Structural equilibrium of DNA represented with different force fields

Benzo(ghi)perylene (BgP) a black tattoo ingredient induced skin toxicity via direct and indirect mode of DNA damage under UVA irradiation

Tattooing is a very common fashion trend across all the ages and gender of the society worldwide. Although skin inflammatory diseases are very frequent among tattoo users because of the active chemical ingredients used in tattoo ink, yet no ingredient-specific toxicity study has been performed. Benzo(ghi)perylene (BgP) is one of the PAHs and an important ingredient of black tattoo ink that shows strong absorption in UVA and UVB radiation of sunlight. Therefore, understanding the hazardous potential of BgP especially under UVA exposure is important for the safety of skin of tattoo users by considering the fact that penetration of UVA is in the dermis region where tattoo ingredients reside. To evaluate the hazardous potential of BgP on human skin under UVA exposure, different experimental tools i.e., in-chemico, in-silico and in-vitro were utilized. Our results illustrated that BgP photosensitized under UVA (1.5 mW/cm²) irradiation shows a degradation pattern till 4 h exposure. Photosensitized BgP reduced significant cell viability (%) at 1 μg/ml concentration. However, the pretreatment of singlet and hydroxyl radical quenchers, restoration of cell viability observed, confirmed the role of type-I and type-II photodynamic reactions in phototoxicity of BgP. Further, intracellular uptake of BgP in HaCaT cells was estimated and confirmed by UHPLC analysis. Molecular docking of BgP with DNA and formation of γ-H2AX foci demonstrated the DNA intercalation and double-stranded DNA damaging potential of BgP. Furthermore, acridine orange and ethidium bromide (AO/EB) dual staining showed apoptotic cell death via photosensitized BgP under UVA irradiation. The above findings suggest that BgP reached the human skin cell and induced dermal toxicity via direct and indirect mode of DNA damage under UVA exposure finally promoting the skin cell death. Thus, BgP-containing tattoo ink may be hazardous and may induce skin damage and diseases, especially in presence of UVA radiation of sunlight. To minimize the risk of skin diseases from synthetic ingredients in tattoo ink, the study highlights the importance of developing eco-friendly and skin-friendly tattoo ingredients by companies.

Benchmark assessment of molecular geometries and energies from small molecule force fields

Background: Force fields are used in a wide variety of contexts for classical molecular simulation, including studies on protein-ligand binding, membrane permeation, and thermophysical property prediction. The quality of these studies relies on the quality of the force fields used to represent the systems. Methods: Focusing on small molecules of fewer than 50 heavy atoms, our aim in this work is to compare nine force fields: GAFF, GAFF2, MMFF94, MMFF94S, OPLS3e, SMIRNOFF99Frosst, and the Open Force Field Parsley, versions 1.0, 1.1, and 1.2. On a dataset comprising 22,675 molecular structures of 3,271 molecules, we analyzed force field-optimized geometries and conformer energies compared to reference quantum mechanical (QM) data. Results: We show that while OPLS3e performs best, the latest Open Force Field Parsley release is approaching a comparable level of accuracy in reproducing QM geometries and energetics for this set of molecules. Meanwhile, the performance of established force fields such as MMFF94S and GAFF2 is generally somewhat worse. We also find that the series of recent Open Force Field versions provide significant increases in accuracy. Conclusions: This study provides an extensive test of the performance of different molecular mechanics force fields on a diverse molecule set, and highlights two (OPLS3e and OpenFF 1.2) that perform better than the others tested on the present comparison. Our molecule set and results are available for other researchers to use in testing.

Changes in Microenvironment Modulate the B- to A-DNA Transition

B- to A-DNA transition is known to be sensitive to the macroscopic properties of the solution, such as salt and ethanol concentrations. Microenvironmental effects on DNA conformational transition have been broadly studied. Providing an intuitive picture of how DNA responds to environmental changes is, however, still needed. Analyzing the chemical equilibrium of B-to-A DNA transition at critical concentrations, employing explicit-solvent simulations, is envisioned to help understand such microenvironmental effects. In the present study, free-energy calculations characterizing the B- to A-DNA transition and the distribution of cations were carried out in solvents with different ethanol concentrations. With the addition of ethanol, the most stable structure of DNA changes from the B- to A-form, in agreement with previous experimental observation. In 60% ethanol, a chemical equilibrium is found, showing reversible transition between B- and A-DNA. Analysis of the microenvironment around DNA suggests that with the increase of ethanol concentration, the cations exhibit a significant tendency to move toward the backbone, and mobility of water molecules around the major groove and backbone decreases gradually, leading eventually to a B-to-A transition. The present results provide a free-energy view of DNA microenvironment and of the role of cation motion in the conformational transition.

Flexibility of short DNA helices with finite-length effect: From base pairs to tens of base pairs

Flexibility of short DNA helices is important for the biological functions such as nucleosome formation and DNA-protein recognition. Recent experiments suggest that short DNAs of tens of base pairs (bps) may have apparently higher flexibility than those of kilo bps, while there is still the debate on such high flexibility. In the present work, we have studied the flexibility of short DNAs with finite-length of 5-50 bps by the all-atomistic molecular dynamics simulations and Monte Carlo simulations with the worm-like chain model. Our microscopic analyses reveal that short DNAs have apparently high flexibility which is attributed to the significantly strong bending and stretching flexibilities of ∼6 bps at each helix end. Correspondingly, the apparent persistence length lp of short DNAs increases gradually from ∼29 nm to ∼45 nm as DNA length increases from 10 to 50 bps, in accordance with the available experimental data. Our further analyses show that the short DNAs with excluding ∼6 bps at each helix end have the similar flexibility with those of kilo bps and can be described by the worm-like chain model with lp ∼ 50 nm.

