Compounds for protecting hydroxyls and methods for their use
First Claim
Patent Images
1. A hydrocarbyldithiomethyl-modified compound comprising the Formula:
- R1—
O—
CH2—
S—
S—
R2or a salt thereof, wherein R1 is an organic molecule; and
R2 is a hydrocarbyl.
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Abstract
A hydrocarbyldithiomethyl-modified compound of the Formula:
R1—O—CH2—S—S—R2
or a salt thereof wherein R1 is an organic molecule and R2 is a hydrocarbyl is useful for protecting and/or blocking hydroxyl groups in organic molecules such as nucleotides. The hydrocarbyldithiomethyl-modified compounds can also be used for chemically synthesizing oligonucleotides and for sequencing nucleic acid compounds.
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Citations
57 Claims
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1. A hydrocarbyldithiomethyl-modified compound comprising the Formula:
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R1—
O—
CH2—
S—
S—
R2or a salt thereof, wherein R1 is an organic molecule; and
R2 is a hydrocarbyl. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15)
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- 16. A hydrocarbyldithiomethyl-modified compound comprising the formula:
- 21. A compound comprising the Formula:
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25. A method for modifying a nucleoside comprising the steps of:
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a) contacting a nucleoside having at least one hallogenomethyl-modified hydroxyl group with a thiosulfonate compound thereby forming a thiosulfonated nucleoside; and
b) contacting said thiosulfonated nucleoside with a hydrocarbylthiol compound thereby forming a hydrocarbyldithiomethyl-modified nucleoside. - View Dependent Claims (26, 27)
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28. A method for sequencing a nucleic acid comprising the steps of:
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a) contacting a target nucleic acid with a primer under conditions wherein said primer anneals to said target nucleic acid in a sequence specific manner and wherein at least a portion of said primer is complementary to a portion of said target nucleic acid;
b) incorporating a hydrocarbyldithiomethyl-modified nucleotide into said primer; and
c) detecting incorporation of said hydrocarbyldithiomethyl-modified nucleotide, wherein said hydrocarbyldithiomethyl-modified nucleotide is complementary to said target nucleic acid at said hydrocarbyldithiomethyl-modified nucleotide'"'"'s site of incorporation thereby identifying the sequence of one nucleobase of said target nucleic acid. - View Dependent Claims (29, 30, 31)
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32. A method for sequencing a nucleic acid comprising the steps of:
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a) contacting a target nucleic acid with a primer under conditions wherein said primer anneals to said target nucleic acid in a sequence specific manner and wherein at least a portion of said primer is complementary to a portion of said target nucleic acid;
b) incorporating a first 3′
-hydrocarbyldithiomethyl-modified nucleotide into said primer;
c) detecting said incorporation of said first 3′
-hydrocarbyldithiomethyl-modified nucleotide thereby identifying the sequence of a nucleobase of said target nucleic acid;
d) removing said hydrocarbyldithiomethyl group from said first incorporated hydrocarbyldithiomethyl-modified nucleotide to form a first elongated primer having a free hydroxyl group;
e) incorporating a second 3′
-hydrocarbyldithiomethyl-modified nucleotide into said first elongated primer; and
f) detecting said second hydrocarbyldithiomethyl-modified nucleotide thereby identifying the sequence of another nucleobase of said target nucleic acid, wherein said first 3′
-hydrocarbyldithiomethyl-modified nucleotide and said second 3′
-hydrocarbyldithiomethyl-modified nucleotide are complementary to said target nucleic acid at each said nucleotide'"'"'s site of incorporation. - View Dependent Claims (33, 34, 35, 36)
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37. A compound comprising the Formula:
- 38. An oligonucleotide synthesis support comprising the formula:
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40. A method for synthesizing an oligonucleotide comprising the steps of:
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a) providing a 5′
protected first nucleoside covalently bonded to a solid support through a linker;
b) deprotecting said first nucleoside at its 5′
position;
c) covalently bonding another 5′
protected nucleoside to said first nucleotide at the 5′
position of said first nucleoside;
d) deprotecting said another nucleoside at its 5′
position; and
e) repeating steps c) and d) for adding additional protected nucleosides, said linker securing said first nucleotide to said solid support via a hydrocarbyldithiomethyl bond. - View Dependent Claims (41, 42, 43, 44)
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45. A method for synthesizing an oligoribonucleotide comprising the steps of:
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a) providing a first protected ribonucleoside covalently bonded to a solid support;
b) covalently linking at least one 2′
-hydrocarbyldithiomethyl-modified ribonucleoside to said first ribonucleoside to form an oligoribonucleotide;
c) partially de-protecting said oligoribonucleotide under acidic or basic conditions; and
d) contacting said oligoribonucleotide with a reducing agent under neutral conditions thereby completely de-protecting said oligoribonucleotide, wherein said method is effective for preventing cleavage or migration of intemucleotide phosphate bonds, and wherein said hydrocarbyldithiomethyl-modified ribonucleoside comprises a hydrocarbyldithiomethyl group bound at the 2′
position of said hydrocarbyldithiomethyl-modified ribonucleoside. - View Dependent Claims (46, 47, 48, 49)
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50. A method for sequencing a nucleic acid comprising the steps of:
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a) providing a primer array comprising a plurality of sequencing primers;
b) contacting a target nucleic acid with said primer array under conditions wherein said sequencing primers anneal to said target nucleic acid in a sequence specific manner thereby forming target-primer complexes between complementary portions of said sequencing primers and said target nucleic acid;
c) incorporating a first 3′
-hydrocarbyldithiomethyl-modified nucleotide into at least one sequencing primer portion of said target-primer complexes, said first 3′
-hydrocarbyldithiomethyl-modified nucleotide being complementary to said target nucleic acid; and
d) detecting said incorporation of said first 3′
-hydrocarbyldithiomethyl-modified nucleotide, wherein said first 3′
-hydrocarbyldithiomethyl-modified nucleotide is complementary to said target sequence at said first 3′
-hydrocarbyldithiomethyl-modified nucleotide'"'"'s site of incorporation. - View Dependent Claims (51, 52, 53, 54)
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55. A method for synthesizing an oligonucleotide comprising the steps of:
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a) providing a 5′
protected first nucleoside covalently bonded to a solid support through a hydrocarbyldithiomethyl containing linker;
b) deprotecting said first nucleoside at its 5′
position;
c) covalently bonding another 5′
protected nucleoside to said first nucleotide at the 5′
position of said first nucleoside;
d) deprotecting said another nucleoside at its 5′
position;
e) optionally repeating steps c) and d) for adding additional protected nucleosides thereby producing an oligonucleotide;
f) optionally selectively cleaving a protecting group from said oligonucleotide thereby forming a partially deprotected oligonucleotide;
g) selectively cleaving said hydrocarbyldithiomethyl containing linker; and
h) isolating said partially deprotected oligonucleotide. - View Dependent Claims (56, 57)
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Specification