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Eugene P Petrov - One of the best experts on this subject based on the ideXlab platform.
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modeling DNA Condensation on freestanding cationic lipid membranes
Physical Chemistry Chemical Physics, 2014Co-Authors: Andrey G Cherstvy, Eugene P PetrovAbstract:Motivated by recent experimental observations of a rapid spontaneous DNA coil–globule transition on freestanding cationic lipid bilayers, we propose simple theoretical models for DNA Condensation on cationic lipid membranes. First, for a single DNA rod, we examine the conditions of full wrapping of a cylindrical DNA-like semi-flexible polyelectrolyte by an oppositely charged membrane. Then, for two parallel DNA rods, we self-consistently analyze the shape and the extent of the membrane enveloping them, focusing on membrane elastic deformations and the membrane–DNA embracing angle, which enables us to compute the membrane-mediated DNA–DNA interactions. We examine the effects of the membrane composition and its charge density, which are the experimentally tunable parameters. We show that membrane-driven rod–rod attraction is more pronounced for higher charge densities and for smaller surface tensions of the membrane. Thus, we demonstrate that for a long DNA chain adhered to a cationic lipid membrane, such membrane-induced DNA–DNA attraction can trigger compaction of DNA.
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DNA Condensation at freestanding cationic lipid bilayers
Biophysical Journal, 2011Co-Authors: Christoph Herold, Petra Schwille, Eugene P PetrovAbstract:We describe a previously unreported coil-globule transition of DNA electrostatically bound to a freestanding fluid cationic lipid membrane [1]. The collapse of a DNA coil into a compact globule takes place after the DNA molecule attaches in an extended conformation to the membrane. DNA Condensation is favored at a higher cationic lipid content, while at lower membrane charge densities coexistence of DNA random coils, partially collapsed conformations, and globules is observed.[1] C. Herold, P. Schwille and E.P. Petrov, Phys. Rev. Lett. 104, 148102 (2010).
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DNA Condensation at freestanding cationic lipid bilayers
Physical Review Letters, 2010Co-Authors: Christoph Herold, Petra Schwille, Eugene P PetrovAbstract:We describe a previously unreported coil-globule transition of DNA electrostatically bound to a freestanding fluid cationic lipid membrane. The collapse of a DNA coil into a compact globule takes place after the DNA molecule attaches in an extended conformation to the membrane. DNA Condensation is favored at a higher cationic lipid content, while at lower membrane charge densities coexistence of DNA random coils, partially collapsed conformations, and globules is observed.
Serge G Lemay - One of the best experts on this subject based on the ideXlab platform.
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charge inversion accompanies DNA Condensation by multivalent ions
Nature Physics, 2007Co-Authors: K Besteman, Serge G Lemay, K Van EijkAbstract:The Condensation of stiff, highly charged DNA molecules into compact structures by condensing agents ranging from multivalent ions1 to small cationic proteins2,3 is of major biological and therapeutic importance4,5, yet the underlying microscopic mechanism remains poorly understood1,6,7,8,9. It has been proposed7,10 that DNA Condensation is a purely electrostatic phenomenon driven by the existence of a strongly correlated liquid (SCL) of counterions at the DNA surface. The same theoretical argument predicts that multivalent counterions overcompensate the DNA charge when present at high concentration11, in turn destabilizing the condensates12. Here, we demonstrate the occurrence of DNA charge inversion by multivalent ions through measurements of the electrophoretic mobility of condensed DNA. By observing the multivalent-ion-induced Condensation of a single DNA molecule using magnetic tweezers, we further show that charge inversion influences Condensation by modulating the barrier for condensate nucleation in a manner consistent with the SCL mechanism.
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role of tension and twist in single molecule DNA Condensation
Physical Review Letters, 2007Co-Authors: K Besteman, S Hage, Nynke H Dekker, Serge G LemayAbstract:Using magnetic tweezers, we study in real time the Condensation of single DNA molecules under tension. We find that DNA Condensation occurs via discrete nucleated events. By measuring the influence of an imposed twist, we show that Condensation is initiated by the formation of a plectonemic supercoil. This demonstrates a strong interplay between the Condensation transition and externally imposed mechanical constraints.
