DNA dynamics in a water drop without counterions

Because of its polyionic character, the DNA double helix is stable and biologically active only in salty aqueous media where its charge is compensated by solvent counterions. Monovalent metal ions are ubiquitous in DNA environment, and they are usually considered as the possible driving force of sequence-dependent modulations of DNA structure that make it recognizable by proteins. In an effort to directly examine this hypothesis, MD simulations of DNA in a water drop surrounded by vacuum were carried out, which relieves the requirement of charge neutrality. Surprisingly, with zero concentration of counterions, a dodecamer DNA duplex appears metastable, and its structure remains similar to that observed in experiment, including the minor groove narrowing in the dodecamer d(CGCGAATTCGCG)(2) often considered as the most evident cation effect. It is suggested that the same computational approach will allow one to simulate dynamics of long DNA chains more efficiently than with periodical boundary conditions.     

Atomic Resolution Insight into Sac7d Protein Binding to DNA and Associated Global Changes by Molecular Dynamics Simulations

Sac7d is a small, thermostable protein that induces large helical deformations in DNA upon association. Starting from multiple initial placements of the unbound Sac7d structure relative to a B‐DNA oligonucleotide, molecular dynamics (MD) simulations were employed to directly follow several successful binding events at atomic resolution that resulted in structures in close agreement with the native complex geometry. The final native complex formed rapidly within tenths of nanoseconds and included simultaneous large‐scale kinking, groove opening, twisting, and intercalation in the target DNA. The simulations indicate that the complex formation process involves initial non‐native contacts that helped in reaching the final bound state, with residues intercalated at the center of the kinked DNA. It was also possible to identify several long‐lived trapped intermediate states of the binding process and to follow sliding processes of Sac7d along the DNA minor groove.     

DNA小沟结合二脒:水分子的识别作用

采用分子动力学模拟了DB921-DNA复合物, 通过7 ns的模拟研究表明: DB921一端的氨基氮原子与一个水分子形成氢键, 同时, 水分子又与DNA的5位A碱基的氮原子形成一个氢键. 水分子在DB921与DNA小沟结合中起了桥连的作用, 使得直线型的芳香二脒化合物DB921通过水桥与DNA小沟结合, 水分子诱导DB921分子与DNA的小沟域构型相适应, 与DNA小沟域的AATTC碱基有较强的结合作用. 在分子水平上提供了DB921与双螺旋DNA相互作用的结构及复合物的动态变化情况, 指出水分子在DNA小沟结合二脒化合物中的识别作用, 为设计出更高生物活性的DNA小沟结合剂提供一定的理论依据.     

Structural and dynamic variations in DNA hexamers containing T-T and F-F single and tandem internal mispairs

Molecular dynamics simulations of double-helical DNA oligomers have been performed to investigate differences in the structure, dynamics, and hydration of F-F and T-T mispairs. Hexamers containing F-F pairs were found to be more dynamic, especially in the region of the mispair itself. This dynamic variability derives from greater flexibility of F-F pairs. The T-T mispairs, on the other hand, were found to be comparatively tightly bound as wobble pairs. The major and minor groove edges of the T-T pairs were observed to be solvated at exposed carbonyl positions by at least one water molecule, while F-F pairs lacked solvating waters. Stacking interactions were nearly identical for T-T and F-F pairs, leading to similar average structures, even though F stacking was more dynamically variable. Solvation differences between F-F and T-T therefore support the steric exclusion model for nucleotide incorporation in DNA replication. Large differences in the orientation of minor groove functional groups, in addition to differences in solvation, further rationalize why F bases present during DNA extension events induce stalls. Two novel nucleotides are proposed to further elucidate minor groove interactions of DNA with polymerase molecules.Electronic Supplementary Material This Material consists of equilibration protocol, plots of center-of-mass stacking, water radial distribution functions, helical parameter dynamics, and dynamics data for a control AT sequence. Supplementary material is available in the online version of this article at Contribution to the Jacopo Tomasi Honorary Issue     

Solvation dynamics of Hoechst 33258 in water: an equilibrium and nonequilibrium molecular dynamics study

