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

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.

journal_name

J Mol Biol

journal_title

Journal of molecular biology

authors

Williams DJ,Hall KB

doi

10.1006/jmbi.2000.3547

keywords:

subject

Has Abstract

pub_date

2000-03-17 00:00:00

pages

251-65

issue

1

eissn

0022-2836

issn

1089-8638

pii

S0022-2836(00)93547-2

journal_volume

297

pub_type

杂志文章

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