Influence of tetraalkyl ammonium lons on the structure of poly (rG-dC).poly (rG-dC): unexpected transitions among the Z, A and B conformations

Jayasena, Sumedha D.; Behe, Michael J.

doi:10.1093/nar/15.9.3907

Cited by 7 publications

(4 citation statements)

References 16 publications

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“…NMR spectroscopy studies have shown that a DNA stretch containing a ribose residue assumes the N‐type (3′endo) puckering while deoxyribose‐containing lengths are mainly in the S‐type (C2′endo) puckering. On the other hand an X‐ray fiber diffraction study on poly(rA) poly(dT) and CD measurements of poly (rG‐dC) poly (rG‐dC) have indicated that they may assume the B‐form character [98]. Recently, the B‐form of DNA‐RNA chimeras (IrCICICIC) 2 and (IrCIrCICIC) 2 in their complexes with distamycin A has been determined [99].…”

Section: High‐pressure Mediated Conformational Changes Of Ribonucleicmentioning

confidence: 99%

The role of water structure in conformational changes of nucleic acids in ambient and high‐pressure conditions

Barciszewski

Jurczak

Porowski

et al. 1999

European Journal of Biochemistry

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This review describes and summarizes data on the structure and properties of water under normal conditions, at high salt concentration and under high pressure. We correlate the observed conformational changes in nucleic acids with changes in water structure and activity, and suggest a mechanism of conformational transitions of nucleic acids which accounts for changes in the water structure. From the biophysical, biochemical and crystallographic data we conclude that the Z-DNA form can be induced only at low water activity produced by high salt concentrations or high pressure, and accompanied by the stabilizing conjugative effect of the cytidine O4 H electrons of the CG base pairs.Keywords: structure of water, high pressure, conformational changes, nucleic acids.Water molecules influence specific interactions in all biological systems and yet it is still extremely difficult to understand their effect in precise atomic models. Recent studies of water effects on biological macromolecules have made molecular biologists aware of the important role that this solvent plays in the structure and function of proteins, nucleic acids and other cell constituents. Also we now realize how little we know about the detailed behaviour of water molecules. In recent years there has been an explosion in the number of new X-ray structures for protein±DNA complexes and other biomolecules. Many of those structures feature water molecules buried at the intermolecular interface, or assign them with reasonable confidence to good geometry of water oxygen atoms, at the coordination space of hydrogen bond donors and acceptors. Thus, hydrogen bonding networks between proteins and nucleic acids often include water molecules, which have not been anticipated from our previous understanding of the molecular basis for macromolecular recognition, which always predicted direct contacts between functional groups. The contribution of hydration to the energetics of macromolecular assembly and catalysis was recognized a long time ago. The cost of removing all the perturbated water, or the benefit of fully hydrating a newly exposed surface is around 3.6±62.7 kJ´mol 21 per 100 A Ê 2 . It is rather high in comparison to ATP molecule hydrolysis which yields 30.5 kcal´mol 21 .We now put forward several basic questions concerning water interactions with proteins and nucleic acids, the strength of these interactions, and their localisation, structure and effect on the conformation of various biological macromolecules. The role of water in biology is not very well understood in detail and is still controversial. Water molecules appear to be both the cement that fills crevices between amino acid building blocks and the lubricant that allows motion of these elements [1]. In consequence, they allow a biological molecule to adopt a tertiary structure without being trapped in a local minimum energy state, as well as to compensate for a poor steric fit of side chains in macromolecule interiors and substrates in the binding sites [2,3]. These interactions of water mol...