Integrated within an appropriate theoretical framework, molecular dynamics (MD) simulations are a powerful tool to complement experimental studies of solvation dynamics. Together, experiment, theory, and simulation have provided substantial insight into the dynamic behavior of polar solvents. MD investigations of solvation dynamics are especially valuable when applied to the heterogeneous environments found in biological systems, where the calculated response of the environment to the electrostatic perturbation of the probe molecule can easily be decomposed by component (e.g., aqueous solvent, biomolecule, ions), greatly aiding the molecular-level interpretation of experiments. A comprehensive equilibrium and nonequilibrium MD study of the solvation dynamics of the fluorescent dye Hoechst 33258 (H33258) in aqueous solution is presented. Many fluorescent probes employed in experimental studies of solvation dynamics in biological systems, such as the DNA minor groove binder H33258, have inherently more conformational flexibility than prototypical fused-ring chromophores. The role of solute flexibility was investigated by developing a fully flexible force-field for the H33258 molecule and by simulating its solvation response. While the timescales for the total solvation response calculated using both rigid (0.16 and 1.3 ps) and flexible (0.17 and 1.4 ps) models of the probe closely matched the experimentally measured solvation response (0.2 and 1.2 ps), there were subtle differences in the response profiles, including the presence of significant oscillations for the flexible probe. A decomposition of the total response of the flexible probe revealed that the aqueous solvent was responsible for the overall decay, while the oscillations result from fluctuations in the electrostatic terms in the solute intramolecular potential energy. A comparison of equilibrium and nonequilibrium approaches for the calculation of the solvation response confirmed that the solvation dynamics of H33258 in water is well-described by linear response theory for both rigid and flexible models of the probe.     

Nature of minor-groove binders-DNA complexes in the gas phase

The structure of noncovalent complexes of DNA duplex with minor groove binders (mG-binders) has been analyzed by state of the art molecular dynamics (MD) simulations. More than 3.3 micros of MD trajectories (including 4 x 0.5 micros trajectories) were collected for the Dickerson's dodecamer bound to DAPI, Hoechst 33258, and Netropsin. Comparison of these trajectories with control simulations in water allowed us to determine that the extreme dehydration and partial neutralization occurring during electrospray experiments does not produce the disruption of the DNA:mG-binder complexes or the dissociation of the two strands of the duplex. Irrespective of the drug and the simulation conditions the mG-binders remains bound to the DNA near the preferential binding position in aqueous conditions. Large distortions appear in the two DNA strands, which maintain however a memory of the original DNA duplex structure in water, and a general helical-like conformation.     

Potential of mean force of water–proton bath and molecular dynamic simulation of proteins at constant pH

An advanced implicit solvent model of water–proton bath for protein simulations at constant pH is presented. The implicit water–proton bath model approximates the potential of mean force of a protein in water solvent in a presence of hydrogen ions. Accurate and fast computational implementation of the implicit water–proton bath model is developed using the continuum electrostatic Poisson equation model for calculation of ionization equilibrium and the corrected MSR6 generalized Born model for calculation of the electrostatic atom–atom interactions and forces. Molecular dynamics (MD) method for protein simulation in the potential of mean force of water–proton bath is developed and tested on three proteins. The model allows to run MD simulations of proteins at constant pH, to calculate pH‐dependent properties and free energies of protein conformations. The obtained results indicate that the developed implicit model of water–proton bath provides an efficient way to study thermodynamics of biomolecular systems as a function of pH, pH‐dependent ionization‐conformation coupling, and proton transfer events. © 2012 Wiley Periodicals, Inc.     

Direct observation of essential DNA dynamics: melting and reformation of the DNA minor groove

The dynamics of bound water and ions present in the minor groove of a dodecamer DNA has been decoupled from that of the long-range twisting/bending of the DNA backbone, using the minor groove binder Hoechst 33258 as a fluorescence reporter in the picosecond-resolved time window. The bound water and ions are essential structural components of the minor groove and are destroyed with the destruction of the minor groove when the dodecamer melts at high temperatures and reforms on subsequent cooling of the melted DNA. The melting and rehybridization of the DNA has been monitored by the changes in secondary structure using circular dichroism (CD) spectroscopy. The change in the relaxation dynamics of the DNA has been studied with picosecond resolution at different temperatures, following the temperature-dependent melting and rehybridization profile of the dodecamer, using time-resolved emission spectra (TRES). At room temperature, the relaxation dynamics of DNA is governed by a 40 ps (30%) and a 12.3 ns (70%) component. The dynamics of bound water and ions present in the minor groove is characterized by the 40 ps component in the relaxation dynamics of the probe bound in the minor groove of the dodecamer DNA. Analyses of the TRES taken at different temperatures show that the contribution of this component decreases and ultimately vanishes with the destruction of the minor groove and reappears again with the reformation of the groove. The dynamical behavior of bound water molecules and ions of a genomic DNA (from salmon testes) at different temperatures is also found to be consistent with that of the dodecamer. The longer component of approximately 10 ns in the DNA dynamics is found to be associated with the long-range bending/twisting of the DNA backbone and the associated counterions. The transition from bound water to free water at the DNA surface, indicative of the change in the hydration number associated with each base pair, has also been ascertained in the case of the genomic DNA at different temperatures by employing densimetric and acoustic techniques.     

