US2020017540A1PendingUtilityA1
Method for the site-specific enzymatic labelling of nucleic acids in vitro by incorporation of unnatural nucleotides
Est. expiryAug 8, 2033(~7 yrs left)· nominal 20-yr term from priority
C12N 15/1024C07H 21/04C07H 19/00C12N 9/22C12Q 1/6832C07H 21/00C07H 19/24C12P 19/34C12N 15/09
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Claims
Abstract
Provided herein are analogs of unnatural nucleotides bearing predominantly hydrophobic nucleobase analogs that form unnatural base pairs during DNA polymerase-mediated replication of DNA or RNA polymerase-mediated transcription of RNA. In this manner, the unnatural nucleobases can be introduced in a site-specific way into oligonucleotides (single or double stranded DNA or RNA), where they can provide for site-specific cleavage, or can provide a reactive linker than can undergo functionalization with a cargo-bearing reagent by means of reaction with a primary amino group or by means of click chemistry with an alkyne group of the unnatural nucleobase linker.
Claims
exact text as granted — not AI-modifiedWhat is claimed is:
1 . A double-stranded oligonucleotide comprising a first strand and a second strand, wherein:
(a) the first strand comprises a first compound of the formula
wherein R 2 is selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl, methoxy, methanethiol, methaneseleno, halogen, cyano, and azido; and
(b) the second strand comprises a second compound selected from the group consisting of
and wherein in the case of each of (a) and (b), the wavy line indicates a bond to a 2′-deoxyribosyl moiety.
2 . The double-stranded oligonucleotide of claim 1 , wherein the first compound and the second compound form a base pair in the double-stranded oligonucleotide.
3 . The double-stranded oligonucleotide of claim 2 , wherein the R 2 is hydrogen or halogen.
4 . The double-stranded oligonucleotide of claim 3 , wherein the R 2 is hydrogen.
5 . The double-stranded oligonucleotide of claim 3 , wherein the R 2 is halogen.
6 . The double-stranded oligonucleotide of claim 5 , wherein the halogen is a fluoro.
7 . The double-stranded oligonucleotide of claim 4 , wherein the second compound is selected from the group consisting of
8 . The double-stranded oligonucleotide of claim 7 , wherein the second compound is selected from the group consisting of
9 . The double-stranded oligonucleotide of claim 8 , wherein the second compound is selected from the group consisting of
10 . The double-stranded oligonucleotide of claim 9 , wherein the second compound is selected from the group consisting of
11 . The double-stranded oligonucleotide of claim 10 , wherein the second compound is
12 . The double-stranded oligonucleotide of claim 10 , wherein the second compound is
13 . A composition comprising:
(a) a 2′-deoxyribonucleic acid (DNA) molecule comprising a first compound of the formula
wherein R 2 is selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl, methoxy, methanethiol, methaneseleno, halogen, cyano, and azido, and wherein the wavy line indicates a bond to a 2′-deoxyribosyl moiety; and
(b) a ribonucleic acid (RNA) molecule comprising a second compound selected from the group consisting of
wherein the wavy line indicates a bond to a ribosyl moiety.
14 . The composition of claim 13 , wherein the first compound and the second compound form a base pair.
15 . The composition of claim 14 , wherein the R 2 is hydrogen or halogen.
16 . The composition of claim 15 , wherein the R 2 is hydrogen.
17 . The composition of claim 16 , wherein the second compound is selected from the group consisting of
18 . The composition of claim 17 , wherein the second compound is selected from the group consisting of
19 . The composition of claim 18 , wherein the second compound is selected from the group consisting of
20 . The composition of claim 19 , wherein the second compound is selected from the group consisting of
21 . The composition of claim 20 , wherein the second compound is
22 . The composition of claim 21 , wherein the second compound is
23 . A composition comprising:
(a) a first ribonucleic acid (RNA) molecule comprising a first compound of the formula
wherein R 2 is selected from the group consisting of hydrogen, alkyl, alkenyl, alkynyl, methoxy, methanethiol, methaneseleno, halogen, cyano, and azido; and
(b) a second ribonucleic acid (RNA) molecule comprising a second compound selected from the group consisting of
and wherein in the case of each of (a) and (b), the wavy line indicates a bond to a ribosyl moiety.
24 . The composition of claim 23 , wherein the first compound and the second compound form a base pair.
25 . The composition of claim 24 , wherein the R 2 is hydrogen.
26 . The composition of claim 25 , wherein the second compound is selected from the group consisting of
27 . The composition of claim 26 , wherein the second compound is selected from the group consisting of
28 . The composition of claim 27 , wherein the second compound is selected from the group consisting of
29 . The composition of claim 28 , wherein the second compound is
30 . The composition of claim 28 , wherein the second compound isJoin the waitlist — get patent alerts
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