Conformational transition dynamics and the mechanism of long-range effects in DNA

A two-component model is proposed to describe the conformational dynamics of DNA macromolecule. A hypothesis on the mechanism of long-distance action transfer in DNA by local conformational transitions is presented. The conditions under which local transitions of B-A type are transmitted along a DNA chain are established.     

DNA structure and dynamics

This review primarily outlines the most recent atomic force microscopy (AFM) studies of DNA structure and dynamics. Sample preparation techniques allowing reliable and reproducible imaging of various DNA topologies are reviewed. Such important issues as imaging of supercoiled DNA conformations at different ionic conditions and detection of local alternative structures that are stabilized by negative DNA supercoiling are discussed in length in the article. The possibility of imaging DNA structural dynamics at different levels is another major focus of the article. Using time-lapse AFM imaging mode of nondried samples, such extensive DNA dynamic processes as transition of one local structure into another (H-DNA to B-form transition), the conformational transitions of DNA Holliday junctions and their branch migration were observed. Potential future applications of this single-molecule dynamics mode of AFM to analyses of various biochemical processes involving DNA are discussed.     

Spontaneous mutational background of microorganisms in the absence of substrate

The dynamics of spontaneous mutagenesis in a population of heterotrophic microorganisms during incubation in the absence of organic substrate was studied. A model of this dynamics was proposed. which is determined by the excitation by an external electromagnetic field of Langmuir proton oscillations activating the tautomeric transitions of nucleotides of DNA. It was shown that the model fits well the experimental data.     

Observation of an A-DNA to B-DNA transition in a nonhelical nucleic acid hairpin molecule using molecular dynamics.

One of the truly challenging problems for molecular dynamics (MD) simulations is demonstrating that the trajectories can sample not only in the vicinity of an experimentally determined structure, but also that the trajectories can find the correct experimental structure starting from some other structure. Frequently these transitions to the correct structure require that the simulations overcome energetic barriers to conformational change. Here we present unrestrained molecular dynamics simulations of the DNA analogs of the RNA 5'-GGACUUCGGUCC-3' hairpin tetraloop. In one simulation we have used deoxyuracil residues, and in the other we have used the native DNA deoxythymine residues. We demonstrate that, on a nanosecond time scale, MD is able to simulate the transitions of both of the A-DNA stems to B-DNA stems within the constraints imposed by the four-base loop that caps the helix. These results suggest that we are now in a position to use MD to address the nature of sequence-dependent structural effects in nonduplex DNA structures.     

DNA lesion alters global conformational dynamics of Y-family DNA polymerase during catalysis

A major product of oxidative damage to DNA, 8-oxo-7,8-dihydro-2'-deoxyguanine (8-oxoG), can lead to genomic mutations if it is bypassed unfaithfully by DNA polymerases in vivo. However, our pre-steady-state kinetic studies show that DNA polymerase IV (Dpo4), a prototype Y-family enzyme from Sulfolobus solfataricus, can bypass 8-oxoG both efficiently and faithfully. For the first time, our stopped-flow FRET studies revealed that a DNA polymerase altered its synchronized global conformational dynamics in response to a DNA lesion. Relative to nucleotide incorporation into undamaged DNA, three of the four domains of Dpo4 undertook different conformational transitions during 8-oxoG bypass and the subsequent extension step. Moreover, the rapid translocation of Dpo4 along DNA induced by nucleotide binding was significantly hindered by the interactions between the embedded 8-oxoG and Dpo4 during the extension step. These results unprecedentedly demonstrate that a Y-family DNA polymerase employs different global conformational dynamics when replicating undamaged and damaged DNA.     

Atomistic basis of force generation,translocation, and coordination in a viral genome packaging motor

Double-stranded DNA viruses package their genomes into pre-assembled capsids using virally-encoded ASCE ATPase ring motors. We present the first atomic-resolution crystal structure of a multimeric ring form of a viral dsDNA packaging motor, the ATPase of the asccφ28 phage, and characterize its atomic-level dynamics via long timescale molecular dynamics simulations. Based on these results, and previous single-molecule data and cryo-EM reconstruction of the homologous φ29 motor, we propose an overall packaging model that is driven by helical-to-planar transitions of the ring motor. These transitions are coordinated by inter-subunit interactions that regulate catalytic and force-generating events. Stepwise ATP binding to individual subunits increase their affinity for the helical DNA phosphate backbone, resulting in distortion away from the planar ring towards a helical configuration, inducing mechanical strain. Subsequent sequential hydrolysis events alleviate the accumulated mechanical strain, allowing a stepwise return of the motor to the planar conformation, translocating DNA in the process. This type of helical-to-planar mechanism could serve as a general framework for ring ATPases.     

