Polynucleotides for use as tags and tag complements, manufacture and use thereof

• US 7,960,537 B2
• Filed: 07/18/2007
• Issued: 06/14/2011
• Est. Priority Date: 01/25/2001
• Status: Expired due to Term

• Current Assignee: Luminex Molecular Diagnostics Incorporated (DiaSorin S.p.A.)
• Original Assignee: Luminex Molecular Diagnostics Incorporated (DiaSorin S.p.A.)
• Inventors: Pancoska, Petr, Benight, Albert S., Bullock, Richard S., Janota, Vit, Kobler, Daniel, Fieldhouse, Daniel, Riccelli, Peter V.
• Primary Examiner(s): Martinell; James
• Application Number:
  US11/779,720
• Publication Number:
  US 20080014587A1
• Time in Patent Office: 1,427 Days
• Field of Search: None
• US Class Current: 536/24.3
• CPC Class Codes: C12Q 1/6855 Ligating adaptors
• CPC Class Codes: C12Q 1/6876 Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
• CPC Class Codes: Y10T 436/13 Tracers or tags
• CPC Class Codes: Y10T 436/143333 Saccharide [e.g., DNA, etc.]

Abstract

A family of minimally cross-hybridizing nucleotide sequences, methods of use, etc. A specific family of 210 24mers is described.

Claims

1. A composition comprising a plurality of chemically synthesized oligonucleotide tag complements, each oligonucleotide having a 5′

residue and a 3′

residue and being characterized in that;

(a) each oligonucleotide is free of either cytosine or guanosine residues;

(b) any two cytosine or guanosine residues are separated by at most 6 non-cytosine or non-guanosine residues, respectively;

(c) the length of each oligonucleotide differs by no more than five bases from the average length of all oligonucleotides in the composition; and

(d) when each oligonucleotide tag complement is exposed to hybridization conditions comprising 0.2M NaCl, 0.1M Tris, 0.08% Triton X-100, pH 8.0 at 37°

C., the maximum degree of hybridization between the tag complement and a tag not fully complementary to the tag complement does not exceed 25% of the degree of hybridization between the tag complement and its fully complementary tag.

2. The composition of claim 1, further characterized in that, when each oligonucleotide contains a cytosine residue or a guanosine residue, each respective oligonucleotide contains either a cytosine or a guanosine residue located within 7 nucleotides of the 5′

residue.

3. The composition of claim 1, further characterized in that the plurality of oligonucleotide tag complements behave isothermally.

4. The composition of claim 1, wherein each oligonucleotide is between 10 and 40 nucleotides in length.

5. The composition of claim 1, wherein the length of each oligonucleotide in the composition differs by no more than one base from the average length of all oligonucleotides in the composition.

6. The composition of claim 1, wherein each oligonucleotide has the same length.

7. The composition of claim 6, wherein each oligonucleotide comprises the same number of either guanosine or cytosine residues.

8. The composition of claim 6, wherein the length is 24 residues.

9. The composition of claim 8, wherein each oligonucleotide contains either 6 guanosine or 6 cytosine residues.

10. The composition of claim 1, wherein, in element (d), the maximum degree of hybridization between the tag complement and a tag not fully complementary to the tag complement does not exceed 20% of the degree of hybridization between the tag complement and its fully complementary tag.

11. The composition of claim 1, wherein, in element (d), the maximum degree of hybridization between the tag complement and a tag not fully complementary to the tag complement does not exceed 11% of the degree of hybridization between the tag complement and its fully complementary tag.

12. The composition of claim 1, wherein the oligonucleotides are attached to a solid phase support.

13. The composition of claim 12, wherein the support is a planar substrate comprising a plurality of spatially addressable regions.

14. The composition of claim 12, wherein the oligonucleotides are covalently linked to microparticles.

15. The composition of claim 14, wherein the microparticles are spectrophotometrically unique and each unique microparticle has a different oligonucleotide attached thereto.

16. A kit for sorting and identifying polynucleotides, the kit comprising one or more solid phase supports each having one or more spatially discrete regions, each such region having a uniform population of identical tag complements covalently attached thereto, and the tag complements each being selected from the set of oligonucleotides as defined in claim 1.

17. A kit according to claim 16, wherein said one or more solid phase supports is a planar substrate and wherein said one or more spatially discrete regions is a plurality of spatially addressable regions.

18. A kit according to claim 16, wherein said one or more solid phase supports is a plurality of microparticles.

19. A kit according to claim 18, wherein said microparticles each have a diameter in the range of from 5 μ

m to 40 μ

m.

20. A kit according to claim 18, wherein each microparticle is spectrophotometrically unique from each other microparticle having a different oligonucleotide attached thereto.