NIRT: A Nanometer-Scale Gene Chip

University Of Illinois At Urbana-Champaign, Urbana IL

Investigators

Abstract

Timp, Gregory CCR-0210843 This proposal was received in response to the Nanoscale Science and Engineering initiative, NSF 01-157, category NIRT. As research in nanotechnology extends its tools for miniaturization and integration to nanometer dimensions (the scale of the secondary structure in a protein or a DNA molecule), new vistas in biology and information science are revealed, which require new multi-disciplinary approaches to both research and education. One new question that emerges is: Can biology be directly integrated with electronics to provide information on physiology? Nature has provided an electrical interface between biology and the environment through ion channels that can now be mimicked using nanotechnology. The main objective of this project is to develop a revolutionary type of silicon integrated circuit that incorporates Metal-Oxide-Semiconductor technology with an on-chip nanopore mechanism for probing the electrical activity of DNA molecules. Ultimately, this biosensor might enable fast, inexpensive characterization of the minimum volume of genetic material, a single strand of DNA. A key constraint is to achieve the required sensitivity. To accomplish these goals, an artificial ion channel (AIC) or nanopore, will be used in conjunction with an amplifier built within one micron from the nanopore, in order to process high-frequency electrical signals occurring when single molecules diffuse through the channel. A membrane having an AIC will be immersed into a buffer solution, and DNA molecules will be pushed through the nanopore by the applied voltage bias a principle that has been tested in a number of recent experiments. Preliminary tests have already successfully demonstrated that ~2-nm diameter nanopores can be reproducibly etched through a ~2-5-nm-thick SiO2 membrane, using a high energy focused electron beam. High-quality, pinhole-free membranes are being used in these experiments. The project will develop artificial ion channels for ultrafast sequencing of single DNA strands. The AIC devices will also be applied for direct measurements of electronic transport properties of DNA molecules. This subject is important since the charge migration in DNA has been linked to the DNA ability to develop and repair defects while being exposed to ionizing radiation. Also, the desire of using single DNA molecules as building blocks for electronic circuits motivates the quest for understanding its transport properties. So far transport properties of DNA have been tested either indirectly or when the molecule is removed from the buffer solution and dried. The AIC device proposed here will be applied to measure directly the long-range charge transfer along DNA, while the molecule is kept in its natural environment in solution. The measurements will be compared with first-principle atomistic simulations. The objective is to understand basic mechanisms that control the charge transport in DNA this controversial topic continues to be strongly debated in the community.