Binding sites and dynamics of ammonium ions in a telomere repeat DNA quadruplex 1 1Edited by I. Tinoco

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

doi:10.1006/jmbi.1998.2327

Cited by 164 publications

(208 citation statements)

References 53 publications

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“…15 N NMR has provided insight into NH 4 + binding, and 205 Tl NMR showed how a K + surrogate stabilizes the [d(T 2 G 4 T 2 )] 4 quadruplex. [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.…”

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

1,544

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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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

1,544

525

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“…Ammonium cations can be used instead [9], as NH 4 + ions also coordinate between G-quartets and thereby stabilize G-quadruplexes in solution [10][11][12]. When sufficient internal energy is provided to the biomolecule, neutral ammonia is lost following proton transfer to the biomolecule.…”

mentioning

confidence: 99%

Ammonium Ion Binding to DNA G-Quadruplexes: Do Electrospray Mass Spectra Faithfully Reflect the Solution-Phase Species?

Balthasart

Plavec

Gabelica

2012

J. Am. Soc. Mass Spectrom.

112

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Abstract. G-quadruplex nucleic acids can bind ammonium ions in solution, and these complexes can be detected by electrospray mass spectrometry (ESI-MS). However, because ammonium ions are volatile, the extent to which ESI-MS quantitatively could provide an accurate reflection of such solution-phase equilibria is unclear. Here we studied five G-quadruplexes having known solution-phase structure and ammonium ion binding constants: the bimolecular G-quadruplexes (dG 4 T 4 G 4 ) 2 , (dG 4 T 3 G 4 ) 2 , and (dG 3 T 4 G 4 ) 2 , and the intramolecular G-quadruplexes dG 4 (T 4 G 4 ) 3 and dG 2 T 2 G 2 TGTG 2 T 2 G 2 (thrombin binding aptamer). We found that not all mass spectrometers are equally suited to reflect the solution phase species. Ion activation can occur in the electrospray source, or in a high-pressure traveling wave ion mobility cell. When the softest instrumental conditions are used, ammonium ions bound between Gquartets, but also additional ammonium ions bound at specific sites outside the external G-quartets, can be observed. However, even specifically bound ammonium ions are in some instances too labile to be fully retained in the gas phase structures, and although the ammonium ion distribution observed by ESI-MS shows biases at specific stoichiometries, the relative abundances in solution are not always faithfully reflected. Ion mobility spectrometry results show that all inter-quartet ammonium ions are necessary to preserve the Gquadruplex fold in the gas phase. Ion mobility experiments, therefore, help assign the number of inner ammonium ions in the solution phase structure.

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“…To date, RNA folding has been investigated by using x-ray footprinting (13), oligonucleotide hybridization, and classical biochemical methods in conjunction with mutational data (14). Although hydrogen exchange rates can be used as reporters of RNA ground-state dynamics and stability (15)(16)(17), RNA hydrogen exchange experiments conducted in a pulse-chase manner fail in most cases because of the high intrinsic exchange rates observed even in folded RNA structures.…”

mentioning

confidence: 99%

Time-resolved NMR methods resolving ligand-induced RNA folding at atomic resolution

Buck

Fürtig²,

Noeske³

et al. 2007

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

132

140

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spectroscopy ͉ riboswitches ͉ dynamics ͉ purine ͉ caged compound S tructural transitions of proteins and RNA constitute an important aspect of cellular function and information transfer. In proteins, the kinetics of these structural transitions, mainly from an unfolded ensemble to a single unique folded state, can be investigated by hydrogen exchange experiments monitored by NMR spectroscopy (1). Such studies have profoundly influenced our understanding of protein-folding pathways. In hydrogen exchange experiments, labile hydrogen atoms become protected against exchange with the bulk solvent during folding. This acquired exchange protection indicates formation of a persistent structure at atomic resolution. Incorporation of structural information derived from exchange experiments into molecular dynamics (MD) simulations (2), including data from methods exhibiting time and atomic resolution together with -value analysis (3) derived from mutational work, has provided detailed structural information of intermediates populated during folding.RNA molecules can adopt a variety of secondary and tertiary conformations (4, 5). In general, the energetic difference between alternate RNA conformations is very small, and the equilibrium distribution is strongly affected through the binding of proteins (6), ions (7), or small metabolites (8-10), or by structural modifications (11). Alternate RNA structures are stabilized by different Watson-Crick base-pairing interactions (12). To date, RNA folding has been investigated by using x-ray footprinting (13), oligonucleotide hybridization, and classical biochemical methods in conjunction with mutational data (14). Although hydrogen exchange rates can be used as reporters of RNA ground-state dynamics and stability (15-17), RNA hydrogen exchange experiments conducted in a pulse-chase manner fail in most cases because of the high intrinsic exchange rates observed even in folded RNA structures.Here, we report on ligand-induced conformational changes of an RNA at atomic resolution by using real-time NMR methods. We investigated the hypoxanthine-induced folding of the guanine-sensing riboswitch aptamer domain (GSR apt ) of the Bacillus subtilis xpt-pbuX operon (18). Riboswitch RNAs have emerged as an important example of macromolecular structural transitions that lead to transcriptional or translational regulation of protein expression induced through the specific binding of a metabolite (reviewed in refs. 19 and 20). Riboswitches are located in the 5Ј-untranslated region (5Ј-UTR) of bacterial mRNA and consist of a highly specific metabolite receptor region (aptamer domain) coupled to a 3Ј-downstream sequence (expression platform). Gene expression is thought to be modulated in response to conformational differences between the ligand-bound and ligand-free conformations of the aptamer domain (21). Crystal structures of the ligand-bound aptamer domains belonging to the class of purine riboswitches (guanineand adenine-sensing riboswitches) have revealed the presence of complex tertiary stru...

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Binding sites and dynamics of ammonium ions in a telomere repeat DNA quadruplex 1 1Edited by I. Tinoco

Cited by 164 publications

References 53 publications

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

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

Ammonium Ion Binding to DNA G-Quadruplexes: Do Electrospray Mass Spectra Faithfully Reflect the Solution-Phase Species?

Time-resolved NMR methods resolving ligand-induced RNA folding at atomic resolution

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