Dynamical control of denaturation bubble nucleation in supercoiled DNA minicircles

Medium viscosity influence on the open states genesis in a DNA molecule

The studies were carried out by the mathematical modeling of DNA mechanical deformations. Numerical calculations done for the interferon alpha 17 gene, which consists of 980 base pairs. It has been established that the genesis and dynamics of open states in the DNA molecule depends on the magnitude of the external influence (torque) and on the viscosity of the environment. In addition, it is shown that the dynamics of open states zones can have a jump-like character with a small change in the magnitude of the torque. When torque is applied to all 980 base pairs of the gene, the following effect is observed: an increase in the viscosity of the medium leads to an increase in the value of the torque necessary for the occurrence of OS and DNA unwinding, i.e. viscosity plays an important stabilizing role in DNA dynamics. Under the influence of a localized torque on different (by the content of A-T and G-C pairs and location) regions of the interferon alpha 17 gene, it was found that the magnitude of the external torque necessary for the occurrence of open states at all calculated values of viscosity depends on the nucleotide composition. The dependence of the torque magnitude required for the open states occurrence on viscosity is observed when the torque is applied to areas close to the gene boundaries. At the same time, the significance of the end effect, which weakens DNA, decreased with increasing viscosity of the medium.

Ratio of AT and GC Pairs in the Zones of Open States Genesis in DNA Molecules

BACKGROUND

There is an assumption about the presence of a specific nucleotides sequence in DNA molecule, which contributes to the genesis of open states (OS). In addition, it would be logical to assume that OS zones should form in DNA regions with a large proportion of Adenine-Thymine (AT) pairs, since they contain fewer hydrogen bonds than Guanine- Cytosine (GC) base pairs. However, studies have shown that in areas rich in AT pairs, the probability of open states will not always be higher.

METHODS

In this work, for two genes containing different numbers of regions with a large AT pairs proportion, we calculated the ratio of AT and GC pairs in the OS zones. For calculations, we used a coarse-grained angular mechanical DNA model.

RESULTS

It has been established that small OS zones can appear on any part of the DNA molecule. They mainly consist of AT pairs, but as the size of OS zones increases, the content of AT pairs in them decreases.

CONCLUSIONS

The occurrence of long-length OS zones is "tied" to regions of the DNA molecule with a large proportion of AT pairs; if there are several such areas, then, depending on the magnitude of the torque, OS zones can arise in different areas of the gene. Thus, the genesis probability of large OS zones in a DNA segment depends not only on the "strength" of the nucleotide sequence of this area, but also on the factors determining the dynamics of DNA.

Large bubble drives circular DNA melting

We investigate the melting transition of non-supercoiled circular DNA of different lengths, employing Brownian dynamics simulations. In the absence of supercoiling, we find that melting of circular DNA is driven by a large bubble, which agrees with the previous predictions of circular DNA melting in the presence of supercoiling. By analyzing sector-wise changes in average base-pair distance, our study reveals that the melting behavior of circular DNA closely resembles that of linear DNA. Additionally, we find a marked difference in the thermal stability of circular DNA over linear DNA at very short length scales, an effect that diminishes as the length of circular DNA increases. The stability of smaller circular DNA is linked to the occurrence of transient small bubbles, characterized by a lower probability of growth.

Kinetics from Metadynamics: Principles, Applications, and Outlook

Metadynamics is a popular enhanced sampling algorithm for computing the free energy landscape of rare events by using molecular dynamics simulation. Ten years ago, Tiwary and Parrinello introduced the infrequent metadynamics approach for calculating the kinetics of transitions across free energy barriers. Since then, metadynamics-based methods for obtaining rate constants have attracted significant attention in computational molecular science. Such methods have been applied to study a wide range of problems, including protein-ligand binding, protein folding, conformational transitions, chemical reactions, catalysis, and nucleation. Here, we review the principles of elucidating kinetics from metadynamics-like approaches, subsequent methodological developments in this area, and successful applications on chemical, biological, and material systems. We also highlight the challenges of reconstructing accurate kinetics from enhanced sampling simulations and the scope of future developments.

