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Nucleic Acids Research, 2003, Vol. 31, No. 3 1108-1117
© 2003 Oxford University Press

Small worlds in RNA structures

Stefan Wuchty*

Department of Physics, 225 Nieuwland Science Hall, University of Notre Dame, IN 45665, USA

*Tel: +1 574 631 3368; Fax: +1 574 631 5952; Email: swuchty{at}nd.edu

I consider conformational spaces of tRNAphe defined by sets of suboptimal structures from the perspective of small-world networks. Herein, the influence of modifications on typical small-world network properties and the shape of energy landscapes is discussed. Results indicate that natural modifications influence the degree of local clustering and mean path lengths far more than random or no modifications. High frequencies in the thermodynamic ensemble coincide with high numbers of neighboring structures that one conformation can adopt by one elementary move. Conformation spaces indicate the existence of modular substructures. It can be shown that modifications leave the nature of small-world topology untouched albeit natural modifications have a reasonable enhancing and streamlining effect on the degree of clustering and therefore on the substructures of the conformational space.


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