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Counter‐ion effects of A‐ and B‐type poly(dG)·Poly(dC) and poly(dA)·Poly(dT) DNA by elongation method
Author(s) -
Xie Peng,
Liu Kai,
Gu Fenglong,
Aoki Yuriko
Publication year - 2012
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.23230
Subject(s) - homo/lumo , elongation , chemistry , guanine , ion , stacking , band gap , ab initio , molecule , crystallography , materials science , physics , condensed matter physics , organic chemistry , metallurgy , ultimate tensile strength , nucleotide , biochemistry , gene
Abstract The elongation method was developed to calculate the local density of states (LDOS) at ab initio molecular orbital (MO) level. This method is performed on eight types of DNA molecules: namely, a pitch of A‐ and B‐ type poly(dA)·poly(dT) and poly(dG)·poly(dC), and they are neutralized by H + and Na + , respectively. The difference of total energy between elongation and conventional calculations in each step is considerably small in the order of 10 −9 hartree/atom for 20 units of B‐type poly(dA)·poly(dT) model. When the figures of total DOS of each model was compared, the energy gap of model containing Na + is smaller than that of corresponding model containing H + . The LDOS for each model estimated by elongation method can well reproduce the results by conventional method. The LDOS figures show that the valence bands in A‐ and B‐type DNA are formed by the highest occupied MOs (HOMOs) of adenine/guanine. Na + can greatly decrease the energy of lowest unoccupied MO (LUMO) and consequently decrease the energy gap between LUMO and HOMO. The electron transfer between stacking adenine/guanine and sodium would play an important role in the conductivity of A‐ and B‐type DNA. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012