Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending 1 1Edited by I. Tinoco

Hud, Nicholas V.; Sklenář, Vladimı́r; Feigon, Juli

doi:10.1006/jmbi.1998.2513

Cited by 208 publications

(207 citation statements)

References 62 publications

Supporting

Mentioning

190

Contrasting

Order By: Relevance

“…This is, to our knowledge, the first evidence for a specific monovalent cation dependence on a DNA structure. The magnitude of the effect is consistent with previous experimental results on the extent and location of NH 4 ϩ binding to A4T4, T4A4, and GCA5CG (53). The ApT step represents a unique and species-dependent tight binding site for monovalent cations, which can coordinate to the two opposing T carbonyls (41,(49)(50)(51)(52)(53)55).…”

Section: Global Bend Of D(caaaattttg)n and D(gttttaaaac)nsupporting

confidence: 90%

“…X-ray crystallography (49,50), molecular dynamics (51), capillary electrophoresis (52), and NMR (53) studies of DNA have shown that, in addition to waters, monovalent cations can bind specifically in the minor groove of A-tracts, although the relative occupancies remain unresolved (54). In our previous NMR studies of A4T4 and T4A4, NH 4 ϩ were found to localize in the narrowest parts of the minor grooves, resulting in a very different distribution of cation localization for the two molecules that was proposed to contribute to A-tract bending (53). NH 4 ϩ has a van der Waals radius about the same as K ϩ , and both are larger than Na ϩ .…”

Section: Global Bend Of D(caaaattttg)n and D(gttttaaaac)nmentioning

confidence: 97%

See 1 more Smart Citation

DNA A-tract bending in three dimensions: Solving the dA ₄ T ₄ vs. dT ₄ A ₄ conundrum

Štefl

Ravindranathan

et al. 2004

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

Self Cite

142

144

View full text Add to dashboard Cite

Section: Global Bend Of D(caaaattttg)n and D(gttttaaaac)nsupporting

confidence: 90%

Section: Global Bend Of D(caaaattttg)n and D(gttttaaaac)nmentioning

confidence: 97%

DNA A-tract bending in three dimensions: Solving the dA ₄ T ₄ vs. dT ₄ A ₄ conundrum

Štefl

Ravindranathan

et al. 2004

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

Self Cite

142

144

View full text Add to dashboard Cite

“…ϩ in both GCA 4 T 4 GC and CGT 4 A 4 CG demonstrated that an ApT step is not needed for ion intrusion into the minor groove (18). The same group previously demonstrated that Mn 2ϩ ions have access to the floor of the minor groove AT tracts of these two dodecamers (19).…”

Section: Nhmentioning

confidence: 86%

Sequence-specific binding of counterions toB-DNA

Денисов

Halle

2000

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

172

154

View full text Add to dashboard Cite

Recent studies by x-ray crystallography, NMR, and molecular simulations have suggested that monovalent counterions can penetrate deeply into the minor groove of B form DNA. Such groovebound ions potentially could play an important role in AT-tract bending and groove narrowing, thereby modulating DNA function in vivo. To address this issue, we report here 23 Na magnetic relaxation dispersion measurements on oligonucleotides, including difference experiments with the groove-binding drug netropsin. The exquisite sensitivity of this method to ions in long-lived and intimate association with DNA allows us to detect sequencespecific sodium ion binding in the minor groove AT tract of three B-DNA dodecamers. The sodium ion occupancy is only a few percent, however, and therefore is not likely to contribute importantly to the ensemble of B-DNA structures. We also report results of ion competition experiments, indicating that potassium, rubidium, and cesium ions bind to the minor groove with similarly weak affinity as sodium ions, whereas ammonium ion binding is somewhat stronger. The present findings are discussed in the light of previous NMR and diffraction studies of sequence-specific counterion binding to DNA.

show abstract

“…6A). Ammonium differs from other monovalent cations as it has protons that can hydrogen bond to acceptor atoms that are accessible in the DNA duplex, which may account for the anomalously high association of ammonium 49 .…”

Section: Competitive Association Of Cations: Assessing the Effects Ofmentioning

confidence: 99%

Quantitative and Comprehensive Decomposition of the Ion Atmosphere around Nucleic Acids

et al. 2007

View full text Add to dashboard Cite

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.

show abstract

Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending 1 1Edited by I. Tinoco

Cited by 208 publications

References 62 publications

DNA A-tract bending in three dimensions: Solving the dA ₄ T ₄ vs. dT ₄ A ₄ conundrum

DNA A-tract bending in three dimensions: Solving the dA ₄ T ₄ vs. dT ₄ A ₄ conundrum

Sequence-specific binding of counterions toB-DNA

Quantitative and Comprehensive Decomposition of the Ion Atmosphere around Nucleic Acids

Contact Info

Product

Resources

About

Localization of ammonium ions in the minor groove of DNA duplexes in solution and the origin of DNA A-tract bending 1 1Edited by I. Tinoco

Cited by 208 publications

References 62 publications

DNA A-tract bending in three dimensions: Solving the dA 4 T 4 vs. dT 4 A 4 conundrum

DNA A-tract bending in three dimensions: Solving the dA 4 T 4 vs. dT 4 A 4 conundrum

Sequence-specific binding of counterions toB-DNA

Quantitative and Comprehensive Decomposition of the Ion Atmosphere around Nucleic Acids

Contact Info

Product

Resources

About

DNA A-tract bending in three dimensions: Solving the dA ₄ T ₄ vs. dT ₄ A ₄ conundrum

DNA A-tract bending in three dimensions: Solving the dA ₄ T ₄ vs. dT ₄ A ₄ conundrum