Helen G. Hansma - One of the best experts on this subject based on the ideXlab platform.
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SURFACE BIOLOGY OF DNA BY ATOMIC FORCE MICROSCOPY
Annual Review of Physical Chemistry, 2001Co-Authors: Helen G. HansmaAbstract:▪ Abstract The atomic force microscope operates on surfaces. Since surfaces occupy much of the space in living organisms, surface biology is a valid and valuable form of biology that has been difficult to investigate in the past owing to a lack of good technology. Atomic force microscopy (AFM) of DNA has been used to investigate DNA Condensation for gene therapy, DNA mapping and sizing, and a few applications to cancer research and to nanotechnology. Some of the most exciting new applications for atomic force microscopy of DNA involve pulling on single DNA molecules to obtain measurements of single-molecule mechanics and thermodynamics.
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DNA toroids stages in Condensation
Biochemistry, 1999Co-Authors: Roxana Golan, Wan Hsieh, Lia I Pietrasanta, Helen G. HansmaAbstract:The effects of polylysine (PLL) and PLL−asialoorosomucoid (AsOR) on DNA Condensation have been analyzed by AFM. Different types of condensed DNA structures were observed, which show a sequence of conformational changes as circular plasmid DNA molecules condense progressively. The structures range from circular molecules with the length of the plasmid DNA to small toroids and short rods with ∼1/6 to 1/8 the contour length of the uncondensed circular DNA. Single plasmid molecules of 6800 base pairs (bp) condense into single toroids of ∼110 nm diameter, measured center-to-center. The results are consistent with a model for DNA Condensation in which circular DNA molecules fold several times into progressively shorter rods. Structures intermediate between toroids and rods suggest that at least some toroids may form by the opening up of rods as proposed by Dunlap et al. [(1997) Nucleic Acids Res. 25, 3095]. Toroids and rods formed at lysine:nucleotide ratios of 5:1 and 6:1. This high lysine:nucleotide ratio is ...
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DNA Condensation for gene therapy as monitored by atomic force microscopy
Nucleic Acids Research, 1998Co-Authors: Helen G. Hansma, Roxana Golan, Wan Hsieh, Charles P Lollo, Patricia Mullenley, Deborah KwohAbstract: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.
Victor A Bloomfield - One of the best experts on this subject based on the ideXlab platform.
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thermodynamics of cationic lipid binding to DNA and DNA Condensation roles of electrostatics and hydrophobicity
Journal of the American Chemical Society, 2002Co-Authors: Daumantas Matulis, Ioulia Rouzina, Victor A BloomfieldAbstract:Alkylammonium binding to DNA was studied by isothermal titration calorimetry. Experimental data, obtained as functions of alkyl chain length, salt concentration, DNA concentration, and temperature, provided a detailed thermodynamic description of lipid−DNA binding reactions leading to DNA Condensation. Lipid binding, counterion displacement, and DNA Condensation were highly cooperative processes, driven by a large increase in entropy and opposed by a relatively small endothermic enthalpy at room temperature. Large negative heat capacity change indicated a contribution from hydrophobic interactions between aliphatic tails.An approximation of lipid−DNA binding as dominated by two factorsionic and hydrophobic interactionsyielded a model that was consistent with experimental data. Chemical group contributions to the energetics of binding were determined and could be used to predict energetics of other lipid binding to DNA. Electrostatic and hydrophobic contributions to Gibbs free energy, enthalpy, entropy, an...
