DNA-Cation Interactions

Egli, Martin

doi:10.1016/s1074-5521(02)00116-3

Cited by 184 publications

(183 citation statements)

References 61 publications

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“…This binding mode is conserved in crystals of the Dickerson-Drew DNA dodecamer and occurs at the site of a facultative bend into the major groove (52,63). Therefore, cation binding in these crystals is not in any way linked to the presence of arabinonucleosides in the central A-tract of dodecamers.…”

Section: Resultsmentioning

confidence: 96%

2‘-Fluoroarabino- and Arabinonucleic Acid Show Different Conformations, Resulting in Deviating RNA Affinities and Processing of Their Heteroduplexes with RNA by RNase H^,

Sarkhel

Wilds

et al. 2006

Biochemistry

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2′-Deoxy-2′-fluoro-arabinonucleic acid (FANA) and arabinonucleic acid (ANA) paired to RNA are substrates of RNase H. The conformation of the natural DNA/RNA hybrid substrates appears to be neither A-form nor B-form. Consistent with this, the conformations of FANA and ANA were found to be intermediate between the A-and B-forms. However, FANA opposite RNA is preferred by RNase H over ANA, and the RNA affinity of FANA considerably exceeds that of ANA. By investigating the conformational boundaries of FANA and ANA residues in crystal structures of A-and B-form DNA duplexes at atomic resolution, we demonstrate that FANA and ANA display subtle conformational differences. The structural data provide insight into the structural requirements at the catalytic site of RNase H. They also allow conclusions with regard to the relative importance of stereoelectronic effects and hydration as modulators of RNA affinity.

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Section: Resultsmentioning

confidence: 96%

2‘-Fluoroarabino- and Arabinonucleic Acid Show Different Conformations, Resulting in Deviating RNA Affinities and Processing of Their Heteroduplexes with RNA by RNase H^,

Sarkhel

Wilds

et al. 2006

Biochemistry

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“…NMR relaxation and atomic absorption spectroscopy measurements with DNA duplexes in solution and DNA fibers, respectively, suggested a preferential interaction with Ca 2+ over Mg 2+ 22, 45 or a similar interaction with these cations 46 . Varying the GC content of the DNA duplex (37%-67%, Supporting Scheme S1 & Table S4) did not change the relative affinities of Ca 2+ and Mg 2+ , providing no indication of a base-specific enhancement of Ca 2+ affinity, as might be anticipated from the apparent preference of inner sphere coordinations of Ca 2+ with guanines 43,47 . Further work will be required to distinguish whether the observed preference arises from a small effective solvation radius for Ca 2+ , from preferential interactions of solvated or partially desolvated Ca 2+ with particular features of the DNA 48 , or from a different mechanism.…”

Section: Competitive Association Of Cations: Assessing the Effects Ofmentioning

confidence: 89%

Quantitative and Comprehensive Decomposition of the Ion Atmosphere around Nucleic Acids

et al. 2007

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The ion atmosphere around nucleic acids critically affects biological and physical processes such as chromosome packing, RNA folding, and molecular recognition. However, the dynamic nature of the ion atmosphere renders it difficult to characterize. The basic thermodynamic description of this atmosphere, a full accounting of the type and number of associated ions, has remained elusive. Here we provide the first complete accounting of the ion atmosphere, using buffer equilibration and atomic emission spectroscopy (BE-AES) to accurately quantitate the cation association and anion depletion. We have examined the influence of ion size and charge on ion occupancy around simple, well-defined DNA molecules. The relative affinity of monovalent and divalent cations correlates inversely with their size. Divalent cations associate preferentially over monovalent cations; e.g., with Na + in four-fold excess of Mg 2+ (20 vs. 5 mM), the ion atmosphere nevertheless has three-fold more Mg 2+ than Na + . Further, the dicationic polyamine putrescine 2+ does not compete effectively for association relative to divalent metal ions, presumably because of its lower charge density. These and other BE-AES results can be used to evaluate and guide the improvement of electrostatic treatments. As a first step, we compare the BE-AES results to predictions from the widely-used nonlinear Poisson Boltzmann (NLPB) theory and assess the applicability and precision of this theory. In the future, BE-AES in conjunction with improved theoretical models, can be applied to complex binding and folding equilibria of nucleic acids and their complexes, to parse the electrostatic contribution from the overall thermodynamics of important biological processes.

