Mechanisms of DNA binding determined in optical tweezers experiments

Abstract

The last decade has seen rapid development in single molecule manipulation of RNA and DNA. Measuring the response force for a particular manipulation has allowed the free energies of various nucleic acid structures and configurations to be determined. Optical tweezers represent a class of single molecule experiments that allows the energies and structural dynamics of DNA to be probed up to and beyond the transition from the double helix to its melted single strands. These experiments are capable of high force resolution over a wide dynamic range. Additionally, these investigations may be compared with results obtained when the nucleic acids are in the presence of proteins or other binding ligands. These ligands may bind into the major or minor groove of the double helix, intercalate between bases or associate with an already melted single strand of DNA. By varying solution conditions and the pulling dynamics, energetic and dynamic information may be deduced about the mechanisms of binding to nucleic acids, providing insight into the function of proteins and the utility of drug treatments. © 2006 Wiley Periodicals, Inc. Biopolymers 85:154–168, 2007.This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com

Biological consequences of tightly bent DNA: The other life of a macromolecular celebrity

“…In these cells, chromosomal DNA is packed in a hierarchical structure. At the lowest level in the hierarchy (and our prime concern here), DNA is wrapped in 147 base pair segments roughly 1 3 4 times around a protein complex (the histone octamer) to form a structure known as the nucleosome as shown in Figure 4.…”

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Nanofluidic structures for single biomolecule fluorescent detection

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Honey, I shrunk the DNA: DNA length as a probe for nucleic‐acid enzyme activity

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