The Experts below are selected from a list of 261 Experts worldwide ranked by ideXlab platform
Michael P Stone - One of the best experts on this subject based on the ideXlab platform.
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binding of the human nucleotide excision repair proteins xpa and xpc hr23b to the 5r thymine glycol lesion and structure of the cis 5r 6s thymine glycol Epimer in the 5 gtgg 3 sequence destabilization of two base pairs at the lesion site
Nucleic Acids Research, 2010Co-Authors: Kyle L Brown, Ashis K. Basu, Marina Roginskaya, Yue Zou, Alvin Altamirano, Michael P StoneAbstract:The 5R thymine glycol (5R-Tg) DNA lesion exists as a mixture of cis-(5R,6S) and trans-(5R,6R) Epimers; these modulate base excision repair. We examine the 7:3 cis-(5R,6S):trans-(5R,6R) mixture of Epimers paired opposite adenine in the 5'-GTgG-3' sequence with regard to nucleotide excision repair. Human XPA recognizes the lesion comparably to the C8-dG acetylaminoflourene (AAF) adduct, whereas XPC/HR23B recognition of Tg is superior. 5R-Tg is processed by the Escherichia coli UvrA and UvrABC proteins less efficiently than the C8-dG AAF adduct. For the cis-(5R, 6S) Epimer Tg and A are inserted into the helix, remaining in the Watson-Crick alignment. The Tg N3H imine and A N(6) amine protons undergo increased solvent exchange. Stacking between Tg and the 3'-neighbor G*C base pair is disrupted. The solvent accessible surface and T(2) relaxation of Tg increases. Molecular dynamics calculations predict that the axial conformation of the Tg CH(3) group is favored; propeller twisting of the Tg*A pair and hydrogen bonding between Tg OH6 and the N7 atom of the 3'-neighbor guanine alleviate steric clash with the 5'-neighbor base pair. Tg also destabilizes the 5'-neighbor G*C base pair. This may facilitate flipping both base pairs from the helix, enabling XPC/HR23B recognition prior to recruitment of XPA.
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Structural Consequences of Epimerization of Thymine Glycol Lesions in Duplex DNA: Implications for DNA Repair
2010Co-Authors: Kyle L Brown, Ashis K. Basu, Marina Roginskaya, Yue Zou, Alvin Altamirano, Michael P StoneAbstract:Thymine glycol (Tg), 5,6-dihydroxy-5,6-dihydrothymine, forms in DNA by reaction of thymine with reactive oxygen species. It exists as two diastereomeric pairs of Epimers, the 5R cis, trans pair (5R,6S;5R,6R) and the 5S cis, trans pair (5S,6R; 5S,6S). The 5R pair is more abundant. At 30 °C, a 70%:30% cis:trans ratio of Epimers is present in this sequence when SR-Tg is opposite dA. For the cis Epimer Tg and A remain in the Watson-Crick alignment. The Tg N3H imine and A N 6 amine protons undergo increased solvent exchange. Stacking between Tg and the 3'-neighbor G•C base pair is disrupted. The solvent accessible surface and T 2 relaxation of Tg increases. Molecular dynamics calculations predict that the axial conformation of the Tg CH 3 group is favored; propeller twisting of the Tg•A pair and hydrogen bonding between Tg OH6 and the N7 atom of the 3'-neighbor guanine alleviate steric clash with the 5'-neighbor base pair. Tg also destabilizes the 5'-neighbor G•C base pair. Under these conditions, the human NER protein XPA binds to the 5R-Tg lesion comparably to the C8-dG acetylaminoflourene (AAF) adduct, whereas XPC/HR23B binding of the Tg lesion is superior than to the AAF adduct. In comparison, this lesion is processed by the Escherichia coli UvrA and UvrABC proteins less efficiently than the C8-dG AAF adduct. The destabilization of two base pairs by the cis Epimer may facilitate flipping both base pairs from the helix, enabling XPC/HR23B binding prior to recruitment of XPA. When 5R-Tg pairs opposite dG in this sequence context only the cis Epimer is observed. Tg assumes the wobble orientation and stacks below the 5'-neighbor dG, while the mismatched dG stacks below the 5'-neighbor dC. Stacking between Tg and the 3'-neighbor G•C base pair is disrupted. Differences in base excision repair of the Tg•G and Tg•A pairs by hNEIL1 may be related to the wobble orientation of the cis Tg Epimer in the Tg•G pair, and the lack of hydrogen bonding between the Tg OH groups and the N7 atom of the 3'-neighbor dG. Hydrogen bonding between Tg 6 OH6→G 7 N7 in the Tg•A pair may increase the energetic barrier with regard to flipping of the Tg lesion into the active site pocket of the glycosylase, hindering repair.