Genesis of Open States Zones in a DNA Molecule Depends on the Localization and Value of the Torque

The formation and dynamics of the open states in a double-stranded DNA molecule are largely determined by its mechanical parameters. The main one is the torque. However, the experimental study of DNA dynamics and the occurrence of open states is limited by the spatial resolution of available biophysical instruments. Therefore, in this work, on the basis of a mechanical mathematical model of DNA, calculations of the torque effect on the process of occurrence and dynamics of open states were carried out for the interferon alpha 17 gene. It was shown that torsion action leads to the occurrence of rotational movements of nitrogenous bases. This influence is nonlinear, and an increase in the amplitude of the torsion action does not lead to an automatic increase in the amplitude of rotational movements and an increase in the zones’ open states. Calculations with a constant torsion moment demonstrate that open states zones are more often formed at the boundaries of the gen and in regions with a predominance of A–T pairs. It is shown, that for the occurrence of open states in the part of the gene that contains a small number of A–T pairs, a large amount of torque is required. When the torque is applied to a certain region of the gene, the probability of the formation of the open state depends on the content of A–T pairs in this region, the size of this region, and on the exposure time. For this mathematical model, open states zones can be closed when the torsion action stops. The simulation results showed that the values of the torsion moment required for the appearance of open states zones, in some cases, are close to experimentally measured (13–15 pN·nm).

Influence of Environmental Parameters on the Stability of the DNA Molecule

Fluctuations in viscosity within the cell nucleus have wide limits. When a DNA molecule passes from the region of high viscosity values to the region of low values, open states, denaturation bubbles, and unweaving of DNA strands can occur. Stabilization of the molecule is provided by energy dissipation-dissipation due to interaction with the environment. Separate sections of a DNA molecule in a twisted state can experience supercoiling stress, which, among other things, is due to complex entropic effects caused by interaction with a solvent. In this work, based on the numerical solution of a mechanical mathematical model for the interferon alpha 17 gene and a fragment of the Drosophila gene, an analysis of the external environment viscosity influence on the dynamics of the DNA molecule and its stability was carried out. It has been shown that an increase in viscosity leads to a rapid stabilization of the angular vibrations of nitrogenous bases, while a decrease in viscosity changes the dynamics of DNA: the rate of change in the angular deviations of nitrogenous bases increases and the angular deformations of the DNA strands increase at each moment of time. These processes lead to DNA instability, which increases with time. Thus, the paper considers the influence of the external environment viscosity on the dissipation of the DNA nitrogenous bases' vibrational motion energy. Additionally, the study on the basis of the described model of the molecular dynamics of physiological processes at different indicators of the rheological behavior of nucleoplasm will allow a deeper understanding of the processes of nonequilibrium physics of an active substance in a living cell to be obtained.

One-Step Polymerase Chain Reaction-Free Nanowire-Based Plasma Cell-Free DNA Assay to Detect EML4-ALK Fusion and to Monitor Resistance in Lung Cancer

BACKGROUND

Next-generation sequencing has mostly been used for genotyping cell-free DNA (cfDNA) in plasma. However, this assay has several clinical limitations. We evaluated the clinical utility of a novel polymerase chain reaction-free nanowire (NW)-based plasma cfDNA assay for detecting ALK fusion and mutations.

PATIENTS, MATERIALS, AND METHODS

We consecutively enrolled 99 patients with advanced non-small cell lung cancer undergoing a fluorescence in situ hybridization (FISH) test for ALK fusion; ALK-positive (n = 36). The NW-based assay was performed using 50-100 μL of plasma collected at pretreatment and every 8 weeks during ALK inhibitor treatment.

RESULTS

There was high concordance between the NW-based assay and the FISH test for identification of ALK fusion (94.9% with a kappa coefficient value of 0.892, 95% confidence interval [CI], 0.799-0.984). There was no difference in the response rate to the first anaplastic lymphoma kinase inhibitor between the ALK-positive patients identified by the NW-based assay and by the FISH test (73.5% vs. 72.2%, p = .931). In the ALK variant analysis, variants 1 and 3 subgroups were detected in 27 (75.0%) and 8 (22.2%) patients, respectively. Among 24 patients treated with crizotinib, variant 3 subgroup was associated with worse median overall survival than variant 1 subgroup (36.5 months; 95% CI, 0.09-87.6 vs. 19.8 months; 95% CI, 9.9-not reached, p = .004]. A serial assessment identified that ALK L1196M resistance mutation emerged before radiologic progression during crizotinib treatment.