Non-equilibrium structural dynamics of supercoiled DNA plasmids exhibits asymmetrical relaxation

Many cellular processes occur out of equilibrium. This includes site-specific unwinding in supercoiled DNA, which may play an important role in gene regulation. Here, we use the Convex Lens-induced Confinement (CLiC) single-molecule microscopy platform to study these processes with high-throughput and without artificial constraints on molecular structures or interactions. We use two model DNA plasmid systems, pFLIP-FUSE and pUC19, to study the dynamics of supercoiling-induced secondary structural transitions after perturbations away from equilibrium. We find that structural transitions can be slow, leading to long-lived structural states whose kinetics depend on the duration and direction of perturbation. Our findings highlight the importance of out-of-equilibrium studies when characterizing the complex structural dynamics of DNA and understanding the mechanisms of gene regulation.     

Molecular dynamics of structural transitions and intercalation in DNA

The large-scale flexibility of DNA and the intercalation of actinomycin D have been studied by computer simulation using molecular dynamics. The stretching and unwinding of B and Z forms of DNA and intercalation in B-DNA were examined through molecular dynamics simulations, and the energetics of transitions were calculated by the conformational energy minimization method. The principal results of this research are as follows: (1) A dynamic conformational pathway is presented for longitudinal stretching and unwinding of the double helix to open an intercalation site. (2) Large-scale transitions are possible in both B and Z forms of DNA through a conformationally allowed kinetic pathway. (3) The stretching and untwisting of a 5′(CG)3′ step is energetically more favorable than for a GC step in B-DNA. (4) The formation of an adjacent second cavity in B-DNA requires larger energy than the formation of the first cavity, affirming the neighbor-exclusion principle of intercalation. (5) Docking an intercalated actinomycin D in the stretched structure is shown to be geometrically and energetically feasible.     

Nucleic acids: theory and computer simulation, Y2K

Molecular dynamics simulations on DNA and RNA that include solvent are now being performed under realistic environmental conditions of water activity and salt. Improvements to force-fields and treatments of long-range interactions have significantly increased the reliability of simulations. New studies of sequence effects, axis bending, solvation and conformational transitions have appeared.     

Insights into the thermal stabilization and conformational transitions of DNA by hyperthermophile protein Sso7d: molecular dynamics simulations and MM-PBSA analysis

In the assembly of DNA-protein complex, the DNA kinking plays an important role in nucleoprotein structures and gene regulation. Molecular dynamics (MD) simulations were performed on specific protein-DNA complexes in this study to investigate the stability and structural transitions of DNA depending on temperature. Furthermore, we introduced the molecular mechanics/Poisson-Boltzmann surface area (MM-PBSA) approach to analyze the interactions between DNA and protein in hyperthermophile. Focused on two specific Sso7d-DNA complexes (PDB codes: 1BNZ and 1BF4), we performed MD simulations at four temperatures (300, 360, 420, and 480?K) and MM-PBSA at 300 and 360?K to illustrate detailed information on the changes of DNA. Our results show that Sso7d stabilizes DNA duplex over a certain temperature range and DNA molecules undergo B-like to A-like form transitions in the binary complex with the temperature increasing, which are consistent with the experimental data. Our work will contribute to a better understanding of protein-DNA interaction.     

Insights into the thermal stabilization and conformational transitions of DNA by hyperthermophile protein Sso7d: molecular dynamics simulations and MM-PBSA analysis

In the assembly of DNA-protein complex, the DNA kinking plays an important role in nucleoprotein structures and gene regulation. Molecular dynamics (MD) simulations were performed on specific protein-DNA complexes in this study to investigate the stability and structural transitions of DNA depending on temperature. Furthermore, we introduced the molecular mechanics/Poisson–Boltzmann surface area (MM-PBSA) approach to analyze the interactions between DNA and protein in hyperthermophile. Focused on two specific Sso7d-DNA complexes (PDB codes: 1BNZ and 1BF4), we performed MD simulations at four temperatures (300, 360, 420, and 480?K) and MM-PBSA at 300 and 360?K to illustrate detailed information on the changes of DNA. Our results show that Sso7d stabilizes DNA duplex over a certain temperature range and DNA molecules undergo B-like to A-like form transitions in the binary complex with the temperature increasing, which are consistent with the experimental data. Our work will contribute to a better understanding of protein-DNA interaction.     

