Nucleic Acid Base Stacking Research Articles

Stacking of nucleic acid bases: optimization of the computational approach\u2014the case of adenine dimers

Stacking interactions play an important role in stabilizing DNA and RNA secondary structure. To select a computational level to study the stacking interactions, both energy and geometric criteria, as well as the time necessary to optimize the system, should be taken into account. In this work, an attempt was made to find the most optimal level of theory describing the stacking interactions in adenine dimers. The obtained results have shown that for this purpose, wB97XD/6-311G(p,d), wB97XD/aug-cc-pvdz, or B97D3/aug-cc-pvdz should be used. What is more, geometry of the most preferable arrangements of molecules was also pointed out, ensuring an optimal starting system for further analyses.

An optimized charge penetration model for use with the AMOEBA force field.

The principal challenge of using classical physics to model biomolecular interactions is capturing the nature of short-range interactions that drive biological processes from nucleic acid base stacking to protein-ligand binding. In particular most classical force fields suffer from an error in their electrostatic models that arises from an ability to account for the overlap between charge distributions occurring when molecules get close to each other, known as charge penetration. In this work we present a simple, physically motivated model for including charge penetration in the AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications) force field. With a function derived from the charge distribution of a hydrogen-like atom and a limited number of parameters, our charge penetration model dramatically improves the description of electrostatics at short range. On a database of 101 biomolecular dimers, the charge penetration model brings the error in the electrostatic interaction energy relative to the ab initio SAPT electrostatic interaction energy from 13.4 kcal mol-1 to 1.3 kcal mol-1. The model is shown not only to be robust and transferable for the AMOEBA model, but also physically meaningful as it universally improves the description of the electrostatic potential around a given molecule.

Investigating the aggregation behaviour of DNA origami frames

We describe the design, synthesis and aggregation behaviour of a biomolecular breadboard in the form of a DNA origami frame. Our findings focus on determining the shortest thermal annealing protocol, yielding correctly folded frames. In addition, we investigate the frames’ chain formation behaviour due to base stacking. By minor alterations in the origami design, we can deliberately avoid or induce this behaviour and influence the relative orientation of frames in the chains.Aggregate formation of DNA origami frames using nucleic acid base stacking.

Impact of Geometry Optimization on Base–Base Stacking Interaction Energies in the Canonical A- and B-Forms of DNA

Base stacking is known to make an important contribution to the stability of DNA and RNA, and accordingly, significant efforts are ongoing to calculate stacking energies using ab initio quantum mechanical methods. To date, impressive improvements have been made in the model chemistries used to perform stacking energy calculations, including extensions that include robust treatments of electron correlation with extended basis sets, as required to treat interactions where dispersion makes a significant contribution. However, those efforts typically use rigid monomer geometries when calculating the interaction energies. To overcome this, in the present work, we describe a novel internal coordinate definition that allows the relative, intermolecular orientation of stacked base monomers to be constrained during geometry optimizations while allowing full optimization of the intramolecular degrees of freedom. Use of the novel reference frame to calculate the impact of full geometry optimization versus constraining the bases to be planar on base monomer stacking energies, combined with density-fitted, spin-component scaling MP2 treatment of electron correlation, shows that full optimization makes the average stacking energy more favorable by -3.4 and -1.5 kcal/mol for the canonical A and B conformations of the 16 5' to 3' base stacked monomers. Thus, treatment of geometry optimization impacts the stacking energies to an extent similar to or greater than the impact of current state of the art increases in the rigor of the model chemistry itself used to treat base stacking. Results also indicate that stacking favors the B-form of DNA, though the average difference versus the A-form decreases from -2.6 to -0.6 kcal/mol when the intramolecular geometry is allowed to fully relax. However, stacking involving cytosine is shown to favor the A-form of DNA, with that contribution generally larger in the fully optimized bases. The present results show the importance of allowing geometry optimization, as well as properly treating the appropriate model chemistry, in studies of nucleic acid base stacking.

