Oligonucleotide replacement for di-tagged and directional libraries
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.
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.