Acta Phys. -Chim. Sin. ›› 2008, Vol. 24 ›› Issue (10): 1917-1921.doi: 10.3866/PKU.WHXB20081031

• Note • Previous Articles     Next Articles

DNA Minor Groove Binding by Diamidine:Water Molecule in Ligand Recognition

MA Guo-Zheng; QIU Ya-Fang; NAN Jun-Min; XIAO Xin   

  1. School of Chemistry &Environment, South China Normal University, Guangzhou 510006, P. R. China
  • Received:2008-06-09 Revised:2008-07-10 Published:2008-10-08
  • Contact: MA Guo-Zheng

Abstract: Molecular dynamics simulations were used to investigate the interaction of DB921 with the DNA oligonucleotide d[CGCGAATTCGCG]2. A 7 ns MD calculation was performed to study the DB921-DNA complex and the results indicated that DB921 was inserted in the minor groove of DNA, binding to the region of duplex AATTC bases. A water molecule forms bifurcated pair of H-bonds between the N atom of benzimidazole ring and N3 atom of the adenine 5 in the DB921-DNA complex. This water molecule performs a key bridging role which induces a more favorable curvature configuration and matches well the DNA minor groove topology. Molecular dynamics studies complemented the structural analysis and offered a clear picture of the water-bridge, providing the theoretical guidance for the design of biologically active minor groove agents.

Key words: Minor grove binding, Diamidine, Water molecule, Molecular recognition


  • O641