Base Flipping in a GCGC Containing DNA Dodecamer: A Comparative Study of the Performance of the Nucleic Acid Force Fields, CHARMM, AMBER, and BMS

The improving quality of empirical force field parameters along with other methodological improvements and ever increasing computational resources have lead to more reliable computations on biological macromolecules. In the case of oligonucleotides, three force fields, namely CHARMM27, AMBER4.1, and BMS, have been developed and are widely used by the simulation community. Testing of these force fields to date has primarily focused on their treatment of the canonical forms of DNA and RNA. However, many biological functions of oligonucleotides involve significant variation of their structures from the canonical forms. In the present work, the three force fields are evaluated via computation of potentials of mean force (PMF) of the base flipping process in a DNA dodecamer, 5'-GTCAGCGCATGG-3'. Results are compared with available experimental data on the equilibrium between the opened and closed (i.e. Watson-Crick base paired) state of the underlined C and its WC partner G. Quantitative analysis shows CHARMM to be in the best agreement with experiment, closely followed by AMBER with BMS in the poorest agreement. Various components contributing to the change in the free energy such as base pair interactions, stacking interactions, solvation effects, and intrinsic potential energy changes were evaluated and compared. The results indicate that while all three force fields reasonably represent the canonical structures, the balance of forces contributing to their structural and dynamic properties differ significantly.

Multivalent ion-mediated nucleic acid helix-helix interactions: RNA versus DNA

Ion-mediated interaction is critical to the structure and stability of nucleic acids. Recent experiments suggest that the multivalent ion-induced aggregation of double-stranded (ds) RNAs and DNAs may strongly depend on the topological nature of helices, while there is still lack of an understanding on the relevant ion-mediated interactions at atomistic level. In this work, we have directly calculated the potentials of mean force (PMF) between two dsRNAs and between two dsDNAs in Co(NH3)6 (3+) (Co-Hex) solutions by the atomistic molecular dynamics simulations. Our calculations show that at low [Co-Hex], the PMFs between B-DNAs and between A-RNAs are both (strongly) repulsive. However, at high [Co-Hex], the PMF between B-DNAs is strongly attractive, while those between A-RNAs and between A-DNAs are still (weakly) repulsive. The microscopic analyses show that for A-form helices, Co-Hex would become 'internal binding' into the deep major groove and consequently cannot form the evident ion-bridge between adjacent helices, while for B-form helices without deep grooves, Co-Hex would exhibit 'external binding' to strongly bridge adjacent helices. In addition, our further calculations show that, the PMF between A-RNAs could become strongly attractive either at very high [Co-Hex] or when the bottom of deep major groove is fixed with a layer of water.

Close encounters with DNA

Over the past ten years, the all-atom molecular dynamics method has grown in the scale of both systems and processes amenable to it and in its ability to make quantitative predictions about the behavior of experimental systems. The field of computational DNA research is no exception, witnessing a dramatic increase in the size of systems simulated with atomic resolution, the duration of individual simulations and the realism of the simulation outcomes. In this topical review, we describe the hallmark physical properties of DNA from the perspective of all-atom simulations. We demonstrate the amazing ability of such simulations to reveal the microscopic physical origins of experimentally observed phenomena. We also discuss the frustrating limitations associated with imperfections of present atomic force fields and inadequate sampling. The review is focused on the following four physical properties of DNA: effective electric charge, response to an external mechanical force, interaction with other DNA molecules and behavior in an external electric field.

Sequence dependent free energy profiles of localized B- to A-form transition of DNA in water

DNA carries an inherent polymorphism, which surfaces under various external conditions. While B-form remains predominant under normal physiological conditions for most of the DNA sequences, low humidity and increased ion concentration cause B- to A-form transition. Certain proteins and molecules also sometimes cause local deformation of the DNA to the specific A-form. Previous experimental and computational studies focused on the overall B- to A-form transition. Here for the first time we investigated thermodynamics and mechanism of B- to A-form transition in water for various DNA sequences at a local dinucleotide base pair level. We introduced a new reaction coordinate Zp', based on the unique order parameter Zp, to drive B- to A-form transition locally and thereby calculate free energy profiles for the same for all the ten different dinucleotide steps embedded in a twelve base pair DNA. Results show that the trend of "A" and "B" philicity observed in experiment is preserved even at this local dinucleotide level, indicating its localized origin. Higher free energy cost obtained here is attributed to the cost of creating B∕A junctions along with formation of B->A transition at dimer level. We find that while water energetically stabilizes A-form for all the ten different dinucleotide steps to various extents, entropy acts against it. Therefore, we find that the stability of B-form DNA in water is entropic in origin. Mechanism of the conversion appears to be triggered by Slide; however, backbone parameters change concertedly.

Optimization of the molecular dynamics method for simulations of DNA and ion transport through biological nanopores

Molecular dynamics (MD) simulations have become a standard method for the rational design and interpretation of experimental studies of DNA translocation through nanopores. The MD method, however, offers a multitude of algorithms, parameters, and other protocol choices that can affect the accuracy of the resulting data as well as computational efficiency. In this chapter, we examine the most popular choices offered by the MD method, seeking an optimal set of parameters that enable the most computationally efficient and accurate simulations of DNA and ion transport through biological nanopores. In particular, we examine the influence of short-range cutoff, integration timestep and force field parameters on the temperature and concentration dependence of bulk ion conductivity, ion pairing, ion solvation energy, DNA structure, DNA-ion interactions, and the ionic current through a nanopore.

