PDBsum entry 201d

DNA

PDB id

201d

Contents

			DNA/RNA

References listed in PDB file

Key reference

Title

Solution structure of the oxytricha telomeric repeat d[g4(t4g4)3] g-Tetraplex.

Authors

Y.Wang, D.J.Patel.

Ref.

J Mol Biol, 1995, 251, 76-94. [DOI no: 10.1006/jmbi.1995.0417]

PubMed id

7643391

Note In the PDB file this reference is annotated as "TO BE PUBLISHED". The citation details given above were identified by an automated search of PubMed on title and author names, giving a perfect match.

Abstract

The solution structure of Oxytricha telomere sequence d[G4(T4G4)3] in 0.1 M Na+ containing solution has been determined using a combined NMR-molecular dynamics approach including relaxation matrix refinement. This four G4 repeat sequence folds intramolecularly into a right-handed G-tetraplex containing four stacked G-tetrads which are connected by two lateral T4 loops and a central diagonal T4 loop. The guanine glycosidic bonds adopt a syn-anti alternation along the full length of the d[G4(T4G4)3] sequence while the orientation around adjacent G-tetrads switches between syn.syn.anti.anti and anti.anti.syn.syn alignments. Four distinct grooves are formed by the parallel (two of medium width) and anti-parallel (one wide and one narrow width) alignment of adjacent G-G-G-G segments in the G-tetraplex. The T4 residues in the diagonal loop are well-defined while the T4 residues in both lateral loops are under-defined and sample multiple conformations. The solution structure of the Na(+)-stabilized Oxytricha d[G4(T4G4)3] G-tetraplex and an earlier solution structure reported from our laboratory on the Na(+)-stabilized human d[AG3(T2AG3)3] G-tetraplex exhibit a common folding topology defined by the same syn/anti distribution of guanine residues along individual strands and around individual G-tetrads, as well as a common central diagonal loop which defines the strand directionalities. The well-resolved proton NMR spectra associated with the d[G4(T4G4)3] G-tetraplex opens the opportunity for studies ranging from cation-dependent characterization of G-tetraplex conformation and hydration to ligand and protein recognition of the distinct grooves associated with this folding topology.



	Figure 6. Figure 6. Stereo views of the six relaxation matrix refined structures of the d[G4 (T4G4 )3 ] G-tetraplex. The G1-G2-G3-G4, G9-G10-G11-G12-T13-T14, T15-T16-G17-G18-G19-G20 and G25-G26-G27-G28 segments are shown in green, magenta, cyan and yellow, respectively. The loop residues that are under-defined are depicted only by their backbone and are shown in white. (A) View normal to the helix axis looking into the medium groove formed by the G9 to G12 (magenta) and G25 to G28 (yellow) segments aligned in parallel. (B) View looking down the helix axis showing only the G-tetrad segments.		Figure 10. Figure 10. Stereo views of the T13-T14-T15-T16 loop linked diagonally to the G1·G17·G28·G12 G-tetrad in the representative relaxation matrix refined structure of the d[G4 (T4G4)3] G-tetraplex. The G-tetrad is shown in yellow, residues T13andT14 in magentaand residues T15andT16 in cyan. Backbones for all residues are shown in white with the phosphate oxygen atoms deleted for clarity. (A) View normal to the helix axis emphasizing that the base planes of T13 and T15 are approximately parallel with the base plane of the G-tetrad and the G12, T13, T14 and T16 residues form approximately a continuous stack. (B) View down the helix axis emphasizing the stacking patterns of T13 on G12 and T15 on G1.

	Headers