CONCLUSION

The newly developed simple NW-based cfDNA assay may be clinically applicable for rapid diagnosis of ALK fusion with its variant forms and early detection of resistance.

IMPLICATIONS FOR PRACTICE

The authors developed a novel one-step polymerase chain reaction-free nanowire (NW)-based plasma cell-free DNA (cfDNA) assay. This study evaluated the clinical utility of this novel method for the diagnosis of EML4-ALK fusion in advanced non-small cell lung cancer (NSCLC). The NW-based assay and FISH test showed high concordance rate in 99 patients with advanced NSCLC. Serial cfDNA assessment demonstrated this method provided early detection of resistance before radiologic progression during crizotinib treatment. Taken together, plasma cfDNA genotyping by the NW-based cfDNA assay may be useful for the rapid diagnosis of ALK fusion, classifying variants, and early detection of resistance.

Anomalous Laterally Stressed Kinetically Trapped DNA Surface Conformations

DNA kinking is inevitable for the highly anisotropic 1D-1D electrostatic interaction with the one-dimensionally periodically charged surface. The double helical structure of the DNA kinetically trapped on positively charged monomolecular films comprising the lamellar templates is strongly laterally stressed and extremely perturbed at the nanometer scale. The DNA kinetic trapping is not a smooth 3D-> 2D conformational flattening but is a complex nonlinear in-plane mechanical response (bending, tensile and unzipping) driven by the physics beyond the scope of the applicability of the linear worm-like chain approximation. Up to now, the DNA molecule adsorbed on a surface was believed to always preserve its native structure. This belief implies a negligible contribution of lateral surface forces during and after DNA adsorption although their impact has never been elucidated. High-resolution atomic force microscopy was used to observe that stiff DNA molecules kinetically trapped on monomolecular films comprising one-dimensional periodically charged lamellar templates as a single layer or as a sublayer are oversaturated by sharp discontinuous kinks and can also be locally melted and supercoiled. We argue that kink/anti-kink pairs are induced by an overcritical lateral bending stress (> 30 pNnm) inevitable for the highly anisotropic 1D-1D electrostatic interaction of DNA and underlying rows of positive surface charges. In addition, the unexpected kink-inducing mechanical instability in the shape of the template-directed DNA confined between the positively charged lamellar sides is observed indicating the strong impact of helicity. The previously reported anomalously low values of the persistence length of the surface-adsorbed DNA are explained by the impact of the surface-induced low-scale bending. The sites of the local melting and supercoiling are convincingly introduced as other lateral stress-induced structural DNA anomalies by establishing a link with DNA high-force mechanics. The results open up the study in the completely unexplored area of the principally anomalous kinetically trapped DNA surface conformations in which the DNA local mechanical response to the surface-induced spatially modulated lateral electrostatic stress is essentially nonlinear. The underlying rich and complex in-plane nonlinear physics acts at the nanoscale beyond the scope of applicability of the worm-like chain approximation.

Current understanding of extrachromosomal circular DNA in cancer pathogenesis and therapeutic resistance

Extrachromosomal circular DNA was recently found to be particularly abundant in multiple human cancer cells, although its frequency varies among different tumor types. Elevated levels of extrachromosomal circular DNA have been considered an effective biomarker of cancer pathogenesis. Multiple reports have demonstrated that the amplification of oncogenes and therapeutic resistance genes located on extrachromosomal DNA is a frequent event that drives intratumoral genetic heterogeneity and provides a potential evolutionary advantage. This review highlights the current understanding of the extrachromosomal circular DNA present in the tissues and circulation of patients with advanced cancers and provides a detailed discussion of their substantial roles in tumor regulation. Confirming the presence of cancer-related extrachromosomal circular DNA would provide a putative testing strategy for the precision diagnosis and treatment of human malignancies in clinical practice.