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Binding of the human nucleotide excision repair proteins XPA and XPC/HR23B to the 5R-thymine glycol lesion and structure of the cis-(5R,6S) thymine glycol Epimer in the 5′-GTgG-3′ sequence: destabilization of two base pairs at the lesion site
Nucleic acids research, 2009Co-Authors: Kyle L Brown, Ashis K. Basu, Marina Roginskaya, Yue Zou, Alvin Altamirano, Michael P StoneAbstract:The 5R thymine glycol (5R-Tg) DNA lesion exists as a mixture of cis-(5R,6S) and trans-(5R,6R) Epimers; these modulate base excision repair. We examine the 7:3 cis-(5R,6S):trans-(5R,6R) mixture of Epimers paired opposite adenine in the 5'-GTgG-3' sequence with regard to nucleotide excision repair. Human XPA recognizes the lesion comparably to the C8-dG acetylaminoflourene (AAF) adduct, whereas XPC/HR23B recognition of Tg is superior. 5R-Tg is processed by the Escherichia coli UvrA and UvrABC proteins less efficiently than the C8-dG AAF adduct. For the cis-(5R, 6S) Epimer Tg and A are inserted into the helix, remaining in the Watson-Crick alignment. The Tg N3H imine and A N(6) amine protons undergo increased solvent exchange. Stacking between Tg and the 3'-neighbor G*C base pair is disrupted. The solvent accessible surface and T(2) relaxation of Tg increases. Molecular dynamics calculations predict that the axial conformation of the Tg CH(3) group is favored; propeller twisting of the Tg*A pair and hydrogen bonding between Tg OH6 and the N7 atom of the 3'-neighbor guanine alleviate steric clash with the 5'-neighbor base pair. Tg also destabilizes the 5'-neighbor G*C base pair. This may facilitate flipping both base pairs from the helix, enabling XPC/HR23B recognition prior to recruitment of XPA.
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interconversion of the cis 5r 6s and trans 5r 6r thymine glycol lesions in duplex dna
Journal of the American Chemical Society, 2008Co-Authors: Kyle L Brown, Ashis K. Basu, Travis Adams, Vijay P Jasti, Michael P StoneAbstract:Thymine glycol (Tg), 5,6-dihydroxy-5,6-dihydrothymine, is formed in DNA by the reaction of thymine with reactive oxygen species. The 5R Tg lesion was incorporated site-specifically into 5′-d(G1T2G3C4G5Tg6G7T8T9T10G11T12)-3′; Tg = 5R Tg. The Tg-modified oligodeoxynucleotide was annealed with either 5′-d(A13C14A15A16A17C18A19C20G21C22A23C24)-3′, forming the Tg6•A19 base pair, corresponding to the oxidative damage of thymine in DNA, or 5′-d(A13C14A15A16A17C18G19C20G21C22A23C24)-3′, forming the mismatched Tg6•G19 base pair, corresponding to the formation of Tg following oxidative damage and deamination of 5-methylcytosine in DNA. At 30 °C, the equilibrium ratio of cis-5R,6S:trans-5R,6R Epimers was 7:3 for the duplex containing the Tg6•A19 base pair. In contrast, for the duplex containing the Tg6•G19 base pair, the cis-5R,6S:trans-5R,6R equilibrium favored the cis-5R,6S Epimer; the level of the trans-5R,6R Epimer remained below the level of detection by NMR. The data suggested that Tg disrupted hydrogen bonding interactions, either when placed opposite to A19 or G19. Thermodynamic measurements indicated a 13 °C reduction of Tm regardless of whether Tg was placed opposite dG or dA in the complementary strand. Although both pairings increased the free energy of melting by 3 kcal/mol, the melting of the Tg•G pair was more enthalpically favored than was the melting of the Tg•A pair. The observation that the position of the equilibrium between the cis-5R,6S and trans-5R,6R thymine glycol Epimers in duplex DNA was affected by the identity of the complementary base extends upon observations that this equilibrium modulates the base excision repair of Tg [Ocampo-Hafalla M. T.; Altamirano A.; Basu A. K.; Chan M. K.; Ocampo J. E.; Cummings A. Jr.; Boorstein R. J.; Cunningham R. P.; Teebor G. W. DNA Repair (Amst)2006, 5, 444−454].
Kyle L Brown - One of the best experts on this subject based on the ideXlab platform.
