title: Detection of local protein structures along DNA using solid-state nanopores.
abstract: Nanopores have been successfully employed as a new tool to rapidly detect single biopolymers, in particular DNA. When a molecule is driven through a nanopore by an externally applied electric field, it causes a characteristic temporary change in the trans-pore current. Here, we examine the translocation of DNA with discrete patches of the DNA-repair protein RecA attached along its length. Using the fact that RecA-coated DNA and bare DNA yield very different current-blockade signatures, we demonstrate that it is possible to map the locations of the proteins along the length of a single molecule using a solid-state nanopore. This is achieved at high speed and without any staining. We currently obtain a spatial resolution of about 8 nm, or 5 RecA proteins binding to 15 base pairs of DNA, and we discuss possible extensions to single protein resolution. The results are a crucial first step toward genomic screening, as they demonstrate the feasibility of reading off information along DNA at high resolution with a solid-state nanopore.
authors.affiliation: Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, Delft, The Netherlands.
authors.forename: Stefan W
authors.initials: SW
authors.lastname: Kowalczyk
authors.forename: Adam R
authors.initials: AR
authors.lastname: Hall
authors.forename: Cees
authors.initials: C
authors.lastname: Dekker
mesh_terms: D004247:DNA / Q000737:chemistry*; D004563:Electrochemistry / Q000379:methods; D018625:Microscopy, Atomic Force / Q000379:methods; D046529:Microscopy, Electron, Transmission; D049329:Nanostructures / Q000737:chemistry*; D036103:Nanotechnology / Q000379:methods*; D009690:Nucleic Acid Conformation; D010100:Oxygen / Q000737:chemistry; D011108:Polymers / Q000737:chemistry; D016062:Porosity; D011938:Rec A Recombinases / Q000737:chemistry; D013499:Surface Properties
chemical_list: D011108:Polymers; D004247:DNA; D011938:Rec A Recombinases; D010100:Oxygen