Electrostatic factors in DNA intercalation

C Medhi, John Blayney Owen Mitchell, S L Price, A B Tabor

Research output: Contribution to journalArticlepeer-review

61 Citations (Scopus)

Abstract

The factors that determine the binding of a chromophore between the base pairs in DNA intercalation complexes are dissected The electrostatic potential in the intercalation plane is calculated using an accurate ab initio based distributed multipole electrostatic model for a range of intercalation sires, involving different sequences of base pairs and relative rn isl angles. There will be a significant electrostatic contribution to the binding energy for chromophores with a predominantly positive electrostatic potential, but this varies significantly with sequence, and somewhat with twist angle. The usefulness of these potential maps for understanding the binding of intercalators is explored by calculating the electrostatic Binding energy for 9-aminoacridine, ethidium, and daunomycin in a variety of model binding sites. The electrostatic forces play a major role in the positioning of an intercalating 9-aminoacridine and a significant stabilizing rob in the binding of ethidium in its sterically constrained position, but the intercalation of daunomycin is determined by the side-chain binding. Sequence preferences are likely to be determined by a complex and subtle mixture of effects, with electrostatics being just one component. The electrostatic binding energy is also unlikely to be a major determinant of the twist angle, as its variation with angle is modest for most intercalation sires. Overall the electrostatic potential maps give guidance on how positively charged chromophores can be chemically adapted by heteroatomic substitution to optimise their binding. (C) 2000 John Wiley & Sons, Inc.

Original languageEnglish
Pages (from-to)84-93
Number of pages10
JournalBiopolymers
Volume52
Issue number2
Publication statusPublished - 1999

Keywords

  • DNA intercalation
  • electrostatic energy
  • distributed multipole analysis
  • 9-aminoacridine
  • ethidium
  • DOUBLE-STRANDED POLYNUCLEOTIDES
  • DISTRIBUTED MULTIPOLE ANALYSIS
  • NUCLEIC ACID INTERACTIONS
  • SEQUENCE SPECIFICITY
  • ETHIDIUM-BROMIDE
  • BASE-PAIRS
  • BINDING AFFINITIES
  • ATOMIC RESOLUTION
  • AQUEOUS-SOLUTION
  • AB-INITIO

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