title: Bacteriophage strain typing by rapid single molecule analysis.
abstract: Rapid characterization of unknown biological samples is under the focus of many current studies. Here we report a method for screening of biological samples by optical mapping of their DNA. We use a novel, one-step chemo-enzymatic reaction to covalently bind fluorophores to DNA at the four-base recognition sites of a DNA methyltransferase. Due to the diffraction limit of light, the dense distribution of labels results in a continuous fluorescent signal along the DNA. The amplitude modulations (AM) of the fluorescence intensity along the stretched DNA molecules exhibit a unique molecular fingerprint that can be used for identification. We show that this labelling scheme is highly informative, allowing accurate genotyping. We demonstrate the method by labelling the genomes of λ and T7 bacteriophages, resulting in a consistent, unique AM profile for each genome. These profiles are also successfully used for identification of the phages from a background phage library. Our method may provide a facile route for screening and typing of various organisms and has potential applications in metagenomics studies of various ecosystems.
authors.affiliation: Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel.
authors.forename: Assaf
authors.initials: A
authors.lastname: Grunwald
authors.affiliation: Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel.
authors.forename: Moran
authors.initials: M
authors.lastname: Dahan
authors.affiliation: Institute of Organic Chemistry, RWTH Aachen University, Aachen D-52056 Germany.
authors.forename: Anna
authors.initials: A
authors.lastname: Giesbertz
authors.affiliation: Department of Astronomy and Theoretical Physics, Lund University, Lund 223 62, Sweden.
authors.forename: Adam
authors.initials: A
authors.lastname: Nilsson
authors.affiliation: Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg 412 96, Sweden.
authors.forename: Lena K
authors.initials: LK
authors.lastname: Nyberg
authors.affiliation: Institute of Organic Chemistry, RWTH Aachen University, Aachen D-52056 Germany.
authors.forename: Elmar
authors.initials: E
authors.lastname: Weinhold
authors.affiliation: Department of Astronomy and Theoretical Physics, Lund University, Lund 223 62, Sweden.
authors.forename: Tobias
authors.initials: T
authors.lastname: Ambjörnsson
authors.affiliation: Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg 412 96, Sweden.
authors.forename: Fredrik
authors.initials: F
authors.lastname: Westerlund
authors.affiliation: Raymond and Beverly Sackler Faculty of Exact Sciences, School of Chemistry, Tel Aviv University, Tel Aviv 6997801, Israel uv@post.tau.ac.il.
authors.forename: Yuval
authors.initials: Y
authors.lastname: Ebenstein
mesh_terms: D001434:Bacteriophage Typing / Q000379:methods*; D001435:Bacteriophages / Q000145:classification / Q000235:genetics; D058893:DNA Barcoding, Taxonomic; D005456:Fluorescent Dyes; D016679:Genome, Viral; D058889:Molecular Typing / Q000379:methods; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific)
chemical_list: D005456:Fluorescent Dyes; C059680:DNA modification methylase TaqI; D015265:Site-Specific DNA-Methyltransferase (Adenine-Specific)