Albany 2013: Book of Abstracts
June 11-15 2013
©Adenine Press (2012)
NMR based structure of berberine bound to parallel stranded DNA quadruplex d-(TTAGGGT)4 containing human telomeric repeat
Stabilization of G-quadruplex structure with quadruplex-interactive ligands leads to in vitro inhibition of telomerase, an enzyme expressed in many tumor cell lines and responsible for the de novo synthesis of telomeric DNA. The rational design of new therapeutic agents that bind to quadruplexes in a structure specific manner is of considerable interest. Berberine, an isoquinoline alkaloid from plants, is a planar molecule with an extended π-delocalized system having a partial positive charge. It has been shown that it binds to G-quadruplex selectively and inhibits telomerase activity. We present here studies on binding of berberine to parallel stranded d-(TTAGGGT)4 containing the human telomeric repeat by proton and phosphorus-31 nuclear magnetic resonance spectroscopy. The H10, H28, and H41,42,43 resonances of berberine are found to shift up field by 0.54, 0.33, and 0.49 ppm on binding to G-quadruplex at 298 K at drug to DNA quadruplex ratio of 1:1 while the nucleotide protons show much smaller up field shifts ~0.02 ppm. All sequential connectivities are observed and the base pairs are found to be intact in the complex. The central G-tetrad core too remains intact on interaction showing characteristic Hoogstein base pairing. Large downfield shifts in phosphorus-31 resonances expected on opening of base pairs are not observed at any base pair step. The inter molecular Nuclear Overhauser Enhancements (NOEs) indicate that H10, H41,42,43 are in close proximity of T1H6, T1H2’, T1H2” protons. The structure obtained from restrained molecular dynamics simulations using inter proton distance restraints shows that berberine binds externally to the quadruplex with no evidence of drug intercalation within the G-quadruplex.