The RNA i-motif.
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.
Snoussi
K
K
Groupe de Biophysique de l' Ecole Polytechnique et de l'UMR 7643 du CNRS, Palasieau, France.
Nonin-Lecomte
S
S
Leroy
J L
JL
D020029:Base Pairing; D001483:Base Sequence; D003596:Cytosine / Q000378:metabolism; D004247:DNA / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D006801:Humans; D006860:Hydrogen Bonding; D008958:Models, Molecular; D009038:Motion; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D009843:Oligoribonucleotides / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D011522:Protons; D012313:RNA / Q000737:chemistry* / Q000235:genetics* / Q000378:metabolism; D020871:RNA Stability; D055672:Static Electricity; D016615:Telomere / Q000235:genetics; D013816:Thermodynamics
D009843:Oligoribonucleotides; D011522:Protons; D012313:RNA; D003596:Cytosine; D004247:DNA