Structure of the B DNA cationic shell as revealed by an X-ray diffraction study of CsDNA

Bartenev, V.N.; Golovamov, Eu.I.; Kapitonova, K. A.; Mokul'Skii, M. A.; Volkova, L. I.; Skuratovskii, I.Ya.

doi:10.1016/s0022-2836(83)80181-8

Cited by 85 publications

(41 citation statements)

References 36 publications

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“…Less apparent hydration in the minor groove and extensive hydration and ion association in the major groove is consistent with the experimental observation of ions in the major groove of A-DNA. A-DNA is presumably stabilized not only by ions and hydration in the major groove, but likely by absence of stabilizing counterion association and, consistent with the ''groove binding model'' (6,12), by hydration in the minor groove.…”

supporting

confidence: 53%

“…Common to each of these means to transition among the various structural forms seems to be both a subtle modulation of the hydration of DNA and the ionic association with the negatively charged phosphate backbone and grooves. Models such as the groove binding model (6,12) explain the stabilization of B-DNA by ions interacting directly with base atoms in the minor groove (Cs ϩ Ͼ K ϩ Ͼ Na ϩ ) or indirectly via water bridges (Li ϩ ). B-DNA is also stabilized by extensive solvation of the grooves and backbone (13), such as the ''spine of hydration'' in the minor groove (14).…”

mentioning

confidence: 99%

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A molecular level picture of the stabilization of A-DNA in mixed ethanol–water solutions

Cheatham

Crowley

Fox

et al. 1997

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

107

126

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Advances in computer power, methodology, and empirical force fields now allow routine ''stable'' nanosecond-length molecular dynamics simulations of DNA in water. The accurate representation of environmental inf luences on structure remains a major, unresolved issue. In contrast to simulations of A-DNA in water (where an A-DNA to B-DNA transition is observed) and in pure ethanol (where disruption of the structure is observed), A-DNA in Ϸ85% ethanol solution remains in a canonical A-DNA geometry as expected. The stabilization of A-DNA by ethanol is likely due to disruption of the spine of hydration in the minor groove and the presence of ion-mediated interhelical bonds and extensive hydration across the major groove.

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supporting

confidence: 53%

mentioning

confidence: 99%

A molecular level picture of the stabilization of A-DNA in mixed ethanol–water solutions

Cheatham

Crowley

Fox

et al. 1997

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

107

126

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“…35 The sodium nmr data clearly show that at least two populations of cations exist in DNA solutions (i.e., free and associated). These populations are in "rapid exchange" and thus cannot be used to deduce the detailed environments of DNA bound sodium.…”

Section: Discussionmentioning

confidence: 97%

Differential electrostatic stabilization of A‐, B‐, and Z‐forms of DNA

Matthew

Richards

1984

Biopolymers

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SynopsisThe static accessibility discrete charge algorithm for protein charge interactions is extended to the case of linear polyelectrolytes. In this model, the effective dielectric value between surface charge sites depends predominantly on the solvent ionic strength and the solvent accessibilities of the charge sites. This treatment accounts for the phenomena of specific ion binding in the context of a general electrostatic effect [Matthew and Richards (1982) Biochemistry 21, 49891. Specific ion sites are determined by locating areas of high electrostatic potential a t the solvent interface of the macromolecule. At a given ionic strength the calculated potential at a site is taken to describe a binding constant and therefore the ion site occupancy. For a 20-base-pair fragment of B-DNA, net charge of -40,16 ion sites are indicated in the minor groove. The partial occupancy of each site increases from 0.2 to 0.5 as the ionic strength is increased from 0.01 to 0.50. Over the same range of ionic strength, the electrostatic free energy of this charge array is calculated to change from +0.6 to -0.05 kcallbp. Parallel behavior is predicted for A-and Z-DNA charge geometries. The most stable configuration, based on electrostatic criteria, at high ionic strength (I = 0.1-0.5) is that of Z-DNA. In this range, the ratio of "bound" sodium to phosphate is predicted to be less than 0.4.

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“…Specifically bound counterions, on the other hand, which are not expected to be fully hydrated, can bind either directly to a phosphate group or may penetrate inside the grooves of DNA with association to the bases. 35 The local order of this association may then very well result in a negative order parameter.…”

Section: Discussionmentioning

confidence: 99%

A study of the quadrupolar NMR splittings of ⁷Li⁺, ²³Na⁺, and ¹³³Cs⁺ counterions in macroscopically oriented DNA fibers

1992

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The hydration and temperature dependencies of the 23Na+, 133Cs+, and 7Li+ quadrupolar splitting have been determined in hydrated, macroscopically oriented DNA fibers. At low water contents the quadrupolar splitting is found to decrease as the water content increases, regardless of counterion, while at high water contents the hydration dependence is reversed. The 23Na+ and 133Cs+ quadrupolar splittings decrease as the temperature increases, while the 7Li+ splitting shows the opposite behavior. At high water contents the 23Na+ and 133Cs+ splittings decrease, and then, after passing zero splitting, increase as the temperature increases. The interpretation of the temperature dependence is discussed in terms of a two-site model (free and bound ions) and a three-site model (free ions and specifically or nonspecifically bound ions). It is suggested that a three-site model is more consistent with the data for the present system. At high water contents, the temperature dependence of the 7Li+ splitting vanishes, indicating counterion condensation. The behavior of the 7Li+ splitting is confirmed by measurements on DNA fibers in equilibrium with a C2H5OD-D2O-LiCl solution. The salt dependence in this system is weak. The counterion quadrupolar splitting is seen to be very sensitive to structural transitions in double-helical DNA.

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Structure of the B DNA cationic shell as revealed by an X-ray diffraction study of CsDNA

Cited by 85 publications

References 36 publications

A molecular level picture of the stabilization of A-DNA in mixed ethanol–water solutions

A molecular level picture of the stabilization of A-DNA in mixed ethanol–water solutions

Differential electrostatic stabilization of A‐, B‐, and Z‐forms of DNA

A study of the quadrupolar NMR splittings of ⁷Li⁺, ²³Na⁺, and ¹³³Cs⁺ counterions in macroscopically oriented DNA fibers

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Structure of the B DNA cationic shell as revealed by an X-ray diffraction study of CsDNA

Cited by 85 publications

References 36 publications

A molecular level picture of the stabilization of A-DNA in mixed ethanol–water solutions

A molecular level picture of the stabilization of A-DNA in mixed ethanol–water solutions

Differential electrostatic stabilization of A‐, B‐, and Z‐forms of DNA

A study of the quadrupolar NMR splittings of 7Li+, 23Na+, and 133Cs+ counterions in macroscopically oriented DNA fibers

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A study of the quadrupolar NMR splittings of ⁷Li⁺, ²³Na⁺, and ¹³³Cs⁺ counterions in macroscopically oriented DNA fibers