Compositions for sorting polynucleotides

• US 6,140,489 A
• Filed: 10/30/1998
• Issued: 10/31/2000
• Est. Priority Date: 10/13/1994
• Status: Expired due to Term

• Current Assignee: Solexa Incorporated (Illumina Incorporated)
• Original Assignee: Lynx Therapeutics, Inc. (Illumina Incorporated)
• Inventors: Brenner, Sydney
• Primary Examiner(s): Elliott, George C.
• Assistant Examiner(s): SHIBUYA, MARK LANCE
• Application Number:
  US09/183,650
• Time in Patent Office: 732 Days
• Field of Search: 435/6, 435/440, 435/471, 435/320.1, 536/23.1, 536/24.2, 536/24.3, 536/24.35, 536/25.4, 536/25.3
• US Class Current: 536/24.3
• CPC Class Codes: B01J 19/00 Chemical, physical or physico-chemical processes in general; Their relevant apparatus
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/005 Beads
• CPC Class Codes: B01J 2219/00572 Chemical means
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/0063 Other, e.g. van der Waals forces, hydrogen bonding
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00648 by the use of solid beads
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: C12N 15/09 Recombinant DNA-technology
• CPC Class Codes: C12N 15/10 Processes for the isolation, preparation or purification of DNA or RNA chemical preparation of DNA or RNA C07H21/00; preparation of non-structural polynucleotides from microorganisms or with enzymes C12P19/34
• CPC Class Codes: C12N 15/1034 Isolating an individual clone by screening libraries
• CPC Class Codes: C12N 15/1065 Preparation or screening of tagged libraries, e.g. tagged microorganisms by STM-mutagenesis, tagged polynucleotides, gene tags
• CPC Class Codes: C12N 15/11 DNA or RNA fragments; Modified forms thereof DNA or RNA not used in recombinant technology, C07H21/00; Non-coding nucleic acids having a biological activity
• CPC Class Codes: C12Q 1/68 involving nucleic acids
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6813 : Hybridisation assays
• CPC Class Codes: C12Q 1/6827 : for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6834 : Enzymatic or biochemical coupling of nucleic acids to a solid phase
• CPC Class Codes: C12Q 1/6839 : Triple helix formation or other higher order conformations in hybridisation assays
• CPC Class Codes: C12Q 1/6855 : Ligating adaptors
• CPC Class Codes: C12Q 1/6869 : Methods for sequencing
• CPC Class Codes: C12Q 1/6874 : involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2521/313 : Type II endonucleases, i.e. cutting outside recognition site
• CPC Class Codes: C12Q 2521/501 : Ligase
• CPC Class Codes: C12Q 2525/161 : incorporating target specific and non-target specific sites
• CPC Class Codes: C12Q 2525/191 : incorporating an adaptor
• CPC Class Codes: C12Q 2563/107 : fluorescence
• CPC Class Codes: C12Q 2563/185 : Nucleic acid dedicated to use as a hidden marker/bar code, e.g. inclusion of nucleic acids to mark art objects or animals
• CPC Class Codes: C12Q 2565/501 : being an array of oligonucleotides
• CPC Class Codes: C12Q 2565/518 : characterised by the immobilisation of the nucleic acid sample or target
• CPC Class Codes: C12Q 2565/519 : characterised by the capture moiety being a single stranded oligonucleotide
• CPC Class Codes: C40B 20/04 : Identifying library members by means of a tag, label, or other readable or detectable entity associated with the library members, e.g. decoding processes
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 70/00 : Tags or labels specially adapted for combinatorial chemistry or libraries, e.g. fluorescent tags or bar codes
• CPC Class Codes: C40B 80/00 : Linkers or spacers specially adapted for combinatorial chemistry or libraries, e.g. traceless linkers or safety-catch linkers
• CPC Class Codes: G01N 37/00 : Details not covered by any other group of this subclass

Abstract

The invention provides a method and materials for sorting polynucleotides with oligonucleotide tags. Oligonucleotide tags of the invention are capable of hybridizing to complementary oligomeric compounds consisting of subunits having enhanced binding strength and specificity as compared to natural oligonucleotides. Such complementary oligomeric compounds are referred to herein as "tag complements." Subunits of tag complements may consist of monomers of non-natural nucleotide analogs, referred to herein as "antisense monomers" or they may comprise oligomers having lengths in the range of 3 to 6 nucleotides or analogs thereof, including antisense monomers, the oligomers being selected from a minimally cross-hybridizing set. In such a set, a duplex made up of an oligomer of the set and the complement of any other oligomer of the set contains at least two mismatches. Preferred antisense monomers include peptide nucleic acid monomers and nucleoside phosphoramidates having a 3'"'"'-NHP(O)(O--)O-5'"'"' linkage with its adjacent nucleoside.

Claims

1. A composition of matter comprising:

a solid phase support having one or more spacially discrete regions; and

a uniform population of substantially identical tag complements covalently attached to the solid phase support in at least one of the one or more spacially discrete regions, the tag complements each comprising a plurality of subunits, each subunit consisting of an oligomer having a length of from three to six monomers and each subunit being selected from a minimally cross-hybridizing set, wherein each of the monomers is selected from a group consisting of nucleoside N3'"'"'→

P5'"'"' phosphoramidates and peptide nucleic acids.

2. The composition of matter of claim 1 wherein said tag complements each have a length in the range of from 10 to 40 monomers.

3. The composition of matter of claim 2 wherein said solid phase support is a microparticle having a single spacially discrete region.

4. The composition of matter of claim 3 wherein said microparticle is made of a material selected from the group consisting of glass, polystyrene, nylon, cellulose, dextran, latex, polyacrolein, and acrylic copolymer.

5. The composistion of matter of claim 4 wherein said microparticle is made of glass or polystyrene.

6. The composition of matter of claim 1 wherein said tag complements each have a length in the range of from 12 to 30 monomers.

7. The composition of matter of claim 6 wherein said solid phase support is a microparticle having a single spacially discrete region.