2011
DOI: 10.1093/nar/gkq1361
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Probing RNA dynamics via longitudinal exchange and CPMG relaxation dispersion NMR spectroscopy using a sensitive 13C-methyl label

Abstract: The refolding kinetics of bistable RNA sequences were studied in unperturbed equilibrium via 13C exchange NMR spectroscopy. For this purpose a straightforward labeling technique was elaborated using a 2′-13C-methoxy uridine modification, which was prepared by a two-step synthesis and introduced into RNA using standard protocols. Using 13C longitudinal exchange NMR spectroscopy the refolding kinetics of a 20 nt bistable RNA were characterized at temperatures between 298 and 310 K, yielding the enthalpy and entr… Show more

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Cited by 53 publications
(53 citation statements)
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“…Longitudinal exchange experiments are based on pulse sequences previously published for 15 N, yielding 13 C, 1 H 2D correlation maps with amplitude modulation of correlation-and exchange-peaks determined by longitudinal exchange rate constants and the kinetics of interconversion. [8,15] For a sample (0.8 mm) of sequence 6, arrays of spectra were recorded at 306, 309, 312, and 315 K with mixing periods of 10, 50, 100, 200, 300, 400, 600, and 800 ms (10,30,60,100,150,250,350,500,600 and 800 ms at 315 K). The size of the data matrices for each spectrum was 1024 48 complex data points, the number of scans was 128 and the interscan delay was 1.5 s, yielding a total measuring time of 30 h at each temperature.…”
Section: Methodsmentioning
confidence: 99%
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“…Longitudinal exchange experiments are based on pulse sequences previously published for 15 N, yielding 13 C, 1 H 2D correlation maps with amplitude modulation of correlation-and exchange-peaks determined by longitudinal exchange rate constants and the kinetics of interconversion. [8,15] For a sample (0.8 mm) of sequence 6, arrays of spectra were recorded at 306, 309, 312, and 315 K with mixing periods of 10, 50, 100, 200, 300, 400, 600, and 800 ms (10,30,60,100,150,250,350,500,600 and 800 ms at 315 K). The size of the data matrices for each spectrum was 1024 48 complex data points, the number of scans was 128 and the interscan delay was 1.5 s, yielding a total measuring time of 30 h at each temperature.…”
Section: Methodsmentioning
confidence: 99%
“…[7] NMR spectroscopy has proven to be well suited for detecting and quantifying distinct folding states of nucleic acids, and for determining the kinetics and the thermodynamics of the refolding process. [8] In this work we present a site-specific 13 Cisotope labeling procedure for DNA and use it to characterize secondary structure heterogeneity of a bistable DNA sequence. [7] We introduce isolated 13 C-spin labels into the methyl groups of thymidines that can be employed to detect and quantify dynamic properties using relaxation-based NMR techniques for 13 CH 3 -spin systems.…”
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confidence: 99%
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“…(Kloiber et al 2011;Korzhnev and Kay 2008;Korzhnev et al 2004b;Schanda et al 2008) These methods were developed primarily for folded substates. Yet they are applicable for intrinsically disordered proteins, too.…”
Section: Nmr Studies Of Excited States Of Proteinsmentioning
confidence: 99%