IP Library › Granted Patent US 12668792
Granted Patent B2
US 12668792 · App. 17/244,365 · Granted Jun 30, 2026

Oligonucleotide replacement for di-tagged and directional libraries

Inventors: Igor Goryshin (Madison, WI); Bradley Baas (San Diego, CA); Ramesh Vaidyanathan (Madison, WI); Mark Maffitt (Madison, WI)
Assignee: Illumina, Inc.
C12N15/1065C07H21/00C12N9/1241C12N15/1093C12P19/34C12Q1/6855C40B50/06
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Quick Facts
Patent No.
US 12668792
App. No.
17/244,365
Granted
Jun 30, 2026
Kind
B2
Abstract

Transposomes and oligonucleotide replacement methods to make DNA libraries that have distinct 5′ and 3′ tags, and to make directional libraries that are enriched for a desired strand.

Claims (89)

1 . An array, comprising:

a surface of the array, the surface comprising a plurality of target nucleic acids; and

a plurality of transposomes bound to the plurality of target nucleic acids, wherein a transposome of the plurality of transposomes comprises:

a tag sequence;

a transposase; and

one or two copies of a transposase end sequence selected from the group consisting of:

(SEQ ID NO: 1)

MRWTGTGHWKAVGARACAV

and

(SEQ ID NO: 2)

NSHBGHSHDDRNGAKACAN.

2 . The array of claim 1 , wherein the transposase end sequence is selected from the group excluding (SEQ ID NO: 3) AGATGTGTATAAGAGACAG.

3 . The array of claim 1 , wherein the transposase end sequence is selected from the group excluding (SEQ ID NO: 5) CGTTGTGTGGACGAGACAG.

4 . The array of claim 1 , wherein the surface comprises a plurality of chambers, and wherein the plurality of transposomes are provided in the plurality of chambers.

5 . The array of claim 1 , wherein the tag sequence comprises one or more affinity tags, one or more reporter moieties, or both.

6 . The array of claim 1 , wherein the one or two copies of the transposase end sequence comprise two copies of the transposase end sequence, wherein the two copies are both SEQ ID NO:1, both SEQ ID NO:2, or are one copy of SEQ ID NO:1 and one copy of SEQ ID NO:2.

7 . The array of claim 1 , wherein the tag sequence of the transposase end comprises a sequence that is different relative to other tag sequences in the plurality of transposomes.

8 . The array of claim 1 , wherein at least one transposase end sequence of the one or two copies of the transposase end sequence is selected from the group consisting of:

(SEQ ID NO: 4)

CGTTGTGTGGACGAGACAC,

(SEQ ID NO: 6)

AGATGTGCATATGATACAG,

(SEQ ID NO: 22)

TGACGCGGGTAAGAGACAA,

(SEQ ID NO: 23)

GGATGCGATGAGGAGACAA,

(SEQ ID NO: 24)

ACATGACCAAGAGAGACAG,

(SEQ ID NO: 25)

AGCGGTGAATAAGAGACAA,

(SEQ ID NO: 26)

AGCGGTGAATAAGAGACAG,

and

(SEQ ID NO: 27)

ACATGAGTATAAGAGACAA.

9 . The array of claim 1 , wherein the surface comprises a solution that comprises the plurality of target nucleic acids.

10 . An array surface, comprising:

a plurality of target nucleic acids disposed in chambers of the array surface; and

a plurality of transposomes bound to the plurality of target nucleic acids, wherein a transposome of the plurality of transposomes comprises:

a tag sequence;

a transposase; and

a transposase end sequence, the transposase end sequence comprising one or two copies of a sequence comprising:

(SEQ ID NO: 1)

MRWTGTGHWKAVGARACAV;

or

(SEQ ID NO: 2)

NSHBGHSHDDRNGAKACAN;

but excluding

(SEQ ID NO: 3)

AGATGTGTATAAGAGACAG.

11 . The array surface of claim 10 , wherein the tag sequence comprises a first barcode sequence and a second barcode sequence.

12 . The array surface of claim 11 , wherein the first barcode sequence and the second barcode sequence are different.

13 . The array surface of claim 11 , wherein the first barcode sequence is the reverse complement of the second barcode sequence.

14 . The array surface of claim 10 , wherein the tag sequence of the transposase end sequence is different relative to other tag sequences in the plurality of transposomes.

15 . The array surface of claim 10 , wherein the one or two copies of the transposase end sequence comprise two copies of the transposase end sequence, wherein the two copies are both SEQ ID NO:1, both SEQ ID NO:2, or are one copy of SEQ ID NO: 1 and one copy of SEQ ID NO:2.

16 . The array surface of claim 10 , wherein the chambers have a solution that comprises the plurality of target nucleic acids.

17 . An array surface, comprising:

a plurality of target nucleic acids; and

a plurality of transposomes bound to the plurality of target nucleic acids, wherein a transposome of the plurality of transposomes comprises:

a transposase; and

a double-stranded nucleic acid, the double-stranded nucleic acid comprising a first strand and a complementary second strand, the first strand comprising:

(SEQ ID NO: 1)

MRWTGTGHWKAVGARACAV;

or

(SEQ ID NO: 2)

NSHBGHSHDDRNGAKACAN;

but excluding

(SEQ ID NO: 3)

AGATGTGTATAAGAGACAG.

18 . The array surface of claim 17 , wherein the complementary second strand comprises (SEQ ID NO: 20) BTGTYTCBTN 1-10 or (SEQ ID NO: 21) NTGTMTCNTN 0-10 .

19 . The array surface of claim 17 , wherein the transposase comprises a hyperactive Tn5 transposase or a Tn5 transposase.

20 . The array surface of claim 17 , wherein the first strand comprises:

(SEQ ID NO: 4)

CGTTGTGTGGACGAGACAC,

(SEQ ID NO: 6)

AGATGTGCATATGATACAG,

(SEQ ID NO: 22)

TGACGCGGGTAAGAGACAA,

(SEQ ID NO: 23)

GGATGCGATGAGGAGACAA,

(SEQ ID NO: 24)

ACATGACCAAGAGAGACAG,

(SEQ ID NO: 25)

AGCGGTGAATAAGAGACAA,

(SEQ ID NO: 26)

AGCGGTGAATAAGAGACAG,

and

(SEQ ID NO: 27)

ACATGAGTATAAGAGACAA.