Model of DNA Dynamics and Replication

Before DNA replication can be initiated a definite number of adenosine triphosphate (ATP) containing pre-replication protein complexes (pre-RCs) must be assembled and bound to DNA like in a super-critical mass. A chemically driven dynamics of the Ginzburg-Landau (GL) type is derived, using the non-equilibrium equation for binding of pre-RCs to DNA and a probabilistic conformational distribution of these protein complexes. This dynamics, in which the DNA-protein system behaves like a nonlinear elastically braced string (NEBS), can control the cell cycle via conformational transitions such that G₂ cells contain exactly twice as much DNA as G₁ cells. After adjustment of previously-made derivations, the model is compared with cell growth data from the T lymphocyte MLA-144.     

Recent developments in single-molecule DNA mechanics

Over the past two decades, measurements on individual stretched and twisted DNA molecules have helped define the basic elastic properties of the double helix and enabled real-time functional assays of DNA-associated molecular machines. Recently, new magnetic tweezers approaches for simultaneously measuring freely fluctuating twist and extension have begun to shed light on the structural dynamics of large nucleoprotein complexes. Related technical advances have facilitated direct measurements of DNA torque, contributing to a better understanding of abrupt structural transitions in mechanically stressed DNA. The new measurements have also been exploited in studies that hint at a developing synergistic relationship between single-molecule manipulation and structural DNA nanotechnology.     

Conformational transitions of DNA induced by changing water content of the sample: a theoretical study

A semi-phenomenological model with spatially distributed parameters is suggested to describe the processes of conformational transitions induced with change of water content of wet DNA samples. It allows describing conformational dynamics of DNA molecules with heterogeneous primary structures. It has been shown that the process of cooperative conformational transition can be simulated as propagating front of a new conformation. The evolution of a conformational perturbation of DNA molecule has been described. It can collapse for finite time or occupy the whole molecule depending on the water content of the sample.     

Theory of low-frequency vibrations in DNA macromolecules

To describe low-frequency dynamics of DNA macromolecules a model is developed taking into account the hydrogen bond stretching in base pairs, the backbone flexibility and intranucleoside mobility. For double-stranded DNA the normal vibrations are found and the structure of low-frequency spectrum is determined. The agreement between theory and Raman spectroscopy data for B-DNA is demonstrated. Conformational dependences of vibration spectrum during the B----A and helix----coil DNA transitions are studied. The contribution coming from low-frequency mobility to the nucleic-protein recognition processes is discussed.     

Shifts in the dynamics of productivity signal ecosystem state transitions at the biome‐scale

Understanding ecosystem dynamics and predicting directional changes in ecosystem in response to global changes are ongoing challenges in ecology. Here we present a framework that links productivity dynamics and ecosystem state transitions based on a spatially continuous dataset of aboveground net primary productivity (ANPP) from the temperate grassland of China. Across a regional precipitation gradient, we quantified spatial patterns in ANPP dynamics (variability, asymmetry and sensitivity to rainfall) and related these to transitions from desert to semi‐arid to mesic steppe. We show that these three indices of ANPP dynamics displayed distinct spatial patterns, with peaks signalling transitions between grassland types. Thus, monitoring shifts in ANPP dynamics has the potential for predicting ecosystem state transitions in the future. Current ecosystem models fail to capture these dynamics, highlighting the need to incorporate more nuanced ecological controls of productivity in models to forecast future ecosystem shifts.     

Dynamics and relative stabilities of parallel- and antiparallel-stranded DNA duplexes.

The dynamics and stability of four DNA duplexes are studied by means of molecular dynamics simulations. The four molecules studied are combinations of 4, 15 bases long, single-stranded oligomers, F1, F2, F3, and F4. The sequence of these single strand oligomers are chosen such that F1-F2 and F3-F4 form parallel (ps) DNA double helices, whereas F1-F4 and F2-F3 form antiparallel-stranded (aps) DNA double helices. Simulations were done at low (100 K) and room (300 K) temperatures. At low temperatures the dynamics are quasi-harmonic and the analysis of the trajectories gives good estimates of the low frequency vibrational modes and density of states. These are used to estimate the linear (harmonic) contribution of local fluctuations to the configurational entropy of the systems. Estimates of the differences in enthalpy between ps and aps duplexes show that aps double helices are more stable than the corresponding ps duplexes, in agreement with experiments. At higher temperatures, the distribution of the fluctuations around the average structures are multimodal and estimates of the configurational entropy cannot be obtained. The multi-basin, nonlinear character of the dynamics at 300 K is established using a novel method which extracts large amplitude nonlinear motions from the molecular dynamics trajectories. Our analysis shows that both ps DNA exhibit much larger fluctuations than the two aps DNA. The large fluctuations of ps DNA are explained in terms of correlated transitions in the beta, epsilon, and zeta backbone dihedral angles.