诺氟沙星-DNA复合物的分子动力学模拟

采用分子模建的方法构建了诺氟沙星-DNA复合物的初始结构, 通过2 ns的分子动力学(MD)模拟研究表明: 诺氟沙星能够和双螺旋d[ATATCGATAT]₂形成稳定的复合物, 药物分子可紧密结合在DNA的小沟区域, 并且能够与DNA的鸟嘌呤碱基形成两个稳定的氢键. 在分子水平上提供了诺氟沙星直接与双螺旋DNA相互作用的结构及复合物的动态变化情况.     

Solvent effects on the conformation of DNA dodecamer segment: a simulation study

Different solvent temperatures with five kinds of counterions are used to investigate solvent effects on the DNA microscopic structure. The dodecamer d (CGCGAATTCGCG) DNA segment is merged into the solvents and its conformation transition is studied with the molecular dynamics simulations in detail. For the simple point charge model of water molecule with Na(+) counterions, as temperature increases from 200 K to 343 K, the duplex DNA changes from stiff B form to a state between A form and B form, which we define as mixed (A-B) structure, with a double helix unwinding. To study the counterions effects, other four alkali cations, Li(+), K(+), Rb(+), or Cs(+) ions, are substituted for Na(+) ions at 298 K and 343 K, respectively. For the cases of Li(+), Rb(+), and Cs(+) ions, the duplex DNA becomes more flexible with sugar configuration changing form C2'-endo to C1'-endo type and the width and depth of minor groove at CpG and GpC steps moving towards A values, as the mass of the counterions decreasing. For the case of K(+) ions, DNA-K(+) interaction widens the width of minor and major grooves at ApA steps and TpT steps, respectively. It seems that the light ions (Li(+) or Na(+)) prefer to interact with the free phosphate oxygen atoms while the heavier ions (Rb(+) and Cs(+)) strongly interact with the base pairs.     

Double-stranded DNA dissociates into single strands when dragged into a poor solvent

DNA displays a richness of biologically relevant supramolecular structures, which depend on both sequence and ambient conditions. The effect of dragging double-stranded DNA (dsDNA) from water into poor solvent on the double-stranded structure is still unclear because of condensation. Here, we employed single molecule techniques based on atomic force microscopy and molecular dynamics (MD) simulations to investigate the change in structure and mechanics of DNA during the ambient change. We found that the two strands are split apart when the dsDNA is pulled at one strand from water into a poor solvent. The findings were corroborated by MD simulations where dsDNA was dragged from water into poor solvent, revealing details of the strand separation at the water/poor solvent interface. Because the structure of DNA is of high polarity, all poor solvents show a relatively low polarity. We speculate that the principle of spontaneous unwinding/splitting of dsDNA by providing a low-polarity (in other word, hydrophobic) micro-environment is exploited as one of the catalysis mechanisms of helicases.     

Fluorescence‐Labeled Bis‐benzamidines as Fluorogenic DNA Minor‐Groove Binders: Photophysics and Binding Dynamics

In recent decades there has been great interest in the design of highly sensitive sequence‐specific DNA binders. The eligibility of the binder depends on the magnitude of the fluorescence increase upon binding, related to its photophysics, and on its affinity and specificity, which is, in turn, determined by the dynamics of the binding process. Therefore, progress in the design of DNA binders requires both thorough photophysical studies and precise determination of the association and dissociation rate constants involved. We have studied two bis‐benzamidine (BBA) derivatives labeled by linkers of various lengths with the dye Oregon Green (OG). These fluorogenic binders show a dramatic fluorescence enhancement upon binding to the minor groove of double‐stranded (ds) DNA, as well as significant improvement in their sequence specificity versus the parent BBA, although with decreased affinity constants. Detailed photophysical analysis shows that static and dynamic quenching of the OG fluorescence by BBA through photoinduced electron transfer is suppressed upon insertion of BBA into the minor groove of DNA. Fluorescence correlation spectroscopy yields precise dynamic rate constants that prove that the association process of these fluorogenic binders to dsDNA is very similar to that of BBA alone and that their lower affinity is mainly a consequence of their weaker attachment to the minor groove and the resultant faster dissociation process. The conclusions of this study will allow us to go one step further in the design of new DNA binders with tunable fluorescence and binding properties.     

