References published by IBA users: Fluorescent labels

  1. Rödiger S, Schierack P, Böhm A, Nitschke J, Berger I, Frömmel U, Schmidt C, Ruhland M, Schimke I, Roggenbuck D, Lehmann W, Schröder C (2012)
    A highly versatile microscope imaging technology platform for the multiplex real-time detection of biomolecules and autoimmune antibodies
    Adv Biochem Engin/Biotechnol 133: 35-74 
  2. Shoura MJ, Vetcher AA, Giovan SM, Bardai F, Bharadwaj A, Kessinger MR, Levene SD (2012)    
    Measurements of DNA-loop formation via Cre-mediated recombination
    Nucleic Acids Research, 1–13 
  3. Rödiger S, Ruhland M, Schmidt C, Schröder C, Grossmann K, Böhm A, Nitschke J, Berger I, Schimke I, Schierack P (2011) 
    Fluorescence dye adsorption assay to quantify carboxyl groups on the surface of poly(methyl methacrylate) microbeads
    Anal. Chem. 83: 3379–3385 
  4. Boudier C, Storchak R, Sharma KK, Didier P, Follenius-Wund A, Muller S, Darlix JL, Mély Y. (2010)
    The mechanism of HIV-1 Tat-directed nucleic acid annealing supports its role in reverse transcription
    Journal of Molecular Biology 400(3):487-501.
  5. Kasper R, Harke B, Forthmann C, Tinnefeld P, Hell SW, Sauer M. (2010)
    Single-molecule STED microscopy with photostable organic fluorophores.
    Small 6(13):1379-84.
  6. Pannecouque C, Szafarowicz B, Volkova N, Bakulev V, Dehaen W, Mély Y, Daelemans D. (2010)
    Inhibition of HIV-1 replication by a bis-thiadiazolbenzene-1,2-diamine that chelates zinc ions from retroviral nucleocapsid zinc fingers.
    Antimicrobial agents and chemotherapy 54(4):1461-8.
  7. Schneider UV, Mikkelsen ND, Jøhnk N, Okkels LM, Westh H, Lisby G. (2010)
    Optimal design of parallel triplex forming oligonucleotides containing Twisted Intercalating Nucleic Acids--TINA.
    Nucleic Acids Research 38(13):4394-403.
  8. Sharma K, Didier P, Darlix JL, de Rocquigny H, Bensikaddour H, Lavergne JP, Pénin F, Lessinger JM, Mély Y. (2010)
    Kinetic analysis of the nucleic acid chaperone activity of the hepatitis C virus core protein.
    Nucleic Acids Research 38(11):3632-42.
  9. Vogelsang J, Cordes T, Forthmann C, Steinhauer C, Tinnefeld P. (2010)
    Intrinsically resolution enhancing probes for confocal microscopy.
    Nano Letters 10(2):672-9.
  10. Avilov SV, Godet J, Piémont E, Mély Y. (2009)
    Site-specific characterization of HIV-1 nucleocapsid protein binding to oligonucleotides with two binding sites.
    Biochemistry 48(11):2422-30.
  11. Cordes T, Vogelsang J, Tinnefeld P. (2009)
    On the mechanism of Trolox as antiblinking and antibleaching reagent.
    Journal of the American Chemical Society 131(14):5018-9.
  12. Didier P, Godet J, Mély Y. (2009)
    Two-photon two-focus fluorescence correlation spectroscopy with a tunable distance between the excitation volumes.
    Journal of Fluorescence 19(3):561-5.
  13. Heilemann M, Hwang LC, Lymperopoulos K, Kapanidis AN. (2009)
    Single-molecule FRET analysis of protein-DNA complexes.
    Methods in Molecular Biology 543:503-21.
  14. Person B, Stein IH, Steinhauer C, Vogelsang J, Tinnefeld P. (2009)
    Correlated movement and bending of nucleic acid structures visualized by multicolor single-molecule spectroscopy.
    Chemphyschem 10(9-10):1455-60.
