Dynamics and Metal Ion Binding in the U6 RNA Intramolecular Stem–Loop as Analyzed by NMR

Blad, Heike; Reiter, Nicholas J.; Abildgaard, Frits; Markley, John L.; Butcher, Samuel E.

doi:10.1016/j.jmb.2005.08.030

Cited by 64 publications

(90 citation statements)

References 50 publications

(89 reference statements)

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“…(the relaxation rate at infinite spin lock power) is estimated from residues that exhibit no exchange. 67 …”

Section: Nmr Studies Of S-ms Motionsmentioning

confidence: 99%

“…20 A second investigation of a 14-nucleotides RNA containing the highly abundant cUUCGg motif also confirmed the rigidity of the structural features of the loop, with the exception of the U6 base, which lacks contacts with other nucleotides. 27 Dynamics of four larger RNAs have been studied as well: the TAR element from HIV, 19,21 the polyadenylation regulatory element 3 0 untranslated region (3 0 UTR) of the mRNA that codes for human U1A, 26 the U6 RNA intramolecular stem-loop 67 and the lead-dependent ribozyme. 66 The TAR RNA activates transcription of the HIV viral genome when Residues that exhibit increased motion on a fast timescale (ns-ps) are red; residues that exhibit increased motion on an intermediate timescale ( s-ms) are green; residues that exhibit dynamics on both timescales are shown in orange.…”

Section: Studies Of Nucleic Acid Dynamics By 13 C Nmrmentioning

confidence: 99%

“…26,66,67 Two of these studies extracted quantitative parameters, such as exchange lifetimes and the populations of each exchanging species. In the lead-dependent ribozyme, the reactive groups rely on thermal fluctuation to switch from a highly populated but inactive state to the low populated active state.…”

Section: Studies Of Nucleic Acid Dynamics By 13 C Nmrmentioning

confidence: 99%

“…81 A recent 13 C T 1 power dependence analysis of this system revealed the presence of a global conformational transition at a rate of about 84 s, that was consistent with the conversion between pH dependent states. 67 Concerning DNA, to date only the terminal residues have displayed flexibility among the oligonucleotides that have been studied. Although local motions in DNA facilitate protein recognition, motion in these systems may exist on timescales that are not easily accessible by solution NMR.…”

Section: Studies Of Nucleic Acid Dynamics By 13 C Nmrmentioning

confidence: 99%

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NMR studies of dynamics in RNA and DNA by ¹³C relaxation

Shajani

Varani

2006

Biopolymers

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T he many functions of RNA in biology very often require this molecule to change its conformation in response to biological signals in the form of small molecules, proteins, or other nucleic acids. 1,2 Although structurally more conservative and therefore dynamically less diverse, local motions in DNA may facilitate protein recognition and allow enzymes acting on DNA to access functional groups on the bases that would otherwise be buried in Watson-Crick base pairs. 3 These statements make a compelling case to study the sequence dependent dynamics in nucleic acids; yet, residue-specific studies of nucleic acid dynamics are relatively few. Fortunately, NMR studies of dynamics of nucleic acids and nucleic acids-protein complexes are gaining increased attention, this spectroscopy being the only way to access information on a residue-by-residue basis. The questions that are being asked are how motion contributes to the affinity and specificity of biological interactions and what trajectories lead to the remarkably large conformational changes that are sometimes observed.RNA and DNA molecules experience motions on a wide range of time scales, ranging from rapid localized motions to much slower collective motions of entire helical domains. Figure 1 summarizes the NMR spectroscopic techniques commonly used to obtain information in each motional regime. Dynamics occurring on time scales that are considered ''fast'' in NMR spectroscopic studies (ps-ns) largely reflects bond librations associated with small amplitude and localized motions.

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“…(the relaxation rate at infinite spin lock power) is estimated from residues that exhibit no exchange. 67 …”

Section: Nmr Studies Of S-ms Motionsmentioning

confidence: 99%

Section: Studies Of Nucleic Acid Dynamics By 13 C Nmrmentioning

confidence: 99%

Section: Studies Of Nucleic Acid Dynamics By 13 C Nmrmentioning

confidence: 99%

Section: Studies Of Nucleic Acid Dynamics By 13 C Nmrmentioning

confidence: 99%

See 2 more Smart Citations

NMR studies of dynamics in RNA and DNA by ¹³C relaxation

Shajani

Varani

2006

Biopolymers

View full text Add to dashboard Cite

show abstract

“…3). Both structures contain two short helices separated by an asymmetric bulge known to form a metal-binding pocket [25][26][27][28][29][30] and are capped by a GNRA-type tetraloop. In addition, they both contain a catalytically critical AGC triad at their 5' ends which interacts with functionally essential divalent cations in group II introns and likely also in the spliceosome.…”

Section: Snrnas and The Group II Self-splicing Intronsmentioning

confidence: 99%