Interaction of Ia and IIa Group Cations with the Guanine Site in Cytosine-guanine Nucleic Acid Base Pair: An Ab Initio Hartree Fock Study in the Absence of Basis Set Superposition Error

Structures and energetics of complexes between guanine...cytosine Watson Crick (GCWC) DNA base pair and various metal cations were investigated by an ab initio Hartree Fock (HF) study in the absence of basis set superposition error. Cations were allowed to interact with N7 and O6 sites of guanine. The BSSE free gradient geometry optimisation were performed in the framework of the SCF-MI (self consistent field for molecular interactions) theory. In particular, the structure of the complex with the mono and bivalent cations, like H+, Na+, K+, Mg++, Ca++ were analysed showing that the coordination to the N7 and O6 sites of the GCWC pair can generate non-WC hydrogen bonding patterns. The results demonstrate that the a priori elimination of the BSSE allows to study molecular clusters of biological interest by employing small basis sets.

[1]  R. Savoie,et al.  Raman spectroscopic study of the effects of Ca2+, Mg2+, Zn2+, and Cd2+ ions on calf thymus DNA: Binding sites and conformational changes , 1990, Biopolymers.

[2]  V. Potaman,et al.  Divalent metal cations upon coordination to the N7 of purines differentially stabilize the PyPuPu DNA triplex due to unequal Hoogsteen-type hydrogen bond enhancement. , 1994, Journal of biomolecular structure & dynamics.

[3]  S. Mansy,et al.  Binding of cis- and trans-dichlorodiammineplatinum(II) to nucleosides. I. Location of the binding sites. , 1973, Journal of the American Chemical Society.

[4]  P. Hobza,et al.  A quantum chemical study of the effect of Na+ on the hydrogen bonds in the adenine-thymine base-pair. , 1984, Biophysical chemistry.

[5]  Ian M. Mills,et al.  Force Constants and Dipole-Moment Derivatives of Molecules from Perturbed Hartree-Fock Calculations. I , 1968 .

[6]  R. M. Izatt,et al.  Thermodynamics of proton dissociation in dilute aqueous solution. 8. pK, change in heat content, and change in entropy values for proton ionization from several pyrimidines and their nucleosides at 25 degrees. , 1967, The Journal of physical chemistry.

[7]  J. Šponer,et al.  Structures and Energies of Hydrogen-Bonded DNA Base Pairs. A Nonempirical Study with Inclusion of Electron Correlation , 1996 .

[8]  Y. Yamaguchi,et al.  A New Dimension to Quantum Chemistry: Analytic Derivative Methods in AB Initio Molecular Electronic Structure Theory , 1994 .

[9]  S. F. Boys,et al.  The calculation of small molecular interactions by the differences of separate total energies. Some procedures with reduced errors , 1970 .

[10]  H. Günthard,et al.  Quantum chemical investigation of stability and structure related to the geometrical isomerism of tautomeric forms of cytosine and uracil , 1992 .

[11]  J. Šponer,et al.  Interaction between the Guanine−Cytosine Watson−Crick DNA Base Pair and Hydrated Group IIa (Mg2+, Ca2+, Sr2+, Ba2+) and Group IIb (Zn2+, Cd2+, Hg2+) Metal Cations , 1998 .

[12]  J. Šponer,et al.  Nature of Nucleic Acid−Base Stacking: Nonempirical ab Initio and Empirical Potential Characterization of 10 Stacked Base Dimers. Comparison of Stacked and H-Bonded Base Pairs , 1996 .

[13]  J. D. Bene.  Molecular orbital study of the lithium(1+) complexes of the DNA bases , 1984 .

[14]  M. Raimondi,et al.  Extension of the SCF-MI Method to the Case of K Fragments one of which is an Open-Shell System. , 1998 .

[15]  Miquel Duran,et al.  How does basis set superposition error change the potential surfaces for hydrogen-bonded dimers? , 1996 .

