Fabrication of patterned arrays

Patent metadata

Field	Value
Publication number	US-2016303534-A1
Application number	US-201415101671-A
Country	US
Kind code	A1
Filing date	Dec 5, 2014
Priority date	Dec 5, 2013
Publication date	Oct 20, 2016
Grant date	—

Abstract

Provided herein are methods and compositions for the fabrication of patterned arrays, such as nucleotide arrays. The methods and compositions are suited for the transfer and reorientation of array components.

First claim

What is claimed is:

1 . A method for generating an array comprising:
providing a template array comprising at least 1,000 different oligonucleotides coupled thereto, coupling said template array to a recipient array having a plurality of oligonucleotides complementary to portions of the at least 1,000 different oligonucleotides, and performing an enzymatic reaction while the template array and the enzymatic array are coupled to one another, thereby generating a recipient array comprising recipient oligonucleotides, wherein at least 40% of the recipient oligonucleotides are complementary or identical to a full-length oligonucleotide from the at least 1,000 different oligonucleotides.

2 . The method of claim 1 , wherein the template array comprises at least 100 spots.

3 . The method of claim 1 , wherein the template array comprises spots at most about 500 μm in size.

4 . The method of claim 1 , wherein the directionality of the recipient oligonucleotides relative to the recipient array is the same as the directionality of the template oligonucleotides relative to the template array.

5 . The method of claim 1 , wherein the directionality of the recipient oligonucleotides relative to the recipient array is the opposite of the directionality of the template oligonucleotides relative to the template array.

6 . The method of claim 1 , wherein a plurality of recipient arrays are generated.

7 . The method of claim 6 , wherein the plurality of recipient oligonucleotides are on average at least 99% identical between one recipient array and another.

8 . The method of claim 6 , wherein the recipient oligonucleotides are at least 99% identical between one recipient array and another.

9 . A method for generating an array comprising: using a template array comprising template oligonucleotides to synthesize a recipient array comprising recipient oligonucleotides wherein the recipient array is coupled to the template array during the synthesis.

10 . The method of claim 9 , wherein at least 40% of the recipient oligonucleotides comprise full-length products.

11 . The method of claim 9 , wherein at least 50% of the recipient oligonucleotides comprise full-length products.

12 . The method of claim 9 , wherein at least 60% of the recipient oligonucleotides comprise full-length products.

13 . The method of claim 9 , wherein the directionality of the recipient oligonucleotides relative to the recipient array is the same as the directionality of the template oligonucleotides relative to the template array.

14 . The method of claim 9 , wherein the directionality of the recipient oligonucleotides relative to the recipient array is the opposite of the directionality of the template oligonucleotides relative to the template array.

15 . The method of claim 9 , wherein a plurality of recipient arrays are generated.

16 . The method of claim 15 , wherein the plurality of recipient oligonucleotides are on average at least 99% identical between one recipient array and another.

17 . The method of claim 15 , wherein the recipient oligonucleotides are at least 99% identical between one recipient array and another.

18 . The method of claim 15 wherein the template array is physically separated from each of the recipient arrays after synthesis of each of the recipient arrays.

19 . The method of claim 15 wherein the template array is separated from each of the recipient arrays after synthesis of each of the recipient arrays by increased temperature.

20 . The method of claim 9 , wherein the template array comprises at least 100 spots.

21 . The method of claim 9 , wherein the template array comprises spots at most about 500 μm in size.

22 . A method for generating a complementary array comprising:
(a) providing a plurality of template oligonucleotides coupled to a first substrate, each of said plurality of template oligonucleotides comprising an adaptor sequence, wherein said adaptor sequence is the same for each of said plurality of template oligonucleotides; (b) providing a plurality of recipient oligonucleotides coupled to a second substrate, each of said plurality of recipient oligonucleotides comprising sequence complementary to said adaptor sequence; (c) hybridizing said adaptor sequence of said template oligonucleotides and said sequence complementary to said adaptor sequence of said recipient oligonucleotides; and (d) conducting extension reactions on said plurality of recipient oligonucleotides using said plurality of template oligonucleotides as templates.

23 . The method of claim 22 , wherein each of said adaptor sequences is located at or near the 3′ end of said template oligonucleotides.

24 . The method of claim 22 , wherein each of said adaptor sequences is located at or near the 5′ end of said template oligonucleotides.

25 . The method of claim 22 , wherein either of said substrates comprises polymer.

26 . The method of claim 22 , wherein either of said substrates comprises acrylamide or polyacrylamide.

27 . The method of claim 22 , wherein the conducting step results in generation of recipient oligonucleotides at least 40% of which are full-length products.

28 . The method of claim 22 , wherein the conducting step results in generation of recipient oligonucleotides at least 50% of which are full-length products.

29 . The method of claim 22 , wherein the conducting step results in generation of recipient oligonucleotides at least 60% of which are full-length products.

30 . The method of claim 22 , wherein the directionality of the recipient oligonucleotides relative to the second substrate is the same as the directionality of the template oligonucleotides relative to the first substrate.

31 . The method of claim 22 , wherein the directionality of the recipient oligonucleotides relative to the second substrate is the opposite of the directionality of the template oligonucleotides relative to the first substrate.

32 . The method of claim 22 , wherein the method is repeated to produce at least 2 recipient arrays.

33 . The method of claim 22 , wherein the template array comprises at least 100 spots.

34 . The method of claim 22 , wherein the template array comprises spots at most about 500 μm in size.

35 . A method for transferring an array, comprising:
(a) providing a substrate comprising a plurality of linker sites; (b) providing an array comprising a plurality of template oligonucleotides; (c) applying reaction mix to said array, said reaction mix comprising enzyme, dNTPs, and a plurality of linker oligonucleotides comprising sequence complementary to an adaptor sequence appended to each of said plurality of template oligonucleotides and further comprising linker molecules capable of binding to said plurality of linker sites; (d) conducting extension reactions of said plurality of said linker oligonucleotides using said plurality of template oligonucleotides as templates, thereby generating a plurality of extension products comprising said linker molecules; (e) contacting said array with said substrate; and (f) linking said linker molecules of said plurality of extension products to said linker sites.

36 . The method of claim 35 , wherein said ad

Assignees

• Zhou Wei
• Crnogorac Filip
• Mcgall Glenn
• Cao Jian
• Centrillion Tech Holdings Corp

Inventors

• Zhou Wei
• Crnogorac Filip
• Mcgall Glenn
• Cao Jian

Classifications

• B01J2219/00709

  Type of synthesis · CPC title

• B01J2219/00722

  Nucleotides · CPC title

• B01J19/0046 Primary

  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 title

• C12Q1/6837 Primary

  using probe arrays or probe chips (C12Q1/6874 takes precedence) · CPC title