Can DNA be created?
Artificial gene synthesis
Artificial gene synthesis, sometimes known as DNA printing is a method in synthetic biology that is used to create artificial genes in the laboratory. Based on solid-phase DNA synthesis, it differs from molecular cloning and polymerase chain reaction (PCR) in that it does not have to begin with preexisting DNA sequences. Therefore, it is possible to make a completely synthetic double-stranded DNA molecule with no apparent limits on either nucleotide sequence or size
Eukaryotic DNA replication
DNA replication is the action of DNA polymerases synthesizing a DNA strand complementary to the original template strand. To synthesize DNA, the double-stranded DNA is unwound by DNA helicases ahead of polymerases, forming a replication fork containing two single-stranded templates. Replication processes permit the copying of a single DNA double helix into two DNA helices, which are divided into the daughter cells at mitosis. The major enzymatic functions carried out at the replication fork are well conserved from prokaryotes to eukaryotes, but the replication machinery in eukaryotic DNA replication is a much larger complex, coordinating many proteins at the site of replication, forming the replisome.
Complementary DNA
Although there are several methods for doing so, cDNA is most often synthesized from mature (fully spliced) mRNA using the enzyme reverse transcriptase. This enzyme, which naturally occurs in retroviruses, operates on a single strand of mRNA, generating its complementary DNA based on the pairing of RNA base pairs (A, U, G and C) to their DNA complements (T, A, C and G, respectively).
Triple-stranded DNA
There are two classes of triplex DNA: intermolecular and intramolecular formations. An intermolecular triplex refers to triplex formation between a duplex and a different (third) strand of DNA. The third strand can either be from a neighboring chromosome or a triplex forming oligonucleotide (TFO). Intramolecular triplex DNA is formed from a duplex with homopurine and homopyrimidine strands with mirror repeat symmetry. The degree of supercoiling in DNA influences the amount of intramolecular triplex formation that occurs. There are two different types of intramolecular triplex DNA: H-DNA and H*-DNA. Formation of H-DNA is stabilized under acidic conditions and in the presence of divalent cations such as Mg. In this conformation, the homopyrimidine strand in the duplex bends back to bind to the purine strand in a parallel fashion. The base triads used to stabilize this conformation are T-A*T and C-G*C. The cytosine of this base triad needs to be protonated in order to form this intramolecular triple helix, which is why this conformation is stabilized under acidic conditions. H*-DNA has favorable formation conditions at neutral pH and in the presence of divalent cations. This intramolecular conformation is formed from the binding of the homopurine and purine strand of the duplex in an antiparallel fashion. It is stabilized by T-A*A and C-G*G base triplets.
Lateral computing
Since the DNA molecule is also a code, but is instead made up of a sequence of four bases that pair up in a predictable manner, many scientists have thought about the possibility of creating a molecular computer. These computers rely on the much faster reactions of DNA nucleotides binding with their complements, a brute force method that holds enormous potential for creating a new generation of computers that would be 100 billion times faster than today's fastest PC. DNA computing has been heralded as the "first example of true nanotechnology", and even the "start of a new era", which forges an unprecedented link between computer science and life science.
Molecular models of DNA
An old standing dynamic problem is how DNA "self-replication" takes place in living cells that should involve transient uncoiling of supercoiled DNA fibers. Although DNA consists of relatively rigid, very large elongated biopolymer molecules called "fibers" or chains (that are made of repeating nucleotide units of four basic types, attached to deoxyribose and phosphate groups), its molecular structure "in vivo" undergoes dynamic configuration changes that involve dynamically attached water molecules and ions. Supercoiling, packing with histones in chromosome structures, and other such supramolecular aspects also involve "in vivo" DNA topology which is even more complex than DNA molecular geometry, thus turning molecular modeling of DNA into an especially challenging problem for both molecular biologists and biotechnologists. Like other large molecules and biopolymers, DNA often exists in multiple stable geometries (that is, it exhibits conformational isomerism) and configurational, quantum states which are close to each other in energy on the potential energy surface of the DNA molecule.
Natural competence
In the natural world DNA usually becomes available by death and lysis of other cells, but in the laboratory it is provided by the researcher, often as a genetically engineered fragment or plasmid. During uptake, DNA is transported across the cell membrane(s), and the cell wall if one is present. Once the DNA is inside the cell it may be degraded to nucleotides, which are reused for DNA replication and other metabolic functions. Alternatively it may be recombined into the cell’s genome by its DNA repair enzymes. If this recombination changes the cell’s genotype the cell is said to have been transformed. Artificial competence and transformation are used as research tools in many organisms ("see Transformation (genetics)").
DNA bank
Scientists are capable of retrieving genetic information from hair, skin, blood, sperm, tissue, and saliva as long as the sample contains intact DNA. Nucleotide sequences between humans differ by only 0.1%. Even so, this 0.1% includes approximately three million bases. DNA can be analyzed through restriction fragment length polymorphism (RFLP) and Polymerase chain reactions (PCR). The RFLP process was introduced in 1988. Restriction enzymes digest portions of the DNA, leaving short fragments. These fragments are sorted through gel electrophoresis. The gel demonstrates the length of the fragments allowing specialists to determine whether the fragments came from the same person. PCR is more commonly used today because it more efficient and requires smaller samples of genetic samples.
Recombinant DNA
Formation of recombinant DNA requires a cloning vector, a DNA molecule that replicates within a living cell. Vectors are generally derived from plasmids or viruses, and represent relatively small segments of DNA that contain necessary genetic signals for replication, as well as additional elements for convenience in inserting foreign DNA, identifying cells that contain recombinant DNA, and, where appropriate, expressing the foreign DNA. The choice of vector for molecular cloning depends on the choice of host organism, the size of the DNA to be cloned, and whether and how the foreign DNA is to be expressed. The DNA segments can be combined by using a variety of methods, such as restriction enzyme/ligase cloning or Gibson assembly.
Synthetic biology
Entire organisms have yet to be created from scratch, although living cells can be transformed with new DNA. Several ways allow constructing synthetic DNA components and even entire synthetic genomes, but once the desired genetic code is obtained, it is integrated into a living cell that is expected to manifest the desired new capabilities or phenotypes while growing and thriving. Cell transformation is used to create biological circuits, which can be manipulated to yield desired outputs.
Exogenous DNA
The use of exogenous DNA to transform cells has spawned the discipline of transgenesis: the use of recombinant DNA techniques to introduce new characters into organisms which were not present previously. The range of organisms that have been created through transgenesis range from bacteria to mammals, including sheep and monkeys, and they have a variety of uses. These include the study of developmental genetics, disease processes and gene regulation. Transgenic farm animals can produce human pharmaceuticals (a method named pharming), and increased milk or meat production. Tissues and organs from transgenic animals can be used in transfusions and transplants with a lesser chance of immune rejection.
DNA condensation
DNA condensation can be induced "in vitro" either by applying external force to bring the double helices together, or by inducing attractive interactions between the DNA segments. The former can be achieved e.g. with the help of the osmotic pressure exerted by crowding neutral polymers in the presence of monovalent salts. In this case, the forces pushing the double helices together are coming from entropic random collisions with the crowding polymers surrounding DNA condensates, and salt is required to neutralize DNA charges and decrease DNA-DNA repulsion. The second possibility can be realized by inducing attractive interactions between the DNA segments by multivalent cationic charged ligands (multivalent metal ions, inorganic cations, polyamines, protamines, peptides, lipids, liposomes and proteins).
DNA replication
DNA is made up of a double helix of two complementary strands. During replication, these strands are separated. Each strand of the original DNA molecule then serves as a template for the production of its counterpart, a process referred to as semiconservative replication. As a result of semi-conservative replication, the new helix will be composed of an original DNA strand as well as a newly synthesized strand. Cellular proofreading and error-checking mechanisms ensure near perfect fidelity for DNA replication.
DNA teleportation
DNA teleportation (also called DNA transduction) is a pseudoscientific claim that DNA produces electromagnetic signals (EMS), measurable when highly diluted in water. This signal can supposedly be recorded, transmitted electronically, and re-emitted on another distant pure water sample, where DNA can replicate through polymerase chain reaction despite the absence of the original DNA in the new water sample. The idea was introduced by the French Nobel laureate Luc Montagnier in 2009. It is similar in principle to water memory, another pseudoscientific concept popularised by another French scientist, Jacques Benveniste, in 1988.
Mutation
A DNA damage can cause an error when the DNA is replicated, and this error of replication can cause a gene mutation that, in turn, could cause a genetic disorder. DNA damages are repaired by the DNA repair system of the cell. Each cell has a number of pathways through which enzymes recognize and repair damages in DNA. Because DNA can be damaged in many ways, the process of DNA repair is an important way in which the body protects itself from disease. Once DNA damage has given rise to a mutation, the mutation cannot be repaired. DNA repair pathways can only recognize and act on "abnormal" structures in the DNA. Once a mutation occurs in a gene sequence it then has normal DNA structure and cannot be repaired.
