Página 1 dos resultados de 1278 itens digitais encontrados em 0.013 segundos

## Polymer induced condensation of DNA supercoils

Bessa Ramos, Jose Esio; Ruggiero Neto, Joao; de Vries, Renko
Fonte: American Institute of Physics (AIP) Publicador: American Institute of Physics (AIP)
Tipo: Artigo de Revista Científica Formato: 6
ENG
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46.3%
Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES); Macromolecular crowding is thought to be a significant factor driving DNA condensation in prokaryotic cells. Whereas DNA in prokaryotes is supercoiled, studies on crowding-induced DNA condensation have so far focused on linear DNA. Here we compare DNA condensation by poly(ethylene oxide) for supercoiled and linearized pUC18 plasmid DNA. It is found that supercoiling has only a limited influence on the critical amount of PEO needed to condense plasmid DNA. In order to pack DNA supercoils in condensates, it seems inevitable that they must be deformed in one way or another, to facilitate dense packing of DNA. Analytical estimates and Monte Carlo simulations indicate that packing of DNA supercoils in condensates is most likely facilitated by a decrease of the superhelical diameter rather than by unwinding of the supercoils.

## Synergy of DNA-bending nucleoid proteins and macromolecular crowding in condensing DNA

Ramos, Esio Bessa; Wintraecken, Kathelijne; Geerling, Ans; De Vried, Renko
Tipo: Artigo de Revista Científica Formato: 259-265
ENG
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56.32%
Many prokaryotic nucleoid proteins bend DNA and form extended helical protein-DNA fibers rather than condensed structures. On the other hand, it is known that such proteins (such as bacterial HU) strongly promote DNA condensation by macromolecular crowding. Using theoretical arguments, we show that this synergy is a simple consequence of the larger diameter and lower net charge density of the protein-DNA filaments as compared to naked DNA, and hence, should be quite general. To illustrate this generality, we use light-scattering to show that the 7kDa basic archaeal nucleoid protein Sso7d from Sulfolobus solfataricus (known to sharply bend DNA) likewise does not significantly condense DNA by itself. However, the resulting protein-DNA fibers are again highly susceptible to crowding-induced condensation. Clearly, if DNA-bending nucleoid proteins fail to condense DNA in dilute solution, this does not mean that they do not contribute to DNA condensation in the context of the crowded living cell. © 2007 World Scientific Publishing Company.

## DNA condensation for gene therapy as monitored by atomic force microscopy.

Hansma, H G; Golan, R; Hsieh, W; Lollo, C P; Mullen-Ley, P; Kwoh, D
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
46.33%
The atomic force microscope (AFM) was used to assay the extent of DNA condensation in approximately 100 different complexes of DNA with polylysine (PL) or PL covalently attached to the glycoproteins asialoorosomucoid (AsOR) or orosomucoid (OR). The best condensation of DNA was obtained with 10 kDa PL covalently attached to AsOR, at a lysine:nucleotide (Lys:nt) ratio of 5:1 or higher. These conditions produce large numbers of toroids and short rods with contour lengths of 300-400 nm. Some DNA condensation into shortened thickened structures was seen with 10 kDa PL attached to AsOR at Lys:nt ratios of 1.6:1 and 3:1. Some DNA condensation was also seen with 4 kDa PL at Lys:nt ratios of 3:1 and higher. Little DNA condensation was seen with PL alone or with PL convalently attached to OR at Lys:nt ratios up to 6:1. AsOR-PL enhanced gene expression in the mouse liver approximately 10- to 50-fold as compared with PL alone.

