An optimized potential function for the calculation of nucleic acid interaction energies I. Base stacking

An optimized potential function for base‐stacking interaction is constructed. Stacking energies between the complementary pairs of a dimer are calculated as a function of the rotational angle and separation distance. Using several different sets of atomic charges, the electrostatic component in the monopole‐monopole approximation (MMA) is compared to the more refined segmented multipole–multipole representation (SMMA); the general features of the stacking minima are found to be correctly reproduced with IEHT or CNDO atomic charges. The electrostatic component is observed to control the location of stacking minima. The MMA, in general, is not a reliable approximation of the SMMA in regions away from minima; however, the MMA is reliable in predicting the location and nature of stacking minima. The attractive part of the Lennard‐Jones 6–12 potential is compared to and parameterized against the expression for the second‐order interaction terms composed of multipole‐bond polarizability for the polarization energy and transition‐dipole bond polarizabilities for approximation of the dispersion energy. The repulsive part of the Lennard‐Jones potential is compared to a Kitaygorodski‐type repulsive function; changing the exponent from its usual value of 12 to 11.7 gives significantly better agreement with the more refined repulsive function. Stacking minima calculated with the optimized potential method are compared with various perturbation‐type treatments. The optimized potential method yields results that compare as well with melting data as do any of the more recent and expensive perturbation methods.

[1]  M. Spencer.  The stereochemistry of deoxyribonucleic acid. I. Covalent bond lengths and angles , 1959 .

[2]  I. Tinoco,et al.  The stability of helical polynucleotides: base contributions. , 1962, Journal of molecular biology.

[3]  Harold A. Scheraga,et al.  Conformational Analysis of Macromolecules. III. Helical Structures of Polyglycine and Poly‐L‐Alanine , 1966 .

[4]  P. Claverie.  Some Practical Improvements in the Calculation of Intermolecular Energies , 1968 .

[5]  C. Giessner-Prettre,et al.  All valence-electrons calculations of the biological purines and pyrimidines , 1968 .

[6]  Robert Rein,et al.  On the calculation of London–Van der Waals interactions in a monopole‐bond polarizability approximation with application to interaction between purine and pyrimidine bases , 1968 .

[7]  A. Lakshminarayanan,et al.  Stereochemistry of nucleic acids and polynucleotides. V. Conformational energy of a ribose‐phosphale unit , 1969 .

[8]  Enrico Clementi,et al.  Study of the electronic structure of molecules. X , 1969 .

[9]  R. Rein,et al.  Theory of intermolecular interactions: The long range terms in the dipole–dipole, monopoles–dipole, and monopoles–bond polarizabilities approximations , 1969 .

[10]  A. Pullman,et al.  Ab initio Calculations on cytosine, thymine and adenine , 1969 .

[11]  A. V. Lakshminarayanan,et al.  Stereochemistry of nucleic acids and polynucleotides. IV. Conformational energy of base‐sugar units , 1969 .

[12]  C. Cantor,et al.  Physicochemical studies on polydeoxyribonucleotides containing defined repeating nucleotide sequences. , 1970, Journal of molecular biology.

[13]  A. Lakshminarayanan,et al.  Stereochemistry of nucleic acids and polynucleotides III. Electronic charge distribution , 1971, Biopolymers.

[14]  R. Rein,et al.  Complementary DNA base interactions: Application of recently refined electrostatic interaction theory , 1972, Biopolymers.

[15]  M. Sundaralingam,et al.  Correlation between the backbone and side chain conformations in 5′‐nucleotides. The concept of a ‘rigid’ nucleotide conformation , 1973 .

[16]  R. Langridge,et al.  Structure of guanosine‐3′,5′‐cytidine monophosphate. I. Semi‐empirical potential energy calculations and model‐building , 1973, Biopolymers.

[17]  Robert Rein,et al.  On Physical Properties and Interactions of Polyatomic Molecules: With Application to Molecular Recognition in Biology , 1973 .

[18]  S. Arnott,et al.  Conformation of keratan sulphate. , 1974, Journal of molecular biology.

[19]  S. Arnott,et al.  The structure of polydeoxyguanylic acid · polydeoxycytidylic acid☆ , 1974 .

[20]  P. Claverie,et al.  Differences of nucleotide stacking patterns in a crystal and in binary complexes— the case of adenine , 1974, Biopolymers.

[21]  S. Arnott,et al.  Structures for the polynucleotide complexes poly(dA) with poly (dT) and poly(dT) with poly(dA) with poly (dT). , 1974, Journal of molecular biology.

[22]  A. Imamura,et al.  A molecular orbital study of stability and the conformation of double-stranded DNA-like polymers. , 1974, Journal of theoretical biology.

[23]  B. I. Sukhorukov,et al.  The influence of nitrous bases interactions on the DNA secondary structure formation. , 1975, Journal of theoretical biology.

[24]  P. Claverie,et al.  Theoretical evaluations of the intermolecular interaction energy of a crystal: application to the analysis of crystal geometry , 1975 .

[25]  V. Danilov,et al.  Quantum mechanical study of bases interactions in various associates in atomic dipole approximation. , 1976, Journal of theoretical biology.