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binding of the human nucleotide excision repair proteins xpa and xpc hr23b to the 5r thymine glycol lesion and structure of the cis 5r 6s thymine glycol Epimer in the 5 gtgg 3 sequence destabilization of two base pairs at the lesion site
Nucleic Acids Research, 2010Co-Authors: Kyle L Brown, Ashis K. Basu, Marina Roginskaya, Yue Zou, Alvin Altamirano, Michael P StoneAbstract:The 5R thymine glycol (5R-Tg) DNA lesion exists as a mixture of cis-(5R,6S) and trans-(5R,6R) Epimers; these modulate base excision repair. We examine the 7:3 cis-(5R,6S):trans-(5R,6R) mixture of Epimers paired opposite adenine in the 5'-GTgG-3' sequence with regard to nucleotide excision repair. Human XPA recognizes the lesion comparably to the C8-dG acetylaminoflourene (AAF) adduct, whereas XPC/HR23B recognition of Tg is superior. 5R-Tg is processed by the Escherichia coli UvrA and UvrABC proteins less efficiently than the C8-dG AAF adduct. For the cis-(5R, 6S) Epimer Tg and A are inserted into the helix, remaining in the Watson-Crick alignment. The Tg N3H imine and A N(6) amine protons undergo increased solvent exchange. Stacking between Tg and the 3'-neighbor G*C base pair is disrupted. The solvent accessible surface and T(2) relaxation of Tg increases. Molecular dynamics calculations predict that the axial conformation of the Tg CH(3) group is favored; propeller twisting of the Tg*A pair and hydrogen bonding between Tg OH6 and the N7 atom of the 3'-neighbor guanine alleviate steric clash with the 5'-neighbor base pair. Tg also destabilizes the 5'-neighbor G*C base pair. This may facilitate flipping both base pairs from the helix, enabling XPC/HR23B recognition prior to recruitment of XPA.
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Structural Consequences of Epimerization of Thymine Glycol Lesions in Duplex DNA: Implications for DNA Repair
2010Co-Authors: Kyle L Brown, Ashis K. Basu, Marina Roginskaya, Yue Zou, Alvin Altamirano, Michael P StoneAbstract:Thymine glycol (Tg), 5,6-dihydroxy-5,6-dihydrothymine, forms in DNA by reaction of thymine with reactive oxygen species. It exists as two diastereomeric pairs of Epimers, the 5R cis, trans pair (5R,6S;5R,6R) and the 5S cis, trans pair (5S,6R; 5S,6S). The 5R pair is more abundant. At 30 °C, a 70%:30% cis:trans ratio of Epimers is present in this sequence when SR-Tg is opposite dA. For the cis Epimer Tg and A remain in the Watson-Crick alignment. The Tg N3H imine and A N 6 amine protons undergo increased solvent exchange. Stacking between Tg and the 3'-neighbor G•C base pair is disrupted. The solvent accessible surface and T 2 relaxation of Tg increases. Molecular dynamics calculations predict that the axial conformation of the Tg CH 3 group is favored; propeller twisting of the Tg•A pair and hydrogen bonding between Tg OH6 and the N7 atom of the 3'-neighbor guanine alleviate steric clash with the 5'-neighbor base pair. Tg also destabilizes the 5'-neighbor G•C base pair. Under these conditions, the human NER protein XPA binds to the 5R-Tg lesion comparably to the C8-dG acetylaminoflourene (AAF) adduct, whereas XPC/HR23B binding of the Tg lesion is superior than to the AAF adduct. In comparison, this lesion is processed by the Escherichia coli UvrA and UvrABC proteins less efficiently than the C8-dG AAF adduct. The destabilization of two base pairs by the cis Epimer may facilitate flipping both base pairs from the helix, enabling XPC/HR23B binding prior to recruitment of XPA. When 5R-Tg pairs opposite dG in this sequence context only the cis Epimer is observed. Tg assumes the wobble orientation and stacks below the 5'-neighbor dG, while the mismatched dG stacks below the 5'-neighbor dC. Stacking between Tg and the 3'-neighbor G•C base pair is disrupted. Differences in base excision repair of the Tg•G and Tg•A pairs by hNEIL1 may be related to the wobble orientation of the cis Tg Epimer in the Tg•G pair, and the lack of hydrogen bonding between the Tg OH groups and the N7 atom of the 3'-neighbor dG. Hydrogen bonding between Tg 6 OH6→G 7 N7 in the Tg•A pair may increase the energetic barrier with regard to flipping of the Tg lesion into the active site pocket of the glycosylase, hindering repair.
