Synthetic Nanopores: Enhancing Optofluidic Detection with Smart Gates

Nanoscopic openings in membranes have been used in single molecule analysis for some time. Typically, changes in ionic current through the pore that are caused by a particle that is moving through and obstructing the opening are detected.

This principle is shown in Fig. 1.

Initially, biological nanopores (a-hemolysin) were used to create blockade signals from single-stranded DNA molecules and have pointed a way towards rapid sequencing of DNA [1]. More recently, nanofabrication methods have been developed to place nanopores in inorganic materials, most commonly silicon nitride membranes [2]. The inherent advantages of artifical pores include robustness and flexibility in size etc.

We are working on integrating nanopores as "smart gates" in integrated optofluidic devices based on liquid-core ARROW waveguides. Fig. 2 shows a cartoon of where a nanopore can be placed on an optofluidic chip to selectively and sequentially introduce single nanoparticles into the optical waveguide channel. Also shown is a nanopore that we prepared and a size comparison with a ribosome (~25nm diameter) [3].

Our goals are to use functional nanotechnology to enhance the functionality of optofluidic devices. The combined use of electrical and optical detection methods with single molecule sensitivity will lead to improved devices for particle detection and studies of single molecules in molecular biology.

This work is funded by the National Institute of Health (NIH/NIBIB), the National Science Foundation (NSF), and the NASA University Affiliated Research Center. We collaborate with the co-inventor of nanopore technology, David Deamer(Biomolecular Engineering, UCSC), and the Nanofabrication Facility at UCSB.

[1] W. Vercoutere, S. Wintres-Hilt, H. Olsen, D. Deamer, D. Haussler, and M. Akeson. "Rapid discrimination among individual DNA hairpin molecules at single-nucleotide resolution using an ion channel", Nat. Biotechnol., 19, 248-252, (2001).

[2] J.Li, D. Stein, C. McMullan, D. Branton, M. J. Aziz, and J. Golovchenko. "Ion-beam sculpting at nanometer length scales", Nature, 412, 166-169, (2001).

[3] M.I. Rudenko, D. Yin, M. Holmes, A.R. Hawkins, and H. Schmidt, "Integration and characterization of SiN nanopores for single-molecule detection in liquid-core ARROW waveguides, Proc SPIE 2007, 6444:64440L.