Genetics
The use of ligation enzymes allows DNA fragments to be connected. By binding ("ligating") fragments of DNA together from different sources, researchers can create recombinant DNA, the DNA often associated with genetically modified organisms. Recombinant DNA is commonly used in the context of plasmids: short circular DNA molecules with a few genes on them. In the process known as molecular cloning, researchers can amplify the DNA fragments by inserting plasmids into bacteria and then culturing them on plates of agar (to isolate clones of bacteria cells—"cloning" can also refer to the various means of creating cloned ("clonal") organisms).
DNA virus
A DNA virus is a virus that has DNA as its genetic material and replicates using a DNA-dependent DNA polymerase. The nucleic acid is usually double-stranded DNA (dsDNA) but may also be single-stranded DNA (ssDNA). DNA viruses belong to either "Group I" or "Group II" of the Baltimore classification system for viruses. Single-stranded DNA is usually expanded to double-stranded in infected cells. Although "Group VII" viruses such as hepatitis B contain a DNA genome, they are not considered DNA viruses according to the Baltimore classification, but rather reverse transcribing viruses because they replicate through an RNA intermediate. Notable diseases like smallpox, herpes, and the chickenpox are caused by such DNA viruses.
DNA vaccination
Alternatively, the DNA may be encapsulated in protein to facilitate cell entry. If this capsid protein is included in the DNA, the resulting vaccine can combine the potency of a live vaccine without reversion risks. In 1983, Enzo Paoletti and Dennis Panicali at the New York Department of Health devised a strategy to produce recombinant DNA vaccines by using genetic engineering to transform ordinary smallpox vaccine into vaccines that may be able to prevent other diseases. They altered the DNA of cowpox virus by inserting a gene from other viruses (namely Herpes simplex virus, hepatitis B and influenza).
Chimeric RNA
DNA encodes the genetic information required for an organism to carry out its life cycle. In effect, DNA serves as the "hard drive" which stores genetic data. DNA is replicated and serves as its own template for replication.
DNA forms a double helix structure and is a composed of a sugar-phosphate backbone and nitrogenous bases; this can be thought of as a ladder structure where the sides of the ladder are constructed of deoxyribose sugar and phosphate while the rungs of the ladder are composed of paired nitrogenous bases. There are four bases in a DNA molecule:
adenine (A), cytosine (C), thymine (T), and guanine (G).
Nucleotides are a structural component of DNA and RNA, being made of a molecule of sugar and a molecule of phosphoric acid. The double helix structure of DNA is composed of two antiparallel strands which are oriented in opposite directions. DNA is composed of base pairs in which adenine pairs with thymine and guanine pairs with cytosine.
While DNA serves as template for production of ribonucleic acid (RNA), RNA is usually responsible for making protein. The process of making RNA from DNA is called transcription. RNA uses a similar set of bases except that thymine is replaced with uracil.
A group of enzymes called RNA polymerases (isolated by biochemists Jerard Hurwitz and Samuel B. Weiss) function in the presence of DNA. These enzymes produce RNA using segments of chromosomal DNA as a template. Unlike replication, where a complete copy of DNA is made, transcription copies only the gene that is to be expressed as a protein.
Evolution
Heritable traits are passed from one generation to the next via DNA, a molecule that encodes genetic information. DNA is a long biopolymer composed of four types of bases. The sequence of bases along a particular DNA molecule specify the genetic information, in a manner similar to a sequence of letters spelling out a sentence. Before a cell divides, the DNA is copied, so that each of the resulting two cells will inherit the DNA sequence. Portions of a DNA molecule that specify a single functional unit are called genes; different genes have different sequences of bases. Within cells, the long strands of DNA form condensed structures called chromosomes. The specific location of a DNA sequence within a chromosome is known as a locus. If the DNA sequence at a locus varies between individuals, the different forms of this sequence are called alleles. DNA sequences can change through mutations, producing new alleles. If a mutation occurs within a gene, the new allele may affect the trait that the gene controls, altering the phenotype of the organism. However, while this simple correspondence between an allele and a trait works in some cases, most traits are more complex and are controlled by quantitative trait loci (multiple interacting genes).
Mutagenesis
DNA damage is an abnormal alteration in the structure of DNA that cannot, itself, be replicated when DNA replicates. In contrast, a mutation is a change in the nucleic acid sequence that can be replicated; hence, a mutation can be inherited from one generation to the next. Damage can occur from chemical addition (adduct), or structural disruption to a base of DNA (creating an abnormal nucleotide or nucleotide fragment), or a break in one or both DNA strands. When DNA containing damage is replicated, an incorrect base may be inserted in the new complementary strand as it is being synthesized (see ). The incorrect insertion in the new strand will occur opposite the damaged site in the template strand, and this incorrect insertion can become a mutation (i.e. a changed base pair) in the next round of replication. Furthermore, double-strand breaks in DNA may be repaired by an inaccurate repair process, non-homologous end joining, which produces mutations. Mutations can ordinarily be avoided if accurate DNA repair systems recognize DNA damage and repair it prior to completion of the next round of replication. At least 169 enzymes are either directly employed in DNA repair or influence DNA repair processes. Of these, 83 are directly employed in the 5 types of DNA repair processes indicated in the chart shown in the article DNA repair.
Artificial gene synthesis
The successful incorporation of a third base pair is a significant breakthrough toward the goal of greatly expanding the number of amino acids which can be encoded by DNA, from the existing 20 amino acids to a theoretically possible 172, thereby expanding the potential for living organisms to produce novel proteins. The artificial strings of DNA do not encode for anything yet, but scientists speculate they could be designed to manufacture new proteins which could have industrial or pharmaceutical uses.
Artificial gene synthesis
DNA sequences have been described which use newly created nucleobases to form a third base pair, in addition to the two base pairs found in nature, A-T (adenine – thymine) and G-C (guanine – cytosine). Multiple research groups have been searching for a third base pair for DNA, including teams led by Steven A. Benner, Philippe Marliere, and Ichiro Hirao. Some new base pairs have been reported.
Eukaryotic DNA replication
The replication fork is the junction between the newly separated template strands, known as the leading and lagging strands, and the double stranded DNA. Since duplex DNA is antiparallel, DNA replication occurs in opposite directions
between the two new strands at the replication fork, but all DNA polymerases synthesize DNA in the 5' to 3' direction with respect to the newly synthesized strand. Further coordination is required during DNA replication. Two replicative polymerases synthesize DNA in opposite orientations. Polymerase ε synthesizes DNA on the "leading" DNA strand continuously as it is pointing in the same direction as DNA unwinding by the replisome. In contrast, polymerase δ synthesizes DNA on the "lagging" strand, which is the opposite DNA template strand, in a fragmented or discontinuous manner.
Okazaki fragments
Newly synthesized DNA, otherwise known as Okazaki fragments, are bound by DNA ligase, which forms a new strand of DNA. There are two strands that are created when DNA is synthesized. The leading strand is continuously synthesized and is elongated during this process to expose the template that is used for the lagging strand (Okazaki fragments). During the process of DNA replication, DNA and RNA primers are removed from the lagging strand of DNA to allow Okazaki fragments to bind to. Since this process is so common, Okazaki maturation will take place around a million times during one completion of DNA replication. For Okazaki maturation to occur, RNA primers must create segments on the fragments to be ligated. This is used as a building block for the synthesis of DNA in the lagging strand. On the template strand, polymerase will synthesize in the opposite direction from the replication fork. Once the template becomes discontinuous, it will create an Okazaki fragment. Defects in the maturation of Okazaki fragments can potentially cause strands in the DNA to break and cause different forms of chromosome abnormality. These mutations in the chromosomes can affect the appearance, the number of sets, or the number of individual chromosomes. Since chromosomes are fixed for each specific species, it can also change the DNA and cause defects in the genepool of that species.
DNA replication
DNA replication (DNA amplification) can also be performed "in vitro" (artificially, outside a cell). DNA polymerases isolated from cells and artificial DNA primers can be used to initiate DNA synthesis at known sequences in a template DNA molecule. Polymerase chain reaction (PCR), ligase chain reaction (LCR), and transcription-mediated amplification (TMA) are examples.
Nuclear DNA
DNA replication begins at a specific site in the DNA molecule called the origin of replication. The enzyme helicase unwinds and separates a portion of the DNA molecule after which single-strand binding proteins react with and stabilize the separated, single-stranded sections of the DNA molecule. The enzyme complex DNA polymerase engages the separated portion of the molecule and initiates the process of replication. DNA polymerase can only connect new DNA nucleotides to a pre-existing chain of nucleotides. Therefore, replication begins as an enzyme called primase assembles an RNA primer at the origin of replication. The RNA primer consists of a short sequence of RNA nucleotides, complementary to a small, initial section of the DNA strand being prepared for replication. DNA polymerase is then able to add DNA nucleotides to the RNA primer and thus begin the process of constructing a new complementary strand of DNA. Later the RNA primer is enzymatically removed and replaced with the appropriate sequence of DNA nucleotides. Because the two complementary strands of the DNA molecule are oriented in opposite directions and the DNA polymerase can only accommodate replication in one direction, two different mechanisms for copying the strands of DNA are employed. One strand is replicated continuously towards the unwinding, separating portion of the original DNA molecule; while the other strand is replicated discontinuously in the opposite direction with the formation of a series of short DNA segments called Okazaki fragments. Each Okazaki fragment requires a separate RNA primer. As the Okazaki fragments are synthesized, the RNA primers are replaced with DNA nucleotides and the fragments are bonded together in a continuous complementary strand.
