Preparation of polynucleotide arrays

• US 20040106110A1
• Filed: 05/22/2002
• Published: 06/03/2004
• Est. Priority Date: 07/30/1998
• Status: Abandoned Application

• Current Assignee: Illumina Cambridge Limited (Illumina Incorporated)
• Original Assignee: Solexa Ltd. (Illumina Incorporated)
• Inventors: Balasubramanian, Shankar, Klenerman, David, Barnes, Colin, Osborne, Mark Allen
• Application Number:
  US10/153,267
• Publication Number:
  US 20040106110A1
• Time in Patent Office: Days
• US Class Current: 435/6
• 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 2219/00317 Microwell devices, i.e. having large numbers of wells
• CPC Class Codes: B01J 2219/00497 Features relating to the solid phase supports
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00529 DNA chips
• CPC Class Codes: B01J 2219/0054 Means for coding or tagging the apparatus or the reagents
• CPC Class Codes: B01J 2219/00572 Chemical means
• CPC Class Codes: B01J 2219/00576 fluorophore
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/00608 DNA chips
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00617 by chemical means
• CPC Class Codes: B01J 2219/00626 Covalent
• 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 2219/00702 Processes involving means for analysing and characterising the products
• CPC Class Codes: B01J 2219/00707 : separated from the reactor apparatus
• CPC Class Codes: B01J 2219/00722 : Nucleotides
• CPC Class Codes: C12Q 1/6837 : using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2525/301 : Hairpin oligonucleotides
• CPC Class Codes: C12Q 2565/507 : characterised by the density of the capture oligonucleotide
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 60/14 : for creating libraries

Abstract

A device comprising an array of molecules immobilised on a solid surface is disclosed, wherein the array has a high density of relatively short molecules and relatively long polynucleotides immobilised on the surface of a solid support, wherein the polynucleotides are at a density that permits individual resolution of those parts thereof that extend beyond the relatively short molecules.

Claims

1. A device comprising a high density array of a plurality of first molecules and a plurality of second polynucleotides immobilised on the surface of a solid support, wherein each molecule of at least a subset of said plurality of first molecules is shorter in length with respect to the distance from the planar surface of the solid support than the length of each of said second polynucleotide of at least a subset of said plurality of second polynucleotides such that said second polynucleotides are of a length and at a density that permits individual resolution of at least two of said second polynucleotides of said subset.

2. The device of claim 1, wherein said second polynucleotide comprises a first portion that corresponds in length with respect to the distance from the planar surface of the solid support to the length of said first molecule and a second portion that extends beyond the first portion and wherein said second portion is interrogated to individually resolve said second polynucleotides.

3. The device of claim 1, wherein each polynucleotide is immobilised by covalent bonding to the surface.

4. The device of claim 1, wherein the polynucleotides and the short molecules contain the same reactive group that attaches to the solid support.

5. The device of claims 1-4, wherein the polynucleotides are immobilised to the solid support via covalent attachment to an intermediate molecule and the short molecules are incapable of undergoing the same covalent attachment to the polynucleotides.

6. The device of claim 5, wherein the intermediate molecule and the short molecules are silane compounds.

7. The device of claims 1-4, wherein adjacent polynucleotides of the array are separated by a distance of at least 10 nm.

8. The device of claims 1-4, wherein the polynucleotides are separated by a distance of at least 100 nm.

9. The device of claims 1-4, wherein the polynucleotides are separated by a distance of at least 250 nm.

10. The device of claims 1-4, wherein the density of the polynucleotides is from 106 to 109 polynucleotides per cm².

11. The device of claims 1-4, wherein the density of the polynucleotides is from 10⁶ to 10⁸ molecules per cm².

12. The device of claims 1-4, wherein the relatively short molecules are polynucleotides.

13. A method of monitoring an interaction with a single polynucleotide, comprising resolving an arrayed polynucleotide with a device comprising a high density array of a plurality of first molecules and a plurality of second polynucleotides immobilised on the surface of a solid support, wherein each molecule of at least a subset of said plurality of first molecules is less in length with respect to the distance from the planar surface of the solid support than the length of each of said second polynucleotide of at least a subset of said plurality of second polynucleotides such that said second polynucleotides are of a length and at a density that permits individual resolution of at least two of said second polynucleotides of said subset.

14. A method for the production of an array of polynucleotides which are at a density that permits individual resolution, comprising arraying on the surface of a solid support, a mixture of relatively long polynucleotides and relatively short molecules, wherein the short molecules are in excess of the polynucleotides.

15. The method of claim 14, wherein the polynucleotides and the short molecules each have the same reactive group that attaches to the solid support or to an intermediate molecule.

16. The method of claim 14 or claim 15, wherein the polynucleotides and short molecules are brought into contact with the solid support in a single composition.

17. The method of claim 14 or claim 15, wherein the short molecules and the polynucleotides are arrayed separately, with the short molecules being brought into contact with the solid support first.

18. The method of claim 17, wherein a minor proportion of the arrayed short molecules comprise a functional group that reacts covalently with a functional group on the polynucleotides to enable the polynucleotides to be arrayed.

19. The method of claim 17, wherein, prior to being arrayed, a minor proportion of short molecules are modified in solution to provide the functional group complementary to that on the polynucleotides.

20. The method of claim 17, wherein the short molecules contain a functional group that is capable of reacting covalently with a complementary group on the polynucleotides, and wherein the polynucleotides are brought into contact with the solid support at a concentration that permits only a minor proportion of the short molecules to undergo reaction with the polynucleotides.

21. The method of claim 20, wherein those molecules that are not reacted with a polynucleotide are reacted with a capping agent.

22. The method of claim 21, wherein the capping agent is a relatively short polynucleotide.

23. The method of claim 14, wherein the relatively short molecules are polynucleotides, and both long and short polynucleotides are reacted with a functional group and then arrayed either directly onto the solid support or to an intermediate molecule bound to the solid support.

24. The method of claim 14, wherein the short molecules are polynucleotides in a hairpin construct, and the relatively long polynucleotides are ligated onto a minor proportion of the short molecules either prior to or after attachment of the short molecules to the solid support.