Role of histone tails in structural stability of the nucleosome

Histone tails play an important role in nucleosome structure and dynamics. Here we investigate the effect of truncation of histone tails H3, H4, H2A and H2B on nucleosome structure with 100 ns all-atom molecular dynamics simulations. Tail domains of H3 and H2B show propensity of -helics formation during the intact nucleosome simulation. On truncation of H4 or H2B tails no structural change occurs in histones. However, H3 or H2A tail truncation results in structural alterations in the histone core domain, and in both the cases the structural change occurs in the H2A3 domain. We also find that the contacts between the histone H2A C terminal docking domain and surrounding residues are destabilized upon H3 tail truncation. The relation between the present observations and corresponding experiments is discussed.

Histone tails are the most common sites of post-translational modifications. Tail modifications alter both inter and intra nucleosomal interactions to disrupt the condensed chromatin structure, thereby playing crucial role in gene access. Here we investigated histone tail functions on the stability of a single nucleosome in atomic detail by selectively truncating tail domains in molecular dynamics simulations. Our study revealed that truncation of H3 or H2A tail results in structural alterations in the nucleosome core whereas truncation of H4 or H2B tail does not. A potential role of H2A C terminal tail in regulating nucleosome stability is discussed. Finally, an -helical domain formation was observed in one of the H3 tails and, upon truncation of this tail, structural changes occurred in closely lying histone domains. The correlation between tail-truncation and structural changes likely sheds light on allosteric regulation of nucleosome stability.

Evaluation of DNA Force Fields in Implicit Solvation

DNA structural deformations and dynamics are crucial to its interactions in the cell. Theoretical simulations are essential tools to explore the structure, dynamics, and thermodynamics of biomolecules in a systematic way. Molecular mechanics force fields for DNA have benefited from constant improvements during the last decades. Several studies have evaluated and compared available force fields when the solvent is modeled by explicit molecules. On the other hand, few systematic studies have assessed the quality of duplex DNA models when implicit solvation is employed. The interest of an implicit modeling of the solvent consists in the important gain in the simulation performance and conformational sampling speed. In this study, respective influences of the force field and the implicit solvation model choice on DNA simulation quality are evaluated. To this end, extensive implicit solvent duplex DNA simulations are performed, attempting to reach both conformational and sequence diversity convergence. Structural parameters are extracted from simulations and statistically compared to available experimental and explicit solvation simulation data. Our results quantitatively expose the respective strengths and weaknesses of the different DNA force fields and implicit solvation models studied. This work can lead to the suggestion of improvements to current DNA theoretical models.

Refinement of the Cornell et al. Nucleic Acids Force Field Based on Reference Quantum Chemical Calculations of Glycosidic Torsion Profiles

We report a reparameterization of the glycosidic torsion χ of the Cornell et al. AMBER force field for RNA, χ(OL). The parameters remove destabilization of the anti region found in the ff99 force field and thus prevent formation of spurious ladder-like structural distortions in RNA simulations. They also improve the description of the syn region and the syn-anti balance as well as enhance MD simulations of various RNA structures. Although χ(OL) can be combined with both ff99 and ff99bsc0, we recommend the latter. We do not recommend using χ(OL) for B-DNA because it does not improve upon ff99bsc0 for canonical structures. However, it might be useful in simulations of DNA molecules containing syn nucleotides. Our parametrization is based on high-level QM calculations and differs from conventional parametrization approaches in that it incorporates some previously neglected solvation-related effects (which appear to be essential for obtaining correct anti/high-anti balance). Our χ(OL) force field is compared with several previous glycosidic torsion parametrizations.

Temperature-induced melting of double-stranded DNA in the absence and presence of covalently bonded antitumour drugs: insight from molecular dynamics simulations

The difference in melting temperature of a double-stranded (ds) DNA molecule in the absence and presence of bound ligands can provide experimental information about the stabilization brought about by ligand binding. By simulating the dynamic behaviour of a duplex of sequence 5′-d(TAATAACGGATTATT)·5′-d(AATAATCCGTTATTA) in 0.1 M NaCl aqueous solution at 400 K, we have characterized in atomic detail its complete thermal denaturation profile in <200 ns. A striking asymmetry was observed on both sides of the central CGG triplet and the strand separation process was shown to be strongly affected by bonding in the minor groove of the prototypical interstrand crosslinker mitomycin C or the monofunctional tetrahydroisoquinolines trabectedin (Yondelis®), Zalypsis® and PM01183®. Progressive helix unzipping was clearly interspersed with some reannealing events, which were most noticeable in the oligonucleotides containing the monoadducts, which maintained an average of 6 bp in the central region at the end of the simulations. These significant differences attest to the demonstrated ability of these drugs to stabilize dsDNA, stall replication and transcription forks, and recruit DNA repair proteins. This stabilization, quantified here in terms of undisrupted base pairs, supports the view that these monoadducts can functionally mimic a DNA interstrand crosslink.

RNA stability under different combinations of amber force fields and solvation models

The proper matching of force field and solvent is critical to obtain correct result in molecular dynamics simulation of bio-molecules. This problem has been intensively investigated for protein but not for RNA yet. In this paper, we use standard molecular dynamics and replica exchange molecular dynamics to take a series of tests on the RNA stability under different combinations of Amber force field parameters (ff98, ff99 and ff99bsc0) and the general Born implicit solvent models (igb1, igb2 and igb5). It is found that only ff98 and ff99bsc0 with igb1 can keep the native conformations of RNA hairpin and duplex. Our results suggest that ff98 plus igb1 may be reasonable choice for molecular dynamics simulation of RNA dynamics.