DNA小沟结合药物DB818的分子动力学模拟和结合自由能分析

采用分子动力学模拟了DNA小沟结合芳香二脒药物DB818形成的复合物. 通过5 ns的模拟研究表明: DB818药物分子可紧密结合在DNA的AATTC小沟区域, 和双螺旋d[CGCGAATTCGCG]2形成稳定的复合物. 由于噻吩硫原子的弱电负性, 使DB818能够以更大的伸展程度与DNA的小沟结合, 形成更强的结合力. DB818苯并咪唑的氮原子能够与DNA 7位和19位T碱基上的氧原子形成两个稳定的氢键, 同时, DB818末端氨基氮原子分别与DNA 的20位T碱基的氧原子和9位C碱基的氧原子形成两个氢键. 另外, 运用MM_PBSA方法计算了DB293-DNA和DB818-DNA复合物的结合自由能, 计算结合能与实验值能较好的吻合, 通过比较其结合自由能, 从热力学能量角度说明了DB818有较大的熵值与较小的焓值贡献, 从而与DNA小沟结合的结合力比DB293强. 本文在分子水平上提供了DB818直接与双螺旋DNA相互作用的结构及复合物的动态变化情况, 为设计出更高生物活性的DNA小沟结合剂提供一定的理论依据.     

Can A Denaturant Stabilize DNA? Pyridine Reverses DNA Denaturation in Acidic pH

The stability of DNA is highly dependent on the properties of the surrounding solvent, such as ionic strength, pH, and the presence of denaturants and osmolytes. Addition of pyridine is known to unfold DNA by replacing π–π stacking interactions between bases, stabilizing conformations in which the nucleotides are solvent exposed. We show here experimental and theoretical evidences that pyridine can change its role and in fact stabilize the DNA under acidic conditions. NMR spectroscopy and MD simulations demonstrate that the reversal in the denaturing role of pyridine is specific, and is related to its character as pseudo groove binder. The present study sheds light on the nature of DNA stability and on the relationship between DNA and solvent, with clear biotechnological implications.     

Can A Denaturant Stabilize DNA? Pyridine Reverses DNA Denaturation in Acidic pH

The stability of DNA is highly dependent on the properties of the surrounding solvent, such as ionic strength, pH, and the presence of denaturants and osmolytes. Addition of pyridine is known to unfold DNA by replacing π–π stacking interactions between bases, stabilizing conformations in which the nucleotides are solvent exposed. We show here experimental and theoretical evidences that pyridine can change its role and in fact stabilize the DNA under acidic conditions. NMR spectroscopy and MD simulations demonstrate that the reversal in the denaturing role of pyridine is specific, and is related to its character as pseudo groove binder. The present study sheds light on the nature of DNA stability and on the relationship between DNA and solvent, with clear biotechnological implications.     

Ultrafast Dynamics of Solvation and Charge Transfer in a DNA‐Based Biomaterial

Charge migration along DNA molecules is a key factor for DNA‐based devices in optoelectronics and biotechnology. The association of a significant amount of water molecules in DNA‐based materials for the intactness of the DNA structure and their dynamic role in the charge‐transfer (CT) dynamics is less documented in contemporary literature. In the present study, we have used a genomic DNA–cetyltrimethyl ammonium chloride (CTMA) complex, a technological important biomaterial, and Hoechest 33258 (H258), a well‐known DNA minor groove binder, as fluorogenic probe for the dynamic solvation studies. The CT dynamics of CdSe/ZnS quantum dots (QDs; 5.2 nm) embedded in the as‐prepared and swollen biomaterial have also been studied and correlated with that of the timescale of solvation. We have extended our studies on the temperature‐dependent CT dynamics of QDs in a nanoenvironment of an anionic, sodium bis(2‐ethylhexyl)sulfosuccinate reverse micelle (AOT RMs), whereby the number of water molecules and their dynamics can be tuned in a controlled manner. A direct correlation of the dynamics of solvation and that of the CT in the nanoenvironments clearly suggests that the hydration barrier within the Arrhenius framework essentially dictates the charge‐transfer dynamics.