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Journal of Biomolecular Structure and Dynamics Volume 16, 1998 - Issue 2
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Original Articles

1H NMR Studies of the Bis-Intercalation of a Homodimeric Oxazole Yellow Dye in DNA Oligonucleotides

Franci Johansen Department of Chemistry, Odense University, Odense M, DK-5230, Denmark
&
Jens Peter Jacobsen Department of Chemistry, Odense University, Odense M, DK-5230, Denmark
Pages 205-222 | Received 29 Jun 1998, Published online: 21 May 2012

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DmitryN. Kaluzhny, VladimirV. Timoshin, OlgaF. Borisova, VictorB. Zhurkin, VladimirL. Florentiev & AnnaK. Shchyolkina. (2008) Intramolecular Recombination R-Triplex in Solution: Stabilization by bis-intercalator YOYO. Journal of Biomolecular Structure and Dynamics 26:3, pages 301-305.
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LoneB. Jørgensen, Poul Nielsen, Jesper Wengel & Jens Peter Jacobsen. (2000) The Solution Structure of a DNA Duplex Containing a Single 1-(2-0,3-C-Ethylene-β-D Arabinofuranosyl)thymidine Nucleoside. Journal of Biomolecular Structure and Dynamics 18:1, pages 45-57.
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ChristinaB. Nielsen, SanjayK. Singh, Jesper Wengel & Jens Peter Jacobsen. (1999) The Solution Structure of a Locked Nucleic Acid (LNA) Hybridized to DNA. Journal of Biomolecular Structure and Dynamics 17:2, pages 175-191.
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Articles from other publishers (61)

Pavel G. Pronkin & Alexander S. Tatikolov. (2023) Fluorescent Probes for Biomacromolecules Based on Monomethine Cyanine Dyes. Chemosensors 11:5, pages 280.
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Christiaan N. Hulleman, Rasmus Ø. Thorsen, Eugene Kim, Cees Dekker, Sjoerd Stallinga & Bernd Rieger. (2021) Simultaneous orientation and 3D localization microscopy with a Vortex point spread function. Nature Communications 12:1.
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Yan Jiang, Theodore Feldman, Julia A. M. Bakx, Darren Yang & Wesley P. Wong. (2020) Stretching DNA to twice the normal length with single-molecule hydrodynamic trapping. Lab on a Chip 20:10, pages 1780-1791.
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Helen L Miller, Sonia Contera, Adam J M Wollman, Adam Hirst, Katherine E Dunn, Sandra Schröter, Deborah O’Connell & Mark C Leake. (2020) Biophysical characterisation of DNA origami nanostructures reveals inaccessibility to intercalation binding sites. Nanotechnology 31:23, pages 235605.
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Tamara Šmidlehner, Andrea Rožman & Ivo Piantanida. (2019) Advances in Cyanine - Amino Acid Conjugates and Peptides for Sensing of DNA, RNA and Protein Structures. Current Protein & Peptide Science 20:11, pages 1040-1045.
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Adam S. BackerAndreas S. BiebricherGraeme A. King, Gijs J. L. Wuite, Iddo Heller & Erwin J. G. Peterman. (2019) Single-molecule polarization microscopy of DNA intercalators sheds light on the structure of S-DNA. Science Advances 5:3.
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Andrea Rožman, Ivo Crnolatac, Todor Deligeorgiev & Ivo Piantanida. (2019) Strong impact of chloro substituent on TOTO and YOYO ds-DNA/RNA sensing. Journal of Luminescence 205, pages 87-96.
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Xiuyan Li, Yangtao Fan, Qingqing Gao, Hu Chen & Yanhui Liu. (2018) Identification of effects of YOYO-1 intercalation on the topological states of circular DNA. Modern Physics Letters B 32:20, pages 1850231.
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Guenyoung Park, Suresh Kumar Chakkarapani, Soyeong Ju, Sujin Ahn & Seong Ho Kang. (2018) Super-resolution morphological dissemination of intercalating dye in single DNA molecules via binding activated localization microscopy. Chinese Chemical Letters 29:3, pages 505-508.
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Chi Jin, David Cerutti & Robert I. Cukier. (2017) Molecular Dynamics of Oxazole Yellow Dye in its Ground and First Excited Electronic States in Solution and when Intercalated in dsDNA. The Journal of Physical Chemistry B 121:44, pages 10242-10248.
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Tamal Roy, Kai Szuttor, Jens Smiatek, Christian Holm & Steffen Hardt. (2017) Electric-field-induced stretching of surface-tethered polyelectrolytes in a microchannel. Physical Review E 96:3.
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Antoine Malabirade, Kai Jiang, Krzysztof Kubiak, Alvaro Diaz-Mendoza, Fan Liu, Jeroen A. van Kan, Jean-François Berret, Véronique Arluison & Johan R.C. van der Maarel. (2017) Compaction and condensation of DNA mediated by the C-terminal domain of Hfq. Nucleic Acids Research 45:12, pages 7299-7308.