A study of nucleic acid base-stacking by the Monte Carlo method: Extended cluster approach

Abstract The adenine-thymine (AT), adenine-uracil (AU) and guanine-cytosine (GC) base associates in clusters containing 400 water molecules were studied using a newly implemented Metropolis Monte Carlo algorithm based on the extended cluster approach. Starting from the hydrogen-bonded Watson-Crick geometries, all three base pairs are transformed into more favorable stacked configurations during the simulation. The obtained results show, for the first time, the transition from planar base pairs to stacked base associates in the Monte Carlo framework. Analysis of the interaction energies shows that, in the water cluster, the stacked dimers are energetically preferable compared to the corresponding Watson-Crick base pairs. This is due to the larger base-water interaction in the stacked structures. The water-water interaction is one of the main factors promoting the formation of stacked dimers, and the obtained data confirm the crucial role of the water-water interactions in base stacking.

A Physical Chemist's Expedition to Explore the World of Membrane Proteins

Despite growing up amid humble surroundings, I ended up receiving an excellent education at the University of California at Berkeley and postdoctoral training at Harvard. My academic career at Caltech was shaped by serendipity, inspirational colleagues, and a stimulating research environment, as well as smart, motivated students and postdocs who were willing to join my search for molecular understanding of complex biological systems. From chemical physics I allowed my research to evolve, beginning with the application of NMR to investigate the base stacking of nucleic acid bases in solution, the dynamic structure of membranes, and culminating with the use of various forms of spectroscopy to elucidate the structure and function of membrane proteins and the early kinetic events in protein folding. The journey was a biased random walk driven by my own intellectual curiosity and instincts and by the pace at which I learned biochemistry from my students and postdocs, my colleagues, and the literature and through osmosis during seminars and scientific meetings.

Nature and magnitude of aromatic stacking of nucleic acid bases

This review summarises recent advances in quantum chemical calculations of base-stacking forces in nucleic acids. We explain in detail the very complex relationship between the gas-phase base-stacking energies, as revealed by quantum chemical (QM) calculations, and the highly variable roles of these interactions in nucleic acids. This issue is rarely discussed in quantum chemical and physical chemistry literature. We further extensively discuss methods that are available for base-stacking studies, complexity of comparison of stacking calculations with gas phase experiments, balance of forces in stacked complexes of nucleic acid bases, and the relation between QM and force field descriptions. We also review all recent calculations on base-stacking systems, including details analysis of the B-DNA stacking. Specific attention is paid to the highest accuracy QM calculations, to the decomposition of the interactions, and development of dispersion-balanced DFT methods. Future prospects of computational studies of base stacking are discussed.

The X3LYP extended density functional accurately describes H-bonding but fails completely for stacking

The performance of the recently introduced X3LYP density functional which was claimed to significantly improve the accuracy for H-bonded and van der Waals complexes was tested for extended H-bonded and stacked complexes (nucleic acid base pairs and amino acid pairs). In the case of planar H-bonded complexes (guanine...cytosine, adenine...thymine) the DFT results nicely agree with accurate correlated ab initio results. For the stacked pairs (uracil dimer, cytosine dimer, adenine...thymine and guanine...cytosine) the DFT fails completely and it was even not able to localize any minimum at the stacked subspace of the potential energy surface. The geometry optimization of all these stacked clusters leads systematically to the planar H-bonded pairs. The amino acid pairs were investigated in the crystal geometry. DFT again strongly underestimates the accurate correlated ab initio stabilization energies and usually it was not able to describe the stabilization of a pair. The X3LYP functional thus behaves similarly to other current functionals. Stacking of nucleic acid bases as well as interaction of amino acids was described satisfactorily by using the tight-binding DFT method, which explicitly covers the London dispersion energy.

