Apparatus and method for sequencing a nucleic acid

Abstract

Disclosed herein are methods and apparatuses for sequencing a nucleic acid. These methods permit a very large number of independent sequencing reactions to be arrayed in parallel, permitting simultaneous sequencing of a very large number (>10,000) of different oligonucleotides.

Description

[0001] RELATED APPLICATIONS [0002] This application claims the benefit of priority to U.S. Ser. No. 10 / 104,280 filed Mar. 21, 2002; which is a CIP of 09 / 814,338 filed Mar. 21, 2001; which is a CIP of U.S. Ser. No. 09 / 664,197 filed Sep. 18, 2000; which is a CIP of U.S. Ser. No. 09 / 398,833 filed Sep. 16, 1999, now U.S. Pat. No. 6,274,320. Each of the above referenced patent and patent applications are incorporated herein by reference in their entireties.FIELD OF THE INVENTION [0003] The invention relates to apparatus and methods for determining the sequence of a nucleic acid. BACKGROUND OF THE INVENTION [0004] Many diseases are associated with particular DNA sequences. The DNA sequences are often referred to as DNA sequence polymorphisms to indicate that the DNA sequence associated with a diseased state differs from the corresponding DNA sequence in non-afflicted individuals. DNA sequence polymorphisms can include, e.g., insertions, deletions, or substitutions of nucleotides in one se...

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Benefits of technology

[0033] The disclosures of one or more embodiments of the invention are set forth in the accompanying description below. Although any methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, the preferred methods and materials are now described. Other features, objects, and advantages of the invention will be apparent from the description and from the claims. In the specification and the appended claims, the singular forms include plural referents unless the context clearly dictates otherwise. Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Unless expressly stated otherwise, the techniques employed or contemplated herein are standard methodologies well known to one of ordinary skill in the art. The examples of embodiments are for illustration purposes only. All patents and publications cited in this specification are incorporated by reference.

Problems solved by technology

Electrophoretic-based separation analyses can be less desirable for applications in which it is desirable to rapidly, economically, and accurately analyze a large number of nucleic acid samples for particular sequence polymorphisms.

For example, electrophoretic-based analysis can require a large amount of input DNA.

In addition, processing the large number of samples required for electrophoretic-based nucleic acid based analyses can be labor intensive.

Furthermore, these techniques can require samples of identical DNA molecules, which must be created prior to electrophoresis at costs that can be considerable.

However, electrophoresis can be ill suited for applications such as clinical sequencing, where relatively cost-effective units with high throughput are needed.

Solid support matrix-based hybridization and sequencing methodologies can require a high sample-DNA concentration and can be hampered by the relatively slow hybridization kinetics of nucleic acid samples with immobilized oligonucleotide probes.

However, PCR can be difficult to incorporate into a solid-phase approach because the amplified DNA is not immobilized onto the surface of the solid support matrix.

However, such radioactive methods are not well suited for routine clinical applications, and hence the development of a simple, highly sensitive non-radioactive method for rapid DNA sequence analysis has also been of great interest.

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