  15. Shvadchak VV, Klymchenko AS, de Rocquigny H, Mély Y. (2009)
    Sensing peptide-oligonucleotide interactions by a two-color fluorescence label: application to the HIV-1 nucleocapsid protein.
    Nucleic Acids Research 37(3):e25.
  16. Shvadchak V, Sanglier S, Rocle S, Villa P, Haiech J, Hibert M, Van Dorsselaer A, Mély Y, de Rocquigny H. (2009)
    Identification by high throughput screening of small compounds inhibiting the nucleic acid destabilization activity of the HIV-1 nucleocapsid protein.
    Biochimie 91(7):916-23.
  17. Tietze LF, Krewer B, Frauendorf H. (2009)
    Investigation of the transformations of a novel anti-cancer agent combining HPLC, HPLC-MS and direct ESI-HRMS analyses.
    Analytical and Bioanalytical Chemistry 395(2):437-48.
  18. Vogelsang J, Cordes T, Tinnefeld P. (2009)
    Single-molecule photophysics of oxazines on DNA and its application in a FRET switch.
    Photochemical & Photobiological Sciences 8(4):486-96.
  19. Vogelsang J, Cordes T, Forthmann C, Steinhauer C, Tinnefeld P. (2009)
    Controlling the fluorescence of ordinary oxazine dyes for single-molecule switching and superresolution microscopy.
    PNAS 106(20):8107-12.
  20. Avilov SV, Piemont E, Shvadchak V, de Rocquigny H, Mély Y. (2008)
    Probing dynamics of HIV-1 nucleocapsid protein/target hexanucleotide complexes by 2-aminopurine.
    Nucleic Acids Research 36(3):885-96.
  21. Bourbigot S, Ramalanjaona N, Boudier C, Salgado GF, Roques BP, Mély Y, Bouaziz S, Morellet N. (2008)
    How the HIV-1 nucleocapsid protein binds and destabilises the (-)primer binding site during reverse transcription.
    Journal of Molecular Biology 383(5):1112-28.
  22. Bugaut A, Balasubramanian S. (2008)
    A sequence-independent study of the influence of short loop lengths on the stability and topology of intramolecular DNA G-quadruplexes.
    Biochemistry 47(2):689-97.
  23. Dietz J, Koch J, Kaur A, Raja C, Stein S, Grez M, Pustowka A, Mensch S, Ferner J, Möller L, Bannert N, Tampé R, Divita G, Mély Y, Schwalbe H, Dietrich U. (2008)
    Inhibition of HIV-1 by a peptide ligand of the genomic RNA packaging signal Psi.
    ChemMedChem 3(5):749-55.
  24. Doeven MK, van den Bogaart G, Krasnikov V, Poolman B. (2008)
    Probing receptor-translocator interactions in the oligopeptide ABC transporter by fluorescence correlation spectroscopy.
    Biophysical Journal 94(10):3956-65.
  25. Fitzner A, Frauendorf H, Laatsch H, Diederichsen U. (2008)
    Formation of gutingimycin: analytical investigation of trioxacarcin A-mediated alkylation of dsDNA.
    Analytical and Bioanalytical Chemistry 390(4):1139-47.
  26. Grohmann D, Godet J, Mély Y, Darlix JL, Restle T. (2008)
    HIV-1 nucleocapsid traps reverse transcriptase on nucleic acid substrates.
    Biochemistry 47(46):12230-40.
  27. Kenfack CA, Piémont E, Ben Gaied N, Burger A, Mély Y. (2008)
    Time-resolved fluorescent properties of 8-vinyl-deoxyadenosine and 2-amino-deoxyribosylpurine exhibit different sensitivity to their opposite base in duplexes.
    The Journal of Physical Chemistry. B 112(32):9736-45.
  28. Kufer SK, Puchner EM, Gumpp H, Liedl T, Gaub HE. (2008)
    Single-molecule cut-and-paste surface assembly.
    Science 319(5863):594-6.