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thermodynamics of DNA binding and Condensation isothermal titration calorimetry and electrostatic mechanism
Journal of Molecular Biology, 2000Co-Authors: Daumantas Matulis, Ioulia Rouzina, Victor A BloomfieldAbstract:Abstract The thermodynamics of binding of the trivalent cations cobalt hexammine and spermidine to plasmid DNA was studied by isothermal titration calorimetry. Two stages were observed in the course of titration, the first attributed to cation binding and the second to DNA Condensation. A standard calorimetric data analysis was extended by applying an electrostatic binding model, which accounted for most of the observed data. Both the binding and Condensation reactions were entropically driven (TΔS∼+10 kcal/mol cation) and enthalpically opposed (ΔH∼+1 kcal/mol cation). As predicted from their relative sizes, the binding constants of the cations were indistinguishable, but cobalt hexammine had a much greater DNA condensing capacity because it is more compact than spermidine. The dependence of both the free energy of cobalt hexammine binding and the critical cobalt hexammine concentration for DNA Condensation on temperature and monovalent cation concentration followed the electrostatic model quite precisely. The heat capacity changes of both stages were positive, perhaps reflecting both the temperature dependence of the dielectric constant of water and the burial of polar surfaces. DNA Condensation occurred when about 67 % of the DNA phosphate charge was neutralized by cobalt hexammine and 87 % by spermidine. During Condensation, the remaining DNA charge was neutralized.
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DNA Condensation by multivalent cations
Biopolymers, 1997Co-Authors: Victor A BloomfieldAbstract:In the presence of multivalent cations, high molecular weight DNA undergoes a dramatic Condensation to a compact, usually highly ordered toroidal structure. This review begins with an overview of DNA Condensation : condensing agents, morphology, kinetics, and reversibility, and the minimum size required to form orderly condensates. It then summarizes the statistical mechanics of the collapse of stiff polymers, which shows why DNA Condensation is abrupt and why toroids are favored structures. Various ways to estimate or measure intermolecular forces in DNA Condensation are discussed, all of them agreeing that the free energy change per base pair is very small, on the order of 1% of thermal energy. Experimental evidence is surveyed showing that DNA Condensation occurs when about 90% of its charge is neutralized by counterions. The various intermolecular forces whose interplay gives rise to DNA Condensation are then reviewed. The entropy loss upon collapse of the expanded wormlike coil costs free energy, and stiffness sets limits on tight curvature. However, the dominant contributions seem to come from ions and water. Electrostatic repulsions must be overcome by high salt concentrations or by the correlated fluctuations of territorially bound multivalent cations. Hydration must be adjusted to allow a cooperative accommodation of the water structure surrounding surface groups on the DNA helices as they approach. Undulations of the DNA in its confined surroundings extend the range of the electrostatic forces. The condensing ions may also subtly modify the local structure of the double helix. © 1998 John Wiley & Sons, Inc. Biopoly 44: 269–282, 1997
Nicholas V Hud - One of the best experts on this subject based on the ideXlab platform.
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integration host factor ihf dictates the structure of polyamine DNA condensates implications for the role of ihf in the compaction of bacterial chromatin
Biochemistry, 2009Co-Authors: Tumpa Sarkar, Anton S Petrov, Jason Vitko, Catherine T Santai, Stephen C Harvey, Ishita Mukerji, Nicholas V HudAbstract:Integration host factor (IHF), a nucleoid-associated protein in bacterial cells, is implicated in a number of chromosomal functions including DNA compaction. IHF binds to all duplex DNA with micromolar affinity and at sequence-specific sites with much higher affinity. IHF is known to induce sharp bends in the helical axis of DNA in both modes of binding, but the role of IHF in controlling DNA Condensation within bacterial cells has remained undetermined. Here we demonstrate that IHF influences the morphology of DNA condensed by polyamines in vitro. In the absence of IHF, spermidine and spermine condense DNA primarily into toroidal structures, whereas in the presence of IHF, polyamines condense DNA primarily into rodlike structures. Computer simulations of DNA Condensation in the absence and presence of IHF binding lend support to our model in which DNA bending proteins, such as IHF and HU, promote the Condensation of DNA into rodlike structures by providing the free energy necessary to bend DNA at the ends of linear bundles of condensed DNA. We propose that a common function of IHF and HU in bacterial cells is to facilitate DNA organization in the nucleoid by the introduction of sharp bends in chromosomal DNA.
