Optical waveguides – With optical coupler – Switch
Reexamination Certificate
2002-02-27
2004-05-04
Ullah, Akm Enayet (Department: 2874)
Optical waveguides
With optical coupler
Switch
C385S012000
Reexamination Certificate
active
06731831
ABSTRACT:
FIELD OF THE INVENTION
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.
BACKGROUND OF THE INVENTION
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 5′-protected nucleosidephosphoramidite “building blocks.” The 5′-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 4,4′-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.
SUMMARY OF THE INVENTION
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
Connelly-Cushwa Michelle R.
Johnsonbaugh Bruce H.
Ullah Akm Enayet
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