  29. Siebrasse JP, Veith R, Dobay A, Leonhardt H, Daneholt B, Kubitscheck U. (2008)
    Discontinuous movement of mRNP particles in nucleoplasmic regions devoid of chromatin.
    PNAS 105(51):20291-6.
  30. Vogelsang J, Kasper R, Steinhauer C, Person B, Heilemann M, Sauer M, Tinnefeld P. (2008)
    A reducing and oxidizing system minimizes photobleaching and blinking of fluorescent dyes.
    Angewandte Chemie (International ed. in english) 47(29):5465-9.
  31. Woźniak AK, Schröder GF, Grubmüller H, Seidel CA, Oesterhelt F. (2008)
    Single-molecule FRET measures bends and kinks in DNA.
    PNAS 105(47):18337-42.
  32. Zhou D, Ying L, Hong X, Hall EA, Abell C, Klenerman D. (2008)
    A compact functional quantum Dot-DNA conjugate: preparation, hybridization, and specific label-free DNA detection.
    Langmuir 24(5):1659-64.
  33. Doose S, Barsch H, Sauer M. (2007)
    Polymer properties of polythymine as revealed by translational diffusion.
    Biophysical Journal 93(4):1224-34.
  34. Egelé C, Piémont E, Didier P, Ficheux D, Roques B, Darlix JL, de Rocquigny H, Mély Y. (2007)
    The single-finger nucleocapsid protein of moloney murine leukemia virus binds and destabilizes the TAR sequences of HIV-1 but does not promote efficiently their annealing.
    Biochemistry 46(50):14650-62.
  35. Friedrich A, Hoheisel JD, Marmé N, Knemeyer JP. (2007)
    DNA-probes for the highly sensitive identification of single nucleotide polymorphism using single-molecule spectroscopy.
    FEBS Letters 581(8):1644-8.
  36. Järve A, Müller J, Kim IH, Rohr K, MacLean C, Fricker G, Massing U, Eberle F, Dalpke A, Fischer R, Trendelenburg MF, Helm M. (2007)
    Surveillance of siRNA integrity by FRET imaging.
    Nucleic Acids Research 35(18):e124.
  37. Kobitski AY, Nierth A, Helm M, Jäschke A, Nienhaus GU. (2007)
    Mg2+-dependent folding of a Diels-Alderase ribozyme probed by single-molecule FRET analysis.
    Nucleic Acids Research 35(6):2047-59.
  38. Morfill J, Kühner F, Blank K, Lugmaier RA, Sedlmair J, Gaub HE. (2007)
    B-S transition in short oligonucleotides.
    Biophysical Journal 93(7):2400-9
  39. Ramalanjaona N, de Rocquigny H, Millet A, Ficheux D, Darlix JL, Mély Y. (2007)
    Investigating the mechanism of the nucleocapsid protein chaperoning of the second strand transfer during HIV-1 DNA synthesis.
    Journal of Molecular Biology 374(4):1041-53.
  40. Schluesche P, Stelzer G, Piaia E, Lamb DC, Meisterernst M. (2007) NC2 mobilizes TBP on core promoter TATA boxes.
    Nature Structural & Molecular Biology 14(12):1196-201.
  41. Ross J, Buschkamp P, Fetting D, Donnermeyer A, Roth CM, Tinnefeld P. (2007)
    Multicolor single-molecule spectroscopy with alternating laser excitation for the investigation of interactions and dynamics.
    The Journal of Physical Chemistry. B 111(2):321-6.
  42. Coban O, Lamb DC, Zaychikov E, Heumann H, Nienhaus GU. (2006)
    Conformational heterogeneity in RNA polymerase observed by single-pair FRET microscopy.
    Biophysical Journal 90(12):4605-17.
  43. Godet J, de Rocquigny H, Raja C, Glasser N, Ficheux D, Darlix JL, Mély Y. (2006)
    During the early phase of HIV-1 DNA synthesis, nucleocapsid protein directs hybridization of the TAR complementary sequences via the ends of their double-stranded stem.
    Journal of Molecular Biology 356(5):1180-92.
