Simulations of dna condensation

Simulations of dna condensation

We introduce a quantitative model of these forces in a Brownian dynamics simulation in addition to a standard mean-field Poisson-Boltzmann repulsion.

The comparison of a theoretical value of the effective diameter calculated from the second virial coefficient in cylindrical geometry with some experimental results allows a quantitative evaluation of the one-parameter attractive potential.

However, under the same conditions the same plasmid without torsional stress does not collapse. The condensed molecules present coexisting open and collapsed plectonemic regions.

This confirms known experimental results. Finally, a simulated DNA molecule confined in a box of variable size also presents some local collapsed zones in 20 mM MgCl 2 above a critical concentration of the DNA. Conformational entropy reduction obtained either by supercoiling or by confinement seems thus to play a crucial role in all forms of condensation of DNA.

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In the latter case, please turn on Javascript support in your web browser and reload this page. Free to read. DNA condensation observed in vitro with the addition of polyvalent counterions is due to intermolecular attractive forces. We introduce a quantitative model of these forces in a Brownian dynamics simulation in addition to a standard mean-field Poisson-Boltzmann repulsion.

simulations of dna condensation

The comparison of a theoretical value of the effective diameter calculated from the second virial coefficient in cylindrical geometry with some experimental results allows a quantitative evaluation of the one-parameter attractive potential.

We show afterward that with a sufficient concentration of divalent salt typically approximately 20 mM MgCl 2supercoiled DNA adopts a collapsed form where opposing segments of interwound regions present zones of lateral contact. However, under the same conditions the same plasmid without torsional stress does not collapse. The condensed molecules present coexisting open and collapsed plectonemic regions. This confirms known experimental results.

DNA condensation at the single molecule level monitored using optical tweezers

Finally, a simulated DNA molecule confined in a box of variable size also presents some local collapsed zones in 20 mM MgCl 2 above a critical concentration of the DNA. Conformational entropy reduction obtained either by supercoiling or by confinement seems thus to play a crucial role in all forms of condensation of DNA. Read article at publisher's site DOI : Nucleic Acids Res43 8 :e54, 17 Feb J Chem Phys401 Jul Cited by: 3 articles PMID: Prog Biophys Mol Biol316 Jul Cited by: 77 articles PMID: Tarmann CJungbauer A.

J Sep Sci31 1401 Aug Cited by: 17 articles PMID: Cited by: 13 articles PMID: To arrive at the top five similar articles we use a word-weighted algorithm to compare words from the Title and Abstract of each citation.

Brownian dynamics simulation of DNA condensation.

Biophys J67 601 Dec Phys Rev Lett1405 Apr Cited by: 11 articles PMID: J Mol Biol201 Nov Cited by: 48 articles PMID: Cited by: articles PMID: Bloomfield VA. Biopolymers44 301 Jan Coronavirus: Find the latest articles and preprints.

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Simple simulations of DNA condensation.

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Coarse-grained molecular dynamics simulations are used to study the condensation of single polyanion chains with block copolymers composed of cationic and neutral blocks. The simulations are an effort to model complexes formed with DNA and cationic copolymers such as polyethylenimine- g -polyethylene glycol which have been used in gene delivery.

The simulations reveal that increases in the cationic block length of the copolymer result in greater condensation of the polyanion. The internal structure of the complex core is shown to be a function of the architecture of the copolymer.

Complexes formed from linear diblock copolymers have homogeneous cores with similarly arranged cationic and anionic beads; however, complexes formed with star-shaped copolymers have a layered core structure, with anionic beads found in the center of the cores.

B, 19 View Author Information. Fax: Cite this: J. B, 19— Article Views Altmetric. Citations Cited By. This article is cited by 37 publications. Schacher, Raffaello Potestio, Kalina Peneva. Biomacromolecules20 12 Macromolecules52 22 The Journal of Physical Chemistry B45 Biomacromolecules19 7 Langmuir34 26 Molecular Pharmaceutics12 8 Smith, and Theresa M.

Biomacromolecules15 5 Tolstyka, Nilesh P. Journal of the American Chemical Society41 The Journal of Physical Chemistry B26 Biomacromolecules12 10 Biomacromolecules12 8 Gallops, Jesse D. Ziebarth, Yongmei Wang. Macromolecular Theory and Simulations29 4 Martini Force Field for Protonated Polyethyleneimine.

simulations of dna condensation

Journal of Computational Chemistry41 4Either your web browser doesn't support Javascript or it is currently turned off. In the latter case, please turn on Javascript support in your web browser and reload this page.

