Experimental and theoretical studies of the effects of deoxyribose substitutions on the stability of the UUCG tetraloop

D. Jeremy Williams, Kathleen B. Hall

Research output: Contribution to journalArticle

35 Scopus citations

Abstract

Experimental and theoretical thermodynamic studies of the consequences of 2'-hydroxyl substitution in the RNA UUCG tetraloop show distinct position dependence consistent with the diverse structural contexts of the four-loop ribose hydroxyls in this motif. The results suggest that even for simple substitutions, such as the replacement of the ribose hydroxyl (2'-OH) with hydrogen (2'-H), the free energy change reflects a complex interplay of hydrogen bonding and solvation effects and is influenced by the intrinsic pucker preferences of the nucleotides. Furthermore, theoretical studies suggest that the effect of these mutations in the single-strand state is sequence dependent, in contrast to what is commonly assumed. Free energy perturbation simulations of ribose-deoxyribose mutations in a single-strand dodecamer and in trinucleotide models suggest that in the denatured state, the magnitude of the free energy change for deoxyribose substitutions is determined to a larger extent by the identity of the nucleotide (A, C, G or U) rather than its structural context. Single-strand mutational effects must be considered when interpreting mutational studies in molecular terms. (C) 2000 Academic Press.

Original languageEnglish
Pages (from-to)251-265
Number of pages15
JournalJournal of Molecular Biology
Volume297
Issue number1
DOIs
StatePublished - Mar 17 2000

Keywords

  • Free energy perturbation
  • RNA
  • Ribose substitutions

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