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Section: High‐pressure Mediated Conformational Changes Of Ribonucleicmentioning

confidence: 99%

The role of water structure in conformational changes of nucleic acids in ambient and high‐pressure conditions

Barciszewski

Jurczak

Porowski

et al. 1999

European Journal of Biochemistry

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“…The thermal modifications were not reversed by decreasing again the temperature: after overnight equilibration at room temperature, the spectra did not show any change. At 0.020 M cadmium, the high temperature spectra suggested a time evolution not towards a Z-but instead an A-form similar to that presented by (G + C)-reach DNA 55 or by poly(rG-dC). 56 The spectral time evolution at 0.010 M cadmium was intermediate between that described for 0.005 and 0.020 M CdCl 2 .…”

Section: Microemulsion Experiments: Polygcmentioning

confidence: 85%

“…The sample, taken back to room temperature yielded a CD spectrum similar to that of the A-form. 55,56 For 0.070 M cadmium the B-to-Z conformational changes are almost reversible: after an overnight equilibration at room temperature the initial B-DNA spectrum was again obtained.…”

Section: Microemulsion Experiments: Polygcmentioning

confidence: 99%

The CdCl2 effects on synthetic DNAs encaged in the nanodomains of a cationic water-in-oil microemulsion

Airoldi

Gennaro

Giomini

et al. 2011

Phys. Chem. Chem. Phys.

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The present work is dedicated to the study of the interactions of CdCl(2) with the synthetic polynucleotides polyAT and polyGC confined in the nanoscopic aqueous compartment of the water-in-oil microemulsion CTAB/pentanol/hexane/water, with the goal to mimic in vitro the situation met by the nucleic acids in vivo. In biological structures, in fact, very long strings of nucleic acids are segregated into very small compartments having a radius exceedingly smaller than the length of the encapsulated macromolecule. For comparison, the behaviour of polyGC was also studied in aqueous solutions of matched composition. The conformational and thermal stabilities of both polynucleotides enclosed in the inner compartment of the microemulsion are scarcely affected by the presence of CdCl(2), whereas in solution immediate and large effects were observed also at room temperature. The lack of effects of CdCl(2) on the properties of the biopolymers entrapped in the aqueous core of the microemulsion has been attributed to the peculiar characteristics of the medium (low dielectric constant, in particular) which cause a total repression of the CdCl(2) dissociation that is not complete even in water. In fact, several of the numerous effects of CdCl(2) observed on the conformational stability of polyGC in aqueous solutions have also been ascribed to the limited dissociation of the cadmium salt.

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“…It is known to exist in the A conformation at moderate salt concentrations and to convert to left-hand helical Z forms at low or high monovalent cation concentration (Wu & Behe, 1984). In solutions containing tetrabutylammonium ions and lacking any competing cations, the polymer can even assume a conformation that yields a circular dichroism spectrum characteristic of B-form DNA (Jayasena & Behe, 1987). Under the solution conditions employed here, however, the unassociated polymer should be firmly in the A form, at least prior to association with histones.…”

Section: Discussionmentioning

confidence: 97%

Nucleosome reconstitution of core-length poly(dG.cntdot.poly(dC) and poly(rG-dC).cntdot.poly(rG-dC)

Jayasena¹,

Behe²

1989

Biochemistry

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The double-stranded polypurine.polypyrimidines poly(dG).poly(dC) and poly[d(A-G)].poly[d(T-C)] and the mixed ribose-deoxyribose polynucleotide poly(rG-dC).poly(rG-dC) have been successfully reconstituted into nucleosomes. The radioactively labeled particles comigrate in gel electrophoresis and sucrose density gradient experiments with authentic nucleosomes derived from chicken erythrocyte chromatin. These results show that nucleosomes are able to accommodate a wider variety of polynucleotides than was previously believed.

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Influence of tetraalkyl ammonium lons on the structure of poly (rG-dC).poly (rG-dC): unexpected transitions among the Z, A and B conformations

Cited by 7 publications

References 16 publications

The role of water structure in conformational changes of nucleic acids in ambient and high‐pressure conditions

The role of water structure in conformational changes of nucleic acids in ambient and high‐pressure conditions

The CdCl2 effects on synthetic DNAs encaged in the nanodomains of a cationic water-in-oil microemulsion

Nucleosome reconstitution of core-length poly(dG.cntdot.poly(dC) and poly(rG-dC).cntdot.poly(rG-dC)

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