Free to read. Molecular dynamics simulations of a simple, bead-spring model of semiflexible polyelectrolytes such as DNA are performed.

simulations of dna condensation

All charges are explicitly treated. Starting from extended, noncondensed conformations, condensed structures form in the simulations with tetravalent or trivalent counterions. No condensates form or are stable for divalent counterions. The mechanism by which condensates form is described. Briefly, condensation occurs because electrostatic interactions dominate entropy, and the favored coulombic structure is a charge-ordered state.

Condensation is a generic phenomenon and occurs for a variety of polyelectrolyte parameters. Toroids and rods are the condensate structures. Toroids form preferentially when the molecular stiffness is sufficiently strong. Read article at publisher's site DOI : Langmuir35 4025 Sep Nucleic Acids Res47 1101 Jun J Mol Recognit31 9 :e, 15 May Cited by: 2 articles PMID: ACS Omega3 918 Sep Soft Matter14 2801 Jul To arrive at the top five similar articles we use a word-weighted algorithm to compare words from the Title and Abstract of each citation.

Ou ZMuthukumar M. J Chem Phys701 Aug Cited by: 28 articles PMID: Bloomfield VA. Biopolymers44 301 Jan Cited by: articles PMID: Biophys J70 601 Jun Manning GS. Cited by: 18 articles PMID: Eriksson MNielsen PE. Q Rev Biophys29 401 Dec Cited by: 33 articles PMID: Coronavirus: Find the latest articles and preprints. Europe PMC requires Javascript to function effectively. Recent Activity.Either your web browser doesn't support Javascript or it is currently turned off.

In the latter case, please turn on Javascript support in your web browser and reload this page. Free to read. Molecular dynamics simulations of a simple, bead-spring model of semiflexible polyelectrolytes such as DNA are performed.

All charges are explicitly treated. Starting from extended, noncondensed conformations, condensed structures form in the simulations with tetravalent or trivalent counterions.

No condensates form or are stable for divalent counterions. The mechanism by which condensates form is described. Briefly, condensation occurs because electrostatic interactions dominate entropy, and the favored coulombic structure is a charge-ordered state. Condensation is a generic phenomenon and occurs for a variety of polyelectrolyte parameters.

Toroids and rods are the condensate structures. Toroids form preferentially when the molecular stiffness is sufficiently strong. Read article at publisher's site DOI : Langmuir35 4025 Sep Nucleic Acids Res47 1101 Jun J Mol Recognit31 9 :e, 15 May Cited by: 2 articles PMID: ACS Omega3 918 Sep Soft Matter14 2801 Jul To arrive at the top five similar articles we use a word-weighted algorithm to compare words from the Title and Abstract of each citation.

Ou ZMuthukumar M. J Chem Phys701 Aug Cited by: 28 articles PMID: Bloomfield VA. Biopolymers44 301 Jan DNA is one the best-recognized molecules. We are all familiar with the famous double-helix that carries instructions for manufacturing and assembling all the components of a living organism. But DNA is more than just a sequence of letters arranged on rigid ladder rungs; it is a polymer with unusual physical properties that, at times, appear to contradict one another.

For example, DNA carries a large negative charge, yet under the right conditions, DNA molecules attract and condense into a compact state. The physical properties of DNA are broadly exploited by cells to perform the molecular feats neccessary for life including storage of information, replication and repair of that information, and regulataion of how that information is expressed.

Hence, elucidation of the molecular mechanisms that govern the behavior of DNA in solution comprises a core thrust of our research. The physical properties of DNA have been suggested to play a central role in spatio-temporal organization of eukaryotic chromosomes.

Experimental correlations have been established between the local nucleotide content of DNA and the frequency of inter- and intra-chromosomal contacts but the underlying physical mechanism remains unknown. Here, we combine fluorescence resonance energy transfer FRET measurements, precipitation assays, and molecular dynamics simulations to characterize the effect of DNA nucleotide content, sequence, and methylation on inter-DNA association and its correlation with DNA looping.

Next, we show that the presence and spatial arrangement of C5 methyl groups determines the strength of inter-DNA attraction, partially explaining why RNA resists condensation. We propose that the differential affinity between DNA regions of varying sequence pattern may drive the phase separation of chromatin into chromosomal subdomains. Here we combine molecular dynamics simulations with single-molecule fluorescence resonance energy transfer experiments to examine the interactions between duplex DNA in the presence of spermine, a biological polycation.