Molecular cloning
Prior to the 1970s, our understanding of genetics and molecular biology was severely hampered by an inability to isolate and study individual genes from complex organisms. This changed dramatically with the advent of molecular cloning methods. Microbiologists, seeking to understand the molecular mechanisms through which bacteria restricted the growth of bacteriophage, isolated restriction endonucleases, enzymes that could cleave DNA molecules only when specific DNA sequences were encountered. They showed that restriction enzymes cleaved chromosome-length DNA molecules at specific locations, and that specific sections of the larger molecule could be purified by size fractionation. Using a second enzyme, DNA ligase, fragments generated by restriction enzymes could be joined in new combinations, termed recombinant DNA. By recombining DNA segments of interest with vector DNA, such as bacteriophage or plasmids, which naturally replicate inside bacteria, large quantities of purified recombinant DNA molecules could be produced in bacterial cultures. The first recombinant DNA molecules were generated and studied in 1972.
Digital DNA
"Digital DNA" is a seven-foot-tall (by five feet across) egg-shaped sculpture made of welded steel and recycled computer silicon circuit boards applied to polystyrene bead foam with an epoxy fiberglass skin, and finished with UV resistant polyurethane clear automotive paint. Sewn into the surface are phrases relating to technology in many languages (Arabic, Russian, French, Italian, Portuguese, Japanese, Etc). It goes deeper into branching, but above all into the origins of what comes to be the adventure of computers. Therefore, through phrases like: “Circuits of Power”, “Ideological Circuits”, “Warfare Circuits”, “Borderless Circuits”, “Sexual Circuits”, “Colonizing Circuits”, “Genetic Circuits, etc, trying to simplistically verify, even if it is a glimpse of consciousness, one of the main tools-objects of our contemporary world.
Francis Crick
The DNA double helix structure proposed by Watson and Crick was based upon "Watson-Crick" bonds between the four bases most frequently found in DNA (A, C, T, G) and RNA (A, C, U, G). However, later research showed that triple-stranded, quadruple-stranded and other more complex DNA molecular structures required Hoogsteen base pairing. The entire field of synthetic biology began with work by researchers such as Erik T. Kool, in which bases other than A, C, T and G are used in a synthetic DNA. In addition to synthetic DNA there are also attempts to construct synthetic codons, synthetic endonucleases, synthetic proteins and synthetic zinc fingers. Using synthetic DNA, instead of there being 4 codons, if there are n new bases there could be as many as n codons. Research is currently being done to see if codons can be expanded to more than 3 bases. These new codons can code for new amino acids. These synthetic molecules can be used not only in medicine, but in creation of new materials.
Synthetic genomics
An unnatural base pair (UBP) is a designed subunit (or nucleobase) of DNA which is created in a laboratory and does not occur in nature. In 2012, a group of American scientists led by Floyd E. Romesberg, a chemical biologist at the Scripps Research Institute in San Diego, California, published that his team designed an unnatural base pair (UBP). The two new artificial nucleotides or "Unnatural Base Pair" (UBP) were named d5SICS and dNaM. More technically, these artificial nucleotides bearing hydrophobic nucleobases, feature two fused aromatic rings that form a (d5SICS–dNaM) complex or base pair in DNA. In 2014 the same team from the Scripps Research Institute reported that they synthesized a stretch of circular DNA known as a plasmid containing natural T-A and C-G base pairs along with the best-performing UBP Romesberg's laboratory had designed, and inserted it into cells of the common bacterium "E. coli" that successfully replicated the unnatural base pairs through multiple generations. This is the first known example of a living organism passing along an expanded genetic code to subsequent generations. This was in part achieved by the addition of a supportive algal gene that expresses a nucleotide triphosphate transporter which efficiently imports the triphosphates of both d5SICSTP and dNaMTP into "E. coli" bacteria. Then, the natural bacterial replication pathways use them to accurately replicate the plasmid containing d5SICS–dNaM.
Scientific method
The history of the discovery of the structure of DNA is a classic example of the elements of the scientific method: in 1950 it was known that genetic inheritance had a mathematical description, starting with the studies of Gregor Mendel, and that DNA contained genetic information (Oswald Avery's "transforming principle"). But the mechanism of storing genetic information (i.e., genes) in DNA was unclear. Researchers in Bragg's laboratory at Cambridge University made X-ray diffraction pictures of various molecules, starting with crystals of salt, and proceeding to more complicated substances. Using clues painstakingly assembled over decades, beginning with its chemical composition, it was determined that it should be possible to characterize the physical structure of DNA, and the X-ray images would be the vehicle. .."2. DNA-hypotheses"
DNA computing
Kevin Cherry and Lulu Qian at Caltech developed a DNA-based artificial neural network that can recognize 100-bit hand-written digits. They achieve this by programming on computer in advance with appropriate set of weights represented by varying concentrations weight molecules which will later be added to the test tube that holds the input DNA strands.
Simon Boulton
DNA is highly reactive and susceptible to damage from things we are exposed to in everyday life. Fortunately, DNA has evolved processes in which it has the ability to repair itself. If the damages are not repaired and it continues to grow, mutagenic changes occur causing ageing and cancer. Boulton is responsible for identifying these new DNA repair genes, understanding how these genes work in DNA, and determining how the defects in these processes contribute to human diseases. To fulfil these tasks, Boulton studies the DNA damage repair inside a specific worm called C. elegans, then extends these findings to human cells. Through this process, he has found "remarkable similarities between the genes and proteins used to repair DNA damage in the worm and in humans...By studying this fundamental process of DNA damage repair, the researchers have contributed to our understanding of how faults in the system can lead to cancer." Boulton's research has resulted in several major breakthroughs that are viewed as highly promising with regard to the potential development of new cancer treatments.
Biosynthesis
DNA is composed of nucleotides that are joined by phosphodiester bonds. DNA synthesis, which takes place in the nucleus, is a semiconservative process, which means that the resulting DNA molecule contains an original strand from the parent structure and a new strand. DNA synthesis is catalyzed by a family of DNA polymerases that require four deoxynucleoside triphosphates, a template strand, and a primer with a free 3'OH in which to incorporate nucleotides.
DNA
In 1933, while studying virgin sea urchin eggs, Jean Brachet suggested that DNA is found in the cell nucleus and that RNA is present exclusively in the cytoplasm. At the time, "yeast nucleic acid" (RNA) was thought to occur only in plants, while "thymus nucleic acid" (DNA) only in animals. The latter was thought to be a tetramer, with the function of buffering cellular pH.
Nucleic acid
Deoxyribonucleic acid (DNA) is a nucleic acid containing the genetic instructions used in the development and functioning of all known living organisms. The DNA segments carrying this genetic information are called genes. Likewise, other DNA sequences have structural purposes, or are involved in regulating the use of this genetic information. Along with RNA and proteins, DNA is one of the three major macromolecules that are essential for all known forms of life.
DNA consists of two long polymers of simple units called nucleotides, with backbones made of sugars and phosphate groups joined by ester bonds. These two strands run in opposite directions to each other and are, therefore, anti-parallel. Attached to each sugar is one of four types of molecules called nucleobases (informally, bases). It is the sequence of these four nucleobases along the backbone that encodes information. This information is read using the genetic code, which specifies the sequence of the amino acids within proteins. The code is read by copying stretches of DNA into the related nucleic acid RNA in a process called transcription.
Within cells DNA is organized into long structures called chromosomes. During cell division these chromosomes are duplicated in the process of DNA replication, providing each cell its own complete set of chromosomes. Eukaryotic organisms (animals, plants, fungi, and protists) store most of their DNA inside the cell nucleus and some of their DNA in organelles, such as mitochondria or chloroplasts. In contrast, prokaryotes (bacteria and archaea) store their DNA only in the cytoplasm. Within the chromosomes, chromatin proteins such as histones compact and organize DNA. These compact structures guide the interactions between DNA and other proteins, helping control which parts of the DNA are transcribed.
Hershey–Chase experiment
Once the Hershey–Chase experiment was published, the scientific community generally acknowledged that DNA was the genetic code material. This discovery led to a more detailed investigation of DNA to determine its composition as well as its 3D structure. Using X-ray crystallography, the structure of DNA was discovered by James Watson and Francis Crick with the help of previously documented experimental evidence by Maurice Wilkins and Rosalind Franklin.
