Fred G. Heineken
CBET Division of Chemical, Bioengineering, Environmental, and Transport Systems
ENG Directorate for Engineering
Start Date:
September 1, 2003
Expires:
August 31, 2008 (Estimated)
Awarded Amount to Date:
$1400000
Investigator(s):
Ronald Larson rlarson@umich.edu (Principal Investigator)
Mark Burns (Co-Principal Investigator) Stella Pang (Co-Principal Investigator) David Burke (Co-Principal Investigator)
Sponsor:
University of Michigan Ann Arbor
3003 South State St.
Ann Arbor, MI 48109 734/764-1817
NSF Program(s):
BIOCHEMICAL & BIOMASS ENG
Field Application(s):
0308000 Industrial Technology
Program Reference Code(s):
BIOT, 9181, 1674
Program Element Code(s):
1402
ABSTRACT
0304316
Larson
This proposal was received in response to Nanoscale Science and Engineering initiative, NSF 02-148, category NIRT. The objective of this proposal is to design and build a microfabricated platform for study of DNA/protein interactions at the nano-scale. These interactions are at the heart of the cellular machinery for maintaining and transcribing DNA, and include transcription factors, as well as histones and other chromatin proteins. These DNA/protein interactions are under active study at the cellular level, but the next steps towards a detailed understanding of them require their study at smaller length scales, including the nanoscale. Therefore, a microfabricated devise will be built, which contains a main channel of length 20 to 30 microns and of width ranging from 20 nm to 2 microns. Individual DNA molecules will be stretched in the channel and positioned using high frequency electric fields, and anchored at gold electrodes using thiol groups chemically attached to the ends of the DNA molecules. This long, very thin, channel will be joined to thin side channels for addition of DNA-interacting proteins locally to specific regions of the DNA molecule. The proteins will be further localized by use of capture electrodes as well as hydrodynamic focusing using flow through other side streams, and other confinement methods. The channels will be etched in silicon, and bonded to a thin glass substrate, to permit examination by optical microscopy. The broader impacts of the proposal include the integration of the proposed research with the introduction of a new Nanoscale Science and Engineering (NSE) curriculum for graduate students. The new course will focus on nano- fabrication issues related to integration of electronic function with microfluidics and transport issues related to the processing of biological samples.
PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH
3. J. H. Kim, V. R. Dukkipati, S. W. Pang, and R. G. Larson. "Stretching and Immobilization of DNA for Studies of DNA-Protein Interactions at the Single-Molecule Level," Nanoscale Research Letters, v.2, 2007, p. 185.
Dukkipati, VR; Pang, SW. "Precise DNA placement and stretching in electrode gaps using electric fields in a microfluidic system," APPLIED PHYSICS LETTERS, v.90, 2007.
Dukkipati, VR; Pang, SW. "Integration of electrodes in Si channels using low temperature polymethylmethacrylate bonding," JOURNAL OF VACUUM SCIENCE & TECHNOLOGY B, v.25, 2007, p. 368-372.
J.H. Kim and R.G. Larson. "Single-molecule analysis of 1D diffusion and transcription elongation of T7 RNA polymerase
along individual stretched DNA molecules," Nucleic Acids Research, v.35, 2007, p. 1.
J.H. Kim, W.X. Shi, and R.G. Larson. "Methods of Stretching DNA Molecules Using Flow Fields," Langmuir, v.23, 2007, p. 755.
Pal, R; Sung, KE; Burns, MA. "Microstencils for the patterning of nontraditional materials," LANGMUIR, v.22, 2006, p. 5392-5397.
Rhee, M; Burns, MA. "Nanopore sequencing technology: nanopore preparations," TRENDS IN BIOTECHNOLOGY, v.25, 2007, p. 174-181.
Sung, KE; Burns, MA. "Optimization of dielectrophoretic DNA stretching in microfabricated devices," ANALYTICAL CHEMISTRY, v.78, 2006, p. 2939-2947.
V. Dukkipati and S. W. Pang,. "Integration of Electrodes in Si Channels using Low Temperature PMMA Bonding," J. Vac. Sci. Technol. B, v.25, 2007, p. 368.
V. Dukkipati, J.H. Kim, S.W. Pang, and R.G. Larson. "Protein-assisted stretching and immobilization of DNA molecules in a microchannel," Nano Letters, v.6, 2006, p. 2499.
W.X. Shi and R.G. Larson. "Atomic force microscopic study of aggregation of RecA-DNA nucleoprotein filaments into
left-handed supercoiled bundles," Nano Letters, v.5, 2006, p. 2476.
W.X. Shi and R.G. Larson. "RecA-ssDNA filaments supercoil in the presence of single-stranded DNA-binding protein," Biochemical and Biophysical Research Communications, v.357, 2007, p. 755.