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Binding of the human nucleotide excision repair proteins XPA and XPC/HR23B to the 5R-thymine glycol lesion and structure of the cis-(5R,6S) thymine glycol Epimer in the 5′-GTgG-3′ sequence: destabilization of two base pairs at the lesion site
Nucleic acids research, 2009Co-Authors: Kyle L Brown, Ashis K. Basu, Marina Roginskaya, Yue Zou, Alvin Altamirano, Michael P StoneAbstract:The 5R thymine glycol (5R-Tg) DNA lesion exists as a mixture of cis-(5R,6S) and trans-(5R,6R) Epimers; these modulate base excision repair. We examine the 7:3 cis-(5R,6S):trans-(5R,6R) mixture of Epimers paired opposite adenine in the 5'-GTgG-3' sequence with regard to nucleotide excision repair. Human XPA recognizes the lesion comparably to the C8-dG acetylaminoflourene (AAF) adduct, whereas XPC/HR23B recognition of Tg is superior. 5R-Tg is processed by the Escherichia coli UvrA and UvrABC proteins less efficiently than the C8-dG AAF adduct. For the cis-(5R, 6S) Epimer Tg and A are inserted into the helix, remaining in the Watson-Crick alignment. The Tg N3H imine and A N(6) amine protons undergo increased solvent exchange. Stacking between Tg and the 3'-neighbor G*C base pair is disrupted. The solvent accessible surface and T(2) relaxation of Tg increases. Molecular dynamics calculations predict that the axial conformation of the Tg CH(3) group is favored; propeller twisting of the Tg*A pair and hydrogen bonding between Tg OH6 and the N7 atom of the 3'-neighbor guanine alleviate steric clash with the 5'-neighbor base pair. Tg also destabilizes the 5'-neighbor G*C base pair. This may facilitate flipping both base pairs from the helix, enabling XPC/HR23B recognition prior to recruitment of XPA.
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interconversion of the cis 5r 6s and trans 5r 6r thymine glycol lesions in duplex dna
Journal of the American Chemical Society, 2008Co-Authors: Kyle L Brown, Ashis K. Basu, Travis Adams, Vijay P Jasti, Michael P StoneAbstract:Thymine glycol (Tg), 5,6-dihydroxy-5,6-dihydrothymine, is formed in DNA by the reaction of thymine with reactive oxygen species. The 5R Tg lesion was incorporated site-specifically into 5′-d(G1T2G3C4G5Tg6G7T8T9T10G11T12)-3′; Tg = 5R Tg. The Tg-modified oligodeoxynucleotide was annealed with either 5′-d(A13C14A15A16A17C18A19C20G21C22A23C24)-3′, forming the Tg6•A19 base pair, corresponding to the oxidative damage of thymine in DNA, or 5′-d(A13C14A15A16A17C18G19C20G21C22A23C24)-3′, forming the mismatched Tg6•G19 base pair, corresponding to the formation of Tg following oxidative damage and deamination of 5-methylcytosine in DNA. At 30 °C, the equilibrium ratio of cis-5R,6S:trans-5R,6R Epimers was 7:3 for the duplex containing the Tg6•A19 base pair. In contrast, for the duplex containing the Tg6•G19 base pair, the cis-5R,6S:trans-5R,6R equilibrium favored the cis-5R,6S Epimer; the level of the trans-5R,6R Epimer remained below the level of detection by NMR. The data suggested that Tg disrupted hydrogen bonding interactions, either when placed opposite to A19 or G19. Thermodynamic measurements indicated a 13 °C reduction of Tm regardless of whether Tg was placed opposite dG or dA in the complementary strand. Although both pairings increased the free energy of melting by 3 kcal/mol, the melting of the Tg•G pair was more enthalpically favored than was the melting of the Tg•A pair. The observation that the position of the equilibrium between the cis-5R,6S and trans-5R,6R thymine glycol Epimers in duplex DNA was affected by the identity of the complementary base extends upon observations that this equilibrium modulates the base excision repair of Tg [Ocampo-Hafalla M. T.; Altamirano A.; Basu A. K.; Chan M. K.; Ocampo J. E.; Cummings A. Jr.; Boorstein R. J.; Cunningham R. P.; Teebor G. W. DNA Repair (Amst)2006, 5, 444−454].
Ashis K. Basu - One of the best experts on this subject based on the ideXlab platform.
