Oligonucleotide tags for sorting and identification

• US 5,846,719 A
• Filed: 06/06/1996
• Issued: 12/08/1998
• Est. Priority Date: 10/13/1994
• Status: Expired due to Term

• Current Assignee: Illumina Incorporated
• Original Assignee: Lynx Therapeutics, Inc. (Illumina Incorporated)
• Inventors: Brenner, Sydney, Macevicz, Stephen C., Albrecht, Glenn
• Primary Examiner(s): Chambers, Jasemine C.
• Assistant Examiner(s): PRIEBE, SCOTT DAVID
• Application Number:
  US08/659,453
• Time in Patent Office: 915 Days
• Field of Search: 435/6, 435/172.3, 435/320.1, 536/23.1, 536/25.4, 536/24.2, 536/24.3
• US Class Current: 506/3
• 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 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00626 Covalent
• 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 15/10 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: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• 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 1/6874 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 2525/204 : specific length of the oligonucleotides
• 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 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

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.

Claims

1. A method of sorting polynucleotides from a population of polynucleotides onto one or more solid phase supports, the method comprising the steps of:

(a) attaching an oligonucleotide tag from a repertoire of tags to each polynucleotide in a population of polynucleotides such that each oligonucleotide tag from the repertoire is selected from a single minimally cross-hybridizing set of oligonucleotides having a length between 12 and 30 nucleotides, wherein each oligonucleotide of the set is separately synthesized and differs from every other oligonucleotide of the set by at least six nucleotides;

(b) sampling the population of polynucleotides such that substantially all different polynucleotides in the population have different oligonucleotide tags attached; and

(c) sorting the polynucleotides from the population by specifically hybridizing the oligonucleotide tags with their respective complements, the respective complements being attached as uniform populations of substantially identical oligonucleotides in spatially discrete regions on the one or more solid phase supports.

2. The method of claim 1 wherein said oligonucleotide tag is single stranded.

3. The method of claim 2 wherein said complement of said oligonucleotide tag is single stranded.

4. The method of claim 3 wherein said repertoire of said oligonucleotide tags contains at least 1000 of said oligonucleotide tags.

5. The method of claim 4 wherein said one or more solid phase supports are microparticles.

6. The method of claim 5 wherein said microparticles have a diameter in the range of from 5 to 40 μ

m.

7. The method of claim 6 wherein said repertoire contains at least 10,000 of said oligonucleotide tags.

8. The method of claim 4 wherein each of said one or more solid phase supports is a planar substrate having a plurality of spatially discrete surface regions, each of such surface regions having attached thereto a uniform population of substantially identical said complements.

9. The method of claim 8 wherein each of said spatially discrete surface regions has an area in the range of from 10 to 1000 μ

m².

10. The method of claim 1 wherein said repertoire contains at least 100 of said oligonucleotide tags.

11. The method of claim 10 wherein each of said oligonucleotide tags consists of an oligonucleotide having a length between 15 and 24 nucleotides.

12. The method of claim 11 wherein said repertoire contains at least 1000 of said oligonucletide tags.

13. A method of sorting polynucleotides from a population of polynucleotides onto one or more solid phase supports, the method comprising the steps of:

(a) attaching an oligonucleotide tag from a repertoire of tags to each polynucleotide in a population of polynucleotides such that each oligonucleotide tag from the repertoire is selected from a single minimally cross-hybridizing set of double stranded oligonucleotides having a length between 18 and 40 nucleotides, wherein each double stranded oligonucleotide of the set is separately synthesized and differs from every other double stranded oligonucleotide of the set by at least six nucleotides;

(b) sampling the population of polynucleotides such that substantially all different polynucleotides in the population have different oligonucleotide tags attached; and

(c) sorting the polynucleotides from the population by specifically hybridizing the oligonucleotide tags with their respective complements, the respective complements being attached as uniform populations of substantially identical oligonucleotides in spatially discrete regions on the one or more solid phase supports.

14. The method of claim 13 wherein said oligonucleotide tag has a first strand and a second strand such that the first strand is homopyrimidine and the second strand is homopurine.

15. The method of claim 14 wherein said complement is homopyrimidine.

16. The method of claim 15 wherein said repertoire of said oligonucleotide tags contains at least 100 of said oligonucleotide tags.

17. The method of claim 16 wherein said one or more solid phase supports are microparticles.

18. The method of claim 17 wherein said microparticles have a diameter in the range of from 5 to 40 μ

m.

19. The method of claim 18 wherein said repertoire contains at least 1000 of said oligonucleotide tags.

20. The method of claim 16 wherein each of said one or more solid phase supports is a planar substrate having a plurality of spatially discrete surface regions, each of such surface regions having attached thereto a uniform population of substantially identical said complements.

21. The method of claim 20 wherein each of said spatially discrete surface regions has an area in the range of from 10 to 1000 μ

m².

22. The method of claim 21 wherein said repertoire contains at least 10 of said oligonucletide tags.

23. The method of claim 22 wherein each of said oligonucleotide tags consists of an oligonucleotide having a length between 15 and 24 base pairs.

24. The method of claim 23 wherein said repertoire contains at least 100 of said oligonucletide tags.

28. The method of claim 22 wherein said one or more solid phase supports are microparticles and wherein said step of sorting said CDNA molecules onto the microparticles produces a subpopulation of loaded microparticles and a subpopulation of unloaded microparticles.

29. The method of claim 28 further including a step of separating said loaded microparticles from said unloaded microparticles.

30. The method of claim 29 further including a step of repeating said steps of sampling, sorting, and separating until a number of said loaded microparticles is accumulated is at least 10,000.

31. The method of claim 30 wherein said number of loaded microparticles is at least 100,000.

33. The method of claim 29 further including a step of repeating said steps of sampling, sorting, and separating until a number of said loaded microparticles is accumulated that is sufficient to estimate the relative abundance of a cDNA molecule present in said population at a frequency within the range of from 0.1% to 5% with a 95% confidence limit no larger than 0.1% of said population.

25. The method of characterizing a population of mRNA molecules, the method comprising the steps of:

forming a population of cDNA molecules from the population of mRNA molecules such that each cDNA molecule has an oligonucleotide tag attached, the olignucleotide tags being selected from a single minimally cross-hybridizing set of olignucleotides having a length of 12 and 30 nucleotides, wherein each olignucleotide of the set is separately synthesized and differs from every other olignucleotide of the set by at least six nucleotides;

sampling the population of cDNA molecules such that substantially all different cDNA molecules have different olignucleotide tags attached;

sorting the cDNA molecules by specifically hybridizing the oligonucleotide tags with their respective complements, the respective complements being attached as uniform populations of substantially identical complements in spatially discrete regions on one or more solid supports;

determining the nucleotide sequence of a portion of each of the sorted cDNA molecules; and

characterizing the population of mRNA molecules by the frequency distribution of the portion of sequences of the cDNA molecules.

26. The method of claim 25 wherein said oligonucleotide tag is single stranded.

27. The method of claim 26 wherein said complement of said oligonucleotide tag is single stranded.

32. The method of claim 32 wherein said number of loaded microparticles is at least 500,000.