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time study of DNA condensate morphology implications regarding the nucleation growth and equilibrium populations of toroids and rods
Biochemistry, 2006Co-Authors: Igor D Vilfan, Christine C Conwell, Tumpa Sarkar, Nicholas V HudAbstract:It is well known that multivalent cations cause free DNA in solution to condense into nanometer-scale particles with toroidal and rod-like morphologies. However, it has not been shown to what degree kinetic factors (e.g., condensate nucleation) versus thermodynamic factors (e.g., DNA bending energy) determine experimentally observed relative populations of toroids and rods. It is also not clear how multimolecular DNA toroids and rods interconvert in solution. We have conducted a series of Condensation studies in which DNA condensate morphology statistics were measured as a function of time and DNA structure. Here, we show that in a typical in vitro DNA Condensation reaction, the relative rod population 2 min after the initiation of Condensation is substantially greater than that measured after morphological equilibrium is reached (ca. 20 min). This higher population of rods at earlier time points is consistent with theoretical studies that have suggested a favorable kinetic pathway for rod nucleation. By using static DNA loops to alter the kinetics and thermodynamics of Condensation, we further demonstrate that reported increases in rod populations associated with decreasing DNA length are primarily due to a change in the thermodynamics of DNA Condensation, rather than a change in the kinetics of condensate nucleation or growth. The results presented also reveal that the redistribution of DNA from rods to toroids is mediated through the exchange of DNA strands with solution.
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evidence that both kinetic and thermodynamic factors govern DNA toroid dimensions effects of magnesium ii on DNA Condensation by hexammine cobalt iii
Biochemistry, 2004Co-Authors: Christine C Conwell, Nicholas V HudAbstract:Millimolar concentrations of divalent cations are shown to affect the size of toroids formed when DNA is condensed by multivalent cations. The origins of this effect were explored by varying the order in which MgCl(2) was added to a series of DNA Condensation reactions with hexammine cobalt chloride. The interplay between Mg(II), temperature, and absolute cation concentration on DNA Condensation was also investigated. These studies reveal that DNA Condensation is extremely sensitive to whether Mg(II) is associated with DNA prior to Condensation or Mg(II) is added concurrently with hexammine cobalt(III) at the time of Condensation. It was also found that, in the presence of Mg(II), temperature and dilution can have opposite effects on the degree of DNA Condensation. A systematic comparison of DNA condensates observed in this study clearly illustrates that, under our low-salt conditions, toroid size is determined by the kinetics of toroid nucleation and growth. However, when Mg(II) is present during Condensation, toroid size can also be limited by a thermodynamic parameter (e.g., undercharging). The path dependence of DNA Condensation presented here illustrates that regardless of which particular factors limit toroid growth, toroids formed under the various conditions of this study are largely nonequilibrium structures.
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controlling the size of nanoscale toroidal DNA condensates with static curvature and ionic strength
Proceedings of the National Academy of Sciences of the United States of America, 2003Co-Authors: Christine C Conwell, Igor D Vilfan, Nicholas V HudAbstract:The process of DNA Condensation into nanometer-scale particles has direct relevance to several fields, including cell biology, virology, and gene delivery for therapeutic purposes. DNA Condensation has also attracted the attention of polymer physicists, as the collapse of DNA molecules from solution into well defined particles represents an exquisite example of a polymer phase transition. Here we present a quantitative study of DNA toroids formed by Condensation of 3 kb DNA with hexammine cobalt (III). The presence or absence of static loops within this DNA molecule demonstrates the effect of nucleation loop size on toroid dimensions and that nucleation is principally decoupled from toroid growth. A comparison of DNA condensates formed at low ionic strength with those formed in the presence of additional salts (NaCl or MgCl2) shows that toroid thickness is a salt-dependant phenomenon. Together, these results have allowed the development of models for DNA toroid formation in which the size of the nucleation loop directly influences the diameter of the fully formed toroid, whereas solution conditions govern toroid thickness. The data presented illustrate the potential that exists for controlling DNA toroid dimensions. Furthermore, this study provides a set of data that should prove useful as a test for theoretical models of DNA Condensation.