Jeffrey Comer

Jeff in Vannes, France

Home Department: Physics

Office Address: Beckman Institute, Room 3023

Email Address: jcomer@ks.uiuc.edu

Education

  • BS with honors, Physics, The University of Akron, 2005

Research Interests

  • Bionanotechnology

Publications

  • "Stretching and unzipping of nucleic acid hairpins using a synthetic nanopore", Q. Zhao, J. Comer, V. Dimitrov, S. Yemenicioglu, A. Aksimentiev, G. Timp, Nucleic Acids Res. , 1-10 (2007).
  • "Detection of DNA sequences using an alternating electric field in a nanopore capacitor", G. Sigalov, J. Comer, G. Timp, A. Aksimentiev, Nano Lett. , (2007).
  • "High voltage SPM oxidation of ZrN: Materials for multiscale applications", N. Farkas, J.R. Comer, G. Zhang, E.A. Evans, R.D. Ramsier, and J.A. Dagata, Nanotechnology 16, 262-266 (2005).
  • "Parallel writing on zirconium nitride thin films by local oxidation nanolithography", N. Farkas, J.R. Comer, G. Zhang, E.A. Evans, R.D. Ramsier, S. Wight, and J.A. Dagata, Appl. Phys. Lett. 85 (23), 5691-5693 (2004).
  • "Chladni plates revisited", J.R. Comer, M.J. Shepard, P.N. Hendricksen, and R.D. Ramsier, Am. J. Phys. 72 (10), 1345-1350 (2004).
  • "Phosphate adsorption on metal oxide surfaces", M.J. Shepard, J.R. Comer, J.S. McNatt, R.D. Ramsier, T.L. Young, J. Rapp-Cross, M.P. Espe, T.R. Robinson, and L.Y. Nelson, Silanes and Other Coupling Agents, Volume 3, K.L. Mittal, Ed., VSP: Leiden, The Netherlands (2004).

Bionanotechnology Tutorial

Bionanotechnology Tutorial
required files

Hairpin movies

1.0 to 1.8 nm pore
A 11.2 ns simulation of a DNA hairpin pulled at 1.0 nm/ns through a conic pore with a bottom diameter of 1.0 nm and a top diameter of 1.8 nm. Note that the opening is too small for the helix and it unzips at the very top of the pore. The portion initially forming the single-stranded coil is shown in blue, while the two portions with complementary sequences, initially forming a double-stranded helix, are shown in yellow and red respectively. The bases of the loop are colored the same as the nearest complementary portion.

1.3 to 2.1 nm pore
A 7.8 ns simulation of a DNA hairpin pulled at 1.0 nm/ns through a conic pore with a bottom diameter of 1.3 nm and a top diameter of 2.1 nm. Here, the hairpin enters a few tenths of nanometers into the pore before unzipping. The portion initially forming the single-stranded coil is shown in blue, while the two portions with complementary sequences, initially forming a double-stranded helix, are shown in yellow and red respectively. The bases of the loop are colored the same as the nearest complementary portion.

1.4 to 2.2 nm pore
A 9.4 ns simulation of a DNA hairpin pulled at 1.0 nm/ns through a conic pore with a bottom diameter of 1.4 nm and a top diameter of 2.2 nm. Note that the double-stranded portion stretches as it moves into the pore, but hydrogen bonds between the bases do not break until this portion reaches the bottom of the pore. At this point, the bases begin to unzip. The portion initially forming the single-stranded coil is shown in blue, while the two portions with complementary sequences, initially forming a double-stranded helix, are shown in yellow and red respectively. The bases of the loop are colored the same as the nearest complementary portion.

1.6 to 2.4 nm pore
A 12.4 ns simulation of a DNA hairpin pulled at 1.0 nm/ns through a conic pore with a bottom diameter of 1.6 nm and a top diameter of 2.4 nm. Because the walls of the pore constrain the molecule, the double-stranded portion does not unzip. Instead, the helix-coil transition proceeds by the stretching route. The portion initially forming the single-stranded coil is shown in blue, while the two portions with complementary sequences, initially forming a double-stranded helix, are shown in yellow and red respectively. The bases of the loop are colored the same as the nearest complementary portion.
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