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DNA intercalation optimized by two-step molecular lock mechanism
Northeastern Univ, Dept Phys, Boston, MA 02115 USA.;King Abdulaziz Univ, Dept Phys, Rabigh 21911, Saudi Arabia..
Uppsala University, Disciplinary Domain of Science and Technology, Chemistry, Department of Chemistry - BMC. Chalmers, Dept Chem & Chem Engn, SE-41296 Gothenburg, Sweden..
Chalmers, Dept Chem & Chem Engn, SE-41296 Gothenburg, Sweden..
Ohio State Univ, Dept Chem & Biochem, Columbus, OH 43210 USA..
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2016 (English)In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 6, article id 37993Article in journal (Refereed) Published
Abstract [en]

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.

Place, publisher, year, edition, pages
2016. Vol. 6, article id 37993
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:uu:diva-312040DOI: 10.1038/srep37993ISI: 000389182900001PubMedID: 27917863OAI: oai:DiVA.org:uu-312040DiVA, id: diva2:1062368
Funder
NIH (National Institute of Health), GM072462Swedish Foundation for Strategic Research Swedish Research Council
Available from: 2017-01-05 Created: 2017-01-04 Last updated: 2017-11-29Bibliographically approved

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