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“…(See the Appendix for the relationship between our analysis and the method from Meisburger et al) It is not clear how accurate this assumption is or whether the same assumption would be valid for highly charged ions (such as Mg 2+ and Sr 2+ ) since the interaction between those ions with nucleic acids is expected to be ion-dependent. [37][38][39][40][41][42] Here, we apply our analysis method to a 25 base-pair duplex DNA. Fig.…”

Section: Duplex Dna In Salt Solutionsmentioning

confidence: 99%

Extracting water and ion distributions from solution x-ray scattering experiments

Nguyên

Pabit

Pollack

et al. 2016

The Journal of Chemical Physics

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Small-angle X-ray scattering measurements can provide valuable information about the solvent environment around biomolecules, but it can be difficult to extract solvent-specific information from observed intensity profiles. Intensities are proportional to the square of scattering amplitudes, which are complex quantities. Amplitudes in the forward direction are real, and the contribution from a solute of known structure (and from the waters it excludes) can be estimated from theory; hence, the amplitude arising from the solvent environment can be computed by difference. We have found that this "square root subtraction scheme" can be extended to non-zero q values, out to 0.1 Å −1 for the systems considered here, since the phases arising from the solute and from the water environment are nearly identical in this angle range. This allows us to extract aspects of the water and ion distributions (beyond their total numbers), by combining experimental data for the complete system with calculations for the solutes. We use this approach to test molecular dynamics and integral-equation (3D-RISM (three-dimensional reference interaction site model)) models for solvent structure around myoglobin, lysozyme, and a 25 base-pair duplex DNA. Comparisons can be made both in Fourier space and in terms of the distribution of interatomic distances in real space. Generally, computed solvent distributions arising from the MD simulations fit experimental data better than those from 3D-RISM, even though the total small-angle X-ray scattering patterns are very similar; this illustrates the potential power of this sort of analysis to guide the development of computational models. Published by AIP Publishing. [http://dx

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DNA-Cation Interactions

Cited by 184 publications

References 61 publications

2‘-Fluoroarabino- and Arabinonucleic Acid Show Different Conformations, Resulting in Deviating RNA Affinities and Processing of Their Heteroduplexes with RNA by RNase H^,

2‘-Fluoroarabino- and Arabinonucleic Acid Show Different Conformations, Resulting in Deviating RNA Affinities and Processing of Their Heteroduplexes with RNA by RNase H^,

Quantitative and Comprehensive Decomposition of the Ion Atmosphere around Nucleic Acids

Extracting water and ion distributions from solution x-ray scattering experiments

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DNA-Cation Interactions

Cited by 184 publications

References 61 publications

2‘-Fluoroarabino- and Arabinonucleic Acid Show Different Conformations, Resulting in Deviating RNA Affinities and Processing of Their Heteroduplexes with RNA by RNase H,

2‘-Fluoroarabino- and Arabinonucleic Acid Show Different Conformations, Resulting in Deviating RNA Affinities and Processing of Their Heteroduplexes with RNA by RNase H,

Quantitative and Comprehensive Decomposition of the Ion Atmosphere around Nucleic Acids

Extracting water and ion distributions from solution x-ray scattering experiments

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2‘-Fluoroarabino- and Arabinonucleic Acid Show Different Conformations, Resulting in Deviating RNA Affinities and Processing of Their Heteroduplexes with RNA by RNase H^,

2‘-Fluoroarabino- and Arabinonucleic Acid Show Different Conformations, Resulting in Deviating RNA Affinities and Processing of Their Heteroduplexes with RNA by RNase H^,