1RME

DNA (5'-D(MCYP*CP*TP*CP*C)-3') tetramer, NMR, 1 structure

Summary for 1RME

• Entry DOI: 10.2210/pdb1rme/pdb
• Descriptor: DNA (5'-D(*(MCY)P*CP*TP*CP*C)-3') (1 entity in total)
• Functional Keywords: deoxyribonucleic acid, i-motif, tetramer, dna
• Biological source: synthetic construct
• Total number of polymer chains: 4
• Total formula weight: 5400.04

Authors

Nonin, S.,Leroy, J.-L. (deposition date: 1996-07-12, release date: 1997-01-11, Last modification date: 2024-05-01)

Primary citation

Nonin, S.,Leroy, J.L.
Structure and conversion kinetics of a bi-stable DNA i-motif: broken symmetry in the [d(5mCCTCC)]4 tetramer.
J.Mol.Biol., 261:399-414, 1996

PubMed Abstract: 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.

PubMed: 8780782
DOI: 10.1006/jmbi.1996.0472

Experimental method

SOLUTION NMR