Single molecule research: When biology meets physics

Current Opinion in Structural Biology, 2002

Physics of Life …, 2010

Single molecule force spectroscopy is a powerful method that uses the mechanical properties of DNA to explore DNA interactions. Here we describe how DNA stretching experiments quantitatively characterize the DNA binding of small molecules and proteins. Small molecules exhibit diverse DNA binding modes, including binding into the major and minor grooves and intercalation between base pairs of double-stranded DNA (dsDNA). Histones bind and package dsDNA, while other nuclear proteins such as high mobility group proteins bind to the backbone and bend dsDNA. Single-stranded DNA (ssDNA) binding proteins slide along dsDNA to locate and stabilize ssDNA during replication. Other proteins exhibit binding to both dsDNA and ssDNA. Nucleic acid chaperone proteins can switch rapidly between dsDNA and ssDNA binding modes, while DNA polymerases bind both forms of DNA with high affinity at distinct binding sites at the replication fork. Single molecule force measurements quantitatively characterize these DNA binding mechanisms, elucidating small molecule interactions and protein function.

Nature, 2003

The basic features of DNA were elucidated during the halfcentury following the discovery of the double helix. But it is only during the past decade that researchers have been able to manipulate single molecules of DNA to make direct measurements of its mechanical properties. These studies have illuminated the nature of interactions between DNA and proteins, the constraints within which the cellular machinery operates, and the forces created by DNA-dependent motors.

Protein Interactions, 2012

Single Molecules, 2000

Structural and functional properties of double stranded deoxyribonucleic acid (dsDNA) are investigated by atomic force microscopy (AFM) on a single molecule level. Here, we characterize different linear and circular DNA systems in terms of their geometry and topology, and visualize enzyme binding of restriction endonuclease Hae III to DNA. Manipulation of single DNA molecules is demonstrated by dissecting individual DNA strands. Furthermore, the elastic response of single DNA molecules to an externally applied force is investigated by AFM force spectroscopy experiments. This gives information about structural properties of the DNA double helix. Specifically, transition from B-form to S-form DNA and a melting transition from double stranded to single stranded DNA is observed. This allows monitoring of specific interaction and binding of small intercalator molecules such as ethidium bromide (EtBr) to DNA by means of a mechanical, non-fluorescent detection scheme.

Physics Today, 2001

By monitoring the response of individual protein and DNA molecules to pulling and twisting, biophysicists can learn much about their structure and their interactions.

Current Opinion in Structural Biology, 2000

During the past decade, physical techniques such as optical tweezers and atomic force microscopy were used to study the mechanical properties of DNA at the single-molecule level. Knowledge of DNA’s stretching and twisting properties now permits these single-molecule techniques to be used in the study of biological processes such as DNA replication and transcription.

Angewandte Chemie International Edition, 2008

Angewandte Chemie International Edition, 2013