By Dagmar Klostermeier, Christian Hammann
Whereas structure-function relationships of proteins were studied for a very long time, structural reports of RNA face extra demanding situations. however, with the continual discovery of novel RNA molecules with key mobile capabilities and of novel pathways and interplay networks, the necessity for structural info of RNA remains to be expanding. This quantity presents an advent into strategies to evaluate constitution and folding of RNA. every one bankruptcy explains the theoretical historical past of 1 procedure, and illustrates probabilities and obstacles in chosen software examples.
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Extra info for RNA Structure and Folding: Biophysical Techniques and Prediction Methods
Zuker M. Mfold web server for nucleic acid folding and hybridization prediction. Nucleic Acids Res. 2003;31:3406–15. 17. Markham NR, Zuker M. DINAMelt web server for nucleic acid melting prediction. Nucleic Acids Res. 2005;33:W577–81. 18. Mathews DH, Turner DH. Prediction of RNA secondary structure by free energy minimization. Curr Opin Struct Biol. 2006;16:270–8. 19. Mathews DH, Turner DH, Zuker M. RNA secondary structure prediction. Curr Protoc Nucleic Acid Chem. 2. 20. Markham NR, Zuker M. UNAFold: software for nucleic acid folding and hybridization.
Li Y, Turner DH. Effects of Mg2+ and the 2’ OH of guanosine on steps required for substrate binding and reactivity with the Tetrahymena ribozyme reveal several local folding transitions. Biochemistry. 1997;36:11131–9. 34. Silverman SK, Cech TR. 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.
Therefore, it is not possible to measure them separately and calculate the CD from their difference. Instead, CD instruments modulate the linearly polarized incident light, such that the illumination of the sample alternates between an excess of the right- and left-handed polarized components with a modulation frequency ω. If the sample shows CD, the intensity of the transmitted light varies with the same modulation frequency ω and the amplitude that reflects the different absorption of the two components.
RNA Structure and Folding: Biophysical Techniques and Prediction Methods by Dagmar Klostermeier, Christian Hammann