Universal bases for nucleic acid analyses, methods for using universal bases, and kits comprising universal bases

• US 7,575,902 B2
• Filed: 04/27/2007
• Issued: 08/18/2009
• Est. Priority Date: 11/07/2001
• Status: Expired due to Fees

• Current Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Original Assignee: Applied Biosystems LLC (Thermo Fisher Scientific Incorporated)
• Inventors: Rosenbaum, Barnett B., Khan, Shaheer H., Jeon, Geun-Sook
• Primary Examiner(s): Riley; Jezia
• Application Number:
  US11/796,555
• Publication Number:
  US 20080274462A1
• Time in Patent Office: 844 Days
• Field of Search: 435/6, 435/91.1, 536/23.1, 536/24.3, 536/24.33
• US Class Current: 435/91.1
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2525/101 incorporating non-naturally occurring nucleotides, e.g. inosine
• CPC Class Codes: C12Q 2525/117 incorporating modified base
• CPC Class Codes: C12Q 2535/101 Sanger sequencing method, i.e. oligonucleotide sequencing using primer elongation and dideoxynucleotides as chain terminators
• CPC Class Codes: C12Q 2535/125 Allele specific primer extension
• CPC Class Codes: Y10S 435/975 Kit

Abstract

Compounds, methods and kits for making and analyzing primer extension products incorporating one or more universal bases are described, including methods and kits for nucleic acid sequencing and microsatellite analysis.

Claims

1. A method of sequencing at least one target nucleic acid template comprising:

(a) forming at least one reaction composition comprising at least one target nucleic acid template, at least one primer, at least one polymerase, at least one universal nucleotide, and at least one specific terminator, wherein the at least one universal nucleotide has a structure

2. The method of claim 1, wherein R², R³, and R⁴ are each independently selected from hydrogen, halogen, alkyl, substituted alkyl, aryl, substituted aryl, and alkylaryl.

3. The method of claim 1, wherein R², R³, and R⁴ are each independently selected from hydrogen, halogen, alkyl, and substituted alkyl.

4. The method of claim 1, wherein R², R³, and R⁴ are each hydrogen.

5. The method of claim 1, wherein R⁵ is hydrogen.

6. The method of claim 1, wherein R⁵ is —

OH.

7. A method of sequencing at least one target nucleic acid template comprising:

(a) forming at least one reaction composition comprising at least one target nucleic acid template, at least one primer, at least one polymerase, at least one universal nucleotide, and at least one specific terminator, wherein the at least one universal nucleotide has a structure

8. The method of claim 7, wherein R², R³, and R⁴ are each independently selected from hydrogen, halogen, alkyl, substituted alkyl, aryl, substituted aryl, and alkylaryl.

9. The method of claim 7, wherein R², R³, and R⁴ are each independently selected from hydrogen, halogen, alkyl, and substituted alkyl.

10. The method of claim 7, wherein R², R³, and R⁴ are each hydrogen.