Knowledge of the structure of DNA led scientists to examine the nature of genetic coding and, in turn, understand the process of protein synthesis. George Gamow proposed that the genetic code was composed of sequences of three DNA base pairs known as triplets or codons which represent one of the twenty amino acids. Genetic coding helped researchers to understand the mechanism of gene expression, the process by which information from a gene is used in protein synthesis. Since then, much research has been conducted to modulate steps in the gene expression process. These steps include transcription, RNA splicing, translation, and post-translational modification which are used to control the chemical and structural nature of proteins. Moreover, genetic engineering gives engineers the ability to directly manipulate the genetic materials of organisms using recombinant DNA techniques. The first recombinant DNA molecule was created by Paul Berg in 1972 when he combined DNA from the monkey virus SV40 with that of the lambda virus.
Extrachromosomal DNA
Extrachromosomal circular DNA (eccDNA) is present in all eukaryotic cells, is usually derived from genomic DNA, and consists of repetitive sequences of DNA found in both coding and non-coding regions of chromosomes. EccDNA can vary in size from less than 2000 base pairs to more than 20,000 base pairs. In plants, eccDNA contains repeated sequences similar to those that are found in the centromeric regions of the chromosomes and in repetitive satellite DNA. In animals, eccDNA molecules have been shown to contain repetitive sequences that are seen in satellite DNA, 5S ribosomal DNA and telomere DNA. Certain organisms, such as yeast, rely on chromosomal DNA replication to produce eccDNA whereas eccDNA formation can occur in other organisms, such as mammals, independently of the replication process. The function of eccDNA has not been widely studied, but it has been proposed that the production of eccDNA elements from genomic DNA sequences adds to the plasticity of the eukaryotic genome and can influence genome stability, cell aging and the evolution of chromosomes.
Expanded genetic code
The successful incorporation of a third base pair into a living micro-organism is a significant breakthrough toward the goal of greatly expanding the number of amino acids which can be encoded by DNA, thereby expanding the potential for living organisms to produce novel proteins. The artificial strings of DNA do not encode for anything yet, but scientists speculate they could be designed to manufacture new proteins which could have industrial or pharmaceutical uses.
XDNA
xDNA (also known as "expanded DNA" or "benzo-homologated DNA") is a size-expanded nucleotide system synthesized from the fusion of a benzene ring and one of the four natural bases: adenine, guanine, cytosine, and thymine. This size expansion produces an 8 letter alphabet which has a larger information density by a factor of 2 compared to natural DNA's (often referred to as B-DNA in literature) 4 letter alphabet. As with normal base-pairing, A pairs with xT, C pairs with xG, G pairs with xC, and T pairs with xA. The double helix is thus 2.4Å wider than a natural double helix. While similar in structure to B-DNA, xDNA has unique absorption, fluorescence, and stacking properties.
DNA
In DNA, fraying occurs when non-complementary regions exist at the end of an otherwise complementary double-strand of DNA. However, branched DNA can occur if a third strand of DNA is introduced and contains adjoining regions able to hybridize with the frayed regions of the pre-existing double-strand. Although the simplest example of branched DNA involves only three strands of DNA, complexes involving additional strands and multiple branches are also possible. Branched DNA can be used in nanotechnology to construct geometric shapes, see the section on uses in technology below.
Dominance (genetics)
The molecular basis of dominance was unknown to Mendel. It is now understood that a gene locus includes a long series (hundreds to thousands) of bases or nucleotides of deoxyribonucleic acid (DNA) at a particular point on a chromosome. The central dogma of molecular biology states that ""DNA makes RNA makes protein"", that is, that DNA is transcribed to make an RNA copy, and RNA is translated to make a protein. In this process, different alleles at a locus may or may not be transcribed, and if transcribed may be translated to slightly different versions of the same protein (called isoforms). Proteins often function as enzymes that catalyze chemical reactions in the cell, which directly or indirectly produce phenotypes. In any diploid organism, the DNA sequences of the two alleles present at any gene locus may be identical (homozygous) or different (heterozygous). Even if the gene locus is heterozygous at the level of the DNA sequence, the proteins made by each allele may be identical. In the absence of any difference between the protein products, neither allele can be said to be dominant (see "co-dominance", above). Even if the two protein products are slightly different (allozymes), it is likely that they produce the same phenotype with respect to enzyme action, and again neither allele can be said to be dominant.
DNA repair
It is important to distinguish between DNA damage and mutation, the two major types of error in DNA. DNA damage and mutation are fundamentally different. Damage results in physical abnormalities in the DNA, such as single- and double-strand breaks, 8-hydroxydeoxyguanosine residues, and polycyclic aromatic hydrocarbon adducts. DNA damage can be recognized by enzymes, and thus can be correctly repaired if redundant information, such as the undamaged sequence in the complementary DNA strand or in a homologous chromosome, is available for copying. If a cell retains DNA damage, transcription of a gene can be prevented, and thus translation into a protein will also be blocked. Replication may also be blocked or the cell may die.
De novo synthesis
"De novo" DNA synthesis is DNA replication without the need for precursor template DNA. It's also referred to as artificial gene synthesis. Primase is an RNA polymerase, and it can add a primer to an existing strand awaiting replication. DNA polymerase cannot add primers, and therefore, needs primase to add the primer "de novo".
Xeno nucleic acid
Not much was done with XNA until the development of special polymerase enzyme, capable of copying XNA from a DNA template as well as copying XNA back into DNA. More recently, synthetic biologists Philipp Holliger and Alexander Taylor, both from the University of Cambridge, managed to create XNAzymes, the XNA equivalent of a Ribozyme, enzymes made of DNA or ribonucleic acid; This demonstrates that XNAs not only store hereditary information, but can also serve as enzymes, raising the possibility that life elsewhere could have begun with something other than RNA or DNA.
Epigenetics in forensic science
DNA methylation is a common epigenetic mark being studied as potential evidence in forensic science. Unlike DNA, realistic DNA methylation is less likely be planted at crime scenes.> Current methods to fabricate DNA usually exclude important methylation marks found in biological tissues making this a way to confirm the identity of an individual when evidence is being assessed.
Evolutionary history of life
Even the simplest members of the three modern domains of life use DNA to record their "recipes" and a complex array of RNA and protein molecules to "read" these instructions and use them for growth, maintenance and self-replication. The discovery that some RNA molecules can catalyze both their own replication and the construction of proteins led to the hypothesis of earlier life-forms based entirely on RNA. These ribozymes could have formed an RNA world in which there were individuals but no species, as mutations and horizontal gene transfers would have meant that the offspring in each generation were quite likely to have different genomes from those that their parents started with. RNA would later have been replaced by DNA, which is more stable and therefore can build longer genomes, expanding the range of capabilities a single organism can have. Ribozymes remain as the main components of ribosomes, modern cells' "protein factories." Evidence suggests the first RNA molecules formed on Earth prior to 4.17 Ga.
DNA supercoil
Positively supercoiled (overwound) DNA is transiently generated during DNA replication and transcription, and, if not promptly relaxed, inhibits (regulates) these processes. The simple figure eight is the simplest supercoil, and is the shape a circular DNA assumes to accommodate one too many or one too few helical twists. The two lobes of the figure eight will appear rotated either clockwise or counterclockwise with respect to one another, depending on whether the helix is over- or underwound. For each additional helical twist being accommodated, the lobes will show one more rotation about their axis. As a general rule, the DNA of most organisms is negatively supercoiled.
DnaG
Once two nucleotides are bound to the primase, DnaG catalyzes the formation of a dinucleotide by forming a phosphodiester bond via dehydration synthesis between the 3' hydroxyl of the nucleotide in the initiation site and the α-phosphate of the nucleotide in the elongation site. This reaction results in a dinucleotide and breaking of the bond between the α and β phosphorus, releasing pyrophosphate. This reaction is irreversible because the pyrophosphate that is formed is hydrolyzed into two inorganic phosphate molecules by the enzyme inorganic pyrophosphatase. This dinucleotide synthesis reaction is the same reaction as any other enzyme that catalyzes the formation of DNA or RNA (DNA Polymerase, RNA Polymerase), therefore DnaG must always synthesize oligonucleotides in the 5' to 3' direction. In "E. coli", primers begin with a triphosphate adenine-guanine (pppAG) dinucleotide at the 5' end.
DNA
For many years, exobiologists have proposed the existence of a shadow biosphere, a postulated microbial biosphere of Earth that uses radically different biochemical and molecular processes than currently known life. One of the proposals was the existence of lifeforms that use arsenic instead of phosphorus in DNA. A report in 2010 of the possibility in the bacterium GFAJ-1, was announced, though the research was disputed, and evidence suggests the bacterium actively prevents the incorporation of arsenic into the DNA backbone and other biomolecules.
Recombinant DNA
Recombinant DNA (rDNA) molecules are DNA molecules formed by laboratory methods of genetic recombination (such as molecular cloning) to bring together genetic material from multiple sources, creating sequences that would not otherwise be found in the genome. Recombinant DNA in a living organism was first achieved in 1973 by Herbert Boyer, of the University of California at San Francisco, and Stanley Cohen, at Stanford University, who used E. coli restriction enzymes to insert foreign DNA into plasmids.
