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1rme
From Proteopedia
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DNA (5'-D(5MCP*CP*TP*CP*C)-3') TETRAMER, NMR, 1 STRUCTURE
Overview
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 interconversion. The interconversion rate is 1.4 s-1 at 0 degree 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-1 at 0 degree C. At 32 degrees C, interconversion is fast on the NMR time scale.
About this Structure
1RME is a Protein complex structure of sequences from [1]. Full crystallographic information is available from OCA.
Reference
Structure and conversion kinetics of a bi-stable DNA i-motif: broken symmetry in the [d(5mCCTCC)]4 tetramer., Nonin S, Leroy JL, J Mol Biol. 1996 Aug 23;261(3):399-414. PMID:8780782
Page seeded by OCA on Sat Nov 24 22:55:39 2007