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binding of the human nucleotide excision repair proteins xpa and xpc hr23b to the 5r thymine glycol lesion and structure of the cis 5r 6s thymine glycol Epimer in the 5 gtgg 3 sequence destabilization of two base pairs at the lesion site
Nucleic Acids Research, 2010Co-Authors: Kyle L Brown, Ashis K. Basu, Marina Roginskaya, Yue Zou, Alvin Altamirano, Michael P StoneAbstract:The 5R thymine glycol (5R-Tg) DNA lesion exists as a mixture of cis-(5R,6S) and trans-(5R,6R) Epimers; these modulate base excision repair. We examine the 7:3 cis-(5R,6S):trans-(5R,6R) mixture of Epimers paired opposite adenine in the 5'-GTgG-3' sequence with regard to nucleotide excision repair. Human XPA recognizes the lesion comparably to the C8-dG acetylaminoflourene (AAF) adduct, whereas XPC/HR23B recognition of Tg is superior. 5R-Tg is processed by the Escherichia coli UvrA and UvrABC proteins less efficiently than the C8-dG AAF adduct. For the cis-(5R, 6S) Epimer Tg and A are inserted into the helix, remaining in the Watson-Crick alignment. The Tg N3H imine and A N(6) amine protons undergo increased solvent exchange. Stacking between Tg and the 3'-neighbor G*C base pair is disrupted. The solvent accessible surface and T(2) relaxation of Tg increases. Molecular dynamics calculations predict that the axial conformation of the Tg CH(3) group is favored; propeller twisting of the Tg*A pair and hydrogen bonding between Tg OH6 and the N7 atom of the 3'-neighbor guanine alleviate steric clash with the 5'-neighbor base pair. Tg also destabilizes the 5'-neighbor G*C base pair. This may facilitate flipping both base pairs from the helix, enabling XPC/HR23B recognition prior to recruitment of XPA.
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Structural Consequences of Epimerization of Thymine Glycol Lesions in Duplex DNA: Implications for DNA Repair
2010Co-Authors: Kyle L Brown, Ashis K. Basu, Marina Roginskaya, Yue Zou, Alvin Altamirano, Michael P StoneAbstract:Thymine glycol (Tg), 5,6-dihydroxy-5,6-dihydrothymine, forms in DNA by reaction of thymine with reactive oxygen species. It exists as two diastereomeric pairs of Epimers, the 5R cis, trans pair (5R,6S;5R,6R) and the 5S cis, trans pair (5S,6R; 5S,6S). The 5R pair is more abundant. At 30 °C, a 70%:30% cis:trans ratio of Epimers is present in this sequence when SR-Tg is opposite dA. For the cis Epimer Tg and A remain in the Watson-Crick alignment. The Tg N3H imine and A N 6 amine protons undergo increased solvent exchange. Stacking between Tg and the 3'-neighbor G•C base pair is disrupted. The solvent accessible surface and T 2 relaxation of Tg increases. Molecular dynamics calculations predict that the axial conformation of the Tg CH 3 group is favored; propeller twisting of the Tg•A pair and hydrogen bonding between Tg OH6 and the N7 atom of the 3'-neighbor guanine alleviate steric clash with the 5'-neighbor base pair. Tg also destabilizes the 5'-neighbor G•C base pair. Under these conditions, the human NER protein XPA binds to the 5R-Tg lesion comparably to the C8-dG acetylaminoflourene (AAF) adduct, whereas XPC/HR23B binding of the Tg lesion is superior than to the AAF adduct. In comparison, this lesion is processed by the Escherichia coli UvrA and UvrABC proteins less efficiently than the C8-dG AAF adduct. The destabilization of two base pairs by the cis Epimer may facilitate flipping both base pairs from the helix, enabling XPC/HR23B binding prior to recruitment of XPA. When 5R-Tg pairs opposite dG in this sequence context only the cis Epimer is observed. Tg assumes the wobble orientation and stacks below the 5'-neighbor dG, while the mismatched dG stacks below the 5'-neighbor dC. Stacking between Tg and the 3'-neighbor G•C base pair is disrupted. Differences in base excision repair of the Tg•G and Tg•A pairs by hNEIL1 may be related to the wobble orientation of the cis Tg Epimer in the Tg•G pair, and the lack of hydrogen bonding between the Tg OH groups and the N7 atom of the 3'-neighbor dG. Hydrogen bonding between Tg 6 OH6→G 7 N7 in the Tg•A pair may increase the energetic barrier with regard to flipping of the Tg lesion into the active site pocket of the glycosylase, hindering repair.