DNA
DNA usually occurs as linear chromosomes in eukaryotes, and circular chromosomes in prokaryotes. The set of chromosomes in a cell makes up its genome; the human genome has approximately 3 billion base pairs of DNA arranged into 46 chromosomes. The information carried by DNA is held in the sequence of pieces of DNA called genes. Transmission of genetic information in genes is achieved via complementary base pairing. For example, in transcription, when a cell uses the information in a gene, the DNA sequence is copied into a complementary RNA sequence through the attraction between the DNA and the correct RNA nucleotides. Usually, this RNA copy is then used to make a matching protein sequence in a process called translation, which depends on the same interaction between RNA nucleotides. In alternative fashion, a cell may simply copy its genetic information in a process called DNA replication. The details of these functions are covered in other articles; here the focus is on the interactions between DNA and other molecules that mediate the function of the genome.
DNA polymerase
Before replication can take place, an enzyme called helicase unwinds the DNA molecule from its tightly woven form, in the process breaking the hydrogen bonds between the nucleotide bases. This opens up or "unzips" the double-stranded DNA to give two single strands of DNA that can be used as templates for replication.
Okazaki fragments
The similarities are the steps for the DNA replication. In both prokaryotes and eukaryotes, replication is accomplished by unwinding the DNA by an enzyme called the DNA helicase. New strands are created by enzymes called DNA polymerases. Both of these follow a similar pattern, called semi-conservative replication, in which individual strands of DNA are produced in different directions, which makes a leading and lagging strand. These lagging strands are synthesized by the production of Okazaki fragments that are soon joined together. Both of these organisms begin new DNA strands which also include small strands of RNA.
Genome
Viral genomes can be composed of either RNA or DNA. The genomes of RNA viruses can be either single-stranded or double-stranded RNA, and may contain one or more separate RNA molecules. DNA viruses can have either single-stranded or double-stranded genomes. Most DNA virus genomes are composed of a single, linear molecule of DNA, but some are made up of a circular DNA molecule.
DNA construct
A DNA construct is an artificially constructed segment of nucleic acid that is to be transplanted into a target tissue or cell. Plasmid DNA constructs often consist of a promoter sequence, followed a by a desired gene, and ended in a transcription termination or polyadenylation signal sequence. A DNA construct may contain a DNA insert, which contains the gene sequence encoding a protein of interest, that has been subcloned into a vector, which contains bacterial resistance genes for growth in bacteria, and promoters for expression in the organism. A DNA construct may express wildtype protein, prevent the expression of certain genes by expressing competitors or inhibitors, or express mutant proteins, such as deletion mutations or missense mutations. A DNA construct is often used in molecular biology to analyze macromolecules such as proteins or RNA in more detail.
Recombinant DNA
Many additional practical applications of recombinant DNA are found in industry, food production, human and veterinary medicine, agriculture, and bioengineering. Some specific examples are identified below.The idea of recombinant DNA was first proposed by Peter Lobban, a graduate student of Prof. Dale Kaiser in the Biochemistry Department at Stanford University Medical School. The first publications describing the successful production and intracellular replication of recombinant DNA appeared in 1972 and 1973, at UCSF and Stanford University. Stanford University applied for a US patent on recombinant DNA in 1974, listing the inventors as Herbert W. Boyer (professor at the University of California, San Francisco) and Stanley N. Cohen (professor at Stanford University); this patent was awarded in 1980. The first licensed drug generated using recombinant DNA technology was human insulin, developed by Genentech and Licensed by Eli Lilly and Company.
DNA sequencing
The concept originated from the idea that single stranded DNA or RNA molecules can be electrophoretically driven in a strict linear sequence through a biological pore that can be less than eight nanometers, and can be detected given that the molecules release an ionic current while moving through the pore. The pore contains a detection region capable of recognizing different bases, with each base generating various time specific signals corresponding to the sequence of bases as they cross the pore which are then evaluated. Precise control over the DNA transport through the pore is crucial for success. Various enzymes such as exonucleases and polymerases have been used to moderate this process by positioning them near the pore’s entrance.
XDNA
Initially synthesized as an enzyme probe by Nelson J. Leonard's group, benzo-homologated adenine was the first base synthesized. Later, Eric T. Kool's group finished synthesizing the remaining three expanded bases, eventually followed by yDNA ("wide" DNA), another benzo-homologated nucleotide system, and naphtho-homologated xxDNA and yyDNA. xDNA is more stable when compared to regular DNA when subjected to higher temperature, and while entire strands of xDNA, yDNA, xxDNA and yyDNA exist, they are currently difficult to synthesize and maintain.Experiments with xDNA provide new insight into the behavior of natural B-DNA. The extended bases xA, xC, xG, and xT are naturally fluorescent, and single strands composed of only extended bases can recognize and bind to single strands of natural DNA, making them useful tools for studying biological systems. xDNA is most commonly formed with base pairs between a natural and expanded nucleobase, however x-nucleobases can also be paired together. Current research supports xDNA as a viable genetic encoding system in the near future.
Recombinant DNA
Recombinant DNA is the general name for a piece of DNA that has been created by the combination of at least two strands. Recombinant DNA is possible because DNA molecules from all organisms share the same chemical structure, and differ only in the nucleotide sequence within that identical overall structure. Recombinant DNA molecules are sometimes called chimeric DNA, because they can be made of material from two different species, like the mythical chimera. R-DNA technology uses palindromic sequences and leads to the production of sticky and blunt ends.
DNA sequencing
DNA sequencing may be used along with DNA profiling methods for forensic identification and paternity testing. DNA testing has evolved tremendously in the last few decades to ultimately link a DNA print to what is under investigation. The DNA patterns in fingerprint, saliva, hair follicles, etc. uniquely separate each living organism from another. Testing DNA is a technique which can detect specific genomes in a DNA strand to produce a unique and individualized pattern. Every living organism ever created has a one of a kind DNA pattern, which can be determined through DNA testing. It is extremely rare that two people have exactly the same DNA pattern, therefore DNA testing is highly successful.
Introduction to evolution
Genes are made of DNA. DNA is a long molecule made up of individual molecules called nucleotides. Genetic information is encoded in the sequence of nucleotides, that make up the DNA, just as the sequence of the letters in words carries information on a page. The genes are like short instructions built up of the "letters" of the DNA alphabet. Put together, the entire set of these genes gives enough information to serve as an "instruction manual" of how to build and run an organism. The instructions spelled out by this DNA alphabet can be changed, however, by mutations, and this may alter the instructions carried within the genes. Within the cell, the genes are carried in chromosomes, which are packages for carrying the DNA. It is the reshuffling of the chromosomes that results in unique combinations of genes in offspring. Since genes interact with one another during the development of an organism, novel combinations of genes produced by sexual reproduction can increase the genetic variability of the population even without new mutations. The genetic variability of a population can also increase when members of that population interbreed with individuals from a different population causing gene flow between the populations. This can introduce genes into a population that were not present before.
DNA nanotechnology
There are potential applications for DNA nanotechnology in nanomedicine, making use of its ability to perform computation in a biocompatible format to make "smart drugs" for targeted drug delivery. One such system being investigated uses a hollow DNA box containing proteins that induce apoptosis, or cell death, that will only open when in proximity to a cancer cell. There has additionally been interest in expressing these artificial structures in engineered living bacterial cells, most likely using the transcribed RNA for the assembly, although it is unknown whether these complex structures are able to efficiently fold or assemble in the cell's cytoplasm. If successful, this could enable directed evolution of nucleic acid nanostructures. 
Scientists at Oxford University reported the self-assembly of four short strands of synthetic DNA into a cage which can enter cells and survive for at least 48 hours. The fluorescently labeled DNA tetrahedra were found to remain intact in the laboratory cultured human kidney cells despite the attack by cellular enzymes after two days. This experiment showed the potential of drug delivery inside the living cells using the DNA ‘cage’. A DNA tetrahedron was used to deliver RNA Interference (RNAi) in a mouse model, reported a team of researchers in MIT. Delivery of the interfering RNA for treatment has showed some success using polymer or lipid, but there are limits of safety and imprecise targeting, in addition to short shelf life in the blood stream. The DNA nanostructure created by the team consists of six strands of DNA to form a tetrahedron, with one strand of RNA affixed to each of the six edges. The tetrahedron is further equipped with targeting protein, three folate molecules, which lead the DNA nanoparticles to the abundant folate receptors found on some tumors. The result showed that the gene expression targeted by the RNAi, luciferase, dropped by more than half. This study shows promise in using DNA nanotechnology as an effective tool to deliver treatment using the emerging RNA Interference technology. The DNA tetrahedron was also used in an effort to overcome the phenomena multidrug resistance. Doxorubicin (DOX) was conjugated with the tetrahedron and was loaded into MCF-7 breast cancer cells that contained the P-glycoprotein drug efflux pump. The results of the experiment showed the DOX was not being pumped out and apoptosis of the cancer cells was achieved.The tetrahedron without DOX was loaded into cells to test its biocompatibility, and the structure showed no cytotoxicity itself.
