INTELLECTUAL MERIT: This research program will explore the interface between hard and soft matter where charged biomolecules are confined to ultra-small, electrostatically actuated, aqueous environments. Success in this effort will add an important new dimension to ?lab-on-a-chip? devices that have the potential to revolutionize medical diagnostics. Nanofluidic structures will directly apply controllable electrostatic forces to a single, charged biomolecule as follows. A negatively charged DNA molecule that is confined to a nanofluidic channel whose width is comparable to the Debye length will be subjected to forces generated by surface potential gradients. By locally tuning the surface potential using gate electrodes, a potential energy landscape will be created that traps DNA at a local minimum. Individual molecules will thereby be confined and manipulated within purely electrostatic walls. The distinct scientific facets of this objective will be addressed through fundamental studies of: (1) the modulation of the electrostatic forces in ionic solution by gated materials, and (2) the conformational and dynamical response of individual DNA polymers to applied electrostatic forces in well-defined, nanofluidic structures. The resulting insight will guide the development of the envisioned ?electro-fluidic? technology. An electrostatically-actuated gate for the manipulation of a single molecule will be demonstrated. The long-term vision of this work includes the integration of electrostatic gates for testing single-molecule dynamics, and to realize ultra-small bioreactors capable of localizing a single enzymatic reaction, such as DNA transcription. The use of gates to selectively control the contents of a silicon-based, artificial cell should also enable experiments in ?bottom-up? biology, in which the biochemical functionality of the cell can be incrementally enhanced.
BROADER IMPACTS: The technology under development in this project not only provides a route to new information about the role of electrostatics in governing the behavior of single polyelectrolyte molecules, it has the potential to provide new control mechanisms for nano-fluidic devices. The project also provides an excellent platform for training of graduate and undergraduate students across the domains of physics, chemistry, biology, and materials science. The PI regularly includes undergraduate students in his research team and is a participant in campus-wide programs that aim to increase the diversity of the scientific workforce. In particular, he is engaged with the Leadership Alliance Program, which seeks to increase participation of underrepresented groups in graduate level programs at leading research institutions, and with the Women in Science and Engineering (WiSE) program, which has served as a channel for attracting female students to join his research group.
NSF award DMR-0805176 enabled our group to develop powerful new methods for controlling the shape and motion of individual DNA molecules in nanofluidic devices. We refer to our methods as "free energy landscaping" because they control the driving force behind DNA’s behavior, which is the free energy landscape. We created nanofluidic devices with an embedded nanotopography – basically a pattern of nano-scale pits inside an otherwise featureless fluidic slit only 100nm high. The topography controls the entropy (a measure of disorder) of DNA, which is one part of its free energy. A nanopit increases the entropy of a polymer like DNA because the extra space there offers more ways for the molecule to configure itself. Consequently, nanopits tend to pin a polymer in place. We studied how DNA navigates arrays of nanopits when carried in an applied fluid flow by collecting and analyzing videos of individual, fluorescently stained DNA molecules. We also developed theoretical models that explain the behavior of DNA in nanofluidic devices with patterned topographies. Finally to demonstrate the technological utility of free energy landscaping, we created a device that funnels long DNA molecules into traps where they adopt the shapes of letters. The ability guide single DNA molecules into traps where they can be studied in detail opens up exciting new possibilities for DNA analysis applications. We also created nanofluidic devices that control DNA by harnessing the nanofluidic version of the field-effect. A negatively charged DNA molecule feels electrostatic forces when it approaches the charged walls of a confining nanoslit. Those electrical forces can be controlled using embedded electrodes that tune the amount of charge at the surface of the nanoslit. In more technical terms, this "electro-fluidic" technology controls the enthalpic part of the free energy of DNA. We created "nanopore transistors," devices featuring a tiny hole in an otherwise insulating membrane that separates two baths of salt water. The voltage-driven current of ions through the nanopore could be controlled by the charge on an annular "gate electrode" (a term borrowed from conventional semiconductor transistors) surrounding the nanopore. Our experimental and theoretical research resulted in a quantitative understanding of how the nanofluidic field-effect works and how it can be harnessed to control the motion of ions or even DNA molecules through the nanopore. The outcomes of this project make a broad impact by advancing "lab-on-a-chip" biomedical technology through the development of new ways to control the shape and motion of single molecules. In particular, field-effect control adds a potent new dimension to fluidic devices, and can leverage integrated circuit technology. Lastly, this NSF project enabled PI Stein to engage students and teachers from the Providence Public School District in science. At the 2010 and 2011 Vartan Gregorian Elementary School Science Conferences, the PI discussed the impact that nanotechnology could make on biology and medicine in the future. Students could easily appreciate the idea of studying single molecules thanks to video data from the funded research, which contrasted single DNA molecules thrashing about due to Brownian motion with molecules that organized themselves into regular shapes inside nanofluidic devices. The PI’s laboratory also hosted two high school science teachers, who both worked on nanofluidics and presented their results at the Brown Summer Research Conference. This Project Outcomes Report for the General Public is displayed verbatim as submitted by the Principal Investigator (PI) for this award. Any opinions, findings, and conclusions or recommendations expressed in this Report are those of the PI and do not necessarily reflect the views of the National Science Foundation; NSF has not approved or endorsed its content.
