8R6H
A quadruplex-duplex hybrid with a three-layered hybrid-2 G-quadruplex topology complexed with Phen-DC3
Summary for 8R6H
| Entry DOI | 10.2210/pdb8r6h/pdb |
| NMR Information | BMRB: 34882 |
| Descriptor | DNA (34-MER), N2,N9-bis(1-methylquinolin-3-yl)-1,10-phenanthroline-2,9-dicarboxamide (2 entities in total) |
| Functional Keywords | (3+1) hybrid, dna, intercalation, phen-dc3, quadruplex-duplex hybrid |
| Biological source | synthetic construct |
| Total number of polymer chains | 1 |
| Total formula weight | 10939.25 |
| Authors | Vianney, Y.M.,Weisz, K. (deposition date: 2023-11-22, release date: 2024-03-06, Last modification date: 2024-07-10) |
| Primary citation | Vianney, Y.M.,Dierks, D.,Weisz, K. Structural Differences at Quadruplex-Duplex Interfaces Enable Ligand-Induced Topological Transitions. Adv Sci, 11:e2309891-e2309891, 2024 Cited by PubMed Abstract: Quadruplex-duplex (QD) junctions, which represent unique structural motifs of both biological and technological significance, have been shown to constitute high-affinity binding sites for various ligands. A QD hybrid construct based on a human telomeric sequence, which harbors a duplex stem-loop in place of a short lateral loop, is structurally characterized by NMR. It folds into two major species with a (3+1) hybrid and a chair-type (2+2) antiparallel quadruplex domain coexisting in a K buffer solution. The antiparallel species is stabilized by an unusual capping structure involving a thymine and protonated adenine base AH of the lateral loop facing the hairpin duplex to form a T·AH·G·C quartet with the interfacial G·C base pair at neutral pH. Addition and binding of Phen-DC to the QD hybrid mixture by its partial intercalation at corresponding QD junctions leads to a topological transition with exclusive formation of the (3+1) hybrid fold. In agreement with the available experimental data, such an unprecedented discrimination of QD junctions by a ligand can be rationalized following an induced fit mechanism. PubMed: 38477454DOI: 10.1002/advs.202309891 PDB entries with the same primary citation |
| Experimental method | SOLUTION NMR |
Structure validation
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