Structure and Conversion Kinetics of a Bi-stable DNA i-motif: Broken Symmetry in the [d(5mCCTCC)]4 Tetramer
Résumé
At slightly acidic pH, protonation of C-rich oligomers results in the formation of a four-stranded structure composed of two parallel duplexes in a head to tail orientation with their hemi-protonated C·C+pairs intercalated in a so-called i-motif. In all cases reported previously the duplexes are identical.
The tetramer formed by the d(5mCCTCC) oligomer is different. The structure is computed on the basis of 55 inter-residue distances derived from NOESY cross-peaks measured at short mixing times. It consists of two intercalated non-equivalent symmetrical duplexes. The base stacking order is C5* C1 C4* C2 (T3*) T3 C2* C4 C1* C5, but the thymidine bases (T3*) of one duplex are looped out and lie in the wide grooves of the tetramer. The thymidine bases T3 stack as a symmetrical T·T pair between the sequentially adjacent C2·C2+pair and the C2*·C2*+pair of the other duplex.
Numerous exchange cross-peaks provide evidence for duplex intercon version. The interconversion rate is 1.4 s−1at 0°C and the activation energy is 94 kJ/mol.
The opening of the T3·T3 pair, the closing of the T3*·T3 pair, and the opening of the C2*·C2*+pair occur simultaneously with the duplex interconversion. This suggests that the concerted opening and closing of the thymidine bases drive the duplex interconversion. Opening of the C4·C4+and C4*·C4*+pairs, and dissociation of the tetramer are not part of the interconversion since they occur at much slower rates. Duplex interconversion within the [d(5mCCTCC)]4 tetramer provides the first structural and kinetics characterization of broken symmetry in a biopolymer.
The tetramer formed by d(5mCCUCC) adopts a similar structure, but the rate of duplex interconversion is faster: 40 s−1at 0°C. At 32°C, interconversion is fast on the NMR time scale.
Domaines
Biologie structurale [q-bio.BM]
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