Molecular dynamics simulation of single DNA stretching reveals a novel structure

Simulating the Helicase Enzymatic Action on ds-DNA: A First-Principles Molecular Dynamics Study

Understanding DNA replication is fundamental for advancements in fields such as genetics, molecular biology, and medical research. In this study, we investigate the mechanical characteristics of three distinct double-stranded DNA molecules (ds-DNA) as each of them is unwound into two individual single strands. To simulate the helicase action, the double strands are subjected to Langevin forces. By use of sequential and helical steering harmonic forces that simulate the enzymatic action of a helicase, each strand of ds-DNA is opened. The research focuses on determining thermal fluctuations, energy changes, charge variations, and individual forces associated with the separation of each base pair in the examined sequences. The findings emphasize the importance of combining quantum mechanical techniques with an implicit force model. This integrative approach is versatile and provides valuable insights into the essential processes governing DNA mechanisms, particularly in relation to cellular functioning, thereby enhancing our understanding of biological molecules.

The emergence of sequence-dependent structural motifs in stretched, torsionally constrained DNA

The double-helical structure of DNA results from canonical base pairing and stacking interactions. However, variations from steady-state conformations resulting from mechanical perturbations in cells have physiological relevance but their dependence on sequence remains unclear. Here, we use molecular dynamics simulations showing sequence differences result in markedly different structural motifs upon physiological twisting and stretching. We simulate overextension on different sequences of DNA ((AA)12, (AT)12, (CC)12 and (CG)12) with supercoiling densities at 200 and 50 mM salt concentrations. We find that DNA denatures in the majority of stretching simulations, surprisingly including those with over-twisted DNA. GC-rich sequences are observed to be more stable than AT-rich ones, with the specific response dependent on the base pair order. Furthermore, we find that (AT)12 forms stable periodic structures with non-canonical hydrogen bonds in some regions and non-canonical stacking in others, whereas (CG)12 forms a stacking motif of four base pairs independent of supercoiling density. Our results demonstrate that 20-30% DNA extension is sufficient for breaking B-DNA around and significantly above cellular supercoiling, and that the DNA sequence is crucial for understanding structural changes under mechanical stress. Our findings have important implications for the activities of protein machinery interacting with DNA in all cells.

An elastic model of DNA under thermal induced stress

DNAs (deoxyribonucleic acids) have the ability to alter its conformation in response to temperature changes to relieve the internal stress. The mistakenly structured DNA can lead to diseases or deformities. The conformation also influences the binding between DNA and other molecular complexes. In the present paper, we investigate the DNA elasticity under the influence of thermal induced stress by employing Kirchhoff's model of a thin elastic rod. The problem is solved by perturbation method to find equilibrium configurations of DNA at different modes. In addition, the model is validated with existing literature in which DNA is stretched or compressed. The behaviors of the helical structure under various temperatures are investigated with the melting temperature of DNA around 80 °C. This elasticity study of DNA could be a groundwork leading to better understandings on the effects of thermal induced stress to DNA's deformation and relevant biological processes in living cells.

Stability of radiation-damaged DNA after multiple strand breaks

Radiation induced double-strand breaks in DNA are more stable against thermal and mechanical stress than usually thought.

The mechanism of the emergence of distinct overstretched DNA states

Although multiple overstretched DNA states were identified in experiments, the mechanism of the emergence of distinct states is still unclear. Molecular dynamics simulation is an ideal tool to clarify the mechanism, but the force loading rates in stretching achieved by conventional all-atom DNA models are much faster, which essentially affect overstretching states. We employed a modified coarse-grained DNA model with an unprecedented low loading rate in simulations to study the overstretching transitions of end-opened double-stranded DNA. We observed two-strand peeling off for DNA with low stability and the S-DNA with high stability under tension. By introducing a melting-forbidden model which prevents base-pair breaking, we still observed the overstretching transition induced by the formation of S-DNA due to the change of dihedral angle. Hence, we confirmed that the competition between the two strain-softening manners, i.e., base-pair breaking and dihedral angle variation, results in the emergence of distinct overstretched DNA states.

Electronic detection of dsDNA transition from helical to zipper conformation using graphene nanopores

Mechanical manipulation of DNA by forced extension can lead double-stranded DNA (dsDNA) to structurally transform from a helical form to a linear zipper-like form. By employing classical molecular dynamics and quantum mechanical nonequilibrium Green's function-based transport simulations, we show the ability of graphene nanopores to discern different dsDNA conformations, in a helical to zipper transition, using transverse electronic conductance. In particular, conductance oscillations due to helical dsDNA vanish as dsDNA extends from a helical form to a zipper form while it is transported through the nanopore. The predicted ability to detect conformational changes in dsDNA via transverse electronic conductance can widen the potential use of graphene-based nanosensors for DNA detection.

