An integrated semiconductor device enabling non-optical genome sequencing.

The seminal importance of DNA sequencing to the life sciences, biotechnology and medicine has driven the search for more scalable and lower-cost solutions. Here we describe a DNA sequencing technology in which scalable, low-cost semiconductor manufacturing techniques are used to make an integrated circuit able to directly perform non-optical DNA sequencing of genomes. Sequence data are obtained by directly sensing the ions produced by template-directed DNA polymerase synthesis using all-natural nucleotides on this massively parallel semiconductor-sensing device or ion chip.

Kinetics of oligonucleotide hybridization to DNA probe arrays on high-capacity porous silica substrates.

We have investigated the kinetics of DNA hybridization to oligonucleotide arrays on high-capacity porous silica films that were deposited by two techniques. Films created by spin coating pure colloidal silica suspensions onto a substrate had pores of approximately 23 nm, relatively low porosity (35%), and a surface area of 17 times flat glass (for a 0.3-microm film).

Kinetics of oligonucleotide hybridization to photolithographically patterned DNA arrays.

The hybridization kinetics of oligonucleotide targets to oligonucleotide probe arrays synthesized using photolithographic fabrication methods developed by Affymetrix have been measured. Values for the fundamental adsorption parameters, k(a), k(d), and K, were determined at both room temperature and 45 degrees C by monitoring the hybridization of fluorescently labeled targets to the array. The values for these parameters and the adsorbed target density ( View Article and Find Full Text PDF

High capacity substrates as a platform for a DNA probe array genotyping assay.

Colloidal silica particles were deposited on a glass substrate to produce high-capacity porous supports for high-density DNA probe arrays. Porous surfaces were used to increase the addressable surface area and number of probes available for hybridization. Surfaces derived from 70-100 nm size particles deposited in films from 0.

Photolithographic synthesis of high-density oligonucleotide probe arrays.

High-density DNA probe arrays provide a massively parallel approach to nucleic acid sequence analysis that is transforming gene-based biomedical research and diagnostics. Light-directed combinatorial oligonucleotide synthesis has enabled the large-scale production of GeneChip probe arrays which contain several hundred of thousand oligonucleotide sequences on glass "chips" about one cm2 in size. Due to their very high information content, GeneChip probe arrays are finding widespread use in the hybridization-based detection and analysis of mutations and polymorphisms ("genotyping"), and in a wide range of gene expression studies.