Molecular dynamics of DNA: comparison of force fields and terminal nucleotide definitions

Despite DNA being a very important target for several proteins and drugs, molecular dynamics simulations with nucleic acids still encompass many challenges, such as the reliability of the chosen force field. In this paper, we carried out molecular dynamics simulations of the Dickerson-Drew dodecamer comparing GROMOS 53A6 and AMBER 03 force fields. While the AMBER force field presents specific topologies for the 5' and 3' terminal nucleotides, the GROMOS force field considers all nucleotides in the same way. To investigate the effects of the terminal nucleotide definitions, both force fields were modified to be applied in the two possible ways: with or without specific terminal nucleotide topologies. The analysis of global stability (rmsd, number of base pairs and hydrogen bonds) showed that both systems simulated with AMBER were stable, while the system simulated with the original GROMOS topologies was very unstable after 5 ns. When specific terminal topologies were included for GROMOS force field, DNA denaturation was delayed until 15 ns, but not avoided. The alpha/gamma transitions also displayed a strong dependence on the force field, but not on the terminal nucleotide definitions: AMBER simulations mainly explored configurations corresponding to the global minimum, while GROMOS simulations exhibited, very early in the simulations, an extensive sampling of local minima that may facilitate transitions to A-DNA isoform. The epsilon/zeta sampling was dependent both on the force field and on the terminal nucleotide definitions: while the AMBER simulations displayed well-defined B-I --> B-II transitions, the GROMOS force field clearly favored the B-I conformation. Also, the system simulated with the original GROMOS topologies displayed uncoupled epsilon/zeta transitions, leading to noncanonical conformations, but this was reverted when the new terminal nucleotide topologies were applied. Finally, the GROMOS force field leads to strong geometrical deformations on the DNA (overestimated groove widths and roll and strongly underestimated twist and slide), which restrict the use of GROMOS force field in long time scale DNA simulations unless a further reparametrization is made.

A model for Structure and Thermodynamics of ssDNA and dsDNA Near a Surface: a Coarse Grained Approach

New methods based on surfaces or beads have allowed measurement of properties of single DNA molecules in very accurate ways. Theoretical coarse grained models have been developed to understand the behavior of single stranded and double stranded DNA. These models have been shown to be accurate and relatively simple for very short systems of 6-8 base pairs near surfaces. Comparatively less is known about the influence of a surface on the secondary structures of longer molecules important to many technologies. Surface fields due to either applied potentials and/or dielectric boundaries are not in current surface mounted coarse grained models. To gain insight into longer and surface mounted sequences we parameterized a discretized worm-like chain model. Each link is considered a sphere of 6 base pairs in length for dsDNA, and 1.5 bases for ssDNA (requiring an always even number of spheres). For this demonstration of the model, the chain is tethered to a surface by a fixed length, non-interacting 0.536 nm linker. Configurational sampling was achieved via Monte-Carlo simulation. Our model successfully reproduces end to end distance averages from experimental results, in agreement with polymer theory and all atom simulations. Our average tilt results are also in agreement with all atom simulations for the case of dense systems.

Force field dependence of phospholipid headgroup and acyl chain properties: comparative molecular dynamics simulations of DMPC bilayers

The reliability of molecular simulations largely depends on the quality of the empirical force field parameters. Force fields used in lipid simulations continue to be improved to enhance the agreement with experiments for a number of different properties. In this work, we have carried out molecular dynamics simulations of neat DMPC bilayers using united-atom Berger force field and three versions of all-atom CHARMM force fields. Three different systems consisting of 48, 72, and 96 lipids were studied. Both particle mesh Ewald (PME) and spherical cut-off schemes were used to evaluate the long-range electrostatic interactions. In total, 21 simulations were carried out and analyzed to find out the dependence of lipid properties on force fields, system size, and schemes to calculate long-range interactions. The acyl chain order parameters calculated from Berger and the recent versions of CHARMM simulations have shown generally good agreement with the experimental results. However, both sets of force fields deviate significantly from the experimentally observed P-C dipolar coupling values for the carbon atoms that link the choline and glycerol groups with the phosphate groups. Significant differences are also observed in several headgroup parameters between CHARMM and Berger simulations. Our results demonstrate that when changes were introduced to improve CHARMM force field using PME scheme, all the headgroup parameters have not been reoptimized. The headgroup properties are likely to play a significant role in lipid-lipid, protein-lipid, and ligand-lipid interactions and hence headgroup parameters in phospholipids require refinement for both Berger and CHARMM force fields.

Prediction of RNA multiloop and pseudoknot conformations from a lattice-based, coarse-grain tertiary structure model

We present a semiquantitative lattice model of RNA folding, which is able to reproduce complex folded structures such as multiloops and pseudoknots without relying on the frequently employed ad hoc generalization of the Jacobson-Stockmayer loop entropy. We derive the model parameters from the Turner description of simple secondary structural elements and pay particular attention to the unification of mismatch and coaxial stacking parameters as well as of border and nonlocal loop parameters, resulting in a reduced, unified parameter set for simple loops of arbitrary type and size. For elementary structures, the predictive power of the model is comparable to the standard secondary structure approaches, from which its parameters are derived. For complex structures, our approach offers a systematic treatment of generic effects of chain connectivity as well as of excluded volume or attractive interactions between and within all elements of the secondary structure. We reproduce the native structures of tRNA multiloops and of viral frameshift signal pseudoknots.