  44. Käppel ND, Dankbar DM, Gauglitz G. (2006)
    DNA Quantification in Nanoliter Volumes.
    Microchimica Acta 154(1-2):65-71.
  45. Kim J, Doose S, Neuweiler H, Sauer M. (2006)
    The initial step of DNA hairpin folding: a kinetic analysis using fluorescence correlation spectroscopy.
    Nucleic Acids Research 34(9):2516-27.
  46. Marmé N, Friedrich A, Müller M, Nolte O, Wolfrum J, Hoheisel JD, Sauer M, Knemeyer JP. (2006)
    Identification of single-point mutations in mycobacterial 16S rRNA sequences by confocal single-molecule fluorescence spectroscopy.
    Nucleic Acids Research 34(13):e90.
  47. Orte A, Clarke R, Balasubramanian S, Klenerman D. (2006)
    Determination of the fraction and stoichiometry of femtomolar levels of biomolecular complexes in an excess of monomer using single-molecule, two-color coincidence detection.
    Analytical Chemistry 78(22):7707-15.
  48. Raja C, Ferner J, Dietrich U, Avilov S, Ficheux D, Darlix JL, de Rocquigny H, Schwalbe H, Mély Y. (2006)
    A tryptophan-rich hexapeptide inhibits nucleic acid destabilization chaperoned by the HIV-1 nucleocapsid protein.
    Biochemistry 45(30):9254-65.
  49. Sánchez-Mosteiro G, van Dijk EM, Hernando J, Heilemann M, Tinnefeld P, Sauer M, Koberlin F, Patting M, Wahl M, Erdmann R, van Hulst NF, García-Parajó MF. (2006)
    DNA-based molecular wires: multiple emission pathways of individual constructs.
    The Journal of Physical Chemistry. B 110(51):26349-53.
  50. Tietze LF, Krewer B, Frauendorf H, Major F, Schuberth I. (2006)
    Investigation of reactivity and selectivity of DNA-alkylating duocarmycin analogues by high-resolution mass spectrometry.
    Angewandte Chemie (International ed. in english) 45(39):6570-4.
  51. Veldhuis G, Hink M, Krasnikov V, van den Bogaart G, Hoeboer J, Visser AJ, Broos J, Poolman B. (2006)
    The oligomeric state and stability of the mannitol transporter, EnzymeII(mtl), from Escherichia coli: a fluorescence correlation spectroscopy study.
    Protein Science 15(8):1977-86.
  52. Beltz H, Clauss C, Piémont E, Ficheux D, Gorelick RJ, Roques B, Gabus C, Darlix JL, de Rocquigny H, Mély Y. (2005)
    Structural determinants of HIV-1 nucleocapsid protein for cTAR DNA binding and destabilization, and correlation with inhibition of self-primed DNA synthesis.
    Journal of Molecular Biology 348(5):1113-26.
  53. Berezhna S, Schaefer S, Heintzmann R, Jahnz M, Boese G, Deniz A, Schwille P. (2005)
    New effects in polynucleotide release from cationic lipid carriers revealed by confocal imaging, fluorescence cross-correlation spectroscopy and single particle tracking.
    Biochimica et Biophysica Acta 1669(2):193-207.
  54. Egelé C, Schaub E, Piémont E, de Rocquigny H, Mély Y. (2005)
    Investigation by fluorescence correlation spectroscopy of the chaperoning interactions of HIV-1 nucleocapsid protein with the viral DNA initiation sequences.
    Comptes rendus biologies 328(12):1041-51.
  55. Habl G, Böhm H, Marmé N, Knemeyer JP. (2005)
    A new assay for single nucleotide polymorphism analysis based on displacement reactions in PNA-DNA double helices.
    International Journal of Environmental Analytical Chemistry 85(9-11):613-623.
  56. Lovullo D, Daniel D, Yodh J, Lohr D, Woodbury NW. (2005)
    A fluorescence resonance energy transfer-based probe to monitor nucleosome structure.
    Analytical Biochemistry 341(1):165-72.