[16]  W. Hehre,et al.  Molecular orbital theory of the properties of inorganic and organometallic compounds 4. Extended basis sets for third‐and fourth‐row, main‐group elements , 1986 .

[17]  Sotiris S. Xantheas,et al.  On the importance of the fragment relaxation energy terms in the estimation of the basis set superposition error correction to the intermolecular interaction energy , 1996 .

[18]  N. V. Riggs.  AN AB INITIO STUDY OF THE STATIONARY STRUCTURES OF THE MAJOR GAS-PHASE TAUTOMER OF ADENINE , 1991 .

[19]  J. Sühnel,et al.  Quantum-chemical ab initio study on the adenine-difluorotoluene complex--a mimic for the adenine-thymine base pair. , 1997, Journal of biomolecular structure & dynamics.

[20]  J. Šponer,et al.  Interaction of DNA Base Pairs with Various Metal Cations (Mg2+, Ca2+, Sr2+, Ba2+, Cu+, Ag+, Au+, Zn2+, Cd2+, and Hg2+): Nonempirical ab Initio Calculations on Structures, Energies, and Nonadditivity of the Interaction , 1997 .

[21]  Pavel Hobza,et al.  Performance of empirical potentials (AMBER, CFF95, CVFF, CHARMM, OPLS, POLTEV), semiempirical quantum chemical methods (AM1, MNDO/M, PM3), and ab initio Hartree–Fock method for interaction of DNA bases: Comparison with nonempirical beyond Hartree–Fock results , 1997 .

[22]  J. Šponer,et al.  Ab Initio Study of the Interaction of Guanine and Adenine with Various Mono- and Bivalent Metal Cations (Li+, Na+, K+, Rb+, Cs+; Cu+, Ag+, Au+; Mg2+, Ca2+, Sr2+, Ba2+; Zn2+, Cd2+, and Hg2+) , 1996 .

[23]  P Hobza,et al.  Hydrogen bonding and stacking of DNA bases: a review of quantum-chemical ab initio studies. , 1996, Journal of biomolecular structure & dynamics.

[24]  Antonino Famulari,et al.  Modification of Roothaan Equations for the Ab-Initio Calculation of Interactions in Large Molecular Systems in the Absence of Basis Set Superposition Error , 1999, LSSC.

[25]  F. J. Luque,et al.  TAUTOMERISM AND PROTONATION OF GUANINE AND CYTOSINE. IMPLICATIONS IN THE FORMATION OF HYDROGEN-BONDED COMPLEXES , 1996 .

[26]  Angelo Liguori,et al.  Gas-phase proton affinity of deoxyribonucleosides and related nucleobases by fast atom bombardment tandem mass spectrometry , 1990 .

[27]  Joel F. Liebman,et al.  Evaluated Gas Phase Basicities and Proton Affinities of Molecules; Heats of Formation of Protonated Molecules , 1984 .

[28]  Pavel Hobza,et al.  Counterpoise-corrected potential energy surfaces of simple H-bonded systems , 1998 .

[29]  Peter Pulay,et al.  Ab initio calculation of force constants and equilibrium geometries in polyatomic molecules , 1969 .

[30]  J. Šponer,et al.  Ability of empirical potentials (AMBER, CHARMM, CVFF, OPLS, Poltev) and semi-empirical quantum chemical methods (AM1, MNDO/M, PM3) to describe H-bonding in DNA base pairs; comparison with ab initio results , 1996 .

[31]  Wolfram Saenger,et al.  Principles of Nucleic Acid Structure , 1983 .

[32]  J. Šponer,et al.  Base stacking and hydrogen bonding in protonated cytosine dimer: the role of molecular ion-dipole and induction interactions. , 1996, Journal of biomolecular structure & dynamics.

[33]  D. Thiele,et al.  Four-stranded nucleic acid structures 25 years later: from guanosine gels to telomer DNA. , 1990, Journal of biomolecular structure & dynamics.