The pathway of oligomeric DNA melting investigated by molecular dynamics simulations

Details of the reaction coordinate for DNA melting are fundamental to much of biology and biotechnology. Recently, it has been shown experimentally that there are at least three states involved. To clarify the reaction mechanism of the melting transition of DNA, we perform 100-ns molecular dynamics simulations of a homo-oligomeric, 12-basepair DNA duplex, d(A(12)).d(T(12)), with explicit salt water at 400 K. Analysis of the trajectory reveals the various biochemically important processes that occur on different timescales. Peeling (including fraying from the ends), searching for Watson-Crick complements, and dissociation are recognizable processes. However, we find that basepair searching for Watson-Crick complements along a strand is not mechanistically tied to or directly accessible from the dissociation steps of strand melting. A three-step melting mechanism is proposed where the untwisting of the duplex is determined to be the major component of the reaction coordinate at the barrier. Though the observations are limited to the characteristics of the system being studied, they provide important insight into the mechanism of melting of other more biologically relevant forms of DNA, which will certainly differ in details from those here.

Strain softening in stretched DNA

The microscopic mechanics of DNA stretching was characterized using extensive molecular dynamics simulations. By employing an anisotropic pressure-control method, realistic force-extension dependences of effectively infinite DNA molecules were obtained. A coexistence of B and S DNA domains was observed during the overstretching transition. The simulations revealed that strain softening may occur in the process of stretching torsionally constrained DNA. The latter observation was qualitatively reconciled with available experimental data using a random-field Ising model.

Effects of long-range electrostatic forces on simulated protein folding kinetics

Molecular dynamics simulations are a useful tool for characterizing protein folding pathways. There are several methods of treating electrostatic forces in these simulations with varying degrees of physical fidelity and computational efficiency. In this article, we compare the reaction field (RF) algorithm, particle-mesh Ewald (PME), and tapered cutoffs with increasing cutoff radii to address the impact of the electrostatics method employed on the folding kinetics. We quantitatively compare different methods by a correlation of quantitative measures of protein folding kinetics. The results of these comparisons show that for protein folding kinetics, the RF algorithm can quantitatively reproduce the kinetics of the more costly PME algorithm. These results not only assist the selection of appropriate algorithms for future simulations, but also give insight on the role that long-range electrostatic forces have in protein folding.

Molecular modeling of nucleic acid structure: setup and analysis

The last in a set of units by these authors, this unit addresses some important remaining questions about molecular modeling of nucleic acids. It describes how to choose an appropriate molecular mechanics force field; how to set up and equilibrate the system for accurate simulation of a nucleic acid in an explicit solvent by molecular dynamics or Monte Carlo simulation; and how to analyze molecular dynamics trajectories.

Probing the interactions of the solvated electron with DNA by molecular dynamics simulations: bromodeoxyuridine substituted DNA

Solvated electrons ((e-)(aq)) are produced during water radiolysis and can interact with biological substrates, including DNA. To augment DNA damage, radiosensitizers such as bromo-deoxyuridine (BUdR), often referred to as an "electron affinic radiosensitizer", are incorporated in place of isosteric thymidine. However, little is known about the primary interactions of (e-)(aq) with DNA. In the present study we addressed this problem by applying molecular modeling and molecular dynamics (MD) simulations to a system of normal (BUdR.A)-DNA and a hydrated electron, where the excess electron was modeled as a localized (e-)(H2O)6 anionic cluster. Our goals were to evaluate the suitability of the MD simulations for this application; to characterize the motion of (e-)(aq) around DNA (e.g., diffusion coefficients); to identify and describe configurational states of close (e-)(aq) localization to DNA; and to evaluate the structural dynamics of DNA in the presence of (e-)(aq). The results indicate that (e-)(aq) has distinct space-preferences for forming close contacts with DNA and is more likely to interact directly with nucleotides other than BUdR. Several classes of DNA - (e-)(aq) contact sites, all within the major groove, were distinguished depending on the structure of the intermediate water layer H-bonding pattern (or its absence, i.e., a direct H-bonding of (e-)(aq) with DNA bases). Large-scale structural perturbations were identified during and after the (e-)(aq) approached the DNA from the major groove side, coupled with deeper penetration of sodium counterions in the minor groove.

Atomistic model of DNA: phonons and base-pair opening

A fully atomistic model of B-DNA using the CHARMM (chemistry at Harvard molecular mechanics) force field is presented. Molecular dynamics simulations were used to prepare an equilibrium structure. The Hessian of interatomic forces obtained from CHARMM for the equilibrium structure was used as input to a large scale phonon calculation. The calculated dispersion relations at low frequency are compared with recently published experimental data, which shows the model to have good accuracy for the low frequency, vibrational modes of DNA. These are discussed in the context of base-pair opening. In addition to the widely reported modes at, or below, approximately 12.5 meV, a continuous band of modes with strong base-pair opening character is found up to 40 meV, which coincides with the typical denaturation temperature of DNA.

Implicit solvent simulations of DNA and DNA-protein complexes: agreement with explicit solvent vs experiment

Molecular dynamics simulations of biomolecules with implicit solvent reduce the computational cost and complexity of such simulations so that longer time scales and larger system sizes can be reached. While implicit solvent simulations of proteins have become well established, the success of implicit solvent in the simulation of nucleic acids has not been fully established to date. Results obtained in this study demonstrate that stable and efficient simulations of DNA and a protein-DNA complex can be achieved with an implicit solvent model based on continuum dielectric electrostatics. Differences in conformational sampling of DNA with two sets of atomic radii that are used to define the dielectric interface between the solute and the continuum dielectric model of the solvent are investigated. Results suggest that depending on the choice of atomic radii agreement is either closer to experimental data or to explicit solvent simulations. Furthermore, partial conformational transitions toward A-DNA conformations when salt is added within the implicit solvent framework are observed.

Nucleic acid solvation: from outside to insight

Nucleic acids are polyanionic molecules that were historically considered to be solely surrounded by a shell of water molecules and a neutralizing cloud of monovalent and divalent cations. In this respect, recent experimental and theoretical reports demonstrate that water molecules within complex nucleic acid structures can display very long residency times, and assist drug binding and catalytic reactions. Finally, anions can also bind to these polyanionic systems. Many of these recent insights are provided by state-of-the-art molecular dynamics simulations of nucleic acid systems, which will be described together with relevant methodological issues.