  57. Pion E, Ullmann GM, Amé JC, Gérard D, de Murcia G, Bombarda E. (2005)
    DNA-induced dimerization of poly(ADP-ribose) polymerase-1 triggers its activation.
    Biochemistry 44(44):14670-81.
  58. Stöhr K, Häfner B, Nolte O, Wolfrum J, Sauer M, Herten DP. (2005)
    Species-specific identification of mycobacterial 16S rRNA PCR amplicons using smart probes.
    Analytical Chemistry 77(22):7195-203.
  59. Woźniak AK, Nottrott S, Kühn-Hölsken E, Schröder GF, Grubmüller H, Lührmann R, Seidel CA, Oesterhelt F. (2005)
    Detecting protein-induced folding of the U4 snRNA kink-turn by single-molecule multiparameter FRET measurements.
    RNA 11(10):1545-54.
  60. Beltz H, Piémont E, Schaub E, Ficheux D, Roques B, Darlix JL, Mély Y. (2004)
    Role of the structure of the top half of HIV-1 cTAR DNA on the nucleic acid destabilizing activity of the nucleocapsid protein NCp7.
    Journal of Molecular Biology 338(4):711-23.
  61. Egelé C, Schaub E, Ramalanjaona N, Piémont E, Ficheux D, Roques B, Darlix JL, Mély Y. (2004)
    HIV-1 nucleocapsid protein binds to the viral DNA initiation sequences and chaperones their kissing interactions.
    Journal of Molecular Biology 342(2):453-66.
  62. Heinze KG, Jahnz M, Schwille P. (2004)
    Triple-color coincidence analysis: one step further in following higher order molecular complex formation. Biophysical Journal 86(1 Pt 1):506-16.
  63. Stote RH, Kellenberger E, Muller H, Bombarda E, Roques BP, Kieffer B, Mély Y. (2004)
    Structure of the His44 --> Ala single point mutant of the distal finger motif of HIV-1 nucleocapsid protein: a combined NMR, molecular dynamics simulation, and fluorescence study.
    Biochemistry 43(24):7687-97.
  64. Azoulay J, Clamme JP, Darlix JL, Roques BP, Mély Y. (2003)
    Destabilization of the HIV-1 complementary sequence of TAR by the nucleocapsid protein through activation of conformational fluctuations.
    Journal of Molecular Biology 326(3):691-700.
  65. Beltz H, Azoulay J, Bernacchi S, Clamme JP, Ficheux D, Roques B, Darlix JL, Mély Y. (2003)
    Impact of the terminal bulges of HIV-1 cTAR DNA on its stability and the destabilizing activity of the nucleocapsid protein NCp7.
    Journal of Molecular Biology 328(1):95-108.
  66. Bernacchi S, Piémont E, Potier N, Dorsselaer A, Mély Y. (2003)
    Excitonic heterodimer formation in an HIV-1 oligonucleotide labeled with a donor-acceptor pair used for fluorescence resonance energy transfer.
    Biophysical Journal 84(1):643-54.
  67. Haustein E, Jahnz M, Schwille P. (2003)
    Triple FRET: a tool for studying long-range molecular interactions.
    Chemphyschem 4(7):745-8.
  68. Pion E, Bombarda E, Stiegler P, Ullmann GM, Mély Y, de Murcia G, Gérard D. (2003)
    Poly(ADP-ribose) polymerase-1 dimerizes at a 5' recessed DNA end in vitro: a fluorescence study.
    Biochemistry 42(42):12409-17.
  69. Bernacchi S, Stoylov S, Piémont E, Ficheux D, Roques BP, Darlix JL, Mély Y. (2002)
    HIV-1 nucleocapsid protein activates transient melting of least stable parts of the secondary structure of TAR and its complementary sequence.
    Journal of Molecular Biology 317(3):385-99.
  70. Bernacchi S, Mély Y. (2001)
    Exciton interaction in molecular beacons: a sensitive sensor for short range modifications of the nucleic acid structure.
    Nucleic Acids Research 29(13):E62-2.