Conformational statistics of short RNA chains

H. Rubin, N. R. Kallenbach

Research output: Contribution to journalArticle

Abstract

The conformational statistics of short ribonucleic acid (RNA) chains have been investigated by a Monte Carlo approach that includes effects due to base-base stacking interations. Using oligoadenylate chains up to ten residues in length as a model, we have determined the dependence of the radial distribution functions and its second moments 〈RN2〉 and 〈SN2〉, the mean square end-to-end distance and radius of gyration respectively, on temperature, due to these stacking interactions. Assuming a helical geometry for stacked residues and different possible coil geometries corresponding to unstacked residues, we find that when stacking is present at low temperatures, the chains are severely non-Gaussian for N ≤ 10, while at high temperatures where stacking interactions diminish, chains are substantially Gaussian for N ≥ 5 residues. Distribution functions for chains with termini constrained to fixed distances have been estimated, in order to permit evaluation of the probability for loop closure of different kinds in short chains. The results are in reasonable agreement with experimental values for short hairpin RNA structures, and predict enthalpic contributions arising from stacking interactions in the process of forming loops from small chains.

Original languageEnglish (US)
Pages (from-to)2766-2776
Number of pages11
JournalThe Journal of chemical physics
Volume62
Issue number7
StatePublished - 1975

Fingerprint

ribonucleic acids
Statistics
statistics
RNA
Distribution functions
Geometry
Temperature
distribution functions
gyration
interactions
geometry
radial distribution
closures
coils
moments
radii
evaluation

ASJC Scopus subject areas

  • Atomic and Molecular Physics, and Optics

Cite this

Rubin, H., & Kallenbach, N. R. (1975). Conformational statistics of short RNA chains. The Journal of chemical physics, 62(7), 2766-2776.

Conformational statistics of short RNA chains. / Rubin, H.; Kallenbach, N. R.

In: The Journal of chemical physics, Vol. 62, No. 7, 1975, p. 2766-2776.

Research output: Contribution to journalArticle

Rubin, H & Kallenbach, NR 1975, 'Conformational statistics of short RNA chains', The Journal of chemical physics, vol. 62, no. 7, pp. 2766-2776.
Rubin, H. ; Kallenbach, N. R. / Conformational statistics of short RNA chains. In: The Journal of chemical physics. 1975 ; Vol. 62, No. 7. pp. 2766-2776.
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