Abstract
RNA double-strand hybridization is a key player in gene expression regulation. Single-stranded RNA of up to 300 nucleotides forms Watson-Crick base pairs with complementary messenger RNA. Fluorescence-based single-molecule methods allow to study RNA-RNA interaction under physiological conditions. Here is described, how the dissociation constant of RNA double strands can be determined by applying fluorescence correlation spectroscopy.
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References
Cech TR, Steitz JA (2014) The noncoding RNA revolution-trashing old rules to forge new ones. Cell 157:77–94
Wilson R, Doudna JA (2013) Molecular mechanisms of RNA interference. Annu Rev Biophys 42:217
Ul Haq I, Brantl S, Müller P (2021) A new role for SR1 from Bacillus subtilis: regulation of sporulation by inhibition of kinA translation. Nucleic Acids Res 49:10589–10603
Mann M, Wright PR, Backofen R (2017) IntaRNA 2.0: enhanced and customizable prediction of RNA–RNA interactions. Nucleic Acids Res 45:W435–WW39
Werner A, Konarev PV, Svergun DI, Hahn U (2009) Characterization of a fluorophore binding RNA aptamer by fluorescence correlation spectroscopy and small angle X-ray scattering. Anal Biochem 389:52–62
Werner A, Hahn U (2009) Fluorescence correlation spectroscopy based characterisation of aptamer ligand interaction. Meth Mol Biol 535:107–114
Eydeler K, Magbanua E, Werner A, Ziegelmüller P, Hahn U (2009) Fluorophore binding aptamers as a tool for RNA visualization. Biophys J 96:3703–3707
Werner A, Skakun VV, Meyer C, Hahn U (2011) RNA dimerization monitored by fluorescence correlation spectroscopy. Eur Biophys J 40:907–921
Rigler R, Elson ES (eds) (2001) Fluorescence correlation spectroscopy: theory and applications. Springer, Berlin
Magde D, Elson ES, Webb WW (1972) Thermodynamic fluctuations in a reacting system – measurement by fluorescence correlation spectroscopy. Phys Rev Lett 29:705–708
Weisshart K, Jungel V, Briddon SJ (2004) The LSM 510 META – ConfoCor 2 system: an integrated imaging and spectroscopic platform for single-molecule detection. Curr Pharm Biotechnol 5:135–154
Fradin C, Zbaida D, Elbaum M (2005) Dissociation of nuclear import cargo complexes by the protein Ran: a fluorescence correlation spectroscopy study. C R Biol 328:1073–1082
Werner A, Skakun VV, Ziegelmüller P, Hahn U (2012) A fluorescence correlation spectroscopy-based enzyme assay for human Dicer. Biol Chem 393:187–193
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Werner, A. (2024). RNA Double-Helix Hybridization Measured by Fluorescence Correlation Spectroscopy. In: Arluison, V., Valverde, C. (eds) Bacterial Regulatory RNA. Methods in Molecular Biology, vol 2741. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3565-0_9
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DOI: https://doi.org/10.1007/978-1-0716-3565-0_9
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Publisher Name: Humana, New York, NY
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Online ISBN: 978-1-0716-3565-0
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