Are Isolated Nucleic Acid Bases Really Planar? A Car−Parrinello Molecular Dynamics Study

Car-Parrinello molecular dynamics simulations of the flexibility of isolated DNA bases have been carried out. The comparison of lowest ring out-of-plane vibrations calculated by using MP2/cc-pvdz and BLYP/PW methods reveals that the DFT method with the plane wave basis set reasonably reproduces out-of-plane deformability of the pyrimidine ring in nucleic acid bases and could be used for reliable modeling of conformational flexibility of nucleobases. The conformational phase space of pyrimidine rings in thymine, cytosine, guanine, and adenine has been investigated by using the ab initio Car-Parrinello molecular dynamics method. It is demonstrated that all nucleic acid bases are highly flexible molecules and possess a nonplanar effective conformation of the pyrimidine ring despite the fact that the planar geometry corresponds to a minimum on the potential energy surface. The population of the planar geometry of the pyrimidine ring does not exceed 30%. Among the nonplanar conformations of the pyrimidine rings, the boat-like and half-chair conformations are the most populated.

Shape effects on the activity of synthetic major-groove binding ligands

In this work we present the results of a molecular simulation study of two different tetracationic bis iron(II) supramolecular cylinders interacting with DNA. One cylinder has been shown to bind in the major groove of DNA and to induce dramatic coiling of the DNA; the second is a derivative of the first, with additional methyl groups attached so as to give a larger cylinder-radius. The simulations show that both cylinders bind strongly to the major groove of the DNA, and induce complex structural changes in A-T rich regions. Whereas the parent cylinder tends to bind along the major groove, the derivatised cylinder tends to twist so that only one end remains within the major groove. Both G-C rich and A-T rich binding sites for the derivatised cylinder are discussed.

Multiple time scales in solvation dynamics of DNA in aqueous solution: the role of water, counterions, and cross-correlations

Recent time domain experiments have explored solvation dynamics of a probe located inside a DNA duplex, in an effort to gain information, e.g., on the dynamics of water molecules in the DNA major and minor grooves and their environment. Multiple time constants in the range of a few picoseconds to several nanoseconds were obtained. We have carried out 15 ns long atomistic molecular dynamics simulations to study the solvation dynamics of bases of a 38 base-pair long DNA duplex in an aqueous solution containing counterions. We have computed the energy-energy time correlation function (TCF) of the four individual bases (A, T, G, and C) to characterize the solvation dynamics. All the TCFs display highly nonexponential decay with time. When the trajectories are analyzed with 100 fs time resolution, the TCF of each base shows initial ultrafast decay (with tau1 approximately equal 60-80 fs) followed by two intermediate components (tau2 approximately equal 1 ps, tau3 approximately equal 20-30 ps), in near complete agreement with a recent time domain experiment on DNA solvation. Interestingly, the solvation dynamics of each of the four different nucleotide bases exhibit rather similar time scales. To explore the existence of slow relaxation at longer times reported recently in a series of experiments, we also analyzed the solvation TCFs calculated with longer time trajectories and with a larger time resolution of 1 ps. In this case, an additional slow component with a time constant of the order of 250 ps is observed. Through an analysis of partial solvation TCFs, we find that the slow decay originates mainly from the interaction of the nucleotides with the dipolar water molecules and the counterions. An interesting negative cross-correlation between water and counterions is observed, which makes an important contribution to relaxation at intermediate to longer times.

Entropy of Water in the Hydration Layer of Major and Minor Grooves of DNA

Transport properties (translational and rotational) of water in the two grooves of the B-DNA duplex are known to be different from those in the bulk. Here, we use a recently developed theoretical scheme to compute the entropies of water molecules in both of the grooves of DNA and compare them with that in the bulk. The scheme requires as input both translational and rotational velocity autocorrelation function (C(V)(t) and C(omega)(t), respectively) data. These velocity autocorrelation functions were computed from an atomistic MD simulation of a B-DNA duplex (36 base pairs long) in explicit water (TIP3P). The average values of the entropy of water at 300 K in both of the grooves of DNA (the TS value in the major groove is 6.71 kcal/mol and that in the minor groove is 6.41 kcal/mol) are found to be significantly lower than that in bulk water (the TS value is 7.27 kcal/mol). Thus, the entropic contribution to the free energy change (TDeltaS) of transferring a minor groove water molecule to the bulk is 0.86 kcal/mol and of transferring a major groove water to the bulk is 0.56 kcal/mol at 300 K, which is to be compared with 1.44 kcal/mol for melting of ice at 273 K. We also calculate the energy of interaction of each water molecule with the rest of the atoms in the system and hence calculate the chemical potential (Helmholtz free energy per water molecule, A = E - TS) in the different domains. The identical free energy value of water molecules in the different domains proves the robustness of the scheme. We propose that the configurational entropy of water in the grooves can be used as a measure of the mobility (or microviscosity) of water molecules in a given domain.