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Yellaiah Tangella, Kesari Lakshmi Manasa, Manda Sathish, Abdullah Alarifi & Ahmed Kamal. (2017) Diphenylphosphoryl Azide (DPPA)-Mediated One-Pot Synthesis of Oxazolo[4,5- c ][1,8]naphthyridin-4(5  H )-ones, Oxazolo[4,5- c ]quinoline-4(5  H )-ones, and Tosyloxazol-5-yl Pyridines . Asian Journal of Organic Chemistry 6:7, pages 898-906.
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Franziska Kriegel, Niklas Ermann & Jan Lipfert. (2017) Probing the mechanical properties, conformational changes, and interactions of nucleic acids with magnetic tweezers. Journal of Structural Biology 197:1, pages 26-36.
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Ying Wang, Andy Sischka, Volker Walhorn, Katja Tönsing & Dario Anselmetti. (2016) Nanomechanics of Fluorescent DNA Dyes on DNA Investigated by Magnetic Tweezers. Biophysical Journal 111:8, pages 1604-1611.
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V. Iarko, E. Werner, L. K. Nyberg, V. Müller, J. Fritzsche, T. Ambjörnsson, J. P. Beech, J. O. Tegenfeldt, K. Mehlig, F. Westerlund & B. Mehlig. (2015) Extension of nanoconfined DNA: Quantitative comparison between experiment and theory. Physical Review E 92:6.
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Maedeh Roushan, Zubair Azad, Shuang Fang Lim, Hong Wang & Robert Riehn. (2015) Interference of ATP with the fluorescent probes YOYO-1 and YOYO-3 modifies the mechanical properties of intercalator-stained DNA confined in nanochannels. Microchimica Acta 182:7-8, pages 1561-1565.
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Kai Jiang, Ce Zhang, Durgarao Guttula, Fan Liu, Jeroen A. van Kan, Christophe Lavelle, Krzysztof Kubiak, Antoine Malabirade, Alain Lapp, Véronique Arluison & Johan R.C. van der Maarel. (2015) Effects of Hfq on the conformation and compaction of DNA. Nucleic Acids Research 43:8, pages 4332-4341.
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Ignác Capek. 2015. DNA Engineered Noble Metal Nanoparticles. DNA Engineered Noble Metal Nanoparticles 515 636 .
Mahesh Akula, Yadagiri Thigulla, Connor Davis, Mukund Jha & Anupam Bhattacharya. (2015) Synthesis of 4-substituted oxazolo[4,5-c]quinolines by direct reaction at the C-4 position of oxazoles. Organic & Biomolecular Chemistry 13:9, pages 2600-2605.
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Johan R. C. van der Maarel, Ce Zhang & Jeroen A. van Kan. (2014) A Nanochannel Platform for Single DNA Studies: From Crowding, Protein DNA Interaction, to Sequencing of Genomic Information. Israel Journal of Chemistry 54:11-12, pages 1573-1588.
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Binu Kundukad, Jie Yan & Patrick S. Doyle. (2014) Effect of YOYO-1 on the mechanical properties of DNA. Soft Matter 10:48, pages 9721-9728.
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Joshua W. Griffis, Mikhail M. Safranovitch, Shilpi P. Vyas, Sean Gerrin, Ekaterina Protozanova, Gene Malkin & Robert H. Meltzer. (2014) Single molecule DNA intercalation in continuous homogenous elongational flow. Lab Chip 14:19, pages 3881-3893.
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M. Maaloum, P. Muller & S. Harlepp. (2013) DNA-intercalator interactions: structural and physical analysis using atomic force microscopy in solution. Soft Matter 9:47, pages 11233.
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Aparna Banerjee Dixit, Krishanu Ray & Lindsay W. Black. (2012) Compression of the DNA substrate by a viral packaging motor is supported by removal of intercalating dye during translocation. Proceedings of the National Academy of Sciences 109:50, pages 20419-20424.
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Ce Zhang, Zongying Gong, Durgarao Guttula, Piravi P. Malar, Jeroen A. van Kan, Patrick S. Doyle & Johan R. C. van der Maarel. (2012) Nanouidic Compaction of DNA by Like-Charged Protein. The Journal of Physical Chemistry B 116:9, pages 3031-3036.
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Alexander S. Tatikolov. (2012) Polymethine dyes as spectral-fluorescent probes for biomacromolecules. Journal of Photochemistry and Photobiology C: Photochemistry Reviews 13:1, pages 55-90.
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Cristina Flors. (2011) DNA and chromatin imaging with super-resolution fluorescence microscopy based on single-molecule localization. Biopolymers 95:5, pages 290-297.
