Nucleic acids labeled with naphthoquinone probe
First Claim
1. A naphthoquinone probe for covalently bonding a nucleic acid target molecule in response to photochemical activation by light irradiation, the naphthoquinone probe having the formula:
- ##STR5## wherein X is a methyl group, and X is positioned on nay of carbon atoms 2-3 and 5-8, wherein said methyl group is capable of alkylation of and covalent bonding to a nucleic acid target molecule due to photochemical activation by light irradiation of the naphthoquinone probe;
wherein L is an N-hydroxy succinimide ester linking group for attaching a probe that localizes to nucleic acid to either ring A or ring B; and
wherein Pr is a nucleic acid probe that preferably localizes to nucleic acid for binding to a nucleic acid target molecule.
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Abstract
A sequence directed reagent is constructed by conjugating a methyl naphthoquinone derivative to a hexamethylamino linker attached to the 5'"'"' terminus of an oligonucleotide. Annealing this modified fragment of DNA to its complementary sequence allows for target modification subsequent to photochemical activation. The product of this reaction is a covalent crosslink between the reagent and target strands resulting from an alkylation of DNA by the photoexcited quinone. The modified sequence is not labile to acid, base or reductants, and blocks the exonuclease activity of the Klenow fragment of DNA polymerase I. In another embodiment, a highly reactive moiety, such as Br is attached to the methyl group of the naphthoquinone derivative. This reagent is similarly linked to an oligonucleotide probe. Activation of this probe linked alkylating agent is by a reductive signal which may either naturally occur within the cell, such as an enzyme, or introduced into the media containing the target molecule.
246 Citations
11 Claims
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1. A naphthoquinone probe for covalently bonding a nucleic acid target molecule in response to photochemical activation by light irradiation, the naphthoquinone probe having the formula:
- ##STR5## wherein X is a methyl group, and X is positioned on nay of carbon atoms 2-3 and 5-8, wherein said methyl group is capable of alkylation of and covalent bonding to a nucleic acid target molecule due to photochemical activation by light irradiation of the naphthoquinone probe;
wherein L is an N-hydroxy succinimide ester linking group for attaching a probe that localizes to nucleic acid to either ring A or ring B; and
wherein Pr is a nucleic acid probe that preferably localizes to nucleic acid for binding to a nucleic acid target molecule. - View Dependent Claims (2, 3, 4, 5)
- ##STR5## wherein X is a methyl group, and X is positioned on nay of carbon atoms 2-3 and 5-8, wherein said methyl group is capable of alkylation of and covalent bonding to a nucleic acid target molecule due to photochemical activation by light irradiation of the naphthoquinone probe;
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6. A naphthoquinone probe for selectively covalently bonding to a nucleic acid target molecule in response to activation by a reductive signal, the naphthoquinone probe having the formula:
- ##STR6## wherein X is located at any of carbon atoms 5-8 of the B ring, and X is selected from the group consisting of CH2 Br, CH2 Cl, CH2 F, CH2 I, CH2 OAc, CH2 OH, CH2 OSO2 CH3, CH2 OSO2 C6 H4 CH3 -p, CH2 OCH2 CH3, CH2 OCONHCH3 and CH2 OCONHCH2 CH2 Cl;
wherein L is an N-hydroxy succinimide ester linking group for attaching a nucleic acid probe to either ring A or ring B; and
wherein Pr is a nucleic acid probe that preferably localizes to a nucleic acid molecule for binding to a nucleic acid target molecule. - View Dependent Claims (7, 8, 9, 10, 11)
- ##STR6## wherein X is located at any of carbon atoms 5-8 of the B ring, and X is selected from the group consisting of CH2 Br, CH2 Cl, CH2 F, CH2 I, CH2 OAc, CH2 OH, CH2 OSO2 CH3, CH2 OSO2 C6 H4 CH3 -p, CH2 OCH2 CH3, CH2 OCONHCH3 and CH2 OCONHCH2 CH2 Cl;
Specification
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- Resources
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Current AssigneeThe Research Foundation for The State University of New York (State University of New York)
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Original AssigneeThe Research Foundation for The State University of New York (State University of New York)
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InventorsChatterjee, Moneesh, Rokita, Steven E.
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Primary Examiner(s)Brown, Johnnie R.
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Assistant Examiner(s)Wilson, James O.
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Application NumberUS07/442,947Time in Patent Office1,560 DaysField of Search514/44, 514/682, 568/328, 536/27, 536/28, 536/29, 536/24.3, 536/25.32, 548/547, 548/548US Class Current536/24.3CPC Class CodesC07H 21/00 Compounds containing two or...
