References published by IBA users

RNA/siRNA
  1. Hands-Taylor KL, Martino L, Tata R, Babon JJ, Bui TT, Drake AF, Beavil RL, Pruijn GJ, Brown PR, Conte MR. (2010)
    Heterodimerization of the human RNase P/MRP subunits Rpp20 and Rpp25 is a prerequisite for interaction with the P3 arm of RNase MRP RNA.
    Nucleic Acids Research 38(12):4052-66.
  2. Brandt DT, Baarlink C, Kitzing TM, Kremmer E, Ivaska J, Nollau P, Grosse R. (2009)
    SCAI acts as a suppressor of cancer cell invasion through the transcriptional control of beta1-integrin.
    Nature Cell Biology 11(5):557-68.
  3. Huber M, Heink S, Grothe H, Guralnik A, Reinhard K, Elflein K, Hünig T, Mittrücker HW, Brüstle A, Kamradt T, Lohoff M. (2009)
    A Th17-like developmental process leads to CD8(+) Tc17 cells with reduced cytotoxic activity.
    European Journal of Immunology 39(7):1716-25.
  4. Konrad A, Wies E, Thurau M, Marquardt G, Naschberger E, Hentschel S, Jochmann R, Schulz TF, Erfle H, Brors B, Lausen B, Neipel F, Stürzl M. (2009)
    A systems biology approach to identify the combination effects of human herpesvirus 8 genes on NF-kappaB activation.
    Journal of Virology 83(6):2563-74.
  5. Goulimari P, Knieling H, Engel U, Grosse R. (2008)
    LARG and mDia1 link Galpha12/13 to cell polarity and microtubule dynamics.
    Molecular Biology of the Cell 19(1):30-40.
  6. Hengesbach M, Meusburger M, Lyko F, Helm M. (2008)
    Use of DNAzymes for site-specific analysis of ribonucleotide modifications.
    RNA 14(1):180-7.
  7. Mariappan M, Radhakrishnan K, Dierks T, Schmidt B, von Figura K. (2008)
    ERp44 mediates a thiol-independent retention of formylglycine-generating enzyme in the endoplasmic reticulum.
    The Journal of Biological Chemistry 283(10):6375-83.
  8. Ohrt T, Mütze J, Staroske W, Weinmann L, Höck J, Crell K, Meister G, Schwille P. (2008)
    Fluorescence correlation spectroscopy and fluorescence cross-correlation spectroscopy reveal the cytoplasmic origination of loaded nuclear RISC in vivo in human cells.
    Nucleic Acids Research 36(20):6439-49.
  9. Brandt DT, Marion S, Griffiths G, Watanabe T, Kaibuchi K, Grosse R. (2007)
    Dia1 and IQGAP1 interact in cell migration and phagocytic cup formation.
    The Journal of Cell Biology 178(2):193-200.
  10. Fechner H, Suckau L, Kurreck J, Sipo I, Wang X, Pinkert S, Loschen S, Rekittke J, Weger S, Dekkers D, Vetter R, Erdmann VA, Schultheiss HP, Paul M, Lamers J, Poller W. (2007)
    Highly efficient and specific modulation of cardiac calcium homeostasis by adenovector-derived short hairpin RNA targeting phospholamban.
    Gene Therapy 14(3):211-8.
  11. Hägerlöf M, Hedman H, Elmroth SK. (2007)
    Platination of the siRNA sense-strand modulates both efficacy and selectivity in vitro.
    Biochemichal and Biophysical Research Communications 361(1):14-9.
  12. Kitzing TM, Sahadevan AS, Brandt DT, Knieling H, Hannemann S, Fackler OT, Grosshans J, Grosse R. (2007)
    Positive feedback between Dia1, LARG, and RhoA regulates cell morphology and invasion.
    Genes & Development 21(12):1478-83.
  13. Schubert S, Rothe D, Werk D, Grunert HP, Zeichhardt H, Erdmann VA, Kurreck J. (2007)
    Strand-specific silencing of a picornavirus by RNA interference: evidence for the superiority of plus-strand specific siRNAs.
    Antiviral Research 73(3):197-205.
  14. Spitzner M, Ousingsawat J, Scheidt K, Kunzelmann K, Schreiber R. (2007)
    Voltage-gated K+ channels support proliferation of colonic carcinoma cells.
    The FASEB Journal 21(1):35-44.
