B. Jayaram

A sequence of ordered solvent peaks in the electron density map of the minor groove region of ApT-rich tracts of the double helix is a characteristic of B-form DNA well established from crystallography. This feature, termed the “spine of hydration”, has been discussed as a stabilizing feature of B-DNA, the structure of which is known to be sensitive to environmental effects. Nanosecond-range molecular dynamics simulations on the DNA duplex of sequence d(CGCGAATTCGCG) have been carried out, including explicit consideration of ∼4000 water molecules and 22 Na+ counterions, and based on the new AMBER 4.1 force field with the particle mesh Ewald summation used in the treatment of long-range interactions. The calculations support a dynamical model of B-DNA closer to the B form than any previously reported. Analysis of the dynamical structure of the solvent revealed that, in over half of the trajectory, a Na+ ion is found in the minor groove localized at the ApT step. This position, termed herein the “ApT pocket”, was noted previously (Lavery, R.; Pullman, B. J. Biomol. Struct. Dyn. 1985, 5, 1021) to be of uniquely low negative electrostatic potential relative to other positions of the groove, a result supported by the location of a Na+ ion in the crystal structure of the dApU miniduplex [Seeman, N.; et al. J. Mol. Biol. 1976, 104, 109) and by additional calculations described herein based on continuum electrostatics. The Na+ ion in the ApT pocket interacts favorably with the thymine O2 atom on opposite strands of the duplex and is well articulated with the water molecules which constitute the remainder of the minor groove spine. This result indicates that counterions may intrude on the minor groove spine of hydration on B-form DNA and subsequently influence the environmental structure and thermodynamics in a sequence-dependent manner. The observed narrowing of the minor groove in the AATT region of the d(CGCGAATTCGCG) structure may be due to direct binding effects and also to indirect modulation of the electrostatic repulsions that occur when a counterion resides in the minor groove “AT pocket”. The idea of localized complexation of otherwise mobile counterions in electronegative pockets in the grooves of DNA helices introduces a heretofore mostly unappreciated source of sequence-dependent effects on local conformational, helicoidal, and morphological structure and may have important implications in understanding the functional energetics and specificity of the interactions of DNA and RNA with regulatory proteins, pharmaceutical agents, and other ligands.

It is well recognized that base sequence exerts a significant influence on the properties of DNA and plays a significant role in protein-DNA interactions vital for cellular processes. Understanding and predicting base sequence effects requires an extensive structural and dynamic dataset which is currently unavailable from experiment. A consortium of laboratories was consequently formed to obtain this information using molecular simulations. This article describes results providing information not only on all 10 unique base pair steps, but also on all possible nearest-neighbor effects on these steps. These results are derived from simulations of 50-100 ns on 39 different DNA oligomers in explicit solvent and using a physiological salt concentration. We demonstrate that the simulations are converged in terms of helical and backbone parameters. The results show that nearest-neighbor effects on base pair steps are very significant, implying that dinucleotide models are insufficient for predicting sequence-dependent behavior. Flanking base sequences can notably lead to base pair step parameters in dynamic equilibrium between two conformational sub-states. Although this study only provides limited data on next-nearest-neighbor effects, we suggest that such effects should be analyzed before attempting to predict the sequence-dependent behavior of DNA.

Electrostatic potentials around DNA are obtained by solving the nonlinear Poisson-Boltzmann (PB) equation. The detailed charge distribution of the DNA and the different polarizabilities of the macromolecule and solvent are included explicitly in the calculations. The PB equation is solved using extensions of a finite difference approach applied previously to proteins. Electrical potentials and ion concentrations are compared to those obtained with simpler models. It is found that the shape of the dielectric boundary between the macromolecule and solvent has significant effects on the calculated potentials near the surface, particularly in the grooves. Sequence-specific patterns are found, the most surprising result being the existence of positive regions of potential near the bases in both the major and minor grooves. The effect of solvent and ionic atmosphere screening of phosphate-phosphate repulsions is studied, and an effective dielectric function, appropriate for molecular mechanics simulations, is derived.

The generalized Born (GB) model provides rapid estimates of the electrostatic free energies of solvation for diverse molecules and molecular ions. This method is expected to be of considerable utility for studies of solvation in macromolecular and biological systems. Calculations on biological molecules are typically based on empirical energy functions, each of which have their own prescriptions for determining net atomic charges. For maximum compatibility, GB parameters tailored to specific force fields are required. The development of parameters compatible with the AMBER force field is described. The method is used to estimate free energies of A and B form structures of DNA obtained from molecular dynamics simulations. The results provide an account of the conformational preferences of right-handed DNA in solution.

BACKGROUND: Computational methods utilizing the structural and functional information help to understand specific molecular recognition events between the target biomolecule and candidate hits and make it possible to design improved lead molecules for the target. RESULTS: Sanjeevini represents a massive on-going scientific endeavor to provide to the user, a freely accessible state of the art software suite for protein and DNA targeted lead molecule discovery. It builds in several features, including automated detection of active sites, scanning against a million compound library for identifying hit molecules, all atom based docking and scoring and various other utilities to design molecules with desired affinity and specificity against biomolecular targets. Each of the modules is thoroughly validated on a large dataset of protein/DNA drug targets. CONCLUSIONS: The article presents Sanjeevini, a freely accessible user friendly web-server, to aid in drug discovery. It is implemented on a tera flop cluster and made accessible via a web-interface at http://www.scfbio-iitd.res.in/sanjeevini/sanjeevini.jsp. A brief description of various modules, their scientific basis, validation, and how to use the server to develop in silico suggestions of lead molecules is provided.