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

Abstract

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.

TATA element recognition by the TATA box-binding protein has been conserved throughout evolution

“…We believe that Hoogsteen base pairs can form at position 7 because the energy barrier for the anti to syn glycosidic torsion angle change is very low for unstacked DNA bases (Ornstein et al 1978), which is precisely the case in the vicinity of the 3Ј kink. Steric clashes between TBP and Watson-Crick C:G or G:C base pairs at position 7 preclude assembly of stable protein-DNA complexes in the absence of further conformational changes in the nucleic acid.…”

“…There is a marked preference for A:T over T:A (frequencies = 83.5% and 13.9%, respectively), which is probably correlated with the frequency of T:A in position 1. T:A on A:T stacking energy is the lowest of all possible combinations (Ornstein et al 1978), again favoring unstacking of the first two base pairs by Phe-148 and Phe-165.…”

“…The EPD survey identifies a marked preference for T (frequency = 79.5%), which may be related to the fact that the energy of T:A stacking on the adjacent base pair is relatively small (except for T:A stacking on C:G) (Ornstein et al 1978) and easy to overcome by intercalation of Phe-148 and Phe-165.…”

Genome-Wide Distribution of TransposedDissociationElements in Maize

“…The various parameters are computationally independent (Liao et al, 2000;Hackett et al, 2007). Such structural computations predict elements of DNA three-dimensional structure, such as local degrees of double helix flexibility versus rigidity (Ornstein et al, 1978;Brukner et al, 1995;Gorin et al, 1995;Olson et al, 1998), and have been used to predict in genomic DNA sequence biologically functional regions, including promoters and transcription start sites (Ohler et al, 2002;Wang and Benham, 2006;Abeel et al, 2008), as well as to profile insertion sites of P element transposons in Drosophila melanogaster and of retroviral and transposon vectors in transgenic animals (Liao et al, 2000;Vigdal et al, 2002;Hackett et al, 2007).…”

4',6-Diamidino-2-phenylindole (DAPI) interacts with rare structures of GC polymers

“…In some measurements, pertaining to FCS studies, the two classes of GC polymers were heated for about 15 min to the melting transition region, at 102°C for the alternating copolymers and 95°C for the homopolymers; stacking energy: 9.7 and 8.2 kcal/ mol per stacked pair, respectively (Ornstein et al 1978). The two stages of the denaturation process were followed by the increase in the absorbed light at 260 nm.…”