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Binding of the human nucleotide excision repair proteins XPA and XPC/HR23B to the 5R-thymine glycol lesion and structure of the cis-(5R,6S) thymine glycol Epimer in the 5′-GTgG-3′ sequence: destabilization of two base pairs at the lesion site
Nucleic acids research, 2009Co-Authors: Kyle L Brown, Ashis K. Basu, Marina Roginskaya, Yue Zou, Alvin Altamirano, Michael P StoneAbstract:The 5R thymine glycol (5R-Tg) DNA lesion exists as a mixture of cis-(5R,6S) and trans-(5R,6R) Epimers; these modulate base excision repair. We examine the 7:3 cis-(5R,6S):trans-(5R,6R) mixture of Epimers paired opposite adenine in the 5'-GTgG-3' sequence with regard to nucleotide excision repair. Human XPA recognizes the lesion comparably to the C8-dG acetylaminoflourene (AAF) adduct, whereas XPC/HR23B recognition of Tg is superior. 5R-Tg is processed by the Escherichia coli UvrA and UvrABC proteins less efficiently than the C8-dG AAF adduct. For the cis-(5R, 6S) Epimer Tg and A are inserted into the helix, remaining in the Watson-Crick alignment. The Tg N3H imine and A N(6) amine protons undergo increased solvent exchange. Stacking between Tg and the 3'-neighbor G*C base pair is disrupted. The solvent accessible surface and T(2) relaxation of Tg increases. Molecular dynamics calculations predict that the axial conformation of the Tg CH(3) group is favored; propeller twisting of the Tg*A pair and hydrogen bonding between Tg OH6 and the N7 atom of the 3'-neighbor guanine alleviate steric clash with the 5'-neighbor base pair. Tg also destabilizes the 5'-neighbor G*C base pair. This may facilitate flipping both base pairs from the helix, enabling XPC/HR23B recognition prior to recruitment of XPA.
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interconversion of the cis 5r 6s and trans 5r 6r thymine glycol lesions in duplex dna
Journal of the American Chemical Society, 2008Co-Authors: Kyle L Brown, Ashis K. Basu, Travis Adams, Vijay P Jasti, Michael P StoneAbstract:Thymine glycol (Tg), 5,6-dihydroxy-5,6-dihydrothymine, is formed in DNA by the reaction of thymine with reactive oxygen species. The 5R Tg lesion was incorporated site-specifically into 5′-d(G1T2G3C4G5Tg6G7T8T9T10G11T12)-3′; Tg = 5R Tg. The Tg-modified oligodeoxynucleotide was annealed with either 5′-d(A13C14A15A16A17C18A19C20G21C22A23C24)-3′, forming the Tg6•A19 base pair, corresponding to the oxidative damage of thymine in DNA, or 5′-d(A13C14A15A16A17C18G19C20G21C22A23C24)-3′, forming the mismatched Tg6•G19 base pair, corresponding to the formation of Tg following oxidative damage and deamination of 5-methylcytosine in DNA. At 30 °C, the equilibrium ratio of cis-5R,6S:trans-5R,6R Epimers was 7:3 for the duplex containing the Tg6•A19 base pair. In contrast, for the duplex containing the Tg6•G19 base pair, the cis-5R,6S:trans-5R,6R equilibrium favored the cis-5R,6S Epimer; the level of the trans-5R,6R Epimer remained below the level of detection by NMR. The data suggested that Tg disrupted hydrogen bonding interactions, either when placed opposite to A19 or G19. Thermodynamic measurements indicated a 13 °C reduction of Tm regardless of whether Tg was placed opposite dG or dA in the complementary strand. Although both pairings increased the free energy of melting by 3 kcal/mol, the melting of the Tg•G pair was more enthalpically favored than was the melting of the Tg•A pair. The observation that the position of the equilibrium between the cis-5R,6S and trans-5R,6R thymine glycol Epimers in duplex DNA was affected by the identity of the complementary base extends upon observations that this equilibrium modulates the base excision repair of Tg [Ocampo-Hafalla M. T.; Altamirano A.; Basu A. K.; Chan M. K.; Ocampo J. E.; Cummings A. Jr.; Boorstein R. J.; Cunningham R. P.; Teebor G. W. DNA Repair (Amst)2006, 5, 444−454].
Lydia Perkins - One of the best experts on this subject based on the ideXlab platform.
