Method for sequencing DNA and RNA by synthesis

Organic compounds -- part of the class 532-570 series – Organic compounds – Carbohydrates or derivatives

Reexamination Certificate

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C536S027620, C536S027810, C536S028500, C536S028530, C536S028520, C536S028540, C536S028100

Reexamination Certificate

active

07544794

ABSTRACT:
This invention relates to the field of nucleic acid chemistry, more specifically to the field of compositions and processes that are nucleic acid analogs. More specifically, this invention relates to compositions that allow the sequencing of oligonucleotides by synthesis, and processes for sequencing by synthesis that exploit these compositions. Most specifically, the instant invention discloses compositions of matter that are 5′-triphosphates of ribo- and 2′-deoxyribonucleosides wherein the 3′-OH group is replaced by a 3′-ONHR group in the alpha configuration, wherein R is either a H or CH3group. Also disclosed are these triphosphates where the nucleobase carries, via a linker, a reporter groups, such as a fluorescent species that can be used in single- or multi-copy DNA sequencing, or a tag that can be visualized by ultramicroscopy. Also disclosed are processes that use these compositions to do sequencing by synthesis.

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Hwang et al., “Evidence for Watson-Crick and Not Hoogsteen or Wobble Base Pairing in the Selection of Nucleotides for Insertion Opposite Pyrimidines and a Thymine Dimer by Yeast DNA Pol n” Biochemistry (2005) vol. 44, pp. 4850-4860.
Burgess et al., “Synthesis of an Oxyamide linked Nucleotide Dimer and Incorporation into Antisense Oligonucleotide Sequences” Journal of the Chemical Society, Chemical Communications (1994) pp. 915-916.
Patent prosecution documents from U.S. Appl. No. 11/513,916, (a) Office action with a mail date of Apr. 14, 2008, raising a 35 USC 102(b) objection, (b) Reply to the above office action, mailed May 7, 2008, traversing the 35USC 102(b) objection, (c) Office action with a mail date of Mar. 23, 2009, maintaining the 35 USC 102(b) objection, (d) Reply to the above office action, mailed Apr. 29, 2009, again traversing the 35 USC 102(b) objection.

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