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Oligonucleotide tags for sorting and identification

Patent 5846719 Issued on December 8, 1998. Estimated Expiration Date: Icon_subject June 6, 2016. Estimated Expiration Date is calculated based on simple USPTO term provisions. It does not account for terminal disclaimers, term adjustments, failure to pay maintenance fees, or other factors which might affect the term of a patent.

Patent References

Multiplex sequencing
Patent #: 4942124
Issued on: 07/17/1990
Inventor: Church

Multiplex analysis of DNA
Patent #: 5149625
Issued on: 09/22/1992
Inventor: Church, et al.

Method and probe composition for detecting multiple sequences in a single assay
Patent #: 5514543
Issued on: 05/07/1996
Inventor: Grossman, et al.

Methods for sorting polynucleotides using oligonucleotide tags
Patent #: 5604097
Issued on: 02/18/1997
Inventor: Brenner

Oligonucleotide population preparation Patent #: 5658736
Issued on: 08/19/1997
Inventor: Wong

Inventors

Assignee

Application

No. 659453 filed on 06/06/1996

US Classes:

435/6, Involving nucleic acid536/23.1, DNA or RNA fragments or modified forms thereof (e.g., genes, etc.)536/24.2, Non-coding sequences having no known regulatory function which are adaptors or linkers for vector or gene contruction536/24.3, Probes for detection of specific nucleotide sequences or primers for the synthesis of DNA or RNA536/25.4Separation or purification of polynucleotides or oligonucleotides

Examiners

Primary: Chambers, Jasemine C.
Assistant: Priebe, Scott D.

Attorney, Agent or Firm

Foreign Patent References

  • 0 303 459 A3 EP. 02/13/1989
  • WO 93/06121 WO. 04/13/1993
  • WO 93/17126 WO. 09/13/1993
  • WO97/31256 WO. 08/13/1997

International Classes

C12Q 001/68
C07H 021/00
C07H 021/04

Abstract

The invention provides a method of tracking, identifying, and/or sorting classes or subpopulations of molecules by the use of oligonucleotide tags. Oligonucleotide tags of the invention comprise oligonucleotides selected from a minimally cross-hybridizing set. Preferably, such oligonucleotides each consist of a plurality of subunits 3 to 9 nucleotides in length. A subunit of a minimally cross-hybridizing set forms a duplex or triplex having two or more mismatches with the complement of any other subunit of the same set. The number of oligonucleotide tags available in a particular embodiment depends on the number of subunits per tag and on the length of the subunit. An important aspect of the invention is the use of the oligonucleotide tags for sorting polynucleotides by specifically hybridizing tags attached to the polynucleotides to their complements on solid phase supports. This embodiment provides a readily automated system for manipulating and sorting polynucleotides, particularly useful in large-scale parallel operations, such as large-scale DNA sequencing, mRNA fingerprinting, and the like, wherein many target polynucleotides or many segments of a single target polynucleotide are sequenced simultaneously.

Other References

  • Brenner and Lerner, "Encoded combinatorial chemistry", Proc. Natl. Acad. Sci. USA 86: 5381-5383, Jun. 1992
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  • Oliphant and Struhl, "Defining the consensus sequences of E. coli promoter elements by random selection," Nucleic Acids Research, 16: 7673-7683 (1988)
  • Gronostajski, "DNA binding of nuclear factor 1: effect of the spacer region," Nucleic Acids Research, 15: 5545-5559 (1987)
  • Matteucci et al, "Targeted random mutagenesis: the use of ambiguously synthesized oligonucleotides to mutagenize sequences immediately 5' of an ATG initiation codon," Nucleic Acids Research, 11: 3113-3121 (1983)
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  • Shoemaker et al, "Quantitative phenotypic analysis of yeast deletion mutants using a highly parallel molecular bar-coding strategy," Nature Genetics, 14: 450-456 (1996)
  • Hensel et al, "Simultaneous identification of bacterial virulence genes by negative selection," Science, 269: 400-403 (1995
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