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Predicting translational diffusion of evolutionary conserved RNA structures by the nucleotide number
KTH, School of Engineering Sciences (SCI), Applied Physics, Experimental Biomolecular Physics.
2011 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 39, no 3, e17- p.Article in journal (Refereed) Published
Abstract [en]

Ribonucleic acids are highly conserved essential parts of cellular life. RNA function is determined to a large extent by its hydrodynamic behaviour. The presented study proposes a strategy to predict the hydrodynamic behaviour of RNA single strands on the basis of the polymer size. By atom-level shell-modelling of high-resolution structures, hydrodynamic radius and diffusion coefficient of evolutionary conserved RNA single strands (ssRNA) were calculated. The diffusion coefficients D of 17-174 nucleotides (nt) containing ssRNA depended on the number of nucleotides N with D = 4.56 x 10(-10) N-0.39 m(2) s(-1). The hydrodynamic radius R-H depended on N with R-H = 5.00 x 10(-10) N-0.38 m. An average ratio of the radius of gyration and the hydrodynamic radius of 0.98 +/- 0.08 was calculated in solution. The empirical law was tested by in solution measured hydrodynamic radii and radii of gyration and was found to be highly consistent with experimental data of evolutionary conserved ssRNA. Furthermore, the hydrodynamic behaviour of several evolutionary unevolved ribonucleic acids could be predicted. Based on atom-level shell-modelling of high-resolution structures and experimental hydrodynamic data, empirical models are proposed, which enable to predict the translational diffusion coefficient and molecular size of short RNA single strands solely on the basis of the polymer size.

Place, publisher, year, edition, pages
2011. Vol. 39, no 3, e17- p.
Keyword [en]
X-RAY-SCATTERING, FLUORESCENCE CORRELATION SPECTROSCOPY, ESCHERICHIA-COLI, RIBOSOMAL-RNA, BIOLOGICAL MACROMOLECULES, LIGHT-SCATTERING, RIBOSWITCH, COEFFICIENTS, MOLECULES, FLUCTUATIONS
National Category
Biophysics
Identifiers
URN: urn:nbn:se:kth:diva-31315DOI: 10.1093/nar/gkq808ISI: 000287257500006Scopus ID: 2-s2.0-79951562206OAI: oai:DiVA.org:kth-31315DiVA: diva2:404819
Note
QC 20110318Available from: 2011-03-18 Created: 2011-03-14 Last updated: 2017-12-11Bibliographically approved

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