This invention relates generally to an optical switch array assembly for DNA probe light synthesis and hybridized DNA probe light detection, and particularly to a micromachined optical switches array assembly that can be selectively actuated for DNA probe light synthesis and hybridized DNA probe light detection.
With the advance of the human genome program, there is a strong movement to diagnose diseases and understand life phenomena by understanding living bodies on the basis of DNA. The main objective of DNA diagnosis is the development of a simple, accurate and cheep technique for DNA screening. The newly developed DNA chips represent a powerful technique for DNA screening. DNA chips have small size, allow a large reduction of sample and reagent consumption, are quick and can be used simply by untrained operators.
DNA arrays have been synthesized using light-directed methods. As an example, light-directed synthesis of oligonucleotides employs 5xe2x80x2-protected nucleosidephosphoramidite xe2x80x9cbuilding blocks.xe2x80x9d The 5xe2x80x2-protecting groups may be either photolabile or acid-labile. A plurality of DNA sequences in predefined regions are synthesized by repeated cycles of deprotection and coupling. Coupling occurs only at sites that have been deprotected. Three methods of light-directed synthesis are: use of photolabile protecting groups and direct photodeprotection; use of acid-labile 4,4xe2x80x2-dimethoxytrityl (DMT) protecting groups and a photoresist; use of DMT protecting groups and a polymer film that contains a photoacid generator (PAG). These methods have many process steps similar to those used in semiconductor integrated circuit manufacturing. These methods also often involve the use of masks that have a predefined image pattern that permits the light used for synthesis of the DNA arrays to reach certain regions of a substrate but not others. The pattern formed on the mask is projected onto a substrate to define which portions of the wafer are to be deprotected and which regions remain protected. In many cases a different mask having a particular predetermined image pattern is used for each separate masking step, and synthesis of a substrate containing many chips requires a plurality of masking steps with different image patterns. For example, synthesis of an array of 20 mers typically requires approximately seventy photolithographic steps and related unique masks. So, using present photolithographic systems and methods, a plurality of different image pattern masks must be pre-generated and changed in the photolithographic system at each masking step. A direct write optical lithography system has been developed to improve the cost, quality, and efficiency of DNA array synthesis by providing a maskless optical lithography system and method where predetermined image patterns can be dynamically changed during photolithographic processing. As such, an optical lithography system is provided to include a means for dynamically changing an intended image pattern without using a mask. One such means includes a spatial light modulator that is electronically controlled by a computer to generate unique predetermined image patterns at each photolithographic step in DNA array synthesis. The spatial light modulators can be, for example, micromachined mechanical modulators or microelectronic devices. One type of mechanical modulator is a micro-mirror array that uses small metal mirrors to selectively reflect a light beam to particular individual features; thus causing the individual features to selectively receive light from a light source (i.e., turning light on and off of the individual features).
Another type of mechanical modulator is designed to modulate transmitted rather than reflected light. An example of a transmission spatial light modulator is a liquid crystal display (LCD). There are a number of drawbacks with this direct write optical lithography system. First, the system consists of several optical active mechanical alignment apparatus including a mechanism for aligning and focusing the chip or substrate, such as an x-y translation stage and a stepping-motor-driven translation stage for moving the substrate by a distance equal to the desired center-to-center distance between chips. The mass production of the DNA probe arrays spends much labor and time and therefore they are very expensive. Particularly when the density of the cells where the probes are fixed, respectively, in a probe array is large, it is getting difficult to produce the probe array at a low cost.
Second, a complicated apparatus is required for optical detection of a hybridized DNA probe array. This apparatus may involve among others moving a sample substrate while simultaneously detecting light transmitted from one or more sample sites on the substrate by sequentially tracking the sample sites as they move. A stage, movable in a first direction, supports the substrate. A detector detects light emanating from an examination region delimited by a detection initiation position and a detection termination position. An optical relay structure transmits light from the examination region to the detector. A scanning mechanism simultaneously moves the optical relay structure and the substrate in the first direction. The optical relay structure tracks the substrate between the detection initiation position and the detection termination position.
The present invention is made for removing the above disadvantages, and an object of the present invention is to provide an optical switch array assembly for DNA probe light synthesis and hybridized DNA probe light detection without any moving apparatus for light alignment and probes tracking.
Another object of the present invention is to provide an optical switch array assembly that is integrated in a substrate with an optical switch array and at least a driving circuit so that not only each site but also each group of sites for DNA probe synthesis can be selectively illuminated.
Still another object of the present invention is to provide an optical switch array that is integrated in a substrate with an optical switch array and at least a driving circuit so that not only each hybridized DNA probe but also each group of hybridized DNA probes can be selectively illuminated for light detection.
Still another object of the present invention is to provide an optical switch array assembly that is integrated in a substrate with an optical switch array and at least a driving circuit so that all sites for DNA probe light synthesis can be directly illuminated without any interference with the reactive liquid.
Still another object of the present invention is to provide an optical switch array assembly that is integrated in a substrate with an optical switch array and at least a driving circuit so that all hybridized DNA probes can be directly illuminated without any cross talk between the adjacent hybridized probes.
Still another object of the present invention is to provide an optical switch array assembly composed of an optical switch array and at least a driving circuit can be batch produced simply using integrated circuit technology and micromachining technology.
Still another object of the present invention is to provide an optical switch array assembly for DNA probe light synthesis and hybridized DNA probe light detection that is simple, cheap and timesaving.
Still another object of the present invention is to provide an optical switch array assembly for DNA probe light synthesis and hybridized DNA probes light detection that can be operated in any laboratory and any hospital.