Atomic-level simulations of seeman DNA nanostructures: the paranemic crossover in salt solution

We use molecular dynamics (MD) simulations to understand the structure and stability of various paranemic crossover (PX) DNA molecules, synthesized recently by Seeman and co-workers at New York University. These studies include all atoms of the PX structures with an explicit description of solvent and ions. The average dynamics structures over the last 1 ns of the 3-ns simulation preserve the Watson-Crick hydrogen bonding as well as the helical structure. The root mean-square deviation in coordinates with respect to the MD averaged structure converges to 2-3 A for PX55, PX65, and PX85, but for PX75 and PX95 the root mean-square deviation in coordinates exhibits large fluctuations, indicating an intrinsic instability. The PX structures are structurally more rigid compared to the canonical B-DNA without crossover. We have developed a strain energy analysis method based on the nearest-neighbor interaction and computed the strain energy for the PX molecules compared to the B-DNA molecules of the same length and sequence. PX65 has the lowest calculated strain energy (approximately -0.77 kcal/mol/bp), and the strain increases dramatically for PX75, PX85, and PX95. PX55 has the highest strain energy (approximately 1.85 kcal/mol/bp) making it unstable, which is in accordance with the experimental results. We find that PX65 has helical twist and other helical structural parameters close to the values for normal B-DNA of similar length and sequence. Vibrational mode analysis shows that compared to other PX motifs, PX65 has the smallest population of the low-frequency modes that are dominant contributors for the conformational entropy of the PX DNA structures. All these results indicate that PX65 is structurally more stable compared to other PX motifs, in agreement with experiments. These results should aid in designing optimized DNA structures for use in nanoscale components and devices.

Simulations of DNA Coiling around a Synthetic Supramolecular Cylinder That Binds in the DNA Major Groove

In this work we present the results of a molecular simulation study of the interaction between a tetracationic bis iron(II) supramolecular cylinder, [Fe2(C25H20N4)3]4+, and DNA. This supramolecular cylinder has been shown to bind in the major groove of DNA and to induce dramatic coiling of the DNA. The simulations have been designed to elucidate the interactions that lead the cylinder to target the major groove and that drive the subsequent DNA conformational changes. Three sets of multi-nanosecond simulations have been performed: one of the uncomplexed d(CCCCCTTTTTCC) d(GGAAAAAGGGGG) dodecamer; one of this DNA complexed with the cylinder molecule; and one of this DNA complexed with a neutralised version of the cylinder. Coiling of the DNA was observed in the DNA-cylinder simulations, giving insight into the molecular level nature of the supramolecular coiling observed experimentally. The cylinder charge was found not to be essential for the DNA coiling, which implies that the DNA response is moderated by the short range interactions that define the molecular shape. Cylinder charge did, however, affect the integrity of the DNA duplex, to the extent that, under some circumstances, the tetracationic cylinder induced defects in the DNA base pairing at locations adjacent to the cylinder binding site.

Oxetane Locked Thymidine in the Dickerson-Drew Dodecamer Causes Local Base Pairing Distortions—An NMR Structure and Hydration Study

The introduction of a North-type sugar conformation constrained oxetane T block, 1-(1',3'-O-anhydro-beta-D-psicofuranosyl) thymine, at the T(7) position of the self-complementary Dickerson-Drew dodecamer, d[(5'-C(1)G(2)C(3)G(4)A(5)A(6)T(7)T(8)C(9)G(10)C(11)G(12)-3')](2), considerably perturbs the conformation of the four central base pairs, reducing the stability of the structure. UV spectroscopy and 1D NMR display a drop in melting temperature of approximately 10 degrees C per modification for the T(7) oxetane modified duplex, where the T(7) block has been introduced in both strands, compared to the native Dickerson-Drew dodecamer. The three dimensional structure has been determined by NMR spectroscopy and has subsequently been compared with the results of 2.4 ns MD simulations of the native and the T(7) oxetane modified duplexes. The modified T(7) residue is found to maintain its constrained sugar- and the related glycosyl torsion conformations in the duplex, resulting in staggered and stretched T(7).A(6) and A(6).T(7) non-linear base pairs. The stacking is less perturbed, but there is an increased roll between the two central residues compared to the native counterpart, which is compensated by tilts of the neighboring base steps. The one dimensional melting profile of base protons of the T(7) and T(8) residues reveals that the introduction of the North-type sugar constrained thymine destabilizes the core of the modified duplex, promoting melting to start simultaneously from the center as well as from the ends. Temperature dependent hydration studies by NMR demonstrate that the central T(7).A(6)/A(6).T(7) base pairs of the T(7) oxetane modified Dickerson-Drew dodecamer have at least one order of magnitude higher water exchange rates (correlated to the opening rate of the base pair) than the corresponding base pairs in the native duplex.

The effect of salt concentration on DNA conformation transition: a molecular-dynamics study

We performed three 3-ns molecular dynamics simulations of d(CGCGAATTCGCG)2 using the AMBER 8 package to determine the effect of salt concentration on DNA conformational transitions. All the simulations were started with A-DNA, with different salt concentrations, and converged with B-DNA with similar conformational parameters. However, the dynamic processes of the three MD simulations were very different. We found that the conformation transition was slow in the solution with higher salt concentration. To determine the cause of this retardation, we performed three additional 1.5-ns simulations starting with B-DNA and with the salt concentrations corresponding to the simulations mentioned above. However, astonishingly, there was no delayed conformation evolution found in any of the three simulations. Thus, our simulation conclusion is that higher salt concentrations slows the A --> B conformation transition, but have no effect on the final stable structure. [Figure: see text].

The physical determinants of the DNA conformational landscape: an analysis of the potential energy surface of single-strand dinucleotides in the conformational space of duplex DNA

A multivariate analysis of the backbone and sugar torsion angles of dinucleotide fragments was used to construct a 3D principal conformational subspace (PCS) of DNA duplex crystal structures. The potential energy surface (PES) within the PCS was mapped for a single-strand dinucleotide model using an empirical energy function. The low energy regions of the surface encompass known DNA forms and also identify previously unclassified conformers. The physical determinants of the conformational landscape are found to be predominantly steric interactions within the dinucleotide backbone, with medium-dependent backbone-base electrostatic interactions serving to tune the relative stability of the different local energy minima. The fidelity of the PES to duplex DNA properties is validated through a correspondence to the conformational distribution of duplex DNA crystal structures and the reproduction of observed sequence specific propensities for the formation of A-form DNA. The utility of the PES is demonstrated through its succinct and accurate description of complex conformational processes in simulations of duplex DNA. The study suggests that stereochemical considerations of the nucleic acid backbone play a role in determining conformational preferences of DNA which is analogous to the role of local steric interactions in determining polypeptide secondary structure.

