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RNA Structure and Folding: Biophysical Techniques and by Dagmar Klostermeier, Christian Hammann

24 February 2017 adminCell Biology

By Dagmar Klostermeier, Christian Hammann

Whereas structure-function relationships of proteins were studied for a very long time, structural reviews of RNA face extra demanding situations. however, with the continual discovery of novel RNA molecules with key mobile services and of novel pathways and interplay networks, the necessity for structural details of RNA continues to be expanding. This quantity presents an advent into concepts to evaluate constitution and folding of RNA. each one bankruptcy explains the theoretical history of 1 procedure, and illustrates probabilities and obstacles in chosen program examples.

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Additional info for RNA Structure and Folding: Biophysical Techniques and Prediction Methods

Example text

2004;43:5870–81. 85. Pilch DS, Kaul M, Barbieri CM, Kerrigan JE. Thermodynamics of aminoglycoside-rRNA recognition. Biopolymers. 2003;70:58–79. 86. Salim NN, Feig AL. Isothermal titration calorimetry of RNA. Methods. 2009;47:198–205. 87. Takach JC, Mikulecky PJ, Feig AL. Salt-dependent heat capacity changes for RNA duplex formation. J Am Chem Soc. 2004;126:6530–1. 88. Vander Meulen KA, Davis JH, Foster TR, Record MT Jr, Butcher SE. Thermodynamics and folding pathway of tetraloop receptor-mediated RNA helical packing.

RNA tertiary folding monitored by fluorescence of covalently attached pyrene. Biochemistry. 1999;38:14224–37. 35. Hall KB. 2-Aminopurine as a probe of RNA conformational transitions. Methods Enzymol. 2009;469:269–85. 36. Ballin JD, Bharill S, Fialcowitz-White EJ, Gryczynski I, Gryczynski Z, Wilson GM. Site-specific variations in RNA folding thermodynamics visualized by 2-aminopurine fluorescence. Biochemistry. 2007;46:13948–60. 37. Sarkar K, Nguyen DA, Gruebele M. Loop and stem dynamics during RNA hairpin folding and unfolding.

6). 45) Experiments at multiple temperatures allow for the direct distinction of a temperature-independent ΔCp (linear relationship between ΔH and T) or temperaturedependent ΔCp (nonlinear dependence of ΔH on T) and thus yield reliable values for ΔCp. 2 Differential scanning calorimetry In DSC, the two-chamber principle of the ITC is also employed; however, the sample cell containing the RNA (in the presence or absence of ligands) and the reference cell are closed (Fig. 4B). Practically, a DSC instrument measures the difference in power that is required to maintain the temperature constant between reference and sample cell.

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