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4 c methoxy 2 deoxy 2 fluoro modified ribonucleotides improve metabolic stability and elicit efficient rnai mediated gene silencing
Journal of the American Chemical Society, 2017Co-Authors: Elise Malekadamian, Dale C Guenther, Shigeo Matsuda, Saul Martinezmontero, Ivan Zlatev, Joel M Harp, Mihai Burai Patrascu, Donald J Foster, Johans Fakhoury, Lydia PerkinsAbstract:We designed novel 4′-modified 2′-deoxy-2′-fluorouridine (2′-F U) analogues with the aim to improve nuclease resistance and potency of therapeutic siRNAs by introducing 4′-C-methoxy (4′-OMe) as the alpha (C4′α) or beta (C4′β) Epimers. The C4′α Epimer was synthesized by a stereoselective route in six steps; however, both α and β Epimers could be obtained by a nonstereoselective approach starting from 2′-F U. 1H NMR analysis and computational investigation of the α-Epimer revealed that the 4′-OMe imparts a conformational bias toward the North-East sugar pucker, due to intramolecular hydrogen bonding and hyperconjugation effects. The α-Epimer generally conceded similar thermal stability as unmodified nucleotides, whereas the β-Epimer led to significant destabilization. Both 4′-OMe Epimers conferred increased nuclease resistance, which can be explained by the close proximity between 4′-OMe substituent and the vicinal 5′- and 3′-phosphate group, as seen in the X-ray crystal structure of modified RNA. siRNAs con...
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4′‑C‑Methoxy-2′-deoxy-2′-fluoro Modified Ribonucleotides Improve Metabolic Stability and Elicit Efficient RNAi-Mediated Gene Silencing
2017Co-Authors: Elise Malek-adamian, Dale C Guenther, Shigeo Matsuda, Ivan Zlatev, Mihai Burai Patrascu, Donald J Foster, Johans Fakhoury, Saúl Martínez-montero, Joel Harp, Lydia PerkinsAbstract:We designed novel 4′-modified 2′-deoxy-2′-fluorouridine (2′-F U) analogues with the aim to improve nuclease resistance and potency of therapeutic siRNAs by introducing 4′-C-methoxy (4′-OMe) as the alpha (C4′α) or beta (C4′β) Epimers. The C4′α Epimer was synthesized by a stereoselective route in six steps; however, both α and β Epimers could be obtained by a nonstereoselective approach starting from 2′-F U. 1H NMR analysis and computational investigation of the α-Epimer revealed that the 4′-OMe imparts a conformational bias toward the North-East sugar pucker, due to intramolecular hydrogen bonding and hyperconjugation effects. The α-Epimer generally conceded similar thermal stability as unmodified nucleotides, whereas the β-Epimer led to significant destabilization. Both 4′-OMe Epimers conferred increased nuclease resistance, which can be explained by the close proximity between 4′-OMe substituent and the vicinal 5′- and 3′-phosphate group, as seen in the X-ray crystal structure of modified RNA. siRNAs containing several C4′α-Epimer monomers in the sense or antisense strands triggered RNAi-mediated gene silencing with efficiencies comparable to that of 2′-F U
Marina Roginskaya - One of the best experts on this subject based on the ideXlab platform.
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Structural Consequences of Epimerization of Thymine Glycol Lesions in Duplex DNA: Implications for DNA Repair
2010Co-Authors: Kyle L Brown, Ashis K. Basu, Marina Roginskaya, Yue Zou, Alvin Altamirano, Michael P StoneAbstract:Thymine glycol (Tg), 5,6-dihydroxy-5,6-dihydrothymine, forms in DNA by reaction of thymine with reactive oxygen species. It exists as two diastereomeric pairs of Epimers, the 5R cis, trans pair (5R,6S;5R,6R) and the 5S cis, trans pair (5S,6R; 5S,6S). The 5R pair is more abundant. At 30 °C, a 70%:30% cis:trans ratio of Epimers is present in this sequence when SR-Tg is opposite dA. For the cis Epimer Tg and A remain in the Watson-Crick alignment. The Tg N3H imine and A N 6 amine protons undergo increased solvent exchange. Stacking between Tg and the 3'-neighbor G•C base pair is disrupted. The solvent accessible surface and T 2 relaxation of Tg increases. Molecular dynamics calculations predict that the axial conformation of the Tg CH 3 group is favored; propeller twisting of the Tg•A pair and hydrogen bonding between Tg OH6 and the N7 atom of the 3'-neighbor guanine alleviate steric clash with the 5'-neighbor base pair. Tg also destabilizes the 5'-neighbor G•C base pair. Under these conditions, the human NER protein XPA binds to the 5R-Tg lesion comparably to the C8-dG acetylaminoflourene (AAF) adduct, whereas XPC/HR23B binding of the Tg lesion is superior than to the AAF adduct. In comparison, this lesion is processed by the Escherichia coli UvrA and UvrABC proteins less efficiently than the C8-dG AAF adduct. The destabilization of two base pairs by the cis Epimer may facilitate flipping both base pairs from the helix, enabling XPC/HR23B binding prior to recruitment of XPA. When 5R-Tg pairs opposite dG in this sequence context only the cis Epimer is observed. Tg assumes the wobble orientation and stacks below the 5'-neighbor dG, while the mismatched dG stacks below the 5'-neighbor dC. Stacking between Tg and the 3'-neighbor G•C base pair is disrupted. Differences in base excision repair of the Tg•G and Tg•A pairs by hNEIL1 may be related to the wobble orientation of the cis Tg Epimer in the Tg•G pair, and the lack of hydrogen bonding between the Tg OH groups and the N7 atom of the 3'-neighbor dG. Hydrogen bonding between Tg 6 OH6→G 7 N7 in the Tg•A pair may increase the energetic barrier with regard to flipping of the Tg lesion into the active site pocket of the glycosylase, hindering repair.
