Force spectroscopy reveals the DNA structural dynamics that govern the slow binding of Actinomycin D

Nucleic Acids Res. 2012 Jun;40(11):4925-32. doi: 10.1093/nar/gks069. Epub 2012 Feb 10.

Abstract

Actinomycin D (ActD) is a small molecule with strong antibiotic and anticancer activity. However, its biologically relevant DNA-binding mechanism has never been resolved, with some studies suggesting that the primary binding mode is intercalation, and others suggesting that single-stranded DNA binding is most important. To resolve this controversy, we develop a method to quantify ActD's equilibrium and kinetic DNA-binding properties as a function of stretching force applied to a single DNA molecule. We find that destabilization of double stranded DNA (dsDNA) by force exponentially facilitates the extremely slow ActD-dsDNA on and off rates, with a much stronger effect on association, resulting in overall enhancement of equilibrium ActD binding. While we find the preferred ActD-DNA-binding mode to be to two DNA strands, major duplex deformations appear to be a pre-requisite for ActD binding. These results provide quantitative support for a model in which the biologically active mode of ActD binding is to pre-melted dsDNA, as found in transcription bubbles. DNA in transcriptionally hyperactive cancer cells will therefore likely efficiently and rapidly bind low ActD concentrations (≈ 10 nM), essentially locking ActD within dsDNA due to its slow dissociation, blocking RNA synthesis and leading to cell death.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Anti-Bacterial Agents / chemistry*
  • Antibiotics, Antineoplastic / chemistry*
  • DNA / chemistry*
  • Dactinomycin / chemistry*
  • Kinetics
  • Models, Molecular
  • Optical Tweezers
  • Spectrum Analysis / methods

Substances

  • Anti-Bacterial Agents
  • Antibiotics, Antineoplastic
  • Dactinomycin
  • DNA