In cells, RNA polymerase (RNAP) must transcribe supercoiled DNA, whose torsional state is constantly changing, but how RNAP deals with DNA supercoiling remains elusive. We report direct measurements of individual Escherichia coli RNAPs as they transcribed supercoiled DNA. We found that a resisting torque slowed RNAP and increased its pause frequency and duration.

The phase diagram of Sr3Ru2O7 shows hallmarks of strong electron correlations despite the modest Coulomb interaction in the Ru 4d shell. We use angle-resolved photoelectron spectroscopy measurements to provide microscopic insight into the formation of the strongly renormalized heavy d-electron liquid that controls the physics of Sr 3Ru2O7. Our data reveal itinerant Ru 4d-states confined over large parts of the Brillouin zone to an energy range of <6 meV, nearly three orders of magnitude lower than the bare band width.

We design and demonstrate electrically controlled optical trapping of individual microparticles and manipulation of biomolecules with nm-scale precision for high throughput applications. This has been realized by integration of photonics, fluidics, and electronics, on-chip. © 2013 The Optical Society.

Methods for exerting and measuring forces on single molecules have revolutionized the study of the physics of biology. However, it is often the case that biological processes involve rotation or torque generation, and these parameters have been more difficult to access experimentally. Recent advances in the single-molecule field have led to the development of techniques that add the capability of torque measurement. By combining force, displacement, torque, and rotational data, a more comprehensive description of the mechanics of a biomolecule can be achieved.

Single-molecule techniques reveal short- and long-range dynamics of supercoiled DNA.

A vital element in integrated optofluidics is dynamic tuning and precise control of photonic devices, especially when employing electronic techniques which are challenging to utilize in an aqueous environment. We overcome this challenge by introducing a new platform in which the photonic device is controlled using electro-optical phase tuning. The phase tuning is generated by the thermo-optic effect using an on-chip electric microheater located outside the fluidic channel, and is transmitted to the optofluidic device through optical waveguides.

We design and demonstrate electrically-enabled optofluidic devices for tuning and reconfiguring lab-on-chip photonic elements in silicon platforms. Optofluidic resonators integrated with electric microheaters for resonance tuning are demonstrated. © OSA 2012.

As the fundamental packing units of DNA in eukaryotes, nucleosomes play a central role in governing DNA accessibility in a variety of cellular processes. Our understanding of the mechanisms underlying this complex regulation has been aided by unique structural and dynamic perspectives offered by single molecule techniques.

DNA unzipping is a powerful tool to study protein-DNA interactions at the single-molecule level. In this chapter, we provide a detailed and practical guide to performing this technique with an optical trap, using nucleosome studies as an example. We detail protocols for preparing an unzipping template, constructing and calibrating the instrument, and acquiring, processing, and analyzing unzipping data. We also summarize major results from utilization of this technique for the studies of nucleosome structure, dynamics, positioning, and remodeling. © 2012 Elsevier Inc.

Helicases are vital enzymes that carry out strand separation of duplex nucleic acids during replication, repair and recombination 1,2. Bacteriophage T7 gene product 4 is a model hexameric helicase that has been observed to use dTTP, but not ATP, to unwind double-stranded (ds)DNA as it translocates from 5′ to 3′ along single-stranded (ss)DNA 2-6. Whether and how different subunits of the helicase coordinate their chemo-mechanical activities and DNA binding during translocation is still under debate 1,7.