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binding of the human nucleotide excision repair proteins xpa and xpc hr23b to the 5r thymine glycol lesion and structure of the cis 5r 6s thymine glycol Epimer in the 5 gtgg 3 sequence destabilization of two base pairs at the lesion site
Nucleic Acids Research, 2010Co-Authors: Kyle L Brown, Ashis K. Basu, Marina Roginskaya, Yue Zou, Alvin Altamirano, Michael P StoneAbstract:The 5R thymine glycol (5R-Tg) DNA lesion exists as a mixture of cis-(5R,6S) and trans-(5R,6R) Epimers; these modulate base excision repair. We examine the 7:3 cis-(5R,6S):trans-(5R,6R) mixture of Epimers paired opposite adenine in the 5'-GTgG-3' sequence with regard to nucleotide excision repair. Human XPA recognizes the lesion comparably to the C8-dG acetylaminoflourene (AAF) adduct, whereas XPC/HR23B recognition of Tg is superior. 5R-Tg is processed by the Escherichia coli UvrA and UvrABC proteins less efficiently than the C8-dG AAF adduct. For the cis-(5R, 6S) Epimer Tg and A are inserted into the helix, remaining in the Watson-Crick alignment. The Tg N3H imine and A N(6) amine protons undergo increased solvent exchange. Stacking between Tg and the 3'-neighbor G*C base pair is disrupted. The solvent accessible surface and T(2) relaxation of Tg increases. Molecular dynamics calculations predict that the axial conformation of the Tg CH(3) group is favored; propeller twisting of the Tg*A pair and hydrogen bonding between Tg OH6 and the N7 atom of the 3'-neighbor guanine alleviate steric clash with the 5'-neighbor base pair. Tg also destabilizes the 5'-neighbor G*C base pair. This may facilitate flipping both base pairs from the helix, enabling XPC/HR23B recognition prior to recruitment of XPA.
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Binding of the human nucleotide excision repair proteins XPA and XPC/HR23B to the 5R-thymine glycol lesion and structure of the cis-(5R,6S) thymine glycol Epimer in the 5′-GTgG-3′ sequence: destabilization of two base pairs at the lesion site
Nucleic acids research, 2009Co-Authors: Kyle L Brown, Ashis K. Basu, Marina Roginskaya, Yue Zou, Alvin Altamirano, Michael P StoneAbstract:The 5R thymine glycol (5R-Tg) DNA lesion exists as a mixture of cis-(5R,6S) and trans-(5R,6R) Epimers; these modulate base excision repair. We examine the 7:3 cis-(5R,6S):trans-(5R,6R) mixture of Epimers paired opposite adenine in the 5'-GTgG-3' sequence with regard to nucleotide excision repair. Human XPA recognizes the lesion comparably to the C8-dG acetylaminoflourene (AAF) adduct, whereas XPC/HR23B recognition of Tg is superior. 5R-Tg is processed by the Escherichia coli UvrA and UvrABC proteins less efficiently than the C8-dG AAF adduct. For the cis-(5R, 6S) Epimer Tg and A are inserted into the helix, remaining in the Watson-Crick alignment. The Tg N3H imine and A N(6) amine protons undergo increased solvent exchange. Stacking between Tg and the 3'-neighbor G*C base pair is disrupted. The solvent accessible surface and T(2) relaxation of Tg increases. Molecular dynamics calculations predict that the axial conformation of the Tg CH(3) group is favored; propeller twisting of the Tg*A pair and hydrogen bonding between Tg OH6 and the N7 atom of the 3'-neighbor guanine alleviate steric clash with the 5'-neighbor base pair. Tg also destabilizes the 5'-neighbor G*C base pair. This may facilitate flipping both base pairs from the helix, enabling XPC/HR23B recognition prior to recruitment of XPA.
