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

  title={An optimized potential function for the calculation of nucleic acid interaction energies I. Base stacking},
  author={Rick L. Ornstein and Robert Rein and Donna L. Breen and Robert D. MacElroy},
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… 
Configurational specificity of stacking interactions in DNA base pairs: A computational analysis
A theoretical study of stacking patterns of various hydrogen‐bonded base pair complexes has been undertaken. Modified Rayleigh‐Schrodinger perturbation theory for intermediate range interactions, has
Conformational studies on polynucleotide chains. V. A comparison between the quantum‐mechanical and the consistent force field approach
Consistent force field (CFF) calculations were performed for the sugar–phosphate–sugar fragment, taken as a model of the polynucleotide backbone. The potential‐energy‐function is the sum of four
RI-MP2 calculations with extended basis sets—a promising tool for study of H-bonded and stacked DNA base pairs
The interaction energies of 9-methyladenine···1-methylthymine H-bonded and 9-methyladenine···9-methylguanine stacked pairs were evaluated at the MP2 and resolution of the identity MP2 (RI-MP2)
Energetics of the protein-DNA-water interaction
The relevant role of hydrophobic interactions and entropy in driving protein-DNA association is indicated by analyses of interaction character showing that, together, the favorable polar and unfavorable polar/hydrophobic-polar interactions mostly cancel.
Molecular dynamics simulations of the bis-intercalated complexes of ditercalinium and Flexi-Di with the hexanucleotide d(GCGCGC)2: theoretical analysis of the interaction and rationale for the sequence binding specificity.
According to the authors' calculations, the electrostatic term is attractive for the stacking interactions between the pyridocarbazole chromophores of these drugs and the base pairs that make up the sandwiched GpC step, but this energy term is repulsive for the base pairing that makes up the boundaries of the bisintercalation site.
Efficient calculation of many stacking and pairing free energies in DNA from a few molecular dynamics simulations.
From analysis of a diverse set of 23 natural and unnatural bases, it appears that stacking free energies and stacking conformations play an important role in pairing of DNA nucleotides.
Empirical energy functions for energy minimization and dynamics of nucleic acids
An improved empirical energy function for energy minimization and dynamics calculations of nucleic acids is developed and evaluated by an examination of its representation of both static and dynamic
The electrostatic contribution to DNA base‐stacking interactions
The Lennard–Jones stacking energy in ideal B‐DNA is found to be essentially independent of sequence, and can be adequately modeled using the Hingerty screening function.


Complementary DNA base interactions: Application of recently refined electrostatic interaction theory
A quantitative approach to the problem of the role of electrostatic interactions in hydrogen bonding in DNA is provided, with obvious impact on the investigation of molecular recognition processes.
Study of the electronic structure of molecules. X
All electrons SCF-LCAO-MO computations for adenine, cytosine, guanine and thyamine are reported. In addition, to compute the total energies and wave functions we have computed the relative gross
Theoretical evaluations of the intermolecular interaction energy of a crystal: application to the analysis of crystal geometry
Simple formulae for the interaction energy between two molecules have been used for writing a program which evaluates the total interaction energy of the molecules in a crystal. These formulae appear
Stereochemistry of nucleic acids and polynucleotides. IV. Conformational energy of base‐sugar units
In this paper, the preferred conformations of the bases with respect to the sugar in various base‐sugar units are worked out using criteria of potential energy. The van der Waals type of intercations
Differences of nucleotide stacking patterns in a crystal and in binary complexes— the case of adenine
It is concluded that, for such configurations with a loosely defined minimum like stacking, crystal structure data may be used only with great caution for assigning a precise configuration to the binary complex.
Theory of intermolecular interactions: The long range terms in the dipole–dipole, monopoles–dipole, and monopoles–bond polarizabilities approximations
The problem of evaluating the long range terms (electrostatic, polarization, dispersion) of the interaction energy between molecules at intermediate distances (i.e. distances of the order of