## DNA condensation by the nucleocapsid protein of HIV-1: a mechanism ensuring DNA protection

Krishnamoorthy, G.; Roques, Bernard; Darlix, Jean-Luc; Mély, Yves
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
46.34%
The nucleocapsid (NC) protein NCp7 of the immunodeficiency virus type 1 is a small basic protein with two zinc finger motifs. NCp7 has key roles in virus replication and structure, which rely on its interactions with nucleic acids. Although most interactions involve RNAs, binding to the viral DNA is thought to be of importance to achieve protection of the DNA against cellular nucleases and its integration into the host genome. We investigated the interaction of NCp7 with plasmid DNA as a model system. The fluorescence probe YOYO-1 was used as the reporter. Binding of NCp7 to DNA caused DNA condensation, as inferred from the dramatic decrease in YOYO-1 fluorescence. Efficient condensation of DNA required the full length NCp7 with the zinc fingers. The fingerless peptide was less efficient in condensing DNA. Binding of both these NC peptides led to freezing of the segmental dynamics of DNA as revealed by anisotropy decay kinetics of YOYO-1. The truncated peptide NC(12–55) which retains the zinc fingers did not lead to DNA condensation despite its ability to bind and partially freeze the segmental motion of DNA. We propose that the histone-like property of NCp7 leading to DNA condensation contributes to viral DNA stability, in vivo.

## Structure of histone H1-DNA complex: Effect of histone H1 on DNA condensation

Hsiang, Myrtle W.; Cole, R. David
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
46.25%
Large doughnut-shaped complexes were formed when histone H1 was mixed with DNA in amounts that extensively neutralized it. The doughnut shape is the most prevalent from observed by electron microscopy for linear double-stranded DNA independent of the molecular weight of the DNA in the range 1.2 × 106 to 25 × 106 at an H1/DNA input weight ratio of 1.3, at ionic strength 0.17. Doughnuts were not observed for single-stranded DNA-H1 complexes; instead, the complexes were globular. The circumference of the doughnutshaped particles indicates that much of the rigidity of duplex DNA in the complex has remained. Evidently, the condensation of the nucleohistone is constrained by the rigidity of duplex DNA and, under this constraint, surface contact with water is minimized by adopting a doughnut shape. Histone H5 causes a type of DNA condensation similar to that of H1 at comparable charge ratios. Core histones H2A-H2b, H3, and H4 complex with DNA to form globular aggregates of such small diameter that the duplex DNA in them must be much more tightly folded than is the case with the doughnut-shaped complexes. Because these histones are designed to fold DNA into nucleosomes 100 Å wide, they must destroy the rigidity of free duplex DNA, perhaps by forming kinks in the chain.

## DNA condensation and self-aggregation of Escherichia coli Dps are coupled phenomena related to the properties of the N-terminus

Ceci, Pierpaolo; Cellai, Sara; Falvo, Elisabetta; Rivetti, Claudio; Rossi, Gian Luigi; Chiancone, Emilia
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
46.33%
Escherichia coli Dps (DNA-binding proteins from starved cells) is the prototype of a DNA-protecting protein family expressed by bacteria under nutritional and oxidative stress. The role of the lysine-rich and highly mobile Dps N-terminus in DNA protection has been investigated by comparing the self-aggregation and DNA-condensation capacity of wild-type Dps and two N-terminal deletion mutants, DpsΔ8 and DpsΔ18, lacking two or all three lysine residues, respectively. Gel mobility and atomic force microscopy imaging showed that at pH 6.3, both wild type and DpsΔ8 self-aggregate, leading to formation of oligomers of variable size, and condense DNA with formation of large Dps–DNA complexes. Conversely, DpsΔ18 does not self-aggregate and binds DNA without causing condensation. At pH 8.2, DpsΔ8 and DpsΔ18 neither self-aggregate nor cause DNA condensation, a behavior also displayed by wild-type Dps at pH 8.7. Thus, Dps self-aggregation and Dps-driven DNA condensation are parallel phenomena that reflect the properties of the N-terminus. DNA protection against the toxic action of Fe(II) and H2O2 is not affected by the N-terminal deletions either in vitro or in vivo, in accordance with the different structural basis of this property.

