PDBsum entry 105d

DNA

PDB id: 105d

Contents

DNA/RNA

References listed in PDB file

Key reference

Title

Solution structures of the i-Motif tetramers of d(tcc), D(5methylcct) and d(t5methylcc): novel noe connections between amino protons and sugar protons.

Authors

J.L.Leroy, M.Guéron.

Ref.

Structure, 1995, 3, 101-120. [DOI no: 10.1016/S0969-2126(01)00138-1]

PubMed id

7743125

Abstract

BACKGROUND: At slightly acid or even neutral pH, oligodeoxynucleotides that include a stretch of cytidines form a tetramer structure in which two parallel-stranded duplexes have their hemi-protonated C.C+ base pairs face-to-face and fully intercalated, in a so-called i-motif, first observed serendipitously in [d(TC5)]4. RESULTS: A high-definition structure of [d(TCC)]4 was computed on the basis of inter-residue distances corresponding to 21 NOESY cross-peaks measured at short mixing times. A similarly defined structure of [d(5mCCT)]4 was also obtained. A small number of very characteristic (amino proton)-(sugar proton) cross-peaks entails the intercalation topology. The structure is generally similar to that of [d(TC5)]4. The sequence d(T5mCC) forms two tetramers in comparable proportions. The intercalation topologies are read off the two patterns of (amino proton)-(sugar proton) cross-peaks: one is the same as in the d(TCC) tetramer, the other has the intercalated strands shifted by one base, which avoids the steric hindrance between the methyl groups of the 5mC pairs of the two duplexes. CONCLUSIONS: The structures obtained in this work and the procedures introduced to characterize them and to solve the problems linked to the symmetry of the structure provide tools for further exploring the conditions required for formation of the i-motif.

Figure 10.
Figure 10. Stereoview, normal to the wide groove, of the lowest-energy conformer of [d(TCC)][4] . T1, green; C2, red; C3 yellow. Figure 10. Stereoview, normal to the wide groove, of the lowest-energy conformer of [d(TCC)][4] . T1, green; C2, red; C3 yellow.

Figure 11.
Figure 11. Views of the eight lowest-energy conformers of the d(TCC) tetramer. (a) View of the wide groove. (b) View of the narrow groove. Colour coding as in Figure 10. Figure 11. Views of the eight lowest-energy conformers of the d(TCC) tetramer. (a) View of the wide groove. (b) View of the narrow groove. Colour coding as in [3]Figure 10.

The above figures are reprinted by permission from Cell Press: Structure (1995, 3, 101-120) copyright 1995.