1i9k

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THE RNA I-MOTIF

Overview

Oligodeoxynucleotides with stretches of cytidine residues associate into a, four-stranded structure, the i-motif, in which two head-to-tail, intercalated, parallel-stranded duplexes are held together by, hemiprotonated C.C+ pairs. We have investigated the possibility of forming, an i-motif structure with C-rich ribonucleic acids. The four C-rich RNAs, studied, r(UC5), r(C5), r(C5U) and r(UC3), associate into multiple, intercalated structures at acidic pH. r(UC5) forms two i-motif structures, that differ by their intercalation topologies. We report on a structural, study of the main form and we analyze the small conformational differences, found by comparison with the DNA i-motif. The stacking topology of the, main structure avoids one of the six 2'-OH/2'-OH repulsive contacts, expected in a fully intercalated structure. The C3'-endo pucker of the RNA, sugars and the orientation of the intercalated C.C+ pairs result in a, modest widening of the narrow grooves at the steps where the hydroxyl, groups are in close contact. The free energy of the RNA i-motif, on, average -4 kJ mol(-1) per C.C+ pair, is half of the value found in DNA, i-motif structures.

About this Structure

1I9K is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.

Reference

The RNA i-motif., Snoussi K, Nonin-Lecomte S, Leroy JL, J Mol Biol. 2001 May 25;309(1):139-53. PMID:11491284

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