1Q2T

Solution structure of d(5mCCTCTCC)4

Summary for 1Q2T

• Entry DOI: 10.2210/pdb1q2t/pdb
• Related: 1RME
• Descriptor: 5'-D(*(MCY)P*CP*TP*CP*TP*CP*C)-3' (1 entity in total)
• Functional Keywords: dna solution structure; i-motif; protonated cytidine; hemiprotonated base-pairs, dna
• Total number of polymer chains: 4
• Total formula weight: 7773.54

Authors

Leroy, J.-L. (deposition date: 2003-07-26, release date: 2003-09-23, Last modification date: 2024-05-22)

Primary citation

Leroy, J.-L.
T.T pair intercalation and duplex inter-conversion within i-motif tetramers
J.Mol.Biol., 333:125-139, 2003

PubMed 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(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.

PubMed: 14516748
DOI: 10.1016/S0022-2836(03)00945-8

Experimental method

SOLUTION NMR