The final result of many experiments in modern biology is a measurement of the expression profile of cultures of cells which have been treated in specifically prescribed ways. In other words, how did the cells in the culture respond to a given set of conditions? What enzymes or other proteins did they produce, and in what quantities? Did they fail to produce particular proteins? If one could grow cells individually rather than in cultures, exposing each to slightly different conditions throughout its life cycle, and then accurately measure the expression profile of each single cell separately, progress on the many open questions in modern biology would accelerate significantly. The quantitation of proteins is currently done with Tandem Mass Spectrometry (MS/MS). MS/MS requires large sample sizes, usually larger than what is available from a single cell. However, the data from MS/MS are often ambiguous, and the protein content of a sample may be reconstructed from the mass spectrum using various techniques, such as time-consuming maximum likelihood methods.
Many technologies exist for the detection of various biological processes and events. Circular dichroism spectroscopy (CD) can detect large changes in the folded fraction of a bulk sample of proteins in solution, for proteins which fold at modest speeds. But a CD spectrum represents only an average over many molecules, and does not yield any information on the folding process in a single molecule. To track fast-folding proteins, CD requires an intense and costly light source (such as the ALS at the Lawrence Berkeley Lab), but again, only the aggregate folded fraction is detected, not single protein molecules.
Fluorescence Resonant Energy Transfer (FRET) is a single molecule method which can track the progress of a folding protein, but it yields information about a limited number of residues only, a small fraction of the number found in a typical globular protein. Furthermore, the information from FRET is simply that pairs of residues either are or are not in close contact, and to some extent, how close that contact is. Hence, FRET measures only degree of progress along the path to the native state, and does not supply information about the nature of the processes which lead to the native state.
“Yeast Songs” can be detected with Atomic Force Microscopy (AFM), but only up to frequencies significantly less than 100 kHz. Furthermore, AFM requires direct mechanical contact with a yeast cell in vivo.
The sequencing of nucleic acids currently requires a substantial amount of sample material, which may usually be amplified via the polymerase chain reaction (PCR). At present, several minutes are needed to determine a single nucleotide in a sequence with reasonable confidence. Thus, the determination of sequences of significant lengths requires a high degree of parallelization and automation.
In some fields, the technique of photoacoustic spectroscopy may be used to study certain bulk properties of quantities of some type of molecule within a medium. In photoacoustic spectroscopy, an intense laser is cyclically pulsed through a transparent medium, which contains a quantity of some type of molecule under study. Energy from the intense laser pulses is transferred to some of the molecules under study, causing them to rapidly heat and cool. This rapid heating/cooling cycle results in cyclical thermal expansion/contraction of the sample. The resulting pressure waves are typically amplified by an acoustic resonance of the test chamber before being detected by sensitive transducers. However, photoacoustic spectroscopy is not suitable for studying non-cyclical events involving one or only a small number of molecules, especially those involving a macromolecule of life transitioning from one inherent, stable state to another inherent, stable state (e.g., a protein folding, an antibody binding to an antigen, DNA supercoiling, DNA replication, and the like).