The Physical Basis of Nucleic Acid Base Stacking in Water

It has been argued that the stacking of adenyl groups in water must be driven primarily by electrostatic interactions, based upon NMR data showing stacking for two adenyl groups joined by a 3-atom linker but not for two naphthyl groups joined by the same linker. In contrast, theoretical work has suggested that adenine stacking is driven primarily by nonelectrostatic forces, and that electrostatic interactions actually produce a net repulsion between adenines stacking in water. The present study provides evidence that the experimental data for the 3-atom-linked bis-adenyl and bis-naphthyl compounds are consistent with the theory indicating that nonelectrostatic interactions drive adenine stacking. First, a theoretical conformational analysis is found to reproduce the observed ranking of the stacking tendencies of the compounds studied experimentally. A geometric analysis identifies two possible reasons, other than stronger electrostatic interactions, why the 3-atom-linked bis-adenyl compounds should stack more than the bis-naphthyl compounds. First, stacked naphthyl groups tend to lie further apart than stacked adenyl groups, based upon both quantum calculations and crystal structures. This may prevent the bis-naphthyl compound from stacking as extensively as the bis-adenyl compound. Second, geometric analysis shows that more stacked conformations are sterically accessible to the bis-adenyl compound than to the bis-naphthyl compound because the linker is attached to the sides of the adenyl groups, but to the ends of the naphthyl groups. Finally, ab initio quantum mechanics calculations and energy decompositions for relevant conformations of adenine and naphthalene dimers support the view that stacking in these compounds is driven primarily by nonelectrostatic interactions. The present analysis illustrates the importance of considering all aspects of a molecular system when interpreting experimental data, and the value of computer models as an adjunct to chemical intuition.

Aromatic Base Stacking in DNA: From ab initio Calculations to Molecular Dynamics Simulations

Aromatic stacking of nucleic acid bases is one of the key players in determining the structure and dynamics of nucleic acids. The arrangement of nucleic acid bases with extensive overlap of their aromatic rings gave rise to numerous often contradictory suggestions about the physical origins of stacking and the possible role of delocalized electrons in stacked aromatic π systems, leading to some confusion about the issue. The recent advance of computer hardware and software finally allowed the application of state of the art quantum-mechanical approaches with inclusion of electron correlation effects to study aromatic base stacking, now providing an ultimitate qualitative description of the phenomenon. Base stacking is determined by an interplay of the three most commonly encountered molecular interactions: dispersion attraction, electrostatic interaction, and short-range repulsion. Unusual (aromatic- stacking specific) energy contributions were in fact not evidenced and are not necessary to describe stacking. The currently used simple empirical potential form, relying on atom-centered constant point charges and Lennard-Jones van der Waals terms, is entirely able to reproduce the essential features of base stacking. Thus, we can conclude that base stacking is in principle one of the best described interactions in current molecular modeling and it allows to study base stacking in DNA using large-scale classical molecular dynamics simulations. Neglect of cooperativity of stacking appears to be the most serious approximation of the currently used force field form. This review summarizes recent developments in the field. It is written for an audience that is not necessarily expert in computational quantum chemistry and follows up on our previous contribution (Sponer et. al., J. Biomol. Struct. Dyn. 14, 117, (1997)). First, the applied methodology, its accuracy, and the physical nature of base stacking is briefly overviewed, including a comment on the accuracy of other molecular orbital methods and force fields. Then, base stacking is contrasted with hydrogen bonding, the other dominant force in nucleic acid structure. The sequence dependence and cooperativity of base stacking is commented on, and finally a brief introduction into recent progress in large-scale molecular dynamics simulations of nucleic acids is provided. Using four stranded DNA assemblies as an example, we demonstrate the efficacy of current molecular dynamics techniques that utilize refined and verified force fields in the study of stacking in nucleic acid molecules.

Finding and visualizing nucleic acid base stacking

Base stacking is one of the primary factors stabilizing nucleic acid structure. Yet, methods for locating stacking interactions in DNA and RNA are rare and methods for displaying stacking are rarer still. We present here simple, automated procedures to search nucleic acid molecules for base-base and base-oxygen stacking and to display these interactions graphically in a manner that readily conveys both the location and the quality of the interaction. The method makes no a priori assumptions about relative base positions when searching for stacking, nor does it rely on empirical energy functions. This is a distinct advantage for two reasons. First, the relative contributions of the forces stabilizing stacked bases are unknown. Second, the electrostatic and hydrophobic components of base stacking are both poorly defined by existing potential energy functions.

