Structure of a DNA-porphyrin complex

  • Lipscomb L
  • Zhou F
  • Presnell S
 et al. 
  • 46

    Readers

    Mendeley users who have this article in their library.
  • 203

    Citations

    Citations of this article.

Abstract

We report the 2.4 Angstrom resolution X-ray structure of a complex in which a small molecule flips a base out of a DNA helical stack, The small molecule is a metalloporphyrin, CuTMPyP4 [copper(II) meso-tetra(N-methyl-4-pyridyl)porphyrin] and the DNA is a hexamer duplex, [d(CGATCG)]2. The porphyrin system, with the copper atom near the helical axis, is located within the helical stack, The porphyrin binds by normal intercalation between the C and G of 5' TCG 3' and by extruding the C of 5' CGA 3'. The DNA forms a distorted right-handed helix with only four normal cross-strand Watson-Crick base pairs, Two pyridyl rings are located in each groove of the DNA, The complex appears to be extensively stabilized by electrostatic interactions between positively charged nitrogen atoms of the pyridyl rings and negatively charged phosphate oxygen atoms of the DNA. Favorable electrostatic interactions appear to draw the porphyrin into the duplex interior, offsetting unfavorable steric clashes between the pyridyl rings and the DNA backbone. These pyridyl-backbone clashes extend the DNA along its axis and preclude formation of van der Waals stacking contacts in the interior of the complex, Stacking contacts are the primary contributor to stability of DNA. The unusual lack of van der Waals stacking contacts in the porphyrin complex destabilizes the DNA duplex and decreases the energetic cost of local melting. Thus extrusion of a base appears to be facilitated by pyridyl-DNA steric clashes.

Get free article suggestions today

Mendeley saves you time finding and organizing research

Sign up here
Already have an account ?Sign in

Find this document

Authors

  • Leigh Ann Lipscomb

  • Fang Xiao Zhou

  • Steven R. Presnell

  • Rebecca J. Woo

  • Mary E. Peek

  • R. Richard Plaskon

Cite this document

Choose a citation style from the tabs below

Save time finding and organizing research with Mendeley

Sign up for free