Biopolym. Cell. 2007; 23(3):167-171.
Does non-empirical quantum chemistry allow understanding nature of purine-purine mismatches formation by high fidelity DNA polymerases?
1Kochina O. S., 2, 3Yurenko Ye. P., 3Hovorun D. M.
  1. Taras Shevchenko National University of Kyiv
    64, Volodymyrska Str., Kyiv, Ukraine, 01033
  2. University Pierre and Marie Curie
    4 place Jussieu 75005 Paris, France
  3. Institute of Molecular Biology and Genetics, NAS of Ukraine
    150, Akademika Zabolotnoho Str., Kyiv, Ukraine, 03680


Based on ab initio quantum chemical calculations at the MP2/6–311++G(d,p)//B3LYP/6–31G(d,p) level of theory, we suggest a new approach, explaining molecular mechanisms of purine-purine mismatches formation by high fidelity DNA polymerases.
Keywords: replication DNA polymerase, purine-purine mismatches of DNA biosynthesis, non-empirical quantum chemistry


[1] Poltev VI, Shuliupina NV, Bruskov VI. [Molecular mechanisms of nucleic acid biosynthesis validity. Comparison of results of computer modeling with experimental data]. Mol Biol (Mosk). 1998;32(2):268-76. Russian.
[2] Beard WA, Wilson SH. Structure and mechanism of DNA polymerase beta. Chem Rev. 2006; 106(2):361–82.
[3] Kunkel TA, Bebenek K. DNA replication fidelity. Annu Rev Biochem. 2000;69:497-529.
[4] Beard WA, Wilson SH. Structural insights into DNA polymerase ? fidelity: hold tight if you want it right. Chem Biol. 1998;5(1):R7–R13.
[5] Tikhomirova A, Beletskaya IV, Chalikian TV. Stability of DNA duplexes containing GG, CC, AA, and TT mismatches. Biochemistry. 2006;45(35):10563-71.
[6] Topal MD, Fresco JR. Complementary base pairing and the origin of substitution mutations. Nature. 1976;263(5575):285-9.
[7] Ahn J, Werneburg BG, Tsai MD. DNA polymerase beta: structure-fidelity relationship from Pre-steady-state kinetic analyses of all possible correct and incorrect base pairs for wild type and R283A mutant. Biochemistry. 1997;36(5):1100-7.
[8] Kretulskie AM, Spratt TE. Structure of purine-purine mispairs during misincorporation and extension by Escherichia coli DNA polymerase I. Biochemistry. 2006;45(11):3740-6.