DNA is strong polyelectrolyte macromolecule making metal ions (counterions) condense to a cloud around the double helix. The counterions may be localized outside the macromolecule and inside the minor and major grooves of the double helix. In the present work, the distribution of condensed counterions between inner and outer regions of DNA has been studied using the approaches of counterion condensation theory. The results have shown that the number of counterions trapped inside the macromolecule should be greater than 0.16 per one phosphate group. The maximal number of counterions that may be localized inside the DNA double helix is limited to about 0.4 per one phosphate group and it is much lower than the total number of condensed counterions. To analyze the structure of counterion cloud the molecular dynamics simulations of \emph{B}-DNA with K$^{+}$ counterions have been performed. The obtained number of the counterions trapped inside the grooves of the double helix is about 0.22$\pm$0.06 per one phosphate group that agree with the model estimations. The developed model describes general features of the structure of counterion cloud around DNA and is able to predict the number of counterions inside the grooves of the double helix.
The structure of DNA double helix is stabilized by metal counterions condensed to a diffuse layer around the macromolecule. The dynamics of counterions in real conditions is governed by the electric fields from DNA and other biological macromolecules. In the present work the molecular dynamics study {was} performed for the system of DNA double helix with neutralizing K$^+$ counterions and for the system of KCl salt solution in the external electric field of different strength (up to 32 mV/Å). The analysis of ionic conductivities of these systems {has shown} that the counterions around the DNA …
Strongly correlated electrostatics of DNA systems has drawn the interest of many groups, especially the condensation and overcharging of DNA by multivalent counterions. By adding counterions of different valencies and shapes, one can enhance or reduce DNA overcharging. In this papers, we focus on the effect of multivalent co-ions, specifically divalent co-ions such as SO$_4^{2-}$. A computational experiment of DNA condensation using Monte$-$Carlo simulation in grand canonical ensemble is carried out where DNA system is in equilibrium with a bulk solution containing a mixture of salt of differe…
Under supercoiling constraints, naked DNA, such as a large part of bacterial DNA, folds into braided structures called plectonemes. The double-helix can also undergo local structural transitions, leading to the formation of denaturation bubbles and other alternative structures. Various polymer models have been developed to capture these properties, with Monte-Carlo (MC) approaches dedicated to the inference of thermodynamic properties. In this chapter, we explain how to perform such Monte-Carlo simulations, following two objectives. On one hand, we present the self-avoiding supercoiled Worm-Li…
We have explored morphology of DNA molecules bound with Cu-complexes of piroxicam molecules, a non-steroidal anti-inflammatory drug (NSAID), under one-dimensional confinement of thin films and have studied the effect of counterions present in a buffer. X-ray reflectivity at and away from the Cu K absorption edge and atomic force microscopy studies reveal that confinement segregates the drug molecules preferentially in a top layer of the DNA film, and counterions enhance this segregation.
Extreme deformations of the DNA double helix attracted a lot of attention during the past decades. Particularly, the determination of the persistence length of DNA with extreme local disruptions, or kinks, has become a crucial problem in the studies of many important biological processes. In this paper we review an approach to calculate the persistence length of the double helix by taking into account the formation of kinks of arbitrary configuration. The reviewed approach improves the Kratky--Porod model to determine the type and nature of kinks that occur in the double helix, by measuring a …
The study of configurational parameters of deformed DNA is a relevant problem in research of such important biological process as double helix compactization in cell. The deformations accompanied with local disruptions of the regular macromolecule structure cause significant bending of the double helix, or kinks. In this paper an approach for Kratky-Porod model to calculate persistence length of DNA macromolecule with kinks is developed. The presented approach considers kinks of arbitrary configuration, including two basic types of kinks, type 1 - sharp kink caused by unstacking a single base …
DNA supercoiling, the under or overwinding of DNA, is a key physical mechanism both participating to compaction of bacterial genomes and making genomic sequences adopt various structural forms. DNA supercoiling may lead to the formation of braided superstructures (plectonemes), or it may locally destabilize canonical B-DNA to generate denaturation bubbles, left-handed Z-DNA and other functional alternative forms. Prediction of the relative fraction of these structures has been limited because of a lack of predictive polymer models that can capture the multiscale properties of long DNA molecule…
DNA nanotubes are tubular structures composed of DNA crossover molecules. We present a bottom up approach for construction and characterization of these structures. Various possible topologies of nanotubes are constructed such as 6-helix, 8-helix and tri-tubes with different sequences and lengths. We have used fully atomistic molecular dynamics simulations to study the structure, stability and elasticity of these structures. Several nanosecond long MD simulations give the microscopic details about DNA nanotubes. Based on the structural analysis of simulation data, we show that 6-helix nanotube…
Recent experiments have shown that trivalent ion, spermidine$^{3+}$, can provoke lateral microphase segregation in DNA brushes. Using molecular simulations and simple theoretical arguments, we explore the effects of trivalent counterions on polyelectrolyte brushes. At a proper range of grafting density, polymer size, and ion concentration, the brush polymers collapse heterogeneously into octopus-like surface micelles. Remarkably, the heterogeneity in brush morphology is maximized and the relaxation dynamics of chain and condensed ion are the slowest at the 1:3 stoichiometric concentration of t…