In order to achieve the above object, in the present invention, an optical switch array assembly is composed of a silicon substrate, an optical switch array disposed in the substrate, a glass plate mounted on the top of the substrate, and a DNA probe array disposed on the surface of the glass plate. The substrate also contains a driving circuit for forcing each optical switch or each group of optical switches on and off and perhaps an addressing circuit for locating each optical switch or each group of optical switches. A plurality of holes is also created in the substrate so that each hole is aligned with an optical switch on the backside and guides an optical beam to the optical switch.
The optical switches are constructed from two parallel thin film mirrors separated by an air gap. As well known, the transmission T of a loss less Fabry-Perot cavity is a function of the reflectivities R1 and R2 of the mirrors and of the air gap h between the mirrors:
T=[(1xe2x88x92R1)(1xe2x88x92R2)]/[(1xe2x88x92{square root over (R1R2)})2+4{square root over (R1R2)}sin2(2xcfx80h/xcex)
where xcex is the working light wavelength.
This expression has maximum and minimum when the sine in the denominator is respectively zero and one. Thus for h being a multiple of xcex/4, the transmission becomes
Tmax=[(1xe2x88x92R1)(1xe2x88x92R2)]/(1xe2x88x92{square root over (R1R2)})2 for h=0,xcex/2,xcex . . . 
Tmin=[(1xe2x88x92R1)(1xe2x88x92R2)]/(1+{square root over (R1R2)})2 for h=xcex/4,3xcex/4 . . . 
The reflectivity of the Fabry-Perot cavity can be become zero only if the mirrors are of equal reflectivity. In this case the above equation is always equal to one. Thus, to get a maximal contract and a maximum reflectivity of the Fabry-Perot cavity, the reflectivities R1 and R2 of the thin film mirrors must be as equal as possible and as high as possible.
It is also known that the reflectivities R1 and R2 of the thin film mirrors are maximum if their thickness is an odd multiple of xcex/(4n), where n is the refractive index of the mirrors material. In this case R1 and R2 of the thin film mirrors can be expressed by       R          1      ,      2        =            (                                    n            2                    -                      n            0                                                n            2                    +                      n            0                              )        2  
where n0 is the refractive index of the underlying medium.
In the present invention the thin film mirrors are made of amorphous silicon carbide or plasma enhanced chemical vapor deposition (PECVD) silicon nitride or lower pressure vapor chemical deposition (LPCVD) silicon nitride. For ultraviolet light silicon dioxide, silicon nitride and silicon carbide are transparent, thus there is no light loss due to absorption. It has been reported that the refractive index of amorphous silicon carbide is 2.48 to 2.65, and the refractive index of silicon nitride is 2.0 to 2.1.
For a freestanding thin film membrane the underlying medium is air and n0=1. Thus the above equation yields values of 52%-56% for R1,2 of amorphous silicon carbide and 40-36% for R1,2 of silicon nitride.
The optical switches based on the Fabry-Perot cavity are operated by electrostatic force. The top mirror of the Fabry-Perot cavity is supported by several flexible beams. Without a voltage applied to the cavity, h equals to odd multiple of xcex/4 so that the transmission of the cavity reaches minimum or the switch is closed. With a voltage applied to the cavity, the flexible beams bend down and the supported mirror moves towards the bottom mirror so that h equals to even multiple of xcex/4. As a result, the transmission of the cavity reaches maximum or the optical switch is opened. As shining light is perpendicularly projected on the backside of the substrate, each hole guides a light beam to a corresponding optical switch. When the optical switch is opened or closed the light beam proceeds forward along the extension direction of the hole or is reflected along a reverse direction.
The applied voltage is directed to a set of selective optical switches by the combination of a driving circuit and an addressing circuit. The driving circuit may be an electrical switch array. The addressing circuit may be a shift register circuit. Both the driving circuit and the addressing circuit may be partially or fully integrated in a same silicon substrate with the optical switch array.
Synthesizing DNA array with the optical switch array assembly using the DMT process may take place as follows. First, a computer file is generated and specifies, for each light illumination step, which optical switches in the optical switch array assembly need to be on and which need to be off to generate a particular predetermined light illumination pattern. Second, the glass plate of the optical switch array assembly is coated with photoresist on the synthesis surface and the optical switch array assembly is mounted in a holder or flow cell so that the synthesis surface is applied with DMT-protected nucleotides containing the desired base (adenine (A), cytosine (C), guanine (G), or thymine (T)). The photoresist may be either positive or negative thus allowing deprotection at locations exposed to the light or deprotection at locations not exposed to the light, respectively. Thirdly, the optical switch array is programmed for the appropriate configuration according to the desired predetermined light illumination pattern, a shutter in an arc lamp is opened, the synthesis surface is illuminated for the desired amount of time, and the shutter is closed. Fourth, the photoresist is developed and etched. Exposure of the glass plate to acid then cleaves the DMT protecting groups from regions of the glass plate where the photoresist has been removed. The remaining photoresist is then stripped. Fifth, DMT-protected nucleotides are coupled to the deprotected oligonucleotides. Sixth, the glass plate of the optical switch array assembly is re-coated with photoresist. These steps are repeated until the DNA array synthesis is complete.
In the analysis procedure, at first, all the components in the sample are labeled with tags such as fluorophores or enzymes. They are placed on the glass plate of the optical switch array assembly for hybridization. If the sample has a component being hybridized with probes on the glass plate, the component is held on the corresponding regions.
The positions of the region emitting fluorescence can be determined by selectively opening the corresponding optical switches of the optical switch array assembly. From the positional information of the fluorescence emitting regions, the probe species being hybridized with the sample components can be determined.