## Alleviation of restriction by DNA condensation and non-specific DNA binding ligands

Keatch, Steven A.; Su, Tsueu-Ju; Dryden, David T. F.
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
46.15%
During conditions of cell stress, the type I restriction and modification enzymes of bacteria show reduced, but not zero, levels of restriction of unmethylated foreign DNA. In such conditions, chemically identical unmethylated recognition sequences also occur on the chromosome of the host but restriction alleviation prevents the enzymes from destroying the host DNA. How is this distinction between chemically identical DNA molecules achieved? For some, but not all, type I restriction enzymes, alleviation is partially due to proteolytic degradation of a subunit of the enzyme. We identify that the additional alleviation factor is attributable to the structural difference between foreign DNA entering the cell as a random coil and host DNA, which exists in a condensed nucleoid structure coated with many non-specific ligands. The type I restriction enzyme is able to destroy the ‘naked’ DNA using a complex reaction linked to DNA translocation, but this essential translocation process is inhibited by DNA condensation and the presence of non-specific ligands bound along the DNA.

## Polar nuclear localization of H1T2, a histone H1 variant, required for spermatid elongation and DNA condensation during spermiogenesis

Martianov, Igor; Brancorsini, Stefano; Catena, Raffaella; Gansmuller, Anne; Kotaja, Noora; Parvinen, Martti; Sassone-Corsi, Paolo; Davidson, Irwin
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
46.16%
Spermiogenesis entails a major biochemical and morphological restructuring of the germ cell involving replacement of the somatic histones by protamines packing the DNA into the condensed spermatid nucleus and elimination of the cytoplasm during the elongation phase. We describe H1T2, an histone H1 variant selectively and transiently expressed in male haploid germ cells during spermiogenesis. In round and elongating spermatids, H1T2 specifically localizes to a chromatin domain at the apical pole, revealing a polarity in the spermatid nucleus. Inactivation by homologous recombination shows that H1T2 is critical for spermiogenesis as male H1t2–/– mice have greatly reduced fertility. Analysis of spermiogenesis in H1t2 mutant mice shows delayed nuclear condensation and aberrant elongation. As a result, mutant spermatids are characterized by the presence of residual cytoplasm, acrosome detachment, and fragmented DNA. Hence, H1T2 is a protein required for proper cell restructuring and DNA condensation during the elongation phase of spermiogenesis.

## Insertion of telomere repeat sequence decreases plasmid DNA condensation by cobalt (III) hexaammine.

Schnell, J R; Berman, J; Bloomfield, V A
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
46.29%
Telomere repeat sequence (TRS) DNA is found at the termini of most eukaryotic chromosomes. The sequences are highly repetitive and G-rich (e.g., [C(1-3)A/TG(1-3)]n for the yeast Saccharomyces cerevisiae) and are packaged into nonnucleosomal protein-DNA structures in vivo. We have used total intensity light scattering and electron microscopy to monitor the effects of yeast TRS inserts on in vitro DNA condensation by cobalt (III) hexaammine. Insertion of 72 bp of TRS into a 3.3-kb plasmid depresses condensation as seen by light scattering and results in a 22% decrease in condensate thickness as measured by electron microscopy. Analysis of toroidal condensate dimensions suggests that the growth stages of condensation are inhibited by the presence of a TRS insert. The depression in total light scattering intensity is greater when the plasmid is linearized with the TRS at an end (39-49%) than when linearized with the TRS in the interior (18-22%). Circular dichroism of a 95-bp fragment containing the TRS insert gives a spectrum that is intermediate between the A-form and B-form, and the anomalous condensation behavior of the TRS suggests a noncanonical DNA structure. We speculate that under conditions in which the plasmid DNA condenses, the telomeric insert assumes a helical geometry that is similar to the A-form and is incompatible with packing into the otherwise B-form lattice of the condensate interior.