Coarse-grained simulations of DNA overstretching

We use a recently developed coarse-grained model to simulate the overstretching of duplex DNA. Overstretching at 23 °C occurs at 74 pN in the model, about 6-7 pN higher than the experimental value at equivalent salt conditions. Furthermore, the model reproduces the temperature dependence of the overstretching force well. The mechanism of overstretching is always force-induced melting by unpeeling from the free ends. That we never see S-DNA (overstretched duplex DNA), even though there is clear experimental evidence for this mode of overstretching under certain conditions, suggests that S-DNA is not simply an unstacked but hydrogen-bonded duplex, but instead probably has a more exotic structure.

Effects of cytosine hydroxymethylation on DNA strand separation

Cytosine hydroxymethylation is an epigenetic control factor in higher organisms. New discoveries of the biological roles of hydroxymethylation serve to raise questions about how this epigenetic modification exerts its functions and how organisms discriminate cytosine hydroxymethylation from methylation. Here, we report investigations that reveal an effect of cytosine hydroxymethylation on mechanical properties of DNA under load. The findings are based on molecular force assay measurements and steered molecular dynamics simulations. Molecular force assay experiments identified significant effects of hydroxymethylation on stretching-induced strand separation; the underlying physical mechanism has been revealed by steered molecular dynamics simulations. We find that hydroxymethylation can either upregulate or downregulate DNA's strand separation propensity, suggesting that hydroxymethylation can control gene expression by facilitating or obstructing the action of transcription machinery or the access to chromosomal DNA.

Competition between Na⁺ and Rb⁺ in the minor groove of DNA

The competition between Na⁺ and Rb⁺ ions in the minor groove of a synthetic B-DNA dodecamer d (CGCGAATTCGCG) is studied using molecular dynamics simulations as the ratio of these two ions changing from 9:1 to 1:9 with the DNA merged into the solvent of water molecule at 298 K. When the concentration of Rb⁺ ions increases, from minority to majority, Na⁺ ions are gradually released from the A tract, and the binding sites in the minor groove are occupied by Rb⁺ ions, extending from the A tract to the whole minor groove. Comparing Na⁺ with Rb⁺ ions, the conformation of the minor groove is influenced strongly by Na⁺ ions.

AN OVERVIEW OF THE STRETCHED INTERMEDIATE MODEL OF B–Z DNA TRANSITION

Recently, the stretched intermediate model was proposed for the B–Z deoxyribonucleic acid (DNA) transition based on simulation results carried out using the Stochastic Difference Equation (SDE) that showed unwinding and elongation of the oligomer during the transition. This model has proven to be successful in resolving the steric dilemma in short oligomers. However, extending the simulation method to larger DNA strands may prove to be computationally challenging. Such difficulty has led us to adopt a mean field approach using phenomenological interaction potentials to simulate the transition. Like the atomistic approach, the SDE simulations based on the mean field approach, also suggest the presence of a stretched intermediate during the transition.

Cytosine methylation alters DNA mechanical properties

DNA methylation plays an essential role in transcriptional control of organismal development in epigenetics, from turning off a specific gene to inactivation of entire chromosomes. While the biological function of DNA methylation is becoming increasingly clear, the mechanism of methylation-induced gene regulation is still poorly understood. Through single-molecule force experiments and simulation we investigated the effects of methylation on strand separation of DNA, a crucial step in gene expression. Molecular force assay and single-molecule force spectroscopy revealed a strong methylation dependence of strand separation. Methylation is observed to either inhibit or facilitate strand separation, depending on methylation level and sequence context. Molecular dynamics simulations provided a detailed view of methylation effects on strand separation, suggesting the underlying physical mechanism. According to our study, methylation in epigenetics may regulate gene expression not only through mechanisms already known but also through changing mechanical properties of DNA.

