Jae-Seok Yu†§, Min-Cheol Lim ‡§, Duyen Thi Ngoc Huynh ‡, Hyung-Jun Kim †, Hyun-Mi Kim †, Young-Rok Kim *‡, and Ki-Bum Kim *†
† Department of Materials Science and Engineering, Seoul National University, Seoul 151-742, Korea
‡ Graduate School of Biotechnology and Department of Food Science and Biotechnology, Kyung Hee University, Yongin 446-701, Korea
§J.Y. and M.L. contributed equally to this work.
*Address correspondence to Young-Rok Kim, Ki-Bum Kim
Solid-state nanopore has been widely studied as an effective tool to detect and analyze small biomolecules, such as DNA, RNA, and proteins, at a single molecule level. In this study, we demonstrate a rapid identification of the location of zinc finger protein (ZFP), which is bound to a specific locus along the length of a double-stranded DNA (dsDNA) to a single protein resolution using a low noise solid-state nanopore. When ZFP labeled DNAs were driven through a nanopore by an externally applied electric field, characteristic ionic current signals arising from the passage of the DNA/ZFP complex and bare DNA were detected, which enabled us to identify the locations of ZFP binding site. We examined two DNAs with ZFP binding sites at different positions and found that the location of the additional current drop derived from the DNA/ZFP complex is well-matched with a theoretical one along the length of the DNA molecule. These results suggest that the protein binding site on DNA can be mapped or that genetic information can be read at a single molecule level using solid-state nanopores.
Keywords: nanopore; zinc finger protein; DNA; single molecule; DNA binding protein