Energetic coupling between DNA bending and base pair opening.

Abstract

The pathway for base pair opening within a B-DNA duplex is investigated by theoretical molecular modeling. The results show that the disruption of a single base pair is energetically compatible with the deductions made from hydrogen exchange measurements. In addition, it is found that the opening process is greatly facilitated by DNA bending and that, conversely, once a base pair is disrupted, DNA can bend very easily. It appears that the energetic coupling between these two processes may play an important role in many biological reactions involving nucleic acid distortion. Despite the accumulation of a wealth of information leading to a better knowledge of the chemical mechanism and of the corresponding time range (1-4), the conformational and energetic details of the pathway for opening and the effect of changes in the tertiary structure of DNA remain unclear. Most notably, the mechanism by which a given base pair manages to accumulate enough energy to spontaneously open and disrupt its hydrogen bonds is still fully unknown. These questions are addressed here by theoretical calculations on a B-DNA oligomer. Using the JUMNA (junction minimization of nucleic acids) molecular modeling program (5), we study the energetics and the conformational route for opening one base within a short DNA fragment and then demonstrate how base pair opening and bending of the DNA double helix are related to one another. METHODSAll of the conformational energy calculations presently described were carried out by using the FLEX parameterization (6, 7) developed over several years in our laboratory and already exploited in a large number of studies of nucleic acids and other biological molecules (see, for example, refs. 8-10). The calculations described here were performed under dielectric damping conditions corresponding to aqueous solution (S = 0.16, D = 78). The next three energy terms represent dispersion-repulsion interactions calculated with a 6-12 dependence using, in part, the parameter set developed by Zhurkin et al. (14). Hydrogen bonds (HB) are dealt with by the latter two of these terms, which take into account their angular dependence. All of these terms are summed over pairs of atoms separated by at least three chemical bonds.The last two terms represent the distortion energy associated with torsion angles T, (including anomeric effects) and valence angles a,-To study the base-opening or bending processes within a DNA fragment it is necessary to have control over the helicoidal parameters describing the position of the bases in space as well as parameters indicating the path of the helical axis so that a given "open" or "bent" state can be maintained while energy optimizing the rest of the DNA conformation. This possibility, which is unavailable in normal molecular mechanics procedures, can be achieved with the recently developed JUMNA procedure (5).The aim of the JUMNA approach is to combine the control over the helicoidal parameters of DNA with the rapidity and ease of treating internal conformation changes, i...

Open complex formation by Escherichia coli RNA polymerase: the mechanism of polymerase‐induced strand separation of double helical DNA

“…The TATA element may be particularly unstable and template supercoiling may further exacerbate this instability. Bending of DNA further increases the probability of opening, and, conversely, base pair opening provides a pathway for DNA bending (Ramstein and Lavery, 1988). It is no doubt significant that many DNA transactions which involve the local melting of DNA occur in bent protein-DNA complexes (Bramhill and Kornberg, 1988;Meyer-Almes etal., 1994;Rees etal., 1993).…”

Functional Architecture of T7 RNA Polymerase Transcription Complexes

“…Effects of mutations in up-and downstream positively charged regions on EC stability. A: Transcripts (13mers) retained ("R") or freed ("F") from halted ECs formed with WT (lanes 1-6), K711C/K713E/K714E (lanes 7-12), K407E/K494E/K332E/K412C (lanes 13-18), or K407E/K412E (lanes 19-24) mutant T7RNAPs in the presence of 0 mM (lanes 1,2,7,8,13,14,19,20), 100 mM (lanes 3,4,9,10,15,16,21,22), or 800 mM (lanes 5,6,11,12,17,18,23,24) NaCl. B: Ratio of Free/Retained transcripts from the experiment in A plotted vs. enzyme and NaCl concentration (error bars give ranges from n=2).…”

Energetics of Base Pairs in B-DNA in Solution: An Appraisal of Potential Functions and Dielectric Treatments

“…The current study gives us an opportunity to characterize some of the recent and popular force fields used in conjunction with different dielectric screening functions, with base pair energies providing a convenient testing ground. Specifically, we have examined the interaction energies between complementary bases involved in Watson-Crick hydrogen bonding adopting a sigmoidal dielectric function (also referred to hereinafter as a modified Hingerty-Lavery function: MHLF), [32][33][34][35][36] to capture the aqueous environment, employing parameters from AM-BER, 37 CHARMM, 38 GROMOS, 39 and OPLS 30,40 force fields. As H-bonds are considered to be mostly electrostatic in nature, it is of interest to estimate the electrostatic contribution to the energetics of base pairs by some state of the art techniques such as the finite difference Poisson-Boltzmann (FDPB) methodology.…”