title: Imaging chromatin nanostructure with binding-activated localization microscopy based on DNA structure fluctuations.
abstract: Advanced light microscopy is an important tool for nanostructure analysis of chromatin. In this report we present a general concept for Single Molecule localization Microscopy (SMLM) super-resolved imaging of DNA-binding dyes based on modifying the properties of DNA and the dye. By careful adjustment of the chemical environment leading to local, reversible DNA melting and hybridization control over the fluorescence signal of the DNA-binding dye molecules can be introduced. We postulate a transient binding as the basis for our variation of binding-activated localization microscopy (BALM). We demonstrate that several intercalating and minor-groove binding DNA dyes can be used to register (optically isolate) only a few DNA-binding dye signals at a time. To highlight this DNA structure fluctuation-assisted BALM (fBALM), we applied it to measure, for the first time, nanoscale differences in nuclear architecture in model ischemia with an anticipated structural resolution of approximately 50 nm. Our data suggest that this approach may open an avenue for the enhanced microscopic analysis of chromatin nano-architecture and hence the microscopic analysis of nuclear structure aberrations occurring in various pathological conditions. It may also become possible to analyse nuclear nanostructure differences in different cell types, stages of development or environmental stress conditions.
authors.affiliation: Institute of Molecular Biology, 55128 Mainz, Germany.
authors.forename: Aleksander
authors.initials: A
authors.lastname: Szczurek
authors.affiliation: University of Manitoba, Cancer Care Manitoba, Winnipeg R3E 0V9, Canada.
authors.forename: Ludger
authors.initials: L
authors.lastname: Klewes
authors.affiliation: Institute of Molecular Biology, 55128 Mainz, Germany.
authors.forename: Jun
authors.initials: J
authors.lastname: Xing
authors.affiliation: Institute of Molecular Biology, 55128 Mainz, Germany.|Physics Department University Mainz (JGU), 55128 Mainz, Germany.
authors.forename: Amine
authors.initials: A
authors.lastname: Gourram
authors.affiliation: Institute of Molecular Biology, 55128 Mainz, Germany.|Physics Department University Mainz (JGU), 55128 Mainz, Germany.
authors.forename: Udo
authors.initials: U
authors.lastname: Birk
authors.affiliation: Département de Médecine, CHUS, Université de Sherbrooke, 3001-12e Avenue Nord, Sherbrooke, Québec J1H 5N4, Canada.|Department of Medicine, Jewish General Hospital, McGill University, 3755 Côte-Ste-Catherine Road, Montreal, Québec H3T 1E2, Canada.
authors.forename: Hans
authors.initials: H
authors.lastname: Knecht
authors.affiliation: Department of Cell Biophysics, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland.
authors.forename: Jurek W
authors.initials: JW
authors.lastname: Dobrucki
authors.affiliation: University of Manitoba, Cancer Care Manitoba, Winnipeg R3E 0V9, Canada.
authors.forename: Sabine
authors.initials: S
authors.lastname: Mai
authors.affiliation: Institute of Molecular Biology, 55128 Mainz, Germany.|Physics Department University Mainz (JGU), 55128 Mainz, Germany.|Kirchhoff Institute of Physics (KIP), and Institute of Pharmacy & Molecular Biotechnology (IPMB), University Heidelberg, Germany.
authors.forename: Christoph
authors.initials: C
authors.lastname: Cremer
mesh_terms: D001205:Ascorbic Acid / Q000494:pharmacology; D001583:Benzoxazoles / Q000737:chemistry; D001665:Binding Sites; D015687:Cell Hypoxia; D002460:Cell Line; D045744:Cell Line, Tumor; D002843:Chromatin / Q000378:metabolism / Q000648:ultrastructure*; D004247:DNA / Q000378:metabolism / Q000648:ultrastructure*; D005456:Fluorescent Dyes / Q000737:chemistry*; D005947:Glucose / Q000172:deficiency; D006367:HeLa Cells; D006576:Heterocyclic Compounds, 4 or More Rings / Q000737:chemistry; D006801:Humans; D006863:Hydrogen-Ion Concentration; D007364:Intercalating Agents / Q000737:chemistry; D008214:Lymphocytes / Q000187:drug effects / Q000378:metabolism / Q000648:ultrastructure; D008856:Microscopy, Fluorescence / Q000379:methods*; D032383:Myocytes, Cardiac / Q000187:drug effects / Q000378:metabolism / Q000648:ultrastructure; D009474:Neurons / Q000187:drug effects / Q000378:metabolism / Q000648:ultrastructure; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D011806:Quinolinium Compounds / Q000737:chemistry
chemical_list: D001583:Benzoxazoles; D002843:Chromatin; D005456:Fluorescent Dyes; D006576:Heterocyclic Compounds, 4 or More Rings; D007364:Intercalating Agents; D011806:Quinolinium Compounds; C075296:1,1'-((4,4,7,7-tetramethyl)-4,7-diazaundecamethylene)bis-4-(3-methyl-2,3-dihydro(benzo-1,3-oxazole)-2-methylidene)quinolinium; D004247:DNA; D005947:Glucose; D001205:Ascorbic Acid