## Structural effects of cobalt-amine compounds on DNA condensation.

Deng, H; Bloomfield, V A
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
46.33%
Light scattering and electron microscopy have been used to investigate the structural effects of the trivalent complexes hexaammine cobalt (III) chloride (Cohex), tris(ethylenediamine) cobalt(III) chloride (Coen), and cobalt(III) sepulchrate chloride (Cosep) on DNA condensation. These cobalt-amine compounds have similar ligand coordination geometries but differ slightly in size. Their hydrophobicity is in the order Cosep > Coen > Cohex, according to the numbers of methylene groups in these ligands. All of these compounds effectively precipitate DNA at high concentrations; but despite a lower surface charge density, Cosep condenses DNA twice as effectively as Coen or Cohex. UV and CD measurements of the supernatants of cobalt-amine/DNA solutions reveal a preferential binding of Delta-Coen over Lambda-Coen to the precipitated DNA, but there is no chiral selectivity for Cosep. Competition experiments show that the binding strengths of these three cobalt-amine compounds to aggregated DNA are comparable. A charge neutralization of 88-90% is required for DNA condensation. Our data indicate that 1) electrostatic interaction is the main driving force for binding of multivalent cations to DNA; 2) DNA condensation is dependent on the structure of the condensing agent; and 3) the hydration pattern or polarization of water molecules on the surface of condensing agents plays an important role in DNA condensation and chiral recognition.

## Brownian dynamics simulation of DNA condensation.

Sottas, P E; Larquet, E; Stasiak, A; Dubochet, J
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
46.21%
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. 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(2)), supercoiled 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. Furthermore, simulations show that circular DNA in 50% methanol solutions with 20 mM MgCl(2) aggregates without the requirement of torsional energy. 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.

## Simultaneous Non-invasive Analysis of DNA Condensation and Stability by Two-step QD-FRET

Chen, Hunter H.; Ho, Yi-Ping; Jiang, Xuan; Mao, Hai-Quan; Wang, Tza-Huei; Leong, Kam W.
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
46.21%
Nanoscale vectors comprised of cationic polymers that condense DNA to form nanocomplexes are promising options for gene transfer. The rational design of more efficient nonviral gene carriers will be possible only with better mechanistic understanding of the critical rate-limiting steps, such as nanocomplex unpacking to release DNA and degradation by nucleases. We present a two-step quantum dot fluorescence resonance energy transfer (two-step QD-FRET) approach to simultaneously and non-invasively analyze DNA condensation and stability. Plasmid DNA, double-labeled with QD (525 nm emission) and nucleic acid dyes, were complexed with Cy5-labeled cationic gene carriers. The QD donor drives energy transfer stepwise through the intermediate nucleic acid dye to the final acceptor Cy5. At least three distinct states of DNA condensation and integrity were distinguished in single particle manner and within cells by quantitative ratiometric analysis of energy transfer efficiencies. This novel two-step QD-FRET method allows for more detailed assessment of the onset of DNA release and degradation simultaneously.

## A universal description for the experimental behavior of salt-(in)dependent oligocation-induced DNA condensation

Korolev, Nikolay; Berezhnoy, Nikolay V.; Eom, Khee Dong; Tam, James P.; Nordenskiöld, Lars
Fonte: Oxford University Press Publicador: Oxford University Press
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
46.27%
We report a systematic study of the condensation of plasmid DNA by oligocations with variation of the charge, Z, from +3 to +31. The oligocations include a series of synthetic linear ε-oligo(l-lysines), (denoted εKn, n = 3–10, 31; n is the number of lysines equal to the ligand charge) and branched α-substituted homologues of εK10: εYK10, εLK10 (Z = +10); εRK10, εYRK10 and εLYRK10 (Z = +20). Data were obtained by light scattering, UV absorption monitored precipitation assay and isothermal titration calorimetry in a wide range concentrations of DNA and monovalent salt (KCl, CKCl). The dependence of EC50 (ligand concentration at the midpoint of DNA condensation) on CKCl shows the existence of a salt-independent regime at low CKCl and a salt-dependent regime with a steep rise of EC50 with increase of CKCl. Increase of the ligand charge shifts the transition from the salt-independent to salt-dependent regime to higher CKCl. A novel and simple relationship describing the EC50 dependence on DNA concentration, charge of the ligand and the salt-dependent dissociation constant of the ligand–DNA complex is derived. For the ε-oligolysines εK3–εK10, the experimental dependencies of EC50 on CKCl and Z are well-described by an equation with a common set of parameters. Implications from our findings for understanding DNA condensation in chromatin are discussed.

