Small worlds in RNA structures

Research output: Contribution to journalReview article

20 Scopus citations

Abstract

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.

Original languageEnglish (US)
Pages (from-to)1108-1117
Number of pages10
JournalNucleic acids research
Volume31
Issue number3
DOIs
StatePublished - Feb 1 2003

ASJC Scopus subject areas

  • Genetics

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