Free Energy Landscaping for Single-Molecule Biophysics

Brown University, Providence RI

Investigators

Abstract

Non-technical: This award by the Biomaterials program in the Division of Materials Research to Brown University is cofunded by the Instrument Development for Biological Research program in the Division of Biological Infrastructure (BIO). This award will study "Lab-on-a-chip" technology in improving healthcare by making biomedical tests smaller, cheaper, and faster. The ultimate limit would be tests on single molecules. This project aims to take an important step in that direction by developing powerful ways of controlling the shape and the motion of single DNA molecules. With this award, techniques will be developed that require nanofluidic device "channels with dimensions only tens to hundreds of nanometers across" because they can exploit physical concepts that only apply at that scale. For instance, a fluidic device with nanoscale topographic features inside it, like nanotrenches, harnesses the entropy of a DNA molecule to guide its motion or even contort it into predetermined shapes. Entropy is a measure of the multitude of microscopically different shapes a polymer can adopt. It is also possible to manipulate a DNA molecule electrostatically, using a nanofluidic version of the field effect upon which transistors are based. The experiments in this project will advance our fundamental understanding of nanofluidics and polymer physics. This project will also apply control over single DNA molecules to obtain overlapping restriction maps of a single molecule, which can increase the throughput of long-range sequence information that complements next-generation genomic sequencing data. This interdisciplinary project will prepare graduate and undergraduate students for careers in a rapidly growing area of the high-technology economy. Furthermore, the videos collected of single DNA molecules being controlled one by one will be used in the classroom at Brown University and in the nearby public elementary schools. Technical: This award is to develop new methods in controlling the configurations and the transport of single DNA molecules inside nanofluidic devices. The proposed methods rely on influencing the free energy landscape for a nanoconfined polyelectrolyte. This researcher will investigate how a series of trenches embedded within a nanoslit governs the configurational entropy of a polymer through the reduction of the number of configurations available in shallow regions as compared with deeper regions. The investigator will also explore how the charged inner surfaces of a device influence the enthalpy of a confined molecule through Coulomb forces, which can be locally tuned using electrodes. These new modalities of control should enable fundamental studies on single DNA molecules and new bio-analytical applications. Stochastic resonance and noise-assisted transport of DNA will be studied in a synthetic, bumpy free energy landscape. A similar device will be used to create overlapping restriction maps of the same DNA molecule by performing multiple restriction digests, sequentially, on the molecule as it is trapped and stretched in a long nanotrench. This project will advance "lab-on-a-chip" applications, provide excellent training opportunities for graduate and undergraduate students, and will support outreach activities to local public schools.