## Thermodynamics of Polyethylenimine-DNA Binding and DNA Condensation

Utsuno, Kuniharu; Uludag, Hasan
Fonte: The Biophysical Society Publicador: The Biophysical Society
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
46.24%
In this study, polyethylenimine (PEI) binding to DNA was examined by isothermal titration calorimetry. Two types of binding modes were found to describe the interactions between these polyelectrolytes in buffers and in water. One type of binding involves PEI binding to the DNA groove because the enthalpy change of this binding mode is positive, and PEI is deprotonated to bind to DNA. Another likely binding mode involves external binding of PEI to the DNA phosphate backbone, accompanied with DNA condensation. The enthalpy change is negative and PEI is protonated when it binds to DNA in this mode. The intrinsic enthalpy change of first binding mode is 1.1 kJ/mol and −0.88 kJ/mol for the second binding mode. This result implies that the PEI is rearranged from the groove to the phosphate backbone of DNA when DNA is condensed. The mechanism of DNA condensation caused by PEI is discussed in this study.

## Evaluation of the effect of vector architecture on DNA condensation and gene transfer efficiency

Canine, Brenda F.; Wang, Yuhua; Hatefi, Arash
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
46.16%
The objective of this study was to evaluate the effect of vector architecture on DNA condensation, particle stability, and gene transfer efficiency. Two recombinant non-viral vectors with the same amino acid compositions but different architectures, composed of lysine-histidine (KH) repeating units fused to fibroblast growth factor, were genetically engineered. In one vector lysine residues were dispersed (KHKHKHKHKK)6-FGF2, whereas in the other they were in clusters (KKKHHHHKKK)6-FGF2. Organization of lysine residues in this manner was inspired by the sequence of DNA condensing motifs that exist in nature (e.g., histones) where lysine residues are organized in clusters. These two constructs were compared in terms of DNA condensation and gene transfer efficiency. It was observed that the construct with KH units in clusters was able to condense pDNA into more stable particles with sizes <150 nm making them suitable for cellular uptake via receptor mediated endocytosis. This in turn resulted in five times higher transfection efficiency for the cKH-FGF2. This study demonstrates that in targeted non-viral gene transfer, the vector architecture plays as significant a role as its amino acid sequence. Thus, in the design of the non-viral vectors (synthetic or recombinant) this factor should be considered of paramount importance.

## Mechanisms of Action of Escapin, a Bactericidal Agent in the Ink Secretion of the Sea Hare Aplysia californica: Rapid and Long-Lasting DNA Condensation and Involvement of the OxyR-Regulated Oxidative Stress Pathway

Ko, Ko-Chun; Tai, Phang C.; Derby, Charles D.
Fonte: American Society for Microbiology Publicador: American Society for Microbiology
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
46.2%
The marine snail Aplysia californica produces escapin, an l-amino acid oxidase, in its defensive ink. Escapin uses l-lysine to produce diverse products called escapin intermediate products of l-lysine (EIP-K), including α-amino-ε-caproic acid, Δ1-piperidine-2-carboxylic acid, and Δ2-piperidine-2-carboxylic acid. EIP-K and H2O2 together, but neither alone, is a powerful bactericide. Here, we report bactericidal mechanisms of escapin products on Escherichia coli. We show that EIP-K and H2O2 together cause rapid and long-lasting DNA condensation: 2-min treatment causes significant DNA condensation and killing, and 10-min treatment causes maximal effect, lasting at least 70 h. We isolated two mutants resistant to EIP-K plus H2O2, both having a single missense mutation in the oxidation regulatory gene, oxyR. A complementation assay showed that the mutated gene, oxyR(A233V), renders resistance to EIP-K plus H2O2, and a gene dosage effect leads to reduction of resistance for strains carrying wild-type oxyR. Temperature stress with EIP-K does not produce the bactericidal effect, suggesting the effect is due to a specific response to oxidative stress. The null mutant for any single DNA-binding protein—Dps, H-NS, Hup, Him, or MukB—was not resistant to EIP-K plus H2O2...

