On the Competition between Water, Sodium Ions, and Spermine in Binding to DNA: A Molecular Dynamics Computer Simulation Study

Korolev, Nikolay; Lyubartsev, Alexander P.; Laaksonen, Aatto; Nordenskiöld, Lars

doi:10.1016/s0006-3495(02)75628-2

Cited by 124 publications

(121 citation statements)

References 56 publications

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“…This has been exemplified by spermine (36)(37)(38) and PCPs (39), in particular, PL, which appears to have modes of DNA binding similar to H1 linker histone (40,41). The X-ray crystal structure of H1 linker histone (42) and circular dichroism studies of drug binding to DNA (43) indicate that positively charged groups of histones are inserted into the DNA minor groove.…”

Section: Model Of Interactions Between Dna and Pcpsmentioning

confidence: 99%

Protection of DNA against Direct Radiation Damage by Complex Formation with Positively Charged Polypeptides

2006

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Radioprotection of DNA from direct-type radiation damage by histones has been studied in model systems using complexes of positively charged polypeptides (PCPs) with DNA. PCPs bind to DNA via ionic interactions mimicking the mode of DNA-histone binding. Direct radiation damage to DNA in films of DNA-PCP complexes was quantified as unaltered base release, which correlates closely with DNA strand breaks. All types of PCPs tested protected DNA from radiation, with the maximum radioprotection being approximately 2.5-fold compared with non-complexed DNA. Conformational changes of the DNA induced by PCPs or repair of free radical damage on the DNA sugar moiety by PCPs are considered the most feasible mechanisms of radioprotection of DNA. The degree of radioprotection of DNA by polylysine (PL) increased dramatically on going from pure DNA to a molar ratio of PL monomer:DNA nucleotide ~1:2, while a further increase in the PL:DNA ratio did not offer more radioprotection. This concentration dependence is in agreement with the model of PCP binding to DNA that assumes preferential binding of positively charged side groups to DNA phosphates in the minor groove, so that the maximum occupancy of all minor-groove PCP binding sites is at a molar ratio of PCP:DNA = 1:2.

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Section: Model Of Interactions Between Dna and Pcpsmentioning

confidence: 99%

Protection of DNA against Direct Radiation Damage by Complex Formation with Positively Charged Polypeptides

2006

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“…We note that interactions between DNA and spermidine or spermine have been studied by techniques like Xray diffraction [48,82], neutron scattering [83], and Raman spectroscopy [84], and by more or less complicated models [48,51,85,86] but the binding properties of the polyamines to DNA are still not clear. Several types of binding have been proposed in the literature, like the location of spermine molecules in the major groove with a single contact with the polyelectrolyte [82], or that the spermine is present in higher concentration close to the minor [86]; also, that polyamines bind to DNA simply by non-specific electrostatic interactions [83,84].…”

Section: Effect Of the Chain Lengthmentioning

confidence: 99%

“…Several types of binding have been proposed in the literature, like the location of spermine molecules in the major groove with a single contact with the polyelectrolyte [82], or that the spermine is present in higher concentration close to the minor [86]; also, that polyamines bind to DNA simply by non-specific electrostatic interactions [83,84]. It is, however, widely accepted that the flexible polyamines have different binding sites, interacting in an irregular way with different sites on DNA [48], forming a short-lived and non-structured [86], mobile [84] atmosphere of ions around the macromolecule. This is the proposed reason for the fact that spermine molecules, for example, are not easily detected by X-ray methods, even though they are present at a high concentration [48].…”

