This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Nanopores are small pores with nanometer-scale radii. They are found in nature, such as the proteinaceous alpha-hemolysin pore [1], but can also be artificially manufactured in silicon-based membranes [2] and polymer wafers [3]. When immersed in aqueous solution and with an applied voltage, nanopores can be used to study the translocation of charged species, such as ions or nucleic acids. There are many promising applications for nanopores;for instance, developing a DNA sequencing technique or building nanofluidic devices. The Resource is working in close collaboration with experimentalists (Gregory Timp UIUC, Zuzanna Siwy UCI) and theoreticians (Jean-Pierre Leburton UIUC, Thorsten Ritz UCI) to understand the physics of synthetic nanopores and improve their usability as sensors. Atomic-scale modeling was carried out in the following directions: (i) translocating DNA-protein complexes through nanopores;(ii) stretching/unzipping DNA hairpins with a nanopore;(iii) sensing DNA sequence with a nanopore capacitor and (iv) modeling of ion interactions inside nanopores.

Agency
National Institute of Health (NIH)
Institute
National Center for Research Resources (NCRR)
Type
Biotechnology Resource Grants (P41)
Project #
5P41RR005969-21
Application #
8172031
Study Section
Special Emphasis Panel (ZRG1-BCMB-E (40))
Project Start
2010-08-01
Project End
2011-07-31
Budget Start
2010-08-01
Budget End
2011-07-31
Support Year
21
Fiscal Year
2010
Total Cost
$50,236
Indirect Cost
Name
University of Illinois Urbana-Champaign
Department
Type
Organized Research Units
DUNS #
041544081
City
Champaign
State
IL
Country
United States
Zip Code
61820
Shim, Jiwook; Banerjee, Shouvik; Qiu, Hu et al. (2017) Detection of methylation on dsDNA using nanopores in a MoS2 membrane. Nanoscale 9:14836-14845
Wolfe, Aaron J; Si, Wei; Zhang, Zhengqi et al. (2017) Quantification of Membrane Protein-Detergent Complex Interactions. J Phys Chem B 121:10228-10241
Decker, Karl; Page, Martin; Aksimentiev, Aleksei (2017) Nanoscale Ion Pump Derived from a Biological Water Channel. J Phys Chem B 121:7899-7906
Radak, Brian K; Chipot, Christophe; Suh, Donghyuk et al. (2017) Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems. J Chem Theory Comput 13:5933-5944
Sun, Chang; Taguchi, Alexander T; Vermaas, Josh V et al. (2016) Q-Band Electron-Nuclear Double Resonance Reveals Out-of-Plane Hydrogen Bonds Stabilize an Anionic Ubisemiquinone in Cytochrome bo3 from Escherichia coli. Biochemistry 55:5714-5725
Belkin, Maxim; Aksimentiev, Aleksei (2016) Molecular Dynamics Simulation of DNA Capture and Transport in Heated Nanopores. ACS Appl Mater Interfaces 8:12599-608
Poudel, Kumud R; Dong, Yongming; Yu, Hang et al. (2016) A time course of orchestrated endophilin action in sensing, bending, and stabilizing curved membranes. Mol Biol Cell 27:2119-32
Vermaas, Josh V; Taguchi, Alexander T; Dikanov, Sergei A et al. (2015) Redox potential tuning through differential quinone binding in the photosynthetic reaction center of Rhodobacter sphaeroides. Biochemistry 54:2104-16
Belkin, Maxim; Chao, Shu-Han; Jonsson, Magnus P et al. (2015) Plasmonic Nanopores for Trapping, Controlling Displacement, and Sequencing of DNA. ACS Nano 9:10598-611
Shen, Rong; Han, Wei; Fiorin, Giacomo et al. (2015) Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments. PLoS Comput Biol 11:e1004368

Showing the most recent 10 out of 371 publications