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Marcel Reuter & David T.F. Dryden. (2010) The kinetics of YOYO-1 intercalation into single molecules of double-stranded DNA. Biochemical and Biophysical Research Communications 403:2, pages 225-229.
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K. Gunther, M. Mertig & R. Seidel. (2010) Mechanical and structural properties of YOYO-1 complexed DNA. Nucleic Acids Research 38:19, pages 6526-6532.
Crossref
C. U. Murade, V. Subramaniam, C. Otto & M. L. Bennink. (2010) Force spectroscopy and fluorescence microscopy of dsDNA-YOYO-1 complexes: implications for the structure of dsDNA in the overstretching region. Nucleic Acids Research 38:10, pages 3423-3431.
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Maria J. Ruedas-Rama, Jose M. Alvarez-Pez, Jose M. Paredes, Eva M. Talavera & Angel Orte. (2010) Binding of BOBO-3 Intercalative Dye to DNA Homo-Oligonucleotides with Different Base Compositions. The Journal of Physical Chemistry B 114:19, pages 6713-6721.
Crossref
Maria J. Ruedas-Rama, Angel Orte, Luis Crovetto, Eva M. Talavera & Jose M. Alvarez-Pez. (2009) Photophysics and Binding Constant Determination of the Homodimeric Dye BOBO-3 and DNA Oligonucleotides. The Journal of Physical Chemistry B 114:2, pages 1094-1103.
Crossref
Ce Zhang, Pei Ge Shao, Jeroen A. van Kan & Johan R. C. van der Maarel. (2009) Macromolecular crowding induced elongation and compaction of single DNA molecules confined in a nanochannel. Proceedings of the National Academy of Sciences 106:39, pages 16651-16656.
Crossref
C.U. Murade, V. Subramaniam, C. Otto & Martin L. Bennink. (2009) Interaction of Oxazole Yellow Dyes with DNA Studied with Hybrid Optical Tweezers and Fluorescence Microscopy. Biophysical Journal 97:3, pages 835-843.
Crossref
Hayriye Özhalıcı-Ünal & Bruce A. Armitage. (2009) Fluorescent DNA Nanotags Based on a Self-Assembled DNA Tetrahedron. ACS Nano 3:2, pages 425-433.
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L. Marcus Wilhelmsson, Ngarita Kingi & Jan Bergman. (2008) Interactions of Antiviral Indolo[2,3- b ]quinoxaline Derivatives with DNA . Journal of Medicinal Chemistry 51:24, pages 7744-7750.
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Ce Zhang, Fang Zhang, Jeroen A. van Kan & Johan R. C. van der Maarel. (2008) Effects of electrostatic screening on the conformation of single DNA molecules confined in a nanochannel. The Journal of Chemical Physics 128:22.
Crossref
Alexandre Fürstenberg & Eric Vauthey. (2007) Ultrafast Excited-State Dynamics of Oxazole Yellow DNA Intercalators. The Journal of Physical Chemistry B 111:43, pages 12610-12620.
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Alexandre Fürstenberg, Todor G. Deligeorgiev, Nikolai I. Gadjev, Aleksey A. Vasilev & Eric Vauthey. (2007) Structure–Fluorescence Contrast Relationship in Cyanine DNA Intercalators: Toward Rational Dye Design. Chemistry – A European Journal 13:30, pages 8600-8609.
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Jasmine I. Daksis & Glen H. Erikson. (2007) Heteropolymeric Triplex-Based Genomic Assay® to Detect Pathogens or Single-Nucleotide Polymorphisms in Human Genomic Samples. PLoS ONE 2:3, pages e305.
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Andrea L. Benvin, Yehuda Creeger, Gregory W. Fisher, Byron Ballou, Alan S. Waggoner & Bruce A. Armitage. (2007) Fluorescent DNA Nanotags:  Supramolecular Fluorescent Labels Based on Intercalating Dye Arrays Assembled on Nanostructured DNA Templates. Journal of the American Chemical Society 129:7, pages 2025-2034.
Crossref
Dilip Venkatrao Jarikote, Nils Krebs, Sebastian Tannert, Beate Röder & Oliver Seitz. (2006) Exploring Base‐Pair‐Specific Optical Properties of the DNA Stain Thiazole Orange. Chemistry – A European Journal 13:1, pages 300-310.
Crossref
Leon M. Bellan, Joshua D. Cross, Elizabeth A. Strychalski, Jose Moran-Mirabal & H. G. Craighead. (2006) Individually Resolved DNA Molecules Stretched and Embedded in Electrospun Polymer Nanofibers. Nano Letters 6:11, pages 2526-2530.
Crossref
Maja Eriksson, Fredrik Westerlund, Merima Mehmedovic, Per Lincoln, Gunnar Westman, Anette Larsson & Björn Åkerman. (2006) Comparing mono- and divalent DNA groove binding cyanine dyes—Binding geometries, dissociation rates, and fluorescence properties. Biophysical Chemistry 122:3, pages 195-205.