A free energy analysis of nucleic acid base stacking in aqueous solution

This paper reports a theoretical study of the free energy contributions to nucleic acid base stacking in aqueous solution. Electrostatic interactions are treated by using the finite difference Poisson-Boltzmann method and nonpolar effects are treated with explicit calculation of van der Waals interactions and/or free energy-surface area relationships. Although for some pairs of bases there is a favorable Coulombic interaction in the stacked conformation, generally the net effect of electrostatic interactions is to oppose stacking. This result is caused by the loss of favorable base-solvent electrostatic interactions, that accompany the partial removal of polar atoms from water in the stacked conformation. Nonpolar interactions, involving the hydrophobic effect and enhancement of van der Waals interactions caused by close-packing, drive stacking. The calculations qualitatively reproduce the experimental dependence of stacking free energy on purine-pyrimidine composition.

Extracting hydrophobic free energies from experimental data: relationship to protein folding and theoretical models

Solubility and vapor pressure measurements of hydrocarbons in water are generally thought to provide estimates of the strength of the hydrophobic effect in the range 20-30 cal/(mol.A2). Our reassessment of the solubility data on the basis of new developments in solution thermodynamics suggests that the hydrophobic surface free energy for hydrocarbon solutes is 46-47 cal/(mol.A2), although the actual value depends strongly on curvature effects [Nicholls et al. (1991) Proteins (in press); Sharp et al. (1991) Science 252, 106-109]. The arguments to support such a significant increase in the estimate of the hydrophobic effect stem partly from theoretical considerations and partly from the experimental results of De Young and Dill [(1990) J. Phys. Chem. 94, 801-809] on benzene partition between water and alkane solvents. Previous estimates of the hydrophobic effect derive from an analysis of solute partition data, which does not fully account for changes in volume entropy. We show here how the ideal gas equations, combined with experimental molar volumes, can account for such changes. Revised solubility scales for the 20 amino acids, based on cyclohexane to water and octanol to water transfer energies, are derived. The agreement between these scales, particularly the octanol scale, and mutant protein stability measurements from Kellis et al. [(1989) Biochemistry 28, 4914-4922] and Shortle et al. [(1990) Biochemistry 29, 8033-8041] is good. The increased strength of the hydrophobic interaction has implications for the energetics of protein folding, substrate binding, and nucleic acid base stacking and the interpretation of computer simulations.

Nature of the stacking of nucleic acid bases in water: a Monte Carlo study

Nature of the stacking of nucleic acid bases in water: a Monte Carlo study

Nature of the stacking of nucleic acid bases in water: A Monte Carlo study

The results of a Monte Carlo simulation of the hydration of uracil and thymine molecules, their stacked dimers and hydrogen-bonded base pairs are presented. Simulations have been performed in a cluster approximation. The semiempirical atom-atom potential functions have been used (cluster consisting of 200 water molecules). It has been shown that stacking interactions of uracil and thymine molecules in water arise mainly due to the increase in the water—water interaction during the transition from monomers to dimer. It has been found that stacked base associates are more favourable than base pairs in water. This is mainly due to the energetically more preferable structure of water around stacks.

Nature of the Stacking of Nucleic Acid Bases in Water: a Monte Carlo Simulation

The results of a Monte Carlo simulation of the hydration of uracil and thymine molecules, their stacked dimers and hydrogen-bonded base pairs are presented. Simulations have been performed in a cluster approximation. The semiempirical atom-atom potential functions have been used (cluster consisting of 200 water molecules). It has been shown that the stacking interactions of uracil and thymine molecules in water arise mainly due to the increase in the water-water interaction during the transition from monomers to dimer. It has been found out that stacked base associates are more preferable than base pairs in water. This preference is mainly due to the energetically more favourable structure of water around the stack.

Kinetics of the stacking of ethidium bromide by the raman laser temperature-jump method

Abstract Raman laser temperature-jump measurements have been made on concentrated solutions of ethidium bromide. Two relaxations were observed. The faster has a lifetime of less than 30 ns and is attributed to rotation of the phenyl ring. The slower relaxation is concentration dependent and is due to the parallel stacking of two dye molecules. The forward and reverse rates for this process are (4.6 ± 1.4) × 10 8 M −1 s −1 and (6.7 ± 1.4)× 10 6 s −1 , respectively, at 25°C. 0.25 M ionic strength, and pH 6.9. This reverse rate and those of three similar reactions are found to fit a linear free energy plot. The implications of these results for studies of nucleic acid base stacking are discussed.