The ends of a large RNA molecule are necessarily close.

ABSTRACT: We show on general theoretical grounds that the two ends of single-stranded (ss) RNA molecules (consisting of roughly equal proportions of A, C, G and U) are necessarily close together, largely independent of their length and sequence. This is demonstrated to be a direct consequence of two generic properties of the equilibrium secondary structures, namely that the average proportion of bases in pairs is ∼60% and that the average duplex length is ∼4. Based on mfold and Vienna computations on large numbers of ssRNAs of various lengths (1000-10 000 nt) and sequences (both random and biological), we find that the 5'-3' distance-defined as the sum of H-bond and covalent (ss) links separating the ends of the RNA chain-is small, averaging 15-20 for each set of viral sequences tested. For random s

SUBMITTER: Yoffe AM 

PROVIDER: S-EPMC3017586 | biostudies-literature | 2011 Jan

REPOSITORIES: biostudies-literature