Effects of the size and concentration of depleting agents on the stabilization of the double-helix structure and DNA condensation: a single molecule force spectroscopy study
Analysis of single-molecule micromanipulation experiments of DNA unzipping process shows some features of the force-distance curve, namely two consequent plateaus in the area of ${\sim}12-14pN$ dependent on nucleotide sequence structure, as well as peaks appearance in the plateau area, to which it was not paid essential attention earlier. Using atom-atom potential function method the estimations of Watson-Crick base pairs opening energies are made. On the basis of this results two possible scenarios of the DNA double helix unzipping process are proposed. According to the first scenario DNA unz…
The thermodynamical stability of DNA minicircles is investigated by means of path integral techniques. Hydrogen bonds between base pairs on complementary strands can be broken by thermal fluctuations and temporary fluctuational openings along the double helix are essential to biological functions such as transcription and replication of the genetic information. Helix unwinding and bubble formation patterns are computed in circular sequences with variable radius in order to analyze the interplay between molecule size and appearance of helical disruptions. The latter are found in minicircles wit…
We report on a way to manipulate the spin transport through double-stranded DNA contacted by normal-metal electrodes. On the basis of an effective model Hamiltonian, the conductance and the spin polarization are calculated in the presence of a gate voltage by using the Landauer-Büttiker formula. Our results indicate that the spin polarization presents strong dependence on the magnitude as well as the direction of the gate voltage. The spin polarization can be significantly enhanced by tuning the gate voltage and shows oscillating behavior with increasing the DNA length.
Experimental data of the DNA cyclization (J-factor) at short length scales, as a way to study the elastic behavior of tightly bent DNA, exceed the theoretical expectation based on the wormlike chain (WLC) model by several orders of magnitude. Here, we propose that asymmetric bending rigidity of the double helix in the groove direction can be responsible for extreme bendability of DNA at short length scales and it also facilitates DNA loop formation at these lengths. To account for the bending asymmetry, we consider the asymmetric elastic rod (AER) model which has been introduced and parametriz…
The mechanism of threshold elongation (overstretching) of DNA macromolecules under the action of external force is studied within the framework of phenomenological approach. When considering the task it is taken into account that double-stranded DNA is a polymorphic macromolecule with a set of metastable states. Accordingly to proposed mechanism, DNA threshold elongation can take place as a cooperative structural transition of macromolecule to metastable form, which is stabilized by the external force. For the description of DNA overstretching, the model included external (stretching) and inte…
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 Cobalt Hexammine ion (Co-Hex) solutions by the atomistic molecular dynamics simulations. Our calculations show that …
Intracellular positive ions neutralise negative charges on the phosphates of a DNA strand conferring greater strength on the hydrogen bonds that connect complementary strands into a double helix and so confer enhanced stability. Beyond a certain value of salt concentration, the DNA molecule displays a unstable nature {\it in vivo} as well as {\it in vitro}. We consider a wide range of salt concentrations and study the stability of the DNA double helix using a statistical model. Through numerical calculations we attempt to explain the different behaviour exhibited by DNA molecules in this range…
A polarizable environment, prominently the solvent, responds to electronic changes in biomolecules rapidly. The knowledge of conformational relaxation of the biomolecule itself, however, may be scarce or missing. In this work, we describe in detail the structural changes in DNA undergoing electron transfer between two adjacent nucleobases. We employ an approach based on averaging of tens to hundreds of thousands of nonequilibrium trajectories generated with molecular dynamics simulation, and a reduction of dimensionality suitable for DNA. We show that the conformational response of the DNA pro…
The model of the deformation of DNA macromolecule is developed with the accounting of two types of components of deformation: external and internal. External components describe the bend, twist and stretch of the double helix. The internal component - the conformational mobility inside of the double helix. In the work the deformation of DNA macromolecule is considered taking into account the coupling of the external component (of deformation) with the internal component (of conformational change). Under the task consideration the macromolecule twist-stretch coupling and coupling between twist …
The translocation of double-stranded DNA through a solid-state nanopore may either decrease or increase the ionic current depending on the ionic concentration of the surrounding solution. Below a certain crossover ionic concentration, the current change inverts from a current blockade to current enhancement. In this paper, we show that the crossover concentration for bundled DNA nanostructures composed of multiple connected DNA double-helices is lower than that of double-stranded DNA. Our measurements suggest that counterion mobility in the vicinity of DNA is reduced depending on the three-dim…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair fluctuations. The latter are all the more important at short length scales in which DNA fragments maintain an intrinsic flexibility. The presented computational method simulates a broad ensemble of possible molecule conformations characterized by a specific average twist and determines the energetically most convenient helical twist by free energy minimizat…
It is suggested that there is an interesting transition in double helices. The transition is between a helix, which has maximal torsion for the constituting helical strands, and a double helix which is nearly optimally packed illustrated by corresponding dual points on the rope curve. The possible physical relevance for denaturation and renaturation of DNA is discussed.
