1I9K

THE RNA I-MOTIF

Summary for 1I9K

• Entry DOI: 10.2210/pdb1i9k/pdb
• Descriptor: 5'-R(*UP*CP*CP*CP*CP*C)-3' (1 entity in total)
• Functional Keywords: rna, i-motif
• Total number of polymer chains: 4
• Total formula weight: 7148.47

Authors

Snoussi, K.,Nonin-Lecomte, S.,Lerou, J.L. (deposition date: 2001-03-20, release date: 2001-05-30, Last modification date: 2024-05-22)

Primary citation

Snoussi, K.,Nonin-Lecomte, S.,Leroy, J.L.
The RNA i-motif.
J.Mol.Biol., 309:139-153, 2001

PubMed Abstract: 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.

PubMed: 11491284
DOI: 10.1006/jmbi.2001.4618

Experimental method

SOLUTION NMR