2KAZ

Folding topology of a bimolecular DNA quadruplex containing a stable mini-hairpin motif within the connecting loop

Summary for 2KAZ

• Entry DOI: 10.2210/pdb2kaz/pdb
• Descriptor: 5'-D(*DGP*DGP*DGP*DAP*DCP*DGP*DTP*DAP*DGP*DTP*DGP*DGP*DG)-3', POTASSIUM ION (2 entities in total)
• Functional Keywords: bimolecular dna quadruplex, dna hairpins, dna, quadruplex
• Total number of polymer chains: 2
• Total formula weight: 8303.53

Authors

Balkwill, G.D.,Garner, T.P.,Williams, H.E.L.,Searle, M.S. (deposition date: 2008-11-18, release date: 2008-12-16, Last modification date: 2024-05-01)

Primary citation

Balkwill, G.D.,Garner, T.P.,Williams, H.E.,Searle, M.S.
Folding topology of a bimolecular DNA quadruplex containing a stable mini-hairpin motif within the diagonal loop
J.Mol.Biol., 385:1600-1615, 2009

PubMed Abstract: We describe the NMR structural characterisation of a bimolecular anti-parallel DNA quadruplex d(G(3)ACGTAGTG(3))(2) containing an autonomously stable mini-hairpin motif inserted within the diagonal loop. A folding topology is identified that is different from that observed for the analogous d(G(3)T(4)G(3))(2) dimer with the two structures differing in the relative orientation of the diagonal loops. This appears to reflect specific base stacking interactions at the quadruplex-duplex interface that are not present in the structure with the T(4)-loop sequence. A truncated version of the bimolecular quadruplex d(G(2)ACGTAGTG(2))(2), with only two core G-tetrads, is less stable and forms a heterogeneous mixture of three 2-fold symmetric quadruplexes with different loop arrangements. We demonstrate that the nature of the loop sequence, its ability to form autonomously stable structure, the relative stabilities of the hairpin loop and core quadruplex, and the ability to form favourable stacking interactions between these two motifs are important factors in controlling DNA G-quadruplex topology.

PubMed: 19070621
DOI: 10.1016/j.jmb.2008.11.050

Experimental method

SOLUTION NMR