Virus
Many viruses can be synthesised de novo ("from scratch") and the first synthetic virus was created in 2002. Although somewhat of a misconception, it is not the actual virus that is synthesised, but rather its DNA genome (in case of a DNA virus), or a cDNA copy of its genome (in case of RNA viruses). For many virus families the naked synthetic DNA or RNA (once enzymatically converted back from the synthetic cDNA) is infectious when introduced into a cell. That is, they contain all the necessary information to produce new viruses. This technology is now being used to investigate novel vaccine strategies. The ability to synthesise viruses has far-reaching consequences, since viruses can no longer be regarded as extinct, as long as the information of their genome sequence is known and permissive cells are available. , the full-length genome sequences of 7454 different viruses, including smallpox, are publicly available in an online database maintained by the National Institutes of Health.
DNA profiling
In August 2009, scientists in Israel raised serious doubts concerning the use of DNA by law enforcement as the ultimate method of identification. In a paper published in the journal "Forensic Science International: Genetics", the Israeli researchers demonstrated that it is possible to manufacture DNA in a laboratory, thus falsifying DNA evidence. The scientists fabricated saliva and blood samples, which originally contained DNA from a person other than the supposed donor of the blood and saliva.
History of genetics
A series of subsequent discoveries led to the realization decades later that the genetic material is made of DNA (deoxyribonucleic acid). In 1941, George Wells Beadle and Edward Lawrie Tatum showed that mutations in genes caused errors in specific steps in metabolic pathways. This showed that specific genes code for specific proteins, leading to the "one gene, one enzyme" hypothesis. Oswald Avery, Colin Munro MacLeod, and Maclyn McCarty showed in 1944 that DNA holds the gene's information. In 1952, Rosalind Franklin and Raymond Gosling produced a strikingly clear x-ray diffraction pattern indicating a helical form, and in 1953, James D. Watson and Francis Crick demonstrated the molecular structure of DNA. Together, these discoveries established the central dogma of molecular biology, which states that proteins are translated from RNA which is transcribed by DNA. This dogma has since been shown to have exceptions, such as reverse transcription in retroviruses.
Mutagenesis
Mammalian nuclear DNA may sustain more than 60,000 damage episodes per cell per day, as listed with references in DNA damage (naturally occurring). If left uncorrected, these adducts, after misreplication past the damaged sites, can give rise to mutations. In nature, the mutations that arise may be beneficial or deleterious—this is the driving force of evolution. An organism may acquire new traits through genetic mutation, but mutation may also result in impaired function of the genes, and in severe cases, cause the death of the organism. In the laboratory, however, mutagenesis is a useful technique for generating mutations that allows the functions of genes and gene products to be examined in detail, producing proteins with improved characteristics or novel functions, as well as mutant strains with useful properties. Initially, the ability of radiation and chemical mutagens to cause mutation was exploited to generate random mutations, but later techniques were developed to introduce specific mutations.
Nirenberg and Leder experiment
Oswald Avery discovered that the substance responsible for producing inheritable change in the disease-causing bacteria was neither a protein nor a lipid, rather deoxyribonucleic acid (DNA). He and his colleagues Colin MacLeod and Maclyn McCarty suggested that DNA was responsible for transferring genetic information. Later, Erwin Chargaff discovered that the makeup of DNA differs from one species to another. These experiments helped pave the way for the discovery of the structure of DNA. In 1953, with the help of Maurice Wilkins and Rosalind Franklin’s X-ray crystallography, James Watson and Francis Crick proposed DNA is structured as a double helix. 
In the 1960s, one main DNA mystery scientists needed to figure out was in translation how many bases would be in each code word, or codon. Scientists knew there were a total of four bases (guanine, cytosine, adenine, and thymine). They also knew that were 20 known amino acids. George Gamow suggested that the genetic code was made of three nucleotides per amino acid. He reasoned that because there are 20 amino acids and only four bases, the coding units could not be single (4 combinations) or pairs (only 16 combinations). Rather, he thought triplets (64 possible combinations) were the coding unit of the genetic code. However, he proposed that the triplets were overlapping and non-degenerate.
Seymour Benzer in the late 1950s had developed an assay using phage mutations which provided the first detailed linearly structured map of a genetic region.
Crick felt he could use mutagenesis and genetic recombination phage to further delineate the nature of the genetic code.
In the Crick, Brenner et al. experiment, using these phages, the triplet nature of the genetic code was confirmed. They used frameshift mutations and a process called reversions, to add and delete various numbers of nucleotides. When a nucleotide triplet was added to or deleted from the DNA sequence, the encoded protein was minimally affected. Thus, they concluded that the genetic code is a triplet code because it did not cause a frameshift in the reading frame. They correctly concluded that the code is degenerate, that triplets are not overlapping, and that each nucleotide sequence is read from a specific starting point.
Nucleotide
An unnatural base pair (UBP) is a designed subunit (or nucleobase) of DNA which is created in a laboratory and does not occur in nature. In 2012, a group of American scientists led by Floyd Romesberg, a chemical biologist at the Scripps Research Institute in San Diego, California, published that his team designed an unnatural base pair (UBP). The two new artificial nucleotides or "Unnatural Base Pair" (UBP) were named d5SICS and dNaM. More technically, these artificial nucleotides bearing hydrophobic nucleobases, feature two fused aromatic rings that form a (d5SICS–dNaM) complex or base pair in DNA. In 2014 the same team from the Scripps Research Institute reported that they synthesized a stretch of circular DNA known as a plasmid containing natural T-A and C-G base pairs along with the best-performing UBP Romesberg's laboratory had designed, and inserted it into cells of the common bacterium "E. coli" that successfully replicated the unnatural base pairs through multiple generations. This is the first known example of a living organism passing along an expanded genetic code to subsequent generations. This was in part achieved by the addition of a supportive algal gene that expresses a nucleotide triphosphate transporter which efficiently imports the triphosphates of both d5SICSTP and dNaMTP into "E. coli" bacteria. Then, the natural bacterial replication pathways use them to accurately replicate the plasmid containing d5SICS–dNaM.
RNA polymerase
RNA polymerase (ribonucleic acid polymerase), both abbreviated RNAP or RNApol, official name DNA-directed RNA polymerase, is a member of a family of enzymes that are essential to life: they are found in all living organisms and many viruses. RNAP locally opens the double-stranded DNA (usually about four turns of the double helix) so that one strand of the exposed nucleotides can be used as a template for the synthesis of RNA, a process called transcription. A transcription factor and its associated transcription mediator complex must be attached to a DNA binding site called a promoter region before RNAP can initiate the DNA unwinding at that position. RNAP has intrinsic helicase activity, therefore no separate enzyme is needed to unwind the DNA (in contrast to DNA polymerase). RNAP not only initiates RNA transcription, it also guides the nucleotides into position, facilitates attachment and elongation, has intrinsic proofreading and replacement capabilities, and termination recognition capability. In eukaryotes, RNAP can build chains as long as 2.4 million nucleotides.
DNA damage theory of aging
In contrast to DNA damage, a mutation is a change in the base sequence of the DNA. A mutation cannot be recognized by enzymes once the base change is present in both DNA strands, and thus a mutation cannot be repaired. At the cellular level, mutations can cause alterations in protein function and regulation. Mutations are replicated when the cell replicates. In a population of cells, mutant cells will increase or decrease in frequency according to the effects of the mutation on the ability of the cell to survive and reproduce. Although distinctly different from each other, DNA damages and mutations are related because DNA damages often cause errors of DNA synthesis during replication or repair and these errors are a major source of mutation.
Molecular cloning
In a conventional molecular cloning experiment, the DNA to be cloned is obtained from an organism of interest, then treated with enzymes in the test tube to generate smaller DNA fragments. Subsequently, these fragments are then combined with vector DNA to generate recombinant DNA molecules. The recombinant DNA is then introduced into a host organism (typically an easy-to-grow, benign, laboratory strain of "E. coli" bacteria). This will generate a population of organisms in which recombinant DNA molecules are replicated along with the host DNA. Because they contain foreign DNA fragments, these are transgenic or genetically modified microorganisms (GMO). This process takes advantage of the fact that a single bacterial cell can be induced to take up and replicate a single recombinant DNA molecule. This single cell can then be expanded exponentially to generate a large amount of bacteria, each of which contain copies of the original recombinant molecule. Thus, both the resulting bacterial population, and the recombinant DNA molecule, are commonly referred to as "clones". Strictly speaking, "recombinant DNA" refers to DNA molecules, while "molecular cloning" refers to the experimental methods used to assemble them. The idea arose that different DNA sequences could be inserted into a plasmid and that these foreign sequences would be carried into bacteria and digested as part of the plasmid. That is, these plasmids could serve as cloning vectors to carry genes.