Crossref
Alexandre Fürstenberg, Marc D. Julliard, Todor G. Deligeorgiev, Nikolai I. Gadjev, Aleksey A. Vasilev & Eric Vauthey. (2006) Ultrafast Excited-State Dynamics of DNA Fluorescent Intercalators:  New Insight into the Fluorescence Enhancement Mechanism. Journal of the American Chemical Society 128:23, pages 7661-7669.
Crossref
R. Lehner, J. Koota, G. Maret & T. Gisler. (2006) Segment Distributions of End-Tethered Polymers in a Good Solvent. Physical Review Letters 96:10.
Crossref
Nabanita Nag, T. Ramreddy, Mamata Kombrabail, P. M. Krishna Mohan, Jacinta D’souza, B. J. Rao, Guy Duportail, Yves Mely & G. Krishnamoorthy. 2006. Reviews in Fluorescence 2006. Reviews in Fluorescence 2006 311 340 .
Jasmine I. DaksisGlen H. Erikson. (2005) Specific Triplex Binding Capacity of Mixed Base Sequence Duplex Nucleic Acids Used for Single-Nucleotide Polymorphism Detection. Genetic Testing 9:2, pages 111-120.
Crossref
Xiaomei Yan, Robert C. Habbersett, Thomas M. Yoshida, John P. Nolan, James H. Jett & Babetta L. Marrone. (2005) Probing the Kinetics of SYTOX Orange Stain Binding to Double-Stranded DNA with Implications for DNA Analysis. Analytical Chemistry 77:11, pages 3554-3562.
Crossref
Patrick T. Underhill & Patrick S. Doyle. (2004) On the coarse-graining of polymers into bead-spring chains. Journal of Non-Newtonian Fluid Mechanics 122:1-3, pages 3-31.
Crossref
Benjamin P. Bowen & Neal W. Woodbury. (2007) TOTO Binding Affinity Analysis Using Single-molecule Fluorescence Spectroscopy¶. Photochemistry and Photobiology 78:6, pages 582-586.
Crossref
Sean Ferree & Harvey W. Blanch. (2003) Electrokinetic Stretching of Tethered DNA. Biophysical Journal 85:4, pages 2539-2546.
Crossref
Benjamin P. Bowen & Neal W. Woodbury. (2003) TOTO Binding Affinity Analysis Using Single-molecule Fluorescence Spectroscopy¶. Photochemistry and Photobiology 78:6, pages 582.
Crossref
S.M Yarmoluk, S.S Lukashov, M.Yu Losytskyy, B Akerman & O.S Kornyushyna. (2002) Interaction of cyanine dyes with nucleic acids. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy 58:14, pages 3223-3232.
Crossref
Jason A. Bordelon, Karl J. Feierabend, Shabana A. Siddiqui, Laura L. Wright & Jeffrey T. Petty. (2002) Viscometry and Atomic Force Microscopy Studies of the Interactions of a Dimeric Cyanine Dye with DNA. The Journal of Physical Chemistry B 106:18, pages 4838-4843.
Crossref
J. M. Kim, T. Ohtani, S. Sugiyama, T. Hirose & H. Muramatsu. (2001) Simultaneous Topographic and Fluorescence Imaging of Single DNA Molecules for DNA Analysis with a Scanning Near-Field Optical/Atomic Force Microscope. Analytical Chemistry 73:24, pages 5984-5991.
Crossref
Jakob Bunkenborg, Nikolai I. Gadjev, Todor Deligeorgiev & Jens Peter Jacobsen. (2000) Concerted Intercalation and Minor Groove Recognition of DNA by a Homodimeric Thiazole Orange Dye. Bioconjugate Chemistry 11:6, pages 861-867.
Crossref
Jeffrey T. Petty, Jason A. Bordelon & Mary E. Robertson. (2000) Thermodynamic Characterization of the Association of Cyanine Dyes with DNA. The Journal of Physical Chemistry B 104:30, pages 7221-7227.
Crossref
J.P Clamme, S Bernacchi, C Vuilleumier, G Duportail & Y Mély. (2000) Gene transfer by cationic surfactants is essentially limited by the trapping of the surfactant/DNA complexes onto the cell membrane: a fluorescence investigation. Biochimica et Biophysica Acta (BBA) - Biomembranes 1467:2, pages 347-361.
Crossref
Katrine E. Nielsen, Sanjay K. Singh, Jesper Wengel & Jens Peter Jacobsen. (2000) Solution Structure of an LNA Hybridized to DNA:  NMR Study of the d(CT L GCT L T L CT L GC):d(GCAGAAGCAG) Duplex Containing Four Locked Nucleotides . Bioconjugate Chemistry 11:2, pages 228-238.
Crossref

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