1q2t
From Proteopedia
|
Solution structure of d(5mCCTCTCC)4
Overview
The i-motif is a four-stranded structure built by intercalation in, head-to-tail orientation of two parallel duplexes associated by, hemi-protonated C.C(+) pairs. Using NMR methods, we investigated the, structure, the base-pair opening kinetics and the internal motions of, three i-motif tetramers: [d(5mCCTCnTCC)](4) (n=1, 2, 3). These tetramers, cannot accommodate the intercalation of two T.T pairs in face-to-face, orientation. They are built by intercalation of two symmetrical duplexes, whose contacting T3/TM thymidine bases (M=5, 6, 7) are either base-paired, or unstacked. The arrangement of the unstacked/paired thymidine bases of, the two T/T groups results in the formation of two different, conformations. One, fully symmetric, whose thymidine bases T3 and TM are, unstacked and base-paired respectively. The other is the asymmetric, assembly of two duplexes: one where both thymidine bases are unstacked and, the other with two T.T pairs. The proportion of the symmetric conformer, increases from a value beyond the detection threshold for n=1, to 19% for, n=2 and up to more than 95% for n=3. The exchange cross-peaks connecting, together the intercalated duplexes of [d(5mCCTCTCC)](4) and, [d(5mCCTCCTCC)](4) reveal a structural interconversion induced by the, simultaneous opening/closing of the contacting T3/TM thymidine bases. In, [d(5mCCTCCTCC)](4) the motion of the T3/T6 groups triggers the, interconversion of the symmetric and asymmetric conformations. In, [d(5mCCTCTCC)](4) the intercalated duplexes exchange their structures in, an apparently concerted motion, suggesting the simultaneous, opening/closing of two distant T3/T5* and T5/T3* switching groups. The, spectrum of [d(5mCCTCCCTCC)](4) is fully symmetric and, for this reason, its spectrum gives no indication for duplex interconversion. Nevertheless, the imino proton exchange kinetics argues for a switching motion of the, T3/T7 group. Duplex interconversion is not detectable in that case, due to, the tetramer symmetry. The origin of the structural conflict hindering the, intercalation of two T.T pairs into the i-motif is discussed.
About this Structure
1Q2T is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
T.T pair intercalation and duplex interconversion within i-motif tetramers., Leroy JL, J Mol Biol. 2003 Oct 10;333(1):125-39. PMID:14516748
Page seeded by OCA on Sun Nov 25 03:28:28 2007
