共 59 条
Quantifying the energetic contributions of desolvation and π-electron density during translesion DNA synthesis
被引:18
作者:
Motea, Edward A.
[2
]
Lee, Irene
[2
]
Berdis, Anthony J.
[1
]
机构:
[1] Case Western Reserve Univ, Dept Pharmacol, Cleveland, OH 44106 USA
[2] Case Western Reserve Univ, Dept Chem, Cleveland, OH 44106 USA
基金:
美国国家卫生研究院;
关键词:
SELECTIVE INCORPORATION OPPOSITE;
APURINIC APYRIMIDINIC SITES;
SINGLE ABASIC SITE;
NONNATURAL NUCLEOTIDES;
BASE-STACKING;
DEOXYRIBONUCLEIC-ACID;
MUTATION-RATES;
HYDROGEN-BONDS;
A-RULE;
POLYMERASE;
D O I:
10.1093/nar/gkq925
中图分类号:
Q5 [生物化学];
Q7 [分子生物学];
学科分类号:
071010 ;
081704 ;
摘要:
This report examines the molecular mechanism by which high-fidelity DNA polymerases select nucleotides during the replication of an abasic site, a non-instructional DNA lesion. This was accomplished by synthesizing several unique 5-substituted indolyl 2'-deoxyribose triphosphates and defining their kinetic parameters for incorporation opposite an abasic site to interrogate the contributions of pi-electron density and solvation energies. In general, the K-d,K- app values for hydrophobic non-natural nucleotides are similar to 10-fold lower than those measured for isosteric hydrophilic analogs. In addition, k(pol) values for nucleotides that contain less pi-electron densities are slower than isosteric analogs possessing higher degrees of pi-electron density. The differences in kinetic parameters were used to quantify the energetic contributions of desolvation and pi-electron density on nucleotide binding and polymerization rate constant. We demonstrate that analogs lacking hydrogen-bonding capabilities act as chain terminators of translesion DNA replication while analogs with hydrogen bonding functional groups are extended when paired opposite an abasic site. Collectively, the data indicate that the efficiency of nucleotide incorporation opposite an abasic site is controlled by energies associated with nucleobase desolvation and pi-electron stacking interactions whereas elongation beyond the lesion is achieved through a combination of base-stacking and hydrogen-bonding interactions.
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页码:1623 / 1637
页数:15
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