Calculation of the Effects of Hydration and Divalent Metal Ions on Nucleotide Base Pairs: Single G–C and Poly(G–C)

Abstract

Model calculation of the effect of hydration on the energy band structure of a nucleotide base stack ENERGY BAND STRUCTURES OF DNA MODELS 5711 distributions obtained in our present calculations are very similar to those obtained for the single base pairs. 17 ACKNOWLEDGMENTSWe wish to express our gratitude to Dr. Richard von Holdt of Lawrence Radiation Laboratory for providing the fast JACOBI eigenvalue routine and for numerous helpful discussions concerning eigenvalue problems. SCF calculations have been carried out for the electronic energy levels and wavefunctions of single G-C and poly(G-C) in the presence of a neutral water molecule or Mg1+ ion. The Pariser-Parr-Pople (P-P-P) approximation was used for the single base pair, and its equivalent, the semiempirical SCF-LCAO-1:rystal-orbital (CO) approximation, for the polymer. Energy levels and energy bands are presented for four different cases. According to the results, the presence of the Mg2+ ion very strongly changes the band structure of the poly (G-C) . The probable consequences of this on the conductive properties of DNA and the possibility of ab initio calculations on periodic DNA models are discussed.

Energy bands in DNA

“…I n the case of the calculation of poly(G-C) with water impurities, both approximations have given the result [24, 251 that the water molecules produced an extra T band between the lowest filled bands and the other bands (their positions, widths and therefore the gaps between them) remained practically unchanged. O n the other hand, in the case of the charged Mg2+ impurities calculated with the aid of the PPP co method, there were drastic changes in the band structure of poly(G-C) [25] : the width of the valence band has broadened to -0.6 eV, that of the conduction band to -0.5 eV and the width of the lowest filled bands to -2.0 eV. The gap between the valence and conduction bands has decreased from -6.1 eV to -2.0 eV.…”

“…To investigate the effect of impurities on the electronic structure of DNA as a first step the band structure of poly(G-C) has been calculated in the tight binding [24] and in the PPP co approximation [25] assuming that one or two water molecules are bound by hydrogen bonds to the -XH, group of each cytosine molecule or/and to the 11 group of each guanine molecule.$ C 0 Further, the band structure of poly(G-C) was recalculated also in the presence of Mg2+ ions, using again the PPP co approximation ~251. In the two calculated models in model I a Mg2f ion is bound to O,, of each guanine molecule by an ionic bond (in this case the ion is in the plane of G-C in a distance of 2 A from 0,J contributing one n orbital and two n-electrons to the n system of G-C.…”

“…Here ZI is the net charge of the ion, the Coulomb integrals y have been taken between the sites r or s and the position N of net charge and the S,,,(O) and ST,s( f 1) overlap integrals have been calculated using Slater orbitals (for further details see Bibliography [25]). It should be noticed that the expressions (I5a) and (I5b) are consistent with the PPP method, if we use the Mulliken approximation for the occurring three center integrals.…”

Calculation of the Effects of Divalent Metal Ions on Nucleotide Base Pairs. II. Single G–C and A–T and Poly(G–C) and (A–T)

“…4, the two 7r electrons contributed by the Mg2+ ion have little significance, because they are localized at the site of the ion. This always happens when the ionization poten tial and electron affinity of the ion are large compared to those of the other atoms of the base.…”