Electrostatic correlations fold DNA

Khan, Malek O.; Jönsson, Bo

doi:10.1002/(sici)1097-0282(199902)49:2<121::aid-bip1>3.0.co;2-2

Cited by 74 publications

(94 citation statements)

References 35 publications

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“…This fact is in agreement with the results obtained by simulation of the compaction induced by trivalent metal ions [37]. Observations for these model systems suggest compaction arising from an approach of relatively extended loops, formed under the local action of the trivalent ions.…”

Section: Discussionsupporting

confidence: 91%

“…Also the internal freedom of the chains is even higher than that found for both proteins, indicating that the estimate is valid. The fact that the degree of compaction induced by trivalent metal ions is not strong has also been pointed out in simulation experiments [37]. Observations for these model systems suggest compaction arising from a closeness of relatively extended loops, formed under the local action of the trivalent ions.…”

Section: Iron[iii]mentioning

confidence: 54%

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Cationic agents for DNA compaction

Gawęda

Morán

Pais

et al. 2008

Journal of Colloid and Interface Science

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Fluorescence microscopy was used to investigate the conformational changes of individual T4 DNA molecules induced by different compacting agents, namely the cationic surfactants, cetyltrimethylammonium bromide (CTAB) and chloride (CTAC), iron(III), lysozyme, and protamine sulfate. A protocol for establishing size estimates is suggested to obtain reproducible results. Observations show that in the presence of lysozyme and protamine sulfate, DNA molecules exhibit a conformational change from an elongated coil structure to compact globules, usually interpreted as a first-order transition. The maximum degree of compaction that is attained when iron(III) or CTAB (CTAC) are used as compacting agents is considerably smaller, and intermediate structures (less elongated coils) are visible even for high concentrations of these agents. Dynamic light scattering experiments were carried out, for some of the systems, to assess the reliability of size estimates from fluorescence microscopy.

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Section: Discussionsupporting

confidence: 91%

Section: Iron[iii]mentioning

confidence: 54%

Cationic agents for DNA compaction

Gawęda

Morán

Pais

et al. 2008

Journal of Colloid and Interface Science

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“…Divalent cations localize near one or more helices, increasing the probability that the helices come together; when they do come together, the local negative charge is increased, facilitating the localization of still more cations, thereby giving progressively increased cation localization and compaction. Collapse of polyanions upon the addition of multivalent cations has been suggested on theoretical grounds from ion-ion correlation effects (43) and entropic effects arising from delocalization of counterions in a collapsed state (44). As the collapse for the Tetrahymena ribozyme occurs before tertiary structure formation, it may result from basic features of RNA and, therefore, may be general for RNA.…”

Section: Methodsmentioning

confidence: 99%

Rapid compaction during RNA folding

Russell

Millett

Täte

et al. 2002

Proc. Natl. Acad. Sci. U.S.A.

217

207

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We have used small angle x-ray scattering and computer simulations with a coarse-grained model to provide a time-resolved picture of the global folding process of the Tetrahymena group I RNA over a time window of more than five orders of magnitude. A substantial phase of compaction is observed on the low millisecond timescale, and the overall compaction and global shape changes are largely complete within one second, earlier than any known tertiary contacts are formed. This finding indicates that the RNA forms a nonspecifically collapsed intermediate and then searches for its tertiary contacts within a highly restricted subset of conformational space. The collapsed intermediate early in folding of this RNA is grossly akin to molten globule intermediates in protein folding.

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“…Here the assumption of uncorrelated positions of the counterions does not hold any longer. The role of counterion correlations as charge density and counterion valency increase is best illustrated by an example from recent calculations by Khan et al (24,25), an example with direct relevance for DNA. Figure 5 shows the end-to-end distance for a polymer as it is progressively charged up.…”

Section: Attractive Ion-ion Correlation Effects For Dna In the Presenmentioning

confidence: 99%

DNA-lipid systems: A physical chemistry study

Dias

Antunes

Miguel

et al. 2002

Braz J Med Biol Res

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It is well known that the interaction of polyelectrolytes with oppositely charged surfactants leads to an associative phase separation; however, the phase behavior of DNA and oppositely charged surfactants is more strongly associative than observed in other systems. A precipitate is formed with very low amounts of surfactant and DNA. DNA compaction is a general phenomenon in the presence of multivalent ions and positively charged surfaces; because of the high charge density there are strong attractive ion correlation effects. Techniques like phase diagram determinations, fluorescence microscopy, and ellipsometry were used to study these systems. The interaction between DNA and catanionic mixtures (i.e., mixtures of cationic and anionic surfactants) was also investigated. We observed that DNA compacts and adsorbs onto the surface of positively charged vesicles, and that the addition of an anionic surfactant can release DNA back into solution from a compact globular complex between DNA and the cationic surfactant. Finally, DNA interactions with polycations, chitosans with different chain lengths, were studied by fluorescence microscopy, in vivo transfection assays and cryogenic transmission electron microscopy. The general conclusion is that a chitosan effective in promoting compaction is also efficient in transfection.

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Electrostatic correlations fold DNA

Cited by 74 publications

References 35 publications

Cationic agents for DNA compaction

Cationic agents for DNA compaction

Rapid compaction during RNA folding

DNA-lipid systems: A physical chemistry study

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