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

Nucleic Acids Research
Thayaparan ParamanathanMark C Williams

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 du...Continue Reading

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Citations

Mar 22, 2014·Physical Chemistry Chemical Physics : PCCP·Kamilla NorregaardLene B Oddershede
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Jun 3, 2021·International Journal of Molecular Sciences·Alejandro Ogazon Del ToroArturo Ponce

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Methods Mentioned

BETA
optical tweezers
force measurements
force measurement

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