3R6R

Structure of the complex of an intramolecular human telomeric DNA with Berberine formed in K+ solution

Summary for 3R6R

• Entry DOI: 10.2210/pdb3r6r/pdb
• Descriptor: DNA (22-mer), POTASSIUM ION, BERBERINE, ... (4 entities in total)
• Functional Keywords: dna-drug complex, g-quadruplex, human telomeric dna, dna, dna-antibiotic complex, dna/antibiotic
• Total number of polymer chains: 1
• Total formula weight: 8407.14

Authors

Ferraroni, M.,Bazzicalupi, C.,Gratteri, P.,Bilia, A.R. (deposition date: 2011-03-22, release date: 2012-02-29, Last modification date: 2023-09-13)

Primary citation

Bazzicalupi, C.,Ferraroni, M.,Bilia, A.R.,Scheggi, F.,Gratteri, P.
The crystal structure of human telomeric DNA complexed with berberine: an interesting case of stacked ligand to G-tetrad ratio higher than 1:1.
Nucleic Acids Res., 41:632-638, 2013

PubMed Abstract: The first crystal structure of human telomeric DNA in complex with the natural alkaloid berberine, produced by different plant families and used in folk medicine for millennia, was solved by X-ray diffraction method. The G-quadruplex unit features all-parallel strands. The overall folding assumed by DNA is the same found in previously reported crystal structures. Similarly to previously reported structures the ligand molecules were found to be stacked onto the external 5' and 3'-end G-tetrads. However, the present crystal structure highlighted for the first time, the presence of two berberine molecules in the two binding sites, directly interacting with each tetrad. As a consequence, our structural data point out a 2:1 ligand to G-tetrad molar ratio, which has never been reported before in a telomeric intramolecular quadruplex structure.

PubMed: 23104378
DOI: 10.1093/nar/gks1001

Experimental method

X-RAY DIFFRACTION (2.4 Å)