Dynamics of Double-Stranded DNA in Confined GeometriesHelmut H. Strey, SUNY at Stony Brook University, DMR 1106044

How the confinement of biomolecules, such as DNA, at nanometer length scales affects their conformational dynamics is still not fully understood. Small channel devices for studying these dynamics have potential applications in genomic sequencing, single biomolecule manipulation, and separations based on topology. Understanding dynamics, such as threading and looping, is also relevant to living systems given the importance of DNA condensation and interaction with enzymes as part of many biological processes in vivo.

We have focused on multiple steps including the double end labeling of the DNA molecules with both fluorescent dyes and quantum dots, characterization of the molecules in solution, novel nanofabrication, and supported lipid bilayers. Characterization of double end labeled molecules in solution required refining the theory and analysis of fluorescence cross correlation spectroscopy.

Top Left: Comparison of different theoretical autocorrelation functions, Top Right: Fitted Experimental auto- and cross- correlation curves, Center/Bottom Left: SEM of straight nanoslits and nanochannels, Bottom Right: Fluorescence Microscopy of nanoslits run with fluorescent dye

• As part of his career development, Stony Brook University graduate student Tomasz Bakowski mentored a summer REU student, Christian Ruiz. He has also delivered two seminars on nanofabrication for two undergraduate classes.

• Christian Ruiz, a junior from City College of the City University of New York, worked on designing an improved defect-free supported lipid bilayer surfaces for studying DNA molecules adsorbed to a 2D surface. His work will complement and strengthen the overall project. He gained experience in several micro- and nano-fabrication techniques.

• We strengthened our collaboration with the nanofabrication and Soft and Biological Nano-materials groups at the Center for Functional Nanomaterials at Brookhaven National Labs.

Left: NSF REU Program in Nanotechnology Undergraduate Christian Ruiz learning techniques in the clean room

Bottom: From left to right, Graduate Student Tomasz Bakowski, REU Director Dr. Gary Halada, Dean of Graduate School, Dr. Charles Taber, Provost Dr. Dennis Assanis, Christian Ruiz

Dynamics of Double-Stranded DNA in Confined GeometriesHelmut H. Strey, SUNY at Stony Brook University, DMR 1106044