Methods for sorting nucleic acids and multiplexed preparative in vitro cloning
First Claim
Patent Images
1. A method of sorting nucleic acid molecules having a predetermined sequence, the method comprising:
- (a) providing a pool of nucleic acid molecules comprising at least two populations of nucleic acid molecules, each population of nucleic acid molecule having a unique target nucleic acid sequence, the target nucleic acid sequence having a 5′
end and a 3′
end;
(b) tagging the 5′
end and the 3′
end of the target nucleic acid molecules with a non-target oligonucleotide tag sequence, wherein the oligonucleotide tag sequence comprises a unique nucleotide tag;
(c) diluting the tagged target nucleic acids;
(d) subjecting the tagged target nucleic acid molecules to a sequencing reaction from both ends to obtain a paired end read; and
(e) sorting the target nucleic acid molecules having the predetermined sequence according to the identity of their corresponding unique pair of oligonucleotide tags.
1 Assignment
0 Petitions
Accused Products
Abstract
Methods and compositions relate to the sorting and cloning of high fidelity nucleic acids using high throughput sequencing. Specifically, nucleic acid molecules having the desired predetermined sequence can be sorted from a pool comprising a plurality of nucleic acids having correct and incorrect sequences.
96 Citations
39 Claims
-
1. A method of sorting nucleic acid molecules having a predetermined sequence, the method comprising:
-
(a) providing a pool of nucleic acid molecules comprising at least two populations of nucleic acid molecules, each population of nucleic acid molecule having a unique target nucleic acid sequence, the target nucleic acid sequence having a 5′
end and a 3′
end;(b) tagging the 5′
end and the 3′
end of the target nucleic acid molecules with a non-target oligonucleotide tag sequence, wherein the oligonucleotide tag sequence comprises a unique nucleotide tag;(c) diluting the tagged target nucleic acids; (d) subjecting the tagged target nucleic acid molecules to a sequencing reaction from both ends to obtain a paired end read; and (e) sorting the target nucleic acid molecules having the predetermined sequence according to the identity of their corresponding unique pair of oligonucleotide tags. - View Dependent Claims (4, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19)
-
-
2. A method of sorting nucleic acid molecules having a predetermined sequence, the method comprising:
-
(a) providing a pool of nucleic acid molecules comprising at least two populations of nucleic acid molecules, each population of nucleic acid molecule having (i) a unique target nucleic acid sequence, the target nucleic acid sequence having a 5′
end and a 3′
end, and (ii) a non-target oligonucleotide tag sequence at the 5′
end and the 3′
end, the oligonucleotide tag sequence comprising a unique oligonucleotide tag;(b) subjecting the tagged target nucleic acid molecules to a sequencing reaction from both ends to obtain a paired end read; and (c) sorting the target nucleic acid molecules having the predetermined sequence according to the identity of their corresponding unique pair of oligonucleotide tags. - View Dependent Claims (3)
-
-
5. The method of claim 5 further comprising amplifying the nucleic acid molecules using primers complementary to at least part of the oligonucleotide tag.
-
20. A method for designing a plurality of oligonucleotides for assembly into a nucleic acid sequence of interest having a predefined sequence, the method comprising:
-
(a) computationally dividing the sequence of each nucleic acid sequence of interest into partially overlapping construction oligonucleotide sequences; (b) selecting a first plurality of construction oligonucleotide sequences such that every two adjacent construction oligonucleotide sequences overlap with each other by N bases, wherein each N-base sequence is at least 4 bases long; (c) comparing the N-base sequences to one another so that one or more of the following constraints are met;
the N-base sequences differ to one another by at least 2 bases, or the N-base sequences differ to one another by at least one base in the last 3 bases of the 5′
end or 3′
end;(d) identifying from the first plurality of construction oligonucleotide sequences, a second plurality of construction oligonucleotide sequences satisfying the constraints; (e) determining the number of oligonucleotides in the second plurality of oligonucleotides; (f) ranking the oligonucleotides from the second plurality of oligonucleotides that meet or exceed the constraints and based on the number of oligonucleotides; (g) using the ranking to design a set of satisfactory partially overlapping construction oligonucleotides. - View Dependent Claims (21, 22, 23, 24, 25, 26, 27)
-
-
28. A method of isolating a nucleic acid having a predefined sequence, the method comprising:
-
(a) providing at least one population of nucleic acid molecules; (b) isolating a clonal population of nucleic acid molecules on a surface; (c) determining the sequence of the clonal population of nucleic acid molecules; (d) localizing the clonal population of nucleic acid molecules having the predefined sequence; and (d) amplifying the nucleic acid molecule having the predefined sequence. - View Dependent Claims (29, 30)
-
-
31. A method for isolating a nucleic acid having a predefined sequence, the method comprising:
-
(a) providing a pool of nucleic acid molecules comprising error-free and error-containing nucleic acid molecules; (b) tagging the nucleic acid molecules; (c) optionally fragmenting the nucleic acid molecules; (d) determining the sequence of the nucleic acid molecules; (e) localizing the error-free and error-containing nucleic acid molecules; and (f) isolating the error-free nucleic acid molecules. - View Dependent Claims (32, 33, 34, 35)
-
-
36. A method of sorting nucleic acid molecules having a predetermined sequence, the method comprising:
-
(a) providing a pool of nucleic acid molecules comprising at least two populations of nucleic acid molecules, each population of nucleic acid molecule having a unique target nucleic acid sequence, the target nucleic acid sequence having a 5′
end and a 3′
end;(b) tagging the 5′
end and the 3′
end of the target nucleic acid molecules with a pair of non-target oligonucleotide tag sequences, wherein each oligonucleotide tag sequence comprises a unique nucleotide tag;(c) diluting the tagged target nucleic acids; (d) amplifying the tagged nucleic acids; (e) dividing the amplified tagged nucleic acids into two pools; (f) subjecting a first pool comprising the tagged target nucleic acid molecules to a sequencing reaction from both ends to obtain a paired end read; (g) subjecting a second pool comprising the tagged target nucleic acid molecules to ligation to form circular nucleic acid molecules thereby bringing the pair of tags in close proximity; (h) sequencing the pair of tags; and (i) sorting the target nucleic acid molecules having the predetermined sequence according to the identity of their corresponding unique pair of oligonucleotide tags.
-
- 37. The method of claim 37 wherein the pair of tags is amplified before being sequenced.
Specification