NMR based structural studies decipher stacking of the alkaloid coralyne to terminal guanines at two different sites in parallel G-quadruplex DNA, [d(TTGGGGT)]4 and [d(TTAGGGT)]4.

ABSTRACT

BACKGROUND: Telomere elongation by telomerase gets inhibited by G-quadruplex DNA found in its guanine rich region. Stabilization of G-quadruplex DNA upon ligand binding has evolved as a promising strategy to target cancer cells in which telomerase is over expressed. METHODS: Interaction of anti-leukemic alkaloid, coralyne, to tetrameric parallel [d(TTGGGGT)]4 (Ttel7), [d(TTAGGGT)]4 (Htel7) and monomeric anti-parallel [dGGGG(TTGGGG)3] (Ttel22) G-quadruplex DNA has been studied using Circular Dichroism (CD) spectroscopy. Titrations of coralyne with Ttel7 and Htel7 were monitored by 1H and 31P NMR spectroscopy. Solution structure of coralyne-Ttel7 complex was obtained by restrained Molecular Dynamics (rMD) simulations using distance restraints from 2D NOESY spectra. Thermal stabilization of DNA was determined by absorption, CD and 1H NMR. RESULTS AND CONCLUSIONS: Binding of coralyne to Ttel7/Htel7 induces negative CD band at 315/300nm. A significant upfield shift in all GNH, downfield shift in T2/T7 base protons and upfield shift (1.8ppm) in coralyne protons indicates stacking interactions. 31P chemical shifts and NOE contacts of G3, G6, T2, T7 protons with methoxy protons reveal proximity of coralyne to T2pG3 and G6pT7 sites. Solution structure reveals stacking of coralyne at G6pT7 and T2pG3 steps with two methoxy groups of coralyne located in the grooves along with formation of a hydrogen bond. Binding stabilizes Ttel7/Htel7 by ~25-35°C in 21 coralyne-Ttel7/Htel7 complex. GENERAL SIGNIFICANCE: The present study is the first report on solution structure of coralyne-Ttel7 complex showing stacking of coralyne with terminal guanine tetrads leading to significant thermal stabilization, which may be responsible for telomerase inhibition.