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- Structural Equilibrium of DNA Represented with Different For...Structural Equilibrium of DNA Represented with Different Force Fields
Biophysical Journal, Volume 75, Issue 1, 1 July 1998, Pages 134-149
Michael Feig and B. Montgomery Pettitt
AbstractWe have recently indicated preliminary evidence of different equilibrium average structures with the CHARMM and AMBER force fields in explicit solvent molecular dynamics simulations on the DNA duplex d(CT) · d(AG) (Feig, M. and B. M. Pettitt, 1997, Experiment vs. Force fields: DNA conformation from molecular dynamics simulations. . . . . 101:7361–7363). This paper presents a detailed comparison of DNA structure and dynamics for both force fields from extended simulation times of 10ns each. Average structures display an A-DNA base geometry with the CHARMM force field and a base geometry that is intermediate between A- and B-DNA with the AMBER force field. The backbone assumes B form on both strands with the AMBER force field, while the CHARMM force field produces heterogeneous structures with the purine strand in A form and the pyrimidine strand in dynamical equilibrium between A and B conformations. The results compare well with experimental data for the cytosine/guanine part but fail to fully reproduce an overall B conformation in the thymine/adenine tract expected from crystallographic data, particularly with the CHARMM force field. Fluctuations between A and B conformations are observed on the nanosecond time scale in both simulations, particularly with the AMBER force field. Different dynamical behavior during the first 4ns indicates that convergence times of several nanoseconds are necessary to fully establish a dynamical equilibrium in all structural quantities on the time scale of the simulations presented here.
Abstract | Full Text | PDF (542 kb) - Stability of Triple-Helical Poly(dT)-Poly(dA)-Poly(dT) DNA w...Stability of Triple-Helical Poly(dT)-Poly(dA)-Poly(dT) DNA with Counterions
Biophysical Journal, Volume 75, Issue 1, 1 July 1998, Pages 70-91
Voichita M. Dadarlat and V.K. Saxena
AbstractStructural conformation of triple-helical poly(dT)-poly(dA)-poly(dT) has been a very controversial issue recently. Earlier investigations, based on fiber diffraction data and molecular modeling, indicated an A-form conformation with sugar pucker. On the other hand, Raman, solution infrared spectral, and NMR studies show a B-form structure with sugars. In accordance with these experimental results, a theoretical model with B-form, sugars was proposed in 1993. In the present work we investigate the dynamics and stability of the two conformations within the effective local field approach applied to the normal mode calculations for the system. The presence of counterions was explicitly taken into account. Stable equilibrium positions for the counterions were calculated by analyzing the normal mode dynamics and free energy of the system. The breathing modes of the triple helix are shifted to higher frequencies over those of the double helix by 4–16cm. The characteristic marker band for the B conformation at 835cm is split up into two marker bands at 830 and 835cm. A detailed comparison of the normal modes and the free energies indicates that the B-form structure, with sugar pucker, is more stable than the A-form structure. The normal modes and the corresponding dipole moments are found to be in close agreement with recent spectroscopic findings.
Abstract | Full Text | PDF (307 kb) - Intrinsic Conformational Properties of Deoxyribonucleosides:...Intrinsic Conformational Properties of Deoxyribonucleosides: Implicated Role for Cytosine in the Equilibrium Among the A, B, and Z Forms of DNA
Biophysical Journal, Volume 76, Issue 6, 1 June 1999, Pages 3206-3218
Nicolas Foloppe and Alexander D. MacKerell
AbstractStructural properties of biomolecules are dictated by their intrinsic conformational energetics in combination with environmental contributions. Calculations using high-level ab initio methods on the deoxyribonucleosides have been performed to investigate the influence of base on the intrinsic conformational energetics of nucleosides. Energy minima in the north and south ranges of the deoxyribose pseudorotation surfaces have been located, allowing characterization of the influence of base on the structures and energy differences between those minima. With all bases, values associated with the south energy minimum are lower than in canonical B-DNA, while values associated with the north energy minimum are close to those in canonical A-DNA. In deoxycytidine, adopts an A-DNA conformation in both the north and south energy minima. Energy differences between the A and B conformations of the nucleosides are <0.5kcal/mol in the present calculations, except with deoxycytidine, where the A form is favored by 2.3kcal/mol, leading the intrinsic conformational energetics of GC basepairs to favor the A form of DNA by 1.5kcal/mol as compared with AT pairs. This indicates that the intrinsic conformational properties of cytosine at the nucleoside level contribute to the A form of DNA containing predominately GC-rich sequences. In the context of a B versus Z DNA equilibrium, deoxycytidine favors the Z form over the B form by 1.6kcal/mol as compared with deoxythymidine, suggesting that the intrinsic conformational properties of cytosine also contribute to GC-rich sequences occurring in Z DNA with a higher frequency than AT-rich sequences. Results show that the east pseudorotation energy barrier involves a decrease in the furanose amplitude and is systematically lower than the inversion barrier, with the energy differences influenced by the base. Energy barriers going from the south (B form) sugar pucker to the east pseudorotation barrier are lower in pyrimidines as compared with purines, indicating that the intrinsic conformational properties associated with base may also influence the sugar pseudorotational population distribution seen in DNA crystal structures and the kinetics of B to A transitions. The present work provides evidence that base composition, in addition to base sequence, can influence DNA conformation.
Abstract | Full Text | PDF (139 kb) - …more
Copyright © 1997 The Biophysical Society. All rights reserved.
Biophysical Journal, Volume 72, Issue 4, 1512-1520, 1 April 1997
doi:10.1016/S0006-3495(97)78799-X
Research Article
Temperature-dependent ultraviolet resonance Raman spectroscopy of the premelting state of dA.dT DNA
S.S. Chan, R.H. Austin, I. Mukerji and T.G. Spiro
Physics Department, Princeton University, New Jersey 08544, USA.
Abstract
Poly(dA).poly(dT) and DNA duplex with four or more adenine bases in a row exhibits a broad, solid-state structural premelting transition at about 35 degrees C. The low-temperature structure is correlated with the phenomena of "bent DNA." We have conducted temperature-dependent ultraviolet resonance Raman measurements of the structural transition using poly(dA).poly(dT) at physiological salt conditions, and are able to identify, between the high and low temperature limits, changes in the vibrational frequencies associated with the C4 carbonyl stretching mode in the thymine ring and the N6 scissors mode of the amine in the adenine ring of poly(dA).poly(dT). This work supports the model that the oligo-dA tracts' solid-state structural premelting transition is due to a set of cross-stand bifurcated hydrogen bonds between consecutive dA. dT pairs.