Gene
The growth, development, and reproduction of organisms relies on cell division; the process by which a single cell divides into two usually identical daughter cells. This requires first making a duplicate copy of every gene in the genome in a process called DNA replication. The copies are made by specialized enzymes known as DNA polymerases, which "read" one strand of the double-helical DNA, known as the template strand, and synthesize a new complementary strand. Because the DNA double helix is held together by base pairing, the sequence of one strand completely specifies the sequence of its complement; hence only one strand needs to be read by the enzyme to produce a faithful copy. The process of DNA replication is semiconservative; that is, the copy of the genome inherited by each daughter cell contains one original and one newly synthesized strand of DNA.
Richard Lathe
Lathe's research has led him to develop a theory that without the Moon, there would be no life on Earth. When life began, Earth orbited much more closely to the Moon than it does now, causing massive tides every few hours, which in turn caused rapid cycling of salinity levels on coastlines and may have driven the evolution of early DNA. Lathe uses polymerase chain reaction (PCR), which amplifies DNA replication in the lab, as an example of the mechanisms that facilitate DNA replication, In the laboratory, PCR synthesis is achieved by cycling DNA between two extreme temperatures in the presence of certain enzymes. At lower temperatures, about 50 °C, single strands of DNA act as templates for building complementary strands. At higher temperatures, about 100 °C, the double strands break apart, doubling the number of molecules. The synthesis of DNA is started again by lowering the temperature, and so forth. Through this process, one DNA molecule can be converted into a trillion identical copies in just 40 cycles. Saline cycles triggered by rapid tidal activity would have amplified molecules such as DNA in a process similar to PCR, says Lathe, "The tidal force is absolutely important, because it provides the energy for association and dissociation" of polymers.
Steven A. Benner
Benner has used synthetic organic chemistry and biophysics to create a "second generation" model for nucleic acid structure. The first generation model of DNA was proposed by James Watson and Francis Crick, based on crystallized X-ray structures being studied by Rosalind Franklin. According to the double-helix model, DNA is composed of two complementary strands of nucleotides coiled around each other. Benner's model emphasizes the role of the sugar and phosphate backbone in the genetic molecular recognition event. The poly-anionic backbone is important in creating the extended structure that helps DNA to replicate.
Base pair
The successful incorporation of a third base pair is a significant breakthrough toward the goal of greatly expanding the number of amino acids which can be encoded by DNA, from the existing 20 amino acids to a theoretically possible 172, thereby expanding the potential for living organisms to produce novel proteins. The artificial strings of DNA do not encode for anything yet, but scientists speculate they could be designed to manufacture new proteins which could have industrial or pharmaceutical uses. Experts said the synthetic DNA incorporating the unnatural base pair raises the possibility of life forms based on a different DNA code.
3-Base Periodicity Property
DNA stores the information required to assemble, maintain and reproduce every living organism. A protein is a large molecule ("macromolecule") made up of smaller subunits, amino acids. DNA sequences are made up of codons, three-long nucleotide stretches, that correspond to specific amino acids. DNA creates RNA which then helps synthesize proteins. Thus, coding DNA is defined as the sections of the genome that are actually transcribed into amino acids in proteins. Noncoding DNA is sections of a DNA sequence that don't necessarily code for proteins. Identification of coding regions is important, as this information can be used in gene identification and then more generally full-genome annotation.
DNA polymerase
It is important to note that the directionality of the newly forming strand (the daughter strand) is opposite to the direction in which DNA polymerase moves along the template strand. Since DNA polymerase requires a free 3' OH group for initiation of synthesis, it can synthesize in only one direction by extending the 3' end of the preexisting nucleotide chain. Hence, DNA polymerase moves along the template strand in a 3'–5' direction, and the daughter strand is formed in a 5'–3' direction. This difference enables the resultant double-strand DNA formed to be composed of two DNA strands that are antiparallel to each other.
DNA
In 1943, Oswald Avery, along with coworkers Colin MacLeod and Maclyn McCarty, identified DNA as the transforming principle, supporting Griffith's suggestion (Avery–MacLeod–McCarty experiment). DNA's role in heredity was confirmed in 1952 when Alfred Hershey and Martha Chase in the Hershey–Chase experiment showed that DNA is the genetic material of the T2 phage.
Late in 1951, Francis Crick started working with James Watson at the Cavendish Laboratory within the University of Cambridge. In 1953, Watson and Crick suggested what is now accepted as the first correct double-helix model of DNA structure in the journal "Nature". Their double-helix, molecular model of DNA was then based on one X-ray diffraction image (labeled as "Photo 51") taken by Rosalind Franklin and Raymond Gosling in May 1952, and the information that the DNA bases are paired. On 28 February 1953 Crick interrupted patrons' lunchtime at The Eagle pub in Cambridge to announce that he and Watson had "discovered the secret of life".
Reproduction
The production of a truly living organism (e.g. a simple bacterium) with no ancestors would be a much more complex task, but may well be possible to some degree according to current biological knowledge. A synthetic genome has been transferred into an existing bacterium where it replaced the native DNA, resulting in the artificial production of a new "M. mycoides" organism.
Nuclear DNA
Nuclear DNA is known as the molecule of life and contains the genetic instructions for the development of all living organisms. It is found in almost every cell in the human body, with exceptions such as red blood cells. Everyone has a unique genetic blueprint, even identical twins. Forensic departments such as the Bureau of Criminal Apprehension (BCA) and Federal Bureau of Investigation (FBI) are able to use techniques involving nuclear DNA to compare samples in a case. Techniques used include polymerase chain reaction (PCR), which allows one to utilize very small amounts of DNA by making copies of targeted regions on the molecule, also known as short tandem repeats (STRs).
DNA
Building blocks of DNA (adenine, guanine, and related organic molecules) may have been formed extraterrestrially in outer space. Complex DNA and RNA organic compounds of life, including uracil, cytosine, and thymine, have also been formed in the laboratory under conditions mimicking those found in outer space, using starting chemicals, such as pyrimidine, found in meteorites. Pyrimidine, like polycyclic aromatic hydrocarbons (PAHs), the most carbon-rich chemical found in the universe, may have been formed in red giants or in interstellar cosmic dust and gas clouds.
DNA origami
DNA is folded into an octahedron and coated with a single bilayer of phospholipid, mimicking the envelope of a virus particle. The DNA nanoparticles, each at about the size of a virion, are able to remain in circulation for hours after injected into mice. It also elicits much lower immune response than the uncoated particles. It presents a potential use in drug delivery, reported by researchers in Wyss Institute at Harvard University.
DNA teleportation
In 2009, Montagnier and his collaborators published a paper titled "Electromagnetic signals are produced by aqueous nanostructures derived from bacterial DNA sequences" in which they showed that bacterial DNA can produce electromagnetic signal (EMS) that is transferred through the cell culture medium. They used the DNA of bacteria "Micoplasma pirum" and "Escherichia coli" cultured in a T lymphocyte (a type of white blood cell) culture medium. They took the solution of the culture medium with all the bacteria filtered off. Absence of bacterial DNA was ascertained by polymerase chain reaction. When the solution was simply incubated for two or three weeks, the bacterial DNA was detected. They diluted the solution several times and tested for electromagnetic radiation using Fourier analysis by a method developed by Jacques Benveniste and his team in 1996. They detected electromagnetic frequencies only at high dilutions, such as ranging from 10 to 10.
ATUM
DNA2.0 (now ATUM) was founded in 2003, in Menlo Park, California. The company is privately held and continues to have all research, development and production in California, currently in their 50,000 sq ft Newark facility. It began and continues as a gene synthesis and protein engineering provider to academia, government and the pharmaceutical, chemical, agricultural and biotechnology industries. Gene Synthesis rapidly replaced molecular cloning for many academic and corporate labs, as "foundries for the biotechnology age" allowing made-to-order genes for biological research. 
DNA2.0 was featured on the PBS show Nova ScienceNow to show how genes are created synthetically in a lab. In 2008, the company supplied some of the DNA stretches used to create a synthetic bacterial genome. 
Dan Rather Reports included DNA2.0 in their episode on Synthetic Biology and how it is solving "some of the most important problems facing the world."
In 2009, The Scientist named the codon design algorithms (now trademarked as GeneGPS) developed by DNA2.0 as one of the Top 10 Innovations of the year for Life Sciences. DNA2.0 developed the Electra Vector System, a universal cloning system that utilizes the type IIS restriction enzyme SapI and T4 DNA ligase in a single-tube reaction. DNA2.0 has made some molecular components, such as synthetic fluorescent proteins, available in open-access collections of DNA parts (BioBricks Foundation). DNA2.0 is a founding member of the International Gene Synthesis Consortium (IGSC) to promote biosecurity in the gene-synthesis industry. There are over 1,200 published scientific articles using DNA2.0 products and/or services, of which 44 include company employees as an author(s).
