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Molecular electrostatic potential of the B‐DNA helix. V. Poly(dG·dC) and poly(dA·dT)
Author(s) -
Perahia D.,
Pullman A.,
Pullman B.
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.560160723
Subject(s) - groove (engineering) , minor groove , helix (gastropod) , multipole expansion , chemistry , dna , base pair , crystallography , physics , materials science , biology , ecology , biochemistry , quantum mechanics , snail , metallurgy
The overlap multipole expansion procedure is ptilized for the evaluation of the electrostatic molecular potential of poly(dC·dC) and poly(dA·dT). lt is shown that the two sequences of base pairs produce different effects in the significant regions of DNA. In the inner regions of the double helix the potentials are deeper in the major groove than in the minor groove in poly(dG·dC), and the reverse is true in poly(dA·dT). At large distances from the helical axis the regions of the backbone and the minor groove are preferred. The shielding of the phosphate groups by Na + ions is shown to have an important effect on the discrimination between the two grooves. The region of the minor groove presents always a negative potential for the sequences considered (up to the explored distance of I7 Å from the helical axis), while negative and positive values of the potentials occur, within that distance, in the region of the major groove.