Section: Effect Of the Chain Lengthmentioning

confidence: 99%

DNA and surfactants in bulk and at interfaces

Dias

Pais

Miguel

et al. 2004

Colloids and Surfaces A: Physicochemical and Engineering Aspect

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Recent investigations of the DNA interactions with cationic surfactants and catanionic mixtures are reviewed. Several techniques have been used such as fluorescence microscopy, dynamic light scattering, electron microscopy, and Monte Carlo simulations.The conformational behaviour of large DNA molecules in the presence of cationic surfactant was followed by fluorescence microscopy and also by dynamic light scattering. These techniques were in good agreement and it was possible to observe a discrete transition from extended coils to collapsed globules and their coexistence for intermediate amphiphile concentrations. The dependence on the surfactant alkyl chain was also monitored by fluorescence microscopy and, as expected, lower concentrations of the more hydrophobic surfactant were required to induce DNA compaction, although an excess of positive charges was still required.Monte Carlo simulations on the compaction of a medium size polyanion with shorter polycations were performed. The polyanion chain suffers a sudden collapse as a function of the concentration of condensing agent, and of the number of charges on the polycation molecules. Further increase in the concentration increases the degree of compaction. The compaction was found to be associated with the polycations promoting bridging between different sites of the polyanion. When the total charge of the polycations was lower than that of the polyanion, a significant translational motion of the compacting agent along the polyanion was observed, producing only a small-degree of intrachain segregation, which can explain the excess of positive charges necessary to compact DNA.Dissociation of the DNA-cationic surfactant complexes and a concomitant release of DNA was achieved by addition of anionic surfactants. The unfolding of DNA molecules, previously compacted with cationic surfactant, was shown to be strongly dependent on the anionic surfactant chain length; lower amounts of a longer chain surfactant were needed to release DNA into solution. On the other hand, no dependence on the hydrophobicity of the compacting agent was observed. The structures of the aggregates formed by the two surfactants, after the interaction with DNA, were imaged by cryogenic transmission electron microscopy. It is possible to predict the structure of the aggregates formed by the surfactants, like vesicles, from the phase behaviour of the mixed surfactant systems.Studies on the interactions between DNA and catanionic mixtures were also performed. It was observed that DNA does not interact with negatively charged vesicles, even though they carry positive amphiphiles; however, in the presence of positively charged vesicles, DNA molecules compact and adsorb on their surface.Finally Monte Carlo simulations were performed on the adsorption of a polyelectrolyte on catanionic surfaces. It was observed that the mobile charges in the surface react to the presence of the polyelectrolyte enabling a strong degree of adsorption even though the membrane was globally neutral. Our observati...

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“…[6,7] Their interaction with the DNA molecule, for instance, has been widely investigated through different experimental techniques. [8][9][10][11][12][13][14] While deregulated amine metabolism is a well-recognized characteristic of animal and human cancers, [15,16] interference with polyamine biosynthesis is presently a rather promising therapeutical approach against proliferative diseases. Moreover, many efforts have lately been devoted to the possible use of polyamines as biochemical markers of cancer.…”

Section: Introductionmentioning

confidence: 99%

Spectroscopic and Theoretical Studies on Solid 1,2‐Ethylenediamine Dihydrochloride Salt

Amado¹,

Otero²,

Marques³

et al. 2004

ChemPhysChem

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A structural study of [H3N(CH2)2NH3)]2+⋅2Cl−, the smallest element of the homologous series of the α,ω‐diamine dihydrochlorides, was carried out by means of Raman and FTIR spectroscopy coupled to ab initio molecular orbital (MO) calculations. As a primary concern, an adequate molecular model for the representation of these solid amine salts was chosen. Thus, several models, varying in the number and position of the counterions as well as in the number of diamine units, were considered. It was found that the best molecular system (i.e., that yielding the best compromise between accuracy and computational requirements) consists of one ethylenediamine cation surrounded by six chloride ions in an arrangement based on the crystal structure reported in the literature for [H3N(CH2)2NH3)]2+⋅2Cl−. This conclusion will hopefully allow for a better understanding of the conformational preferences, in the solid state, of these biologically relevant linear polyamines.

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On the Competition between Water, Sodium Ions, and Spermine in Binding to DNA: A Molecular Dynamics Computer Simulation Study

Cited by 124 publications

References 56 publications

Protection of DNA against Direct Radiation Damage by Complex Formation with Positively Charged Polypeptides

Protection of DNA against Direct Radiation Damage by Complex Formation with Positively Charged Polypeptides

DNA and surfactants in bulk and at interfaces

Spectroscopic and Theoretical Studies on Solid 1,2‐Ethylenediamine Dihydrochloride Salt

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