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Molecular mechanics studies of sequence‐specific repair of DNA alkylated by EMS in the laci gene of Escherichia coli
Author(s) -
Foley C. K.,
Pedersen L. G.,
Darden T. A.,
Anderson M. W.
Publication year - 2009
Publication title -
international journal of quantum chemistry
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.484
H-Index - 105
eISSN - 1097-461X
pISSN - 0020-7608
DOI - 10.1002/qua.560360705
Subject(s) - dna , escherichia coli , lac repressor , dna repair , nucleotide excision repair , chemistry , biophysics , microbiology and biotechnology , binding site , gene , biology , biochemistry , lac operon
Aspects of sequence‐specific UvrABC excision repair in DNA have been studied by calculating binding energies of oligomers containing central 3mers of the type XGeY, where X and Y are bases corresponding to specific sites in the lacI gene of Escherichia coli and the central Ge is O 6 ‐ethylguanine. Binding energies were determined by first calculating the total energy of the double strand for a given sequence in B‐DNA form and subtracting the total energy of the two separate single strands. A plot of binding energy vs. the ratio of mutations at sites in repair‐deficient and repair‐proficient strains of E. coli show that the weaker the binding of the DNA helix the more efficiently ethylguanine lesions are repaired. A model is proposed that relates the local binding energies of ethylguanine‐containing strands to the fraction of mutations remaining in an excision‐repair‐deficient strain of E. coli . This model indicates that site‐specific variations in the efficiency of UvrABC excision repair of ethylguanine lesions may be controlled by variations in local helix geometry caused by weaker or tighter binding of the DNA helix.