The B- to A-DNA transition and the reorganization of solvent at the DNA surface

DNA geometry depends on relative humidity. Using the CHARMM22 force field to push B-DNA to A-DNA, a molecular dynamics simulation of a mixed-sequence 24-basepair DNA double-stranded oligomer, starting from B-DNA, was carried out to explore both the mechanism of the transition and the evolution of hydration patterns on the surface of DNA. Over the 11-ns trajectory, the transition recapitulates the slide-first, roll-later mechanism, is opposed by DNA electrostatics, and is favored by an increasing amount of condensed sodium ions. Hydration was characterized by counting the hydrogen bonds between water and DNA, and by the number of water bridges linking two DNA atoms. The number of hydrogen bonds between water and DNA remains constant during the transition, but there is a 40% increase in the number of water bridges, in agreement with the principle of economy of hydration. Water bridges emerge as delicate sensors of both structure and dynamics of DNA. Both local flexibility and the frustration of the water network on the surface of DNA probably account for the low populations and short residence times of the bridges, and for the lubricant role of water in ligand-DNA interactions.

Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps

We describe herein a computationally intensive project aimed at carrying out molecular dynamics (MD) simulations including water and counterions on B-DNA oligomers containing all 136 unique tetranucleotide base sequences. This initiative was undertaken by an international collaborative effort involving nine research groups, the "Ascona B-DNA Consortium" (ABC). Calculations were carried out on the 136 cases imbedded in 39 DNA oligomers with repeating tetranucleotide sequences, capped on both ends by GC pairs and each having a total length of 15 nucleotide pairs. All MD simulations were carried out using a well-defined protocol, the AMBER suite of programs, and the parm94 force field. Phase I of the ABC project involves a total of approximately 0.6 mus of simulation for systems containing approximately 24,000 atoms. The resulting trajectories involve 600,000 coordinate sets and represent approximately 400 gigabytes of data. In this article, the research design, details of the simulation protocol, informatics issues, and the organization of the results into a web-accessible database are described. Preliminary results from 15-ns MD trajectories are presented for the d(CpG) step in its 10 unique sequence contexts, and issues of stability and convergence, the extent of quasiergodic problems, and the possibility of long-lived conformational substates are discussed.

The stability of Seeman JX DNA topoisomers of paranemic crossover (PX) molecules as a function of crossover number

We use molecular dynamics simulations in explicit water and salt (Na+) to determine the effect of varying the number of crossover points on the structure and stability of the PX65 paranemic crossover DNA molecule and its JXM topoisomers (M denotes the number of missing crossover points), recently synthesized by the Seeman group at New York University. We find that PX65, with six crossover points, is the most stable, and that the stability decreases monotonically with the number of crossover points PX65 > JX1 > JX2 > JX3 > JX4, with 6, 5, 4, 3 and 2 crossover points, respectively. Thus, for PX65/JX1, the strain energy is approximately 3 kcal/mol/bp, while it is approximately 13 kcal/mol/bp for JX2, JX3 and JX4. Another measure of the stability is the change in the structure from the minimum energy structure to the equilibrium structure at 300 K, denoted as root-mean-square deviation in coordinates (CRMSD). We find that CRMSD is approximately 3.5 A for PX65, increases to 6 A for JX1 and increases to 10 A for JX2/JX3/JX4. As the number of crossover points decreases, the distance between the two double helical domains of the PX/JX molecules increases from approximately 20 A for PX65 to 23 A for JX4. This indicates that JX2, JX3 and JX4 are less likely to form, at least in with Na+. However, in all the cases, the two double helical domains have average helicoidal parameters similar to a typical B-DNA of similar length and base sequence.

Daunomycin Intercalation Stabilizes Distinct Backbone Conformations of DNA

Daunomycin is a widely used antibiotic of the anthracycline family. In the present study we reveal the structural properties and important intercalator-DNA interactions by means of molecular dynamics. As most of the X-ray structures of DNA-daunomycin intercalated complexes are short hexamers or octamers of DNA with two drug molecules per doublehelix we calculated a self complementary 14-mer oligodeoxyribonucleotide duplex d(CGCGCGATCGCGCG)2 in the B-form with two putative intercalation sites at the 5'-CGA-3' step on both strands. Consequently we are able to look at the structure of a 1:1 complex and exclude crystal packing effects normally encountered in most of the X-ray crystallographic studies conducted so far. We performed different 10 to 20 ns long molecular dynamics simulations of the uncomplexed DNA structure, the DNA-daunomycin complex and a 1:2 complex of DNA-daunomycin where the two intercalator molecules are stacked into the two opposing 5'-CGA-3' steps. Thereby--in contrast to X-ray structures--a comparison of a complex of only one with a complex of two intercalators per doublehelix is possible. The chromophore of daunomycin is intercalated between the 5'-CG-3' bases while the daunosamine sugar moiety is placed in the minor groove. We observe a flexibility of the dihedral angle at the glycosidic bond, leading to three different positions of the ammonium group responsible for important contacts in the minor groove. Furthermore a distinct pattern of BI and BII around the intercalation site is induced and stabilized. This indicates a transfer of changes in the DNA geometry caused by intercalation to the DNA backbone.