High density single-molecule-bead arrays for parallel single molecule force spectroscopy

Parallelized DNA tethered bead measurements to scrutinize DNA mechanical structure

Tethering beads to DNA offers a panel of single molecule techniques for the refined analysis of the conformational dynamics of DNA and the elucidation of the mechanisms of enzyme activity. Recent developments include the massive parallelization of these techniques achieved by the fabrication of dedicated nanoarrays by soft nanolithography. We focus here on two of these techniques: the Tethered Particle motion and Magnetic Tweezers allowing analysis of the behavior of individual DNA molecules in the absence of force and under the application of a force and/or a torque, respectively. We introduce the experimental protocols for the parallelization and discuss the benefits already gained, and to come, for these single molecule investigations.

Microarrays and single molecules: an exciting combination

Biomolecules positioned at interfaces have spawned many applications in bioanalysis, biophysics, and cell biology. This Highlight describes recent developments in the research areas of protein and DNA arrays, and single-molecule sensing. We cover the ultrasensitive scanning of conventional microarrays as well as the generation of arrays composed of individual molecules. The combination of these tools has improved the detection limits and the dynamic range of microarray analysis, helped develop powerful single-molecule sequencing approaches, and offered biophysical examination with high throughput and molecular detail. The topic of this Highlight integrates several disciplines and is written for interested chemists, biophysicists and nanotechnologists.

Progress toward the application of molecular force spectroscopy to DNA sequencing

Many recent advances in DNA sequencing have taken advantage of single-molecule techniques using fluorescently labeled oligonucleotides as the principal mode of detection. However, in spite of the successes of fluorescent-based sequencers, avoidance of labeled nucleotides could substantially reduce the costs of sequencing. This article discusses the development of an alternative sequencing method in which unlabeled DNA can be manipulated directly on a massively parallel scale using single-molecule force spectroscopy. We combine a wide-field optical detection technique (evanescent field excitation) with one of two methods of applying force in parallel, magnetic or dielectrophoretic tweezers, to attain near single-base sensitivity in the double-stranded character of DNA. This article will discuss the developments of such a single-molecule force spectroscopy technique as a potential technology for genome sequencing.

Unraveling protein-protein interactions in clathrin assemblies via atomic force spectroscopy

Atomic force microscopy (AFM), single molecule force spectroscopy (SMFS), and single particle force spectroscopy (SPFS) are used to characterize intermolecular interactions and domain structures of clathrin triskelia and clathrin-coated vesicles (CCVs). The latter are involved in receptor-mediated endocytosis (RME) and other trafficking pathways. Here, we subject individual triskelia, bovine-brain CCVs, and reconstituted clathrin-AP180 coats to AFM-SMFS and AFM-SPFS pulling experiments and apply novel analytics to extract force-extension relations from very large data sets. The spectroscopic fingerprints of these samples differ markedly, providing important new information about the mechanism of CCV uncoating. For individual triskelia, SMFS reveals a series of events associated with heavy chain alpha-helix hairpin unfolding, as well as cooperative unraveling of several hairpin domains. SPFS of clathrin assemblies exposes weaker clathrin-clathrin interactions that are indicative of inter-leg association essential for RME and intracellular trafficking. Clathrin-AP180 coats are energetically easier to unravel than the coats of CCVs, with a non-trivial dependence on force-loading rate.