Simultaneous and Different Binding Mechanisms of 4′,6-Diamidino-2-phenylindole to DNA Hexamer (d(CGATCG))2

Abstract

The solution structure of the complex between 4', 6-diamidino-2-phenylindole (DAPI) and DNA oligomer (d(CGATCG))2 at a 2:1 drug/duplex ratio has been characterized by combined use of proton one- and two-dimensional NMR spectroscopy, molecular mechanics, and molecular dynamics computations. Intermolecular nuclear Overhauser effects (NOEs), DNA structure perturbations, and resonance shifts induced by binding provide evidence that DAPI interacts with DNA hexamer by two different binding mechanisms, in fast exchange on the NMR time scale, without any significant distortion of the B-type conformation of DNA hexamer. The results indicate that the ligand binds into the minor groove of the central 5'-ATC-3' region of the hexamer and on the outside of the oligomer by a pi,pi-stacking interaction with the terminal C1:G6 base pairs. A model for both binding mechanisms that accounts for all experimental data was generated by molecular mechanics and dynamics calculations based on experimental NOEs. In the minor groove binding, N2 amino group of G2 precludes a deep insertion of phenyl ring of DAPI into the groove. Position and orientation of the drug in the external stacking interaction resemble those suggested for intercalation of DAPI between C:G base pairs.

Dicationic DNA Minor Groove Binders as Antimicrobial Agents

“…DAPI binds in the minor groove of DNA at AT sites [70]. A second, weaker binding interaction has been ascribed to intercalation at GC sites [71][72][73][74]. An alternate explanation for the weaker binding interaction has been offered [75], however NMR studies clearly indicate intercalation at GC sites [73,74].…”

“…A second, weaker binding interaction has been ascribed to intercalation at GC sites [71][72][73][74]. An alternate explanation for the weaker binding interaction has been offered [75], however NMR studies clearly indicate intercalation at GC sites [73,74]. X-ray structures have been reported for complexes between DAPI and two different oligomers, both of which contain AATT-binding sites [76,77].…”

DAPI binding to the DNA minor groove: a continuum solvent analysis

“…However, the observed contacts cannot easily be translated into energetic contributions to binding and interpretation of thermodynamic results is therefore difficult. For this reason there has been some controversy with regard to the relative contribution of electrostatic, hydrogen-bonding and steric interactions to binding affinity and sequence specificity (Vlieghe et al, 1999;Trotta et al, 1996). In addition, the contribution of small, ligand-induced DNA conformational changes to binding affinity and specificity cannot be straightforwardly extracted from structural and biochemical studies alone.…”

Application of the RISM Method to Estimate the Relative Gibbs Free Energies of 4',6-Diamidino-2-phenylindole Binding Within the Minor Groove of a DNA Along Simulation Trajectory

“…Это сайт AATT в последовательности d(CGCGAATTCGCG)2 [18] и сайт ATTG в додекамере d(GGCCAATTGG)2 [19]. Так как DAPI обычно связывается с AT-богатой последовательностью в малом желобе, где стесненное окружение стабилизирует связывание [18,20,21], а с GC-богатой последовательностью предпочитает взаимодействовать в большом желобе [22][23][24], можно было бы ожидать, что в додекамере d(GGCCAATTGG)2 он будет локализован именно на AATT последовательности. Однако в эксперименте показано, что DAPI специфично взаимодействует с последовательностью ATTG в додекамере d(GGCCAATTGG)2 [19].…”