Kinetics of Sodium Ion Binding to DNA Quadruplexes

Deng, Hong; Braunlin, William H.

doi:10.1006/jmbi.1996.0039

Cited by 88 publications

(105 citation statements)

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“…An increase in the 23 Na NMR linewidth of [d(G 4 T 4 G 4 )] 2 was observed as the temperature raised (33, 42, and 53 Hz linewidths at 298, 308, and 318 K, respectively), suggesting that conditions of a slow exchange were attained in solution in the whole range of temperatures. This finding is in line with the results of earlier studies, [36,40] where the intense 23 Na NMR signal observed in G-quadruplex DNA solutions (0 ppm) was attributed to sodium ions in fast exchange between the bulk and unspecific binding sites at the quadruplex surface and in slow exchange with ions specifically bound within the quadruplex.…”

Section: Resultssupporting

confidence: 93%

Competitive binding exchange between alkali metal ions (K⁺, Rb⁺, and Cs⁺) and Na⁺ ions bound to the dimeric quadruplex [d(G₄T₄G₄)]₂: a ²³Na and ¹H NMR study

Marincola

Virno

Randazzo

et al. 2009

Magnetic Reson in Chemistry

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A comparative study of the competitive cation exchange between the alkali metal ions K+, Rb+, and Cs+ and the Na+ ions bound to the dimeric quadruplex [d(G4T4G4)]2 was performed in aqueous solution by a combined use of the 23Na and 1H NMR spectroscopy. The titration data confirm the different binding affinities of these ions for the G-quadruplex and, in particular, major differences in the behavior of Cs+ as compared to the other ions were found. Accordingly, Cs+ competes with Na+ only for the binding sites at the quadruplex surface (primarily phosphate groups), while K+ and Rb+ are also able to replace sodium ions located inside the quadruplex. Furthermore, the 1H NMR results relative to the CsCl titration evidence a close approach of Cs+ ions to the phosphate groups in the narrow groove of [d(G4T4G4)]2. Based on a three-site exchange model, the 23Na NMR relaxation data lead to an estimate of the relative binding affinity of Cs+ versus Na+ for the quadruplex surface of 0.5 at 298 K. Comparing this value to those reported in the literature for the surface of the G-quadruplex formed by 5'-guanosinemonophosphate and for the surface of double-helical DNA suggests that topology factors may have an important influence on the cation affinity for the phosphate groups on DNA.

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Section: Resultssupporting

confidence: 93%

Competitive binding exchange between alkali metal ions (K⁺, Rb⁺, and Cs⁺) and Na⁺ ions bound to the dimeric quadruplex [d(G₄T₄G₄)]₂: a ²³Na and ¹H NMR study

Marincola

Virno

Randazzo

et al. 2009

Magnetic Reson in Chemistry

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“…[212,213] Although 23 Na NMR spectroscopy in solution provides dynamic information, it gives no structural insight. [214] There is a need, therefore, for techniques that detect DNA-bound metals. The high-resolution crystal structures of lipophilic G-quadruplexes synthesized from G (1) [29][30][31][32][33] have helped validate such new methods, namely solid-state 23 Na and 39 K NMR spectroscopy and extended Xray absorption fine structure (EXAFS).…”

Section: Crystal Structures Of Lipophilic G-quadruplexes: Models For mentioning

confidence: 99%

G‐Quartets 40 Years Later: From 5′‐GMP to Molecular Biology and Supramolecular Chemistry

Davis¹

2004

Angew Chem Int Ed

1,533

525

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Molecular self-assembly is central to many processes in both biology and supramolecular chemistry. The G-quartet, a hydrogen-bonded macrocycle formed by cation-templated assembly of guanosine, was first identified in 1962 as the basis for the aggregation of 5'-guanosine monophosphate. We now know that many nucleosides, oligonucleotides, and synthetic derivatives form a rich array of functional G-quartets. The G-quartet surfaces in areas ranging from structural biology and medicinal chemistry to supramolecular chemistry and nanotechnology. This Review integrates and summarizes knowledge gained from these different areas, with emphasis on G-quartet structure, function, and molecular recognition.