## Dependence of DNA condensation on the correlation distance between condensed counterions

Liu, Yanhui; Wang, Wenbo; Hu, Lin
Fonte: Springer Netherlands Publicador: Springer Netherlands
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
46.26%
Based on the ground state of counterions condensed on a DNA molecule, a model has been developed to successfully detect the process of DNA condensation. Through further investigation, the process of DNA condensation strongly depends on the correlation distance between condensed counterions on DNA molecules. Generally, there are two routes. The process of DNA condensation with the correlation distance between condensed counterions being 2 nm or 4 nm is different from the one with the correlation distance between condensed counterions being 3 nm or 5 nm. Effects of ionic strength on the diameter of toroidal condensates originate from the increase of correlation distance between condensed counterions.

## Time-Dependent DNA Condensation Induced by Amyloid β-Peptide

Yu, Haijia; Ren, Jinsong; Qu, Xiaogang
Fonte: Biophysical Society Publicador: Biophysical Society
Tipo: Artigo de Revista Científica
EN
Relevância na Pesquisa
46.34%
The major protein component of the amyloid deposition in Alzheimer's disease is a 39–43 residue peptide, amyloid β (Aβ). Aβ is toxic to neurons, although the mechanism of neurodegeneration is uncertain. Evidence exists for non-B DNA conformation in the hippocampus of Alzheimer's disease brains, and Aβ was reportedly able to transform DNA conformation in vitro. In this study, we found that DNA conformation was altered in the presence of Aβ, and Aβ induced DNA condensation in a time-dependent manner. Furthermore, Aβ sheets, serving as condensation nuclei, were crucial for DNA condensation, and Cu2+ and Zn2+ ions inhibited Aβ sheet-induced DNA condensation. Our results suggest DNA condensation as a mechanism of Aβ toxicity.

## Theory and simulations of toroidal and rod-like structures in single-molecule DNA condensation

Cortini, Ruggero; Caré, Bertrand R.; Victor, Jean-Marc; Barbi, Maria
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
46.34%
DNA condensation by multivalent cations plays a crucial role in genome packaging in viruses and sperm heads, and has been extensively studied using single-molecule experimental methods. In those experiments, the values of the critical condensation forces have been used to estimate the amplitude of the attractive DNA-DNA interactions. Here, to describe these experiments, we developed an analytical model and a rigid body Langevin dynamics assay to investigate the behavior of a polymer with self-interactions, in the presence of a traction force applied at its extremities. We model self-interactions using a pairwise attractive potential, thereby treating the counterions implicitly. The analytical model allows to accurately predict the equilibrium structures of toroidal and rod-like condensed structures, and the dependence of the critical condensation force on the DNA length. We find that the critical condensation force depends strongly on the length of the DNA, and finite-size effects are important for molecules of length up to 10^5 {\mu}m. Our Langevin dynamics simulations show that the force-extension behavior of the rod-like structures is very different from the toroidal ones, so that their presence in experiments should be easily detectable. In double-stranded DNA condensation experiments...

## Grand-canonical simulation of DNA condensation with two salts, affect of divalent counterion size

Nguyen, Toan T.
Tipo: Artigo de Revista Científica
Relevância na Pesquisa
46.33%
The problem of DNA$-$DNA interaction mediated by divalent counterions is studied using a generalized Grand-canonical Monte-Carlo simulation for a system of two salts. The effect of the divalent counterion size on the condensation behavior of the DNA bundle is investigated. Experimentally, it is known that multivalent counterions has strong effect on the DNA condensation phenomenon. While tri- and tetra-valent counterions are shown to easily condense free DNA molecules in solution into torroidal bundles, the situation with divalent counterions are not as clear cut. Some divalent counterions like Mg$^{+2}$ are not able to condense free DNA molecules in solution, while some like Mn$^{+2}$ can condense them into disorder bundles. In restricted environment such as in two dimensional system or inside viral capsid, Mg$^{+2}$ can have strong effect and able to condense them, but the condensation varies qualitatively with different system, different coions. It has been suggested that divalent counterions can induce attraction between DNA molecules but the strength of the attraction is not strong enough to condense free DNA in solution. However, if the configuration entropy of DNA is restricted, these attractions are enough to cause appreciable effects. The variations among different divalent salts might be due to the hydration effect of the divalent counterions. In this paper...