DNA–DNA interactions

Methyl groups of thymine acts as a steric block, relocating spermine from major grooves to interhelical regions, thereby increasing DNA—DNA attraction. Recent genome-wide chromosome organization studies showed that remote contact frequencies are higher for AT-rich and methylated DNA, suggesting that direct DNA—DNA interactions that we report here may play a role in the chromosome organization and gene regulation.

Spontaneous assembly of DNA molecules into compact structures is ubiquitous in biological systems. Experiment has shown that polycations can turn electrostatic self-repulsion of DNA into attraction, yet the physical mechanism of DNA condensation has remained elusive. Here, we report the results of atomistic molecular dynamics simulations that elucidated the microscopic structure of dense DNA assemblies and the physics of interactions that makes such assemblies possible.

Reproducing the setup of the DNA condensation experiments, we measured the internal pressure of DNA arrays as a function of the DNA—DNA distance, showing a quantitative agreement between the results of our simulations and the experimental data. While side-by-side interactions between two or more DNA molecules have been the subject of many studies, end-to-end interaction of duplex DNA and its role in cell biology and DNA nanotechnology remains almost entirely unexplored.

To determine the microscopic origin, magnitude and range of forces driving this spectacular self-assembly, we carried out the first direct study of end-to-end association using the all-atom molecular dynamics method. Our state-of-the-art free energy calculations combined with brute-force simulations of spontaneous self-assembly revealed the standard binding free energy and kinetic rate constants for the end-to-end interaction.

We found the end-to-end force to be strong, short-range, hydrophobic and only weakly dependent on the ion concentration. This work is described in a report appearing in Nucleic Acids Research. The concept of "ion atmosphere" is prevalent in both theoretical and experimental studies of nucleic acid systems, yet the spatial arrangement and the composition of ions in the ion atmosphere remain elusive, in particular when several ionic species e.

Complementing the experimental study of Bai and co-workers J. We demonstrate that our improved parametrization of the all-atom model can quantitatively reproduce the experimental ion-count data.

Our simulations determine the size of the ion atmosphere, the concentration profiles of ionic species competing to neutralize the DNA charge, and the sites of the cations' preferential binding at the surface of double-stranded DNA.

We find that the effective size of the ion atmosphere depends on both the bulk concentration and valence of ions: increasing either reduces the size of the atmosphere. Within the DNA grooves, the relative concentrations of cations depend on their bulk values. DNA is so famously known as the carrier of genetic information that the structural and dynamical aspects of the molecule are often neglected. However, most cellular processes that involve DNA cannot be understood without consideration of its interactions with other DNA and proteins.

simulations of dna condensation

Such interactions can give rise self-assembled structures, for example DNA supercoils, which we strive to understand using a bottom-up approach by examining the most basic constituents of a larger more complex system.

Thus, in collaboration with the groups of Ralf Seidel at the University of Technology in Dresden and Gero Wedemann at the University of Applied Sciences Stralsund, we have examined the interactions between DNA helices in plectonemic supercoils using magnetic tweezers, coarse-grained Monte Carlo and atomistic molecular dynamics simulations.

Building on our previous workour group characterized the effective forces between parallel DNA in monovalent electrolytes at different ion concentrations.Molecular dynamics simulations of a simple, bead-spring model of semiflexible polyelectrolytes such as DNA are performed.

All charges are explicitly treated. Starting from extended, noncondensed conformations, condensed structures form in the simulations with tetravalent or trivalent counterions. No condensates form or are stable for divalent counterions. The mechanism by which condensates form is described.

Briefly, condensation occurs because electrostatic interactions dominate entropy, and the favored coulombic structure is a charge-ordered state. Condensation is a generic phenomenon and occurs for a variety of polyelectrolyte parameters. Toroids and rods are the condensate structures.

Toroids form preferentially when the molecular stiffness is sufficiently strong. National Center for Biotechnology InformationU. Journal List Biophys J v.

Biophys J. M J Stevens. Author information Copyright and License information Disclaimer. Sandia National Laboratory, P. Copyright notice. This article has been cited by other articles in PMC. Abstract Molecular dynamics simulations of a simple, bead-spring model of semiflexible polyelectrolytes such as DNA are performed. Bloomfield VA. Condensation of DNA by multivalent cations: considerations on mechanism.

DNA condensation. Curr Opin Struct Biol. Cationic silanes stabilize intermediates in DNA condensation.


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