DNA intercalation optimized by two-step molecular lock mechanism.

Ali A Almaqwashi,Ioulia Rouzina,Mark C Williams,Johanna Andersson,Per Lincoln,Fredrik Westerlund

doi:10.1038/srep37993

Abstract

The diverse properties of DNA intercalators, varying in affinity and kinetics over several orders of magnitude, provide a wide range of applications for DNA-ligand assemblies. Unconventional intercalation mechanisms may exhibit high affinity and slow kinetics, properties desired for potential therapeutics. We used single-molecule force spectroscopy to probe the free energy landscape for an unconventional intercalator that binds DNA through a novel two-step mechanism in which the intermediate and final states bind DNA through the same mono-intercalating moiety. During this process, DNA undergoes significant structural rearrangements, first lengthening before relaxing to a shorter DNA-ligand complex in the intermediate state to form a molecular lock. To reach the final bound state, the molecular length must increase again as the ligand threads between disrupted DNA base pairs. This unusual binding mechanism results in an unprecedented optimized combination of high DNA binding affinity and slow kinetics, suggesting a new paradigm for rational design of DNA intercalators.

Highlights

DNA intercalation represents an invasive, yet reversible, mode of DNA-ligand binding
In this work we introduce a new mechanism of DNA intercalation, where the intercalating moiety is converted from a fast assembling conventional intercalative state to a slow assembling final intercalative state
The quantified dynamic DNA deformations show that two-step intercalation exhibits a molecular lock mechanism, in which equilibrium DNA deformation in the final state is less than the dynamic DNA deformation that is required for the full DNA-ligand assembly process

Summary

Introduction

DNA intercalation represents an invasive, yet reversible, mode of DNA-ligand binding. It shows clusters of two different types of ligands. We used dual-beam optical tweezers to conduct single-molecule force spectroscopy experiments using a force clamp, allowing us to fully characterize the affinity, kinetics, and the governing structural dynamics of this unique intercalating system We found that this ligand possesses the highest DNA binding affinity measured with this method, combined with one of the slowest dissociation rates from the final intercalative state (Fig. 1A)

Methods

Results

Conclusion