T·T Pair Intercalation and Duplex Interconversion Within i-Motif Tetramers

Abstract

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(5mCCTC nTCC)] 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/T M 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 T M 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/T M 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.