Quantifying force-dependent and zero-force DNA intercalation by single-molecule stretching

Ioana D. Vladescu, Micah J. McCauley, Megan E. Nuñez, Ioulia Rouzina, Mark C. Williams

Research output: Contribution to journalArticlepeer-review

107 Scopus citations


We used single DNA molecule stretching to investigate DNA intercalation by ethidium and three ruthenium complexes. By measuring ligand-induced DNA elongation at different ligand concentrations, we determined the binding constant and site size as a function of force. Both quantities depend strongly on force and, in the limit of zero force, converge to the known bulk solution values, when available. This approach allowed us to distinguish the intercalative mode of ligand binding from other binding modes and allowed characterization of intercalation with binding constants ranging over almost six orders of magnitude, including ligands that do not intercalate under experimentally accessible solution conditions. As ligand concentration increased, the DNA stretching curves saturated at the maximum amount of ligand intercalation. The results showed that the applied force partially relieves normal intercalation constraints. We also characterized the flexibility of intercalator-saturated dsDNA for the first time.

Original languageEnglish (US)
Pages (from-to)517-522
Number of pages6
JournalNature Methods
Issue number6
StatePublished - Jun 2007

Bibliographical note

Funding Information:
We acknowledge funding from the US National Science Foundation (MCB0238190), US National Institutes of Health (GM072462) and American Chemical Society Petroleum Research Fund.

Copyright 2008 Elsevier B.V., All rights reserved.


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