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“…[212,213] Ein 23 Na-NMR-Spektrum in Lösung liefert zwar Informationen zur Dynamik, aber nicht zur Struktur. [214] Demnach besteht ein Bedarf an Methoden, mit denen sich DNAgebundene Metalle nachweisen lassen. Hochaufgelöste Kristallstrukturen [29][30][31][32][33] der lipophilen G-Quadruplexe aus G (1) trugen dazu bei, die Gültigkeit neuer Methoden wie der 23 Naund 39 K-Festkörper-NMR-Spektroskopie und der EXAFSRöntgenspektroskopie (EXAFS = extended X-ray absorption fine structure) zu bestätigen.…”

Section: Zusammenfassung Der Für Die G-quadruplexstruktur Und Die Molunclassified

40 Jahre G‐Quartetts: von 5′‐GMP zur Molekularbiologie und Supramolekularen Chemie

Davis

2004

Angewandte Chemie

234

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Die molekulare Selbstorganisation spielt bei vielen Prozessen in der Biologie und der Supramolekularen Chemie eine zentrale Rolle. Das G‐Quartett, ein durch Selbstorganisation von Guanosin an einem kationischen Templat gebildeter, wasserstoffverbrückter Makrocyclus, wurde erstmals 1962 als Basiseinheit der Aggregation von 5′‐Guanosinmonophosphat nachgewiesen. Inzwischen weiß man, dass viele Nucleoside, Oligonucleotide und synthetische Derivate eine Vielzahl funktionaler G‐Quartetts bilden. Das G‐Quartett spielt in vielen Bereichen eine Rolle, angefangen von der Strukturbiologie und der Medizinischen Chemie bis zur Supramolekularen Chemie und Nanotechnologie. Dieser Aufsatz fasst die Ergebnisse aus den unterschiedlichen Gebieten zusammen, wobei der Schwerpunkt auf der Struktur, der Funktion und der molekularen Erkennung des G‐Quartetts liegt.

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Kinetics of Sodium Ion Binding to DNA Quadruplexes

Cited by 88 publications

References 0 publications

Competitive binding exchange between alkali metal ions (K⁺, Rb⁺, and Cs⁺) and Na⁺ ions bound to the dimeric quadruplex [d(G₄T₄G₄)]₂: a ²³Na and ¹H NMR study

Competitive binding exchange between alkali metal ions (K⁺, Rb⁺, and Cs⁺) and Na⁺ ions bound to the dimeric quadruplex [d(G₄T₄G₄)]₂: a ²³Na and ¹H NMR study

G‐Quartets 40 Years Later: From 5′‐GMP to Molecular Biology and Supramolecular Chemistry

40 Jahre G‐Quartetts: von 5′‐GMP zur Molekularbiologie und Supramolekularen Chemie

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Kinetics of Sodium Ion Binding to DNA Quadruplexes

Cited by 88 publications

References 0 publications

Competitive binding exchange between alkali metal ions (K+, Rb+, and Cs+) and Na+ ions bound to the dimeric quadruplex [d(G4T4G4)]2: a 23Na and 1H NMR study

Competitive binding exchange between alkali metal ions (K+, Rb+, and Cs+) and Na+ ions bound to the dimeric quadruplex [d(G4T4G4)]2: a 23Na and 1H NMR study

G‐Quartets 40 Years Later: From 5′‐GMP to Molecular Biology and Supramolecular Chemistry

40 Jahre G‐Quartetts: von 5′‐GMP zur Molekularbiologie und Supramolekularen Chemie

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Competitive binding exchange between alkali metal ions (K⁺, Rb⁺, and Cs⁺) and Na⁺ ions bound to the dimeric quadruplex [d(G₄T₄G₄)]₂: a ²³Na and ¹H NMR study

Competitive binding exchange between alkali metal ions (K⁺, Rb⁺, and Cs⁺) and Na⁺ ions bound to the dimeric quadruplex [d(G₄T₄G₄)]₂: a ²³Na and ¹H NMR study