DNA
Deoxyribonucleic acid (; DNA) is a molecule composed of two chains that coil around each other to form a double helix carrying the genetic instructions used in the growth, development, functioning, and reproduction of all known living organisms and many viruses. DNA and ribonucleic acid (RNA) are nucleic acids; alongside proteins, lipids and complex carbohydrates (polysaccharides), nucleic acids are one of the four major types of macromolecules that are essential for all known forms of life.
Split gene theory
To answer this, he made two basic assumptions: (i) before a self-replicating cell could come into existence, DNA molecules were synthesized in the primordial soup by random addition of the 4 nucleotides without the help of templates and (ii) the nucleotide sequences that code for proteins were selected from these preexisting random DNA sequences in the primordial soup, and not by construction from shorter coding sequences. He also surmised that codons must have been established prior to the origin of the first genes. If primordial DNA did contain random nucleotide sequences, he asked: Was there an upper limit in the coding-sequence lengths, and, if so, did this limit play a crucial role in the formation of the structural features of genes at the very beginning of the origin of genes?
Fail-safes in nanotechnology
DNA within our bodies naturally breaks down, replicates itself, and rebuilds itself every time a cell divides. These processes are all controlled and completed by various enzymes. DNA molecules are composed of corresponding base pair nucleotides in a double-helix formation, which makes these processes very efficient, accurate, and predictable. Due to the ease with which DNA molecules can be fashioned, many publications in the academic society are geared towards creating nanostructures using DNA. With a DNA-based nano-device, synthetic proteins could be created, designed to deactivate a nano-device. These synthetic proteins would be injected into the body to break down the DNA and render a nano-device harmless in the event of a malfunction.
Sequence-controlled polymer
In nature, DNA, RNA, proteins and other macromolecules can also be recognized as sequence-controlled polymers for their well-ordered structural skeletons. DNA, based on A-T, C-G base pairs, are formed in well-aligned sequences. Through precise sequences of DNA, 20 amino acids are able to generate sequential peptide chains with three-dimensional structures by virtue of transcription and translation process. These ordered sequences of different constituents endow organisms with complicated and diverse functions.
Genetics
DNA normally exists as a double-stranded molecule, coiled into the shape of a double helix. Each nucleotide in DNA preferentially pairs with its partner nucleotide on the opposite strand: A pairs with T, and C pairs with G. Thus, in its two-stranded form, each strand effectively contains all necessary information, redundant with its partner strand. This structure of DNA is the physical basis for inheritance: DNA replication duplicates the genetic information by splitting the strands and using each strand as a template for synthesis of a new partner strand.
In vitro recombination
Recombinant DNA (rDNA), or molecular cloning, is the process by which a single gene, or segment of DNA, is isolated and amplified. Recombinant DNA is also known as in vitro recombination. A cloning vector is a DNA molecule that carries foreign DNA into a host cell, where it replicates, producing many copies of itself along with the foreign DNA. There are many types of cloning vectors such plasmids and phages. In order to carry out recombination between vector and the foreign DNA, it is necessary the vector and DNA to be cloned by digestion, ligase the foreign DNA into the vector with the enzyme DNA ligase. And DNA is inserted by introducing the DNA into bacteria cells by transformation.
DNA
DNA is a long polymer made from repeating units called nucleotides. The structure of DNA is dynamic along its length, being capable of coiling into tight loops and other shapes. In all species it is composed of two helical chains, bound to each other by hydrogen bonds. Both chains are coiled around the same axis, and have the same pitch of 34 ångströms (3.4 nanometres). The pair of chains has a radius of 10 ångströms (1.0 nanometre). According to another study, when measured in a different solution, the DNA chain measured 22 to 26 ångströms wide (2.2 to 2.6 nanometres), and one nucleotide unit measured 3.3 Å (0.33 nm) long. Although each individual nucleotide repeating unit is very small, DNA polymers can be very large molecules containing hundreds of millions of nucleotides. For instance, the DNA in the largest human chromosome, chromosome number 1, consists of approximately 220 million base pairs and would be 85 mm long if straightened.
Introduction to genetics
DNA can be copied very easily and accurately because each piece of DNA can direct the creation of a new copy of its information. This is because DNA is made of two strands that pair together like the two sides of a zipper. The nucleotides are in the center, like the teeth in the zipper, and pair up to hold the two strands together. Importantly, the four different sorts of nucleotides are different shapes, so for the strands to close up properly, an A nucleotide must go opposite a T nucleotide, and a G opposite a C. This exact pairing is called base pairing.
DNA
DNA can be damaged by many sorts of mutagens, which change the DNA sequence. Mutagens include oxidizing agents, alkylating agents and also high-energy electromagnetic radiation such as ultraviolet light and X-rays. The type of DNA damage produced depends on the type of mutagen. For example, UV light can damage DNA by producing thymine dimers, which are cross-links between pyrimidine bases. On the other hand, oxidants such as free radicals or hydrogen peroxide produce multiple forms of damage, including base modifications, particularly of guanosine, and double-strand breaks. A typical human cell contains about 150,000 bases that have suffered oxidative damage. Of these oxidative lesions, the most dangerous are double-strand breaks, as these are difficult to repair and can produce point mutations, insertions, deletions from the DNA sequence, and chromosomal translocations. These mutations can cause cancer. Because of inherent limits in the DNA repair mechanisms, if humans lived long enough, they would all eventually develop cancer. DNA damages that are naturally occurring, due to normal cellular processes that produce reactive oxygen species, the hydrolytic activities of cellular water, etc., also occur frequently. Although most of these damages are repaired, in any cell some DNA damage may remain despite the action of repair processes. These remaining DNA damages accumulate with age in mammalian postmitotic tissues. This accumulation appears to be an important underlying cause of aging.
RNA spike-in
RNA spike-ins can be synthesized by any means of creating RNA synthetically, or by using cells to transcribe DNA to RNA "in vivo" (in cells). RNA can be produced "in vitro" (cell free) using RNA polymerase and DNA with the desired sequence. Large scale biotech manufacturers produce RNA synthetically via high-throughput techniques and provide solutions of RNA spike-ins at predetermined concentration. Bacteria containing DNA (usually on plasmids) for transcription to spike-ins are also commercially available. The purified RNA can be stored long-term in a buffered solution at low temperature.
Complementary DNA
In genetics, complementary DNA (cDNA) is DNA synthesized from a single-stranded RNA (e.g., messenger RNA (mRNA) or microRNA) template in a reaction catalyzed by the enzyme reverse transcriptase. cDNA is often used to clone eukaryotic genes in prokaryotes. When scientists want to express a specific protein in a cell that does not normally express that protein (i.e., heterologous expression), they will transfer the cDNA that codes for the protein to the recipient cell. cDNA is also produced naturally by retroviruses (such as HIV-1, HIV-2, simian immunodeficiency virus, etc.) and then integrated into the host's genome, where it creates a provirus.
P1 phage
In the viral particle the DNA molecule is longer (110Kbp) than the actual length of the genome. It is created by cutting an appropriately sized fragment from a concatemeric DNA chain having multiple copies of the genome (see the section below on lysis for how this is made). Due to this the ends of the DNA molecule are identical. This is referred to as being terminally redundant. This is important for the DNA to be circularized in the host. Another consequence of the DNA being cut out of a concatemer is that a given linear molecule can start at any location on the circular genome. This is called a cyclical permutation.
DNA replication
DNA is always synthesized in the 5' to 3' direction. Since the leading and lagging strand templates are oriented in opposite directions at the replication fork, a major issue is how to achieve synthesis of nascent (new) lagging strand DNA, whose direction of synthesis is opposite to the direction of the growing replication fork.
Humanized antibody
It is possible to produce a humanized antibody without creating a chimeric intermediate. "Direct" creation of a humanized antibody can be accomplished by inserting the appropriate CDR coding segments (so-called 'donor', responsible for the desired binding properties) into a human antibody "scaffold" (so-called 'acceptor'). As discussed above, this is achieved through recombinant DNA methods using an appropriate vector and expression in mammalian cells. That is, after an antibody is developed to have the desired properties in a mouse (or other non-human), the DNA coding for that antibody can be isolated, cloned into a vector and sequenced. The DNA sequence corresponding to the antibody CDRs can then be determined. Once the precise sequence of the desired CDRs are known, a strategy can be devised for inserting these sequences appropriately into a construct containing the DNA for a human antibody variant. The strategy may also employ synthesis of linear DNA fragments based on the reading of CDR sequences.
Deoxyribozyme
Deoxyribozymes, also called DNA enzymes, DNAzymes, or catalytic DNA, are DNA oligonucleotides that are capable of performing a specific chemical reaction, often but not always catalytic. This is similar to the action of other biological enzymes, such as proteins or ribozymes (enzymes composed of RNA).
However, in contrast to the abundance of protein enzymes in biological systems and the discovery of biological ribozymes in the 1980s,
there are no known naturally occurring deoxyribozymes.
Deoxyribozymes should not be confused with DNA aptamers which are oligonucleotides that selectively bind a target ligand, but do not catalyze a subsequent chemical reaction.