B-DNA to zip-DNA: simulating a DNA transition to a novel structure with enhanced charge-transport characteristics

The forced extension of a DNA segment is studied in a series of steered molecular dynamics simulations, employing a broad range of pulling forces. Throughout the entire force range, the formation of a zipper-like (zip-) DNA structure is observed. In that structure, first predicted by Lohikoski et al., the bases of the DNA strands interdigitate with each other and form a single-base aromatic stack. Similar motifs, albeit only a few base pairs in extent, have been observed in experimental crystal structures. Analysis of the dynamics of structural changes in pulled DNA shows that S-form DNA, thought to be adopted by DNA under applied force, serves as an intermediate between B-DNA and zip-DNA. Therefore, the phase transition plateau observed in force-extension curves of DNA is suggested to reflect the B-DNA to zip-DNA structural transition. Electronic structure analysis of purine bases in zip-DNA indicates a several-fold to order of magnitude increase in the π-π electronic coupling among nearest-neighbor nucleobases, compared to B-DNA. We further observe that zip-DNA does not require base pair complementarity between DNA strands, and we predict that the increased electronic coupling in zip-DNA will result in a much higher rate of charge transfer through an all-purine zip-DNA compared to B-DNA of equal length.

Stretching chimeric DNA: a test for the putative S-form

Double-stranded DNA "overstretches" at a pulling force of about 65 pN, increasing in length by a factor of 1.7. The nature of the overstretched state is unknown, despite its considerable importance for DNA's biological function and technological application. Overstretching is thought by some to be a force-induced denaturation and by others to consist of a transition to an elongated, hybridized state called S-DNA. Within a statistical mechanical model, we consider the effect upon overstretching of extreme sequence heterogeneity. "Chimeric" sequences possessing halves of markedly different AT composition elongate under fixed external conditions via distinct, spatially segregated transitions. The corresponding force-extension data vary with pulling rate in a manner that depends qualitatively and strikingly upon whether the hybridized S-form is accessible. This observation implies a test for S-DNA that could be performed in experiment.

Force induced DNA melting

When pulled along the axis, double-strand DNA undergoes a large conformational change and elongates by roughly twice its initial contour length at a pulling force of about 70 pN. The transition to this highly overstretched form of DNA is very cooperative. Applying a force perpendicular to the DNA axis (unzipping), double-strand DNA can also be separated into two single-stranded DNA, this being a fundamental process in DNA replication. We study the DNA overstretching and unzipping transition using fully atomistic molecular dynamics (MD) simulations and argue that the conformational changes of double-strand DNA associated with either of the above mentioned processes can be viewed as force induced DNA melting. As the force at one end of the DNA is increased the DNA starts melting abruptly/smoothly above a critical force depending on the pulling direction. The critical force f(m), at which DNA melts completely decreases as the temperature of the system is increased. The melting force in the case of unzipping is smaller compared to the melting force when the DNA is pulled along the helical axis. In the case of melting through unzipping, the double-strand separation has jumps which correspond to the different energy minima arising due to sequence of different base pairs. The fraction of Watson-Crick base pair hydrogen bond breaking as a function of force does not show smooth and continuous behavior and consists of plateaus followed by sharp jumps.

Simulation of the mechanical strength of a single collagen molecule

We perform atomistic simulations on a single collagen molecule to determine its intrinsic molecular strength. A tensile pull simulation to determine the tensile strength and Young's modulus is performed, and a simulation that separates two of the three helices of collagen examines the internal strength of the molecule. The magnitude of the calculated tensile forces is consistent with the strong forces of bond stretching and angle bending that are involved in the tensile deformation. The triple helix unwinds with increasing tensile force. Pulling apart the triple helix has a smaller, oscillatory force. The oscillations are due to the sequential separation of the hydrogen-bonded helices. The force rises due to reorienting the residues in the direction of the separation force. The force drop occurs once the hydrogen bond between residues on different helices break and the residues separate.

Assessing the Mechanical Properties of a Molecular Spring

We report on the dramatic effect of increasing helix diameter on the hybridization of oligopyridine-dicarboxamide strands into double helices. Upon replacing a single pyridine by a 1,8-diazaanthracene unit within an oligomeric strand, a 4.7 A enlargement of the helix diameter occurs parallel to the long anthracene axis. This structure change results in a spectacular stabilization of the double helical hybrids derived from these strands (factors of over 10(7)). Detailed investigations of the hybridization process using X-ray crystallography, NMR, fluorescence measurements and molecular mechanics calculations allowed us to assign the duplex stabilization to two enthalpic effects. First, the increase in diameter results in an augmented surface, involved in intermolecular pi-pi stacking. Second, the enlarged diameter leads to a lower tilt angle of the helical strand, with respect to the helix axis, which in turn results in smaller dihedral angles at the aryl-amide linkages and thus a considerably lowered enthalpic cost of the spring-like extension of the strands during the hybridization process. These results provide novel insights into how subtle tuning of molecular components may result in considerable and rationalizable changes in double helical supramolecular architectures.