Complementary DNA base interactions: Application of recently refined electrostatic interaction theory

Stamatiadou, Mary N.; Swissler, Thomas J.; Rabinowitz, James R.; Rein, Robert

doi:10.1002/bip.1972.360110608

Cited by 20 publications

(6 citation statements)

References 19 publications

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“…Another approach that has been studied very extensively involves expressing V(7r) as a multipole expansion, written in terms of one or more centers (46)(47)(48). In a recent adaptation of this technique, designed to facilitate the treatment of large biological molecules, each overlap term in the electronic density function was replaced by a one-center expansion that went as far as the quadrupole terms (49).…”

Section: Methods Of Calculating the Electrostatic Potentialmentioning

confidence: 99%

Molecular electrostatic potentials: an effective tool for the elucidation of biochemical phenomena.

Politzer¹,

Laurence²,

Jayasuriya³

1985

Environ Health Perspect

698

139

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The electrostatic potential V(r) that is created in the space around a molecule by its nuclei and electrons (treated as static distributions of charge) is a very useful property for analyzing and predicting molecular reactive behavior. It is rigorously defined and can be determined experimentally as well as computationally. The potential has been particularly useful as an indicator of the sites or regions of a molecule to which an approaching electrophile is initially attracted, and it has also been applied successfully to the study of interactions that involve a certain optimum relative orientation of the reactants, such as between a drug and its cellular receptor. A variety of methods for calculating V(r) is available, at different levels of rigor. For large biologically active molecules, multipole expansions and superposition of potentials computed for subunits have been found to be effective. A large number of chemical and biochemical systems and processes have now been studied in terms of electrostatic potentials. Three examples of such applications are surveyed in this paper. These deal with: (a) reactive properties of nucleic acids, including their component bases; (b) biological recognition processes, including drug-receptors and enzyme-substrate interactions; and (c) chemical carcinogenesis, referring specifically to the polycyclic aromatic hydrocarbons and halogenated olefins and their epoxides. For each of these areas, examples of the use of electrostatic potentials in elucidating structure-activity patterns are given.

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Section: Methods Of Calculating the Electrostatic Potentialmentioning

confidence: 99%

Molecular electrostatic potentials: an effective tool for the elucidation of biochemical phenomena.

Politzer¹,

Laurence²,

Jayasuriya³

1985

Environ Health Perspect

698

139

View full text Add to dashboard Cite

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“…The magnitude of this difference follows closely the trend set by the differences in angular minima as predicted by the SMMA and MMA electrostatic calculations. (8) -6.57 (7) t%I t E 1 (9) -12.1 (7) -7.02 (7) -6.78 (6) t K 1 See footnote a, Poly(dG).poly(dC)…”

Section: (4)mentioning

confidence: 98%

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

et al. 1978

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An optimized potential function for base-stacking interactions 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 expressions for the second-order interaction terms composed of multipole-bond polarizability for the polarization energy and transition-dipole bond polariz abilities 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.

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“…The present study, i.e., the inclusion of terms up to octopole interactions and the subsequent decomposition into inverse powers of R , gives a better insight into the convergence problem than the previous study [6]. With respect to electrostatic interactions it was observed that after some oscillations.…”

Section: Discussion and Resultsmentioning

confidence: 65%

“…By expanding both charge distributions in a Taylor series the interaction energies can be expressed as a series of multipole-multipole terms. We list below only those terms involving octopole interactions and refer the reader to other sources [5,6] for a description of terms in the series up to quadrupole-quadrupole interactions. Buckingham [ 121 describes the electrostatic octopole moment as (3) .…”

Section: Electrostatic Energymentioning

confidence: 99%

“…A detailed description of the electrostatic interactions between biomolecules has been given in a series of papers from this laboratory [l-71. Fundamental to these calculations is the representation of the electrostatic potential at biological distances of interest in terms of convergent series of successive multipole moments. Prior studies by Stamatiadou and coworkers [6] have been made on nucleotide base interactions using terms as high as quadrupole-quadrupole interactions. The results indicated that while the electrostatic interaction tended to converge at hydrogen bonding distances, terms higher than quadrupole might be needed to assure complete convergence.…”

Section: Introductionmentioning

confidence: 99%

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Some improvements in DNA interaction calculations

Egan

Swissler

Rein

2009

Int. J. Quantum Chem.

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Calculations are made on specific DNA-type compleles using refined e\pressions for electrostatic and polariiation energies. Dispersion and repulsive terms are included in the evaluation of the total interaction energy. It is shown that the expansion of the electrostatic potential to include multipole moments up to octopole is necessary to achieve convergence of first-order energies. Polarization energies are not as sensitive to this expansion. The calculations also support the usefulness of the hard sphere model for DNA hydrogen bonds and indicate how stacking interactions are influenced by second-order energies.

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Complementary DNA base interactions: Application of recently refined electrostatic interaction theory

Cited by 20 publications

References 19 publications

Molecular electrostatic potentials: an effective tool for the elucidation of biochemical phenomena.

Molecular electrostatic potentials: an effective tool for the elucidation of biochemical phenomena.

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

Some improvements in DNA interaction calculations

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