  15. Hägerlöf M, Papsai P, Chow CS, Elmroth SK. (2006)
    More pronounced salt dependence and higher reactivity for platination of the hairpin r(CGCGUUGUUCGCG) compared with d(CGCGTTGTTCGCG).
    Journal of Biological Inorganic Chemistry 11(8):974-90.
  16. Löseke S, Grage-Griebenow E, Heine H, Wagner A, Akira S, Bauer S, Bufe A. (2006)
    In vitro-generated viral double-stranded RNA in contrast to polyinosinic:polycytidylic acid induces interferon-alpha in human plasmacytoid dendritic cells.
    Scandinavian Journal of Immunology 63(4):264-74.
  17. Marquis J, Paillard L, Audic Y, Cosson B, Danos O, Le Bec C, Osborne HB. (2006)
    CUG-BP1/CELF1 requires UGU-rich sequences for high-affinity binding.
    The Biochemical Journal 400(2):291-301.
  18. Nagel JH, Flamm C, Hofacker IL, Franke K, de Smit MH, Schuster P, Pleij CW. (2006)
    Structural parameters affecting the kinetics of RNA hairpin formation.
    Nucleic Acids Research 34(12):3568-76.
  19. Ohrt T, Merkle D, Birkenfeld K, Echeverri CJ, Schwille P. (2006)
    In situ fluorescence analysis demonstrates active siRNA exclusion from the nucleus by Exportin 5.
    Nucleic Acids Research 34(5):1369-80.
  20. Ren X, Li H, Clarke RW, Alves DA, Ying L, Klenerman D, Balasubramanian S. (2006)
    Analysis of human telomerase activity and function by two color single molecule coincidence fluorescence spectroscopy.
    Journal of the American Chemical Society 128(15):4992-5000.
  21. Klar J, Sigl M, Obermayer B, Schweda F, Krämer BK, Kurtz A. (2005)
    Calcium inhibits renin gene expression by transcriptional and posttranscriptional mechanisms.
    Hypertension 46(6):1340-6.
  22. Schubert S, Grünweller A, Erdmann VA, Kurreck J. (2005)
    Local RNA target structure influences siRNA efficacy: systematic analysis of intentionally designed binding regions.
    Journal of Molecular Biology 348(4):883-93.
  23. Najafi-Shoushtari SH, Mayer G, Famulok M. (2004)
    Sensing complex regulatory networks by conformationally controlled hairpin ribozymes.
    Nucleic Acids Research 32(10):3212-9.
  24. Olsthoorn RC, Laurs M, Sohet F, Hilbers CW, Heus HA, Pleij CW. (2004)
    Novel application of sRNA: stimulation of ribosomal frameshifting.
    RNA 10(11):1702-3.
  25. Wieland G, Orthaus S, Ohndorf S, Diekmann S, Hemmerich P. (2004)
    Functional complementation of human centromere protein A (CENP-A) by Cse4p from Saccharomyces cerevisiae.
    Molecular and Cellular Biology 24(15):6620-30.
  26. Grünweller A, Gillen C, Erdmann VA, Kurreck J. (2003)
    Cellular uptake and localization of a Cy3-labeled siRNA specific for the serine/threonine kinase Pim-1
    Oligonucleotides 13(5):345-52.
  27. Grünweller A, Wyszko E, Bieber B, Jahnel R, Erdmann VA, Kurreck J. (2003)
    Comparison of different antisense strategies in mammalian cells using locked nucleic acids, 2'-O-methyl RNA, phosphorothioates and small interfering RNA.
    Nucleic Acids Research 31(12):3185-93.
  28. Persson T, Cuzic S, Hartmann RK. (2003)
    Catalysis by RNase P RNA: unique features and unprecedented active site plasticity.
    The Journal of Biological Chemistry 278(44):43394-401.
  29. Werner S, Vogel-Bachmayr K, Hollinderbäumer B, Wöhrl BM. (2001)
    Requirements for minus-strand transfer catalyzed by Rous sarcoma virus reverse transcriptase.
    Journal of Virology 75(21):10132-8.
Fluorescence/FRET
  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.
Surface binding/immobilization/microarrays
  1. Huang C, Stakenborg T, Cheng Y, Colle F, Steylaerts T, Jans K, Van Dorpe P, Lagae L. (2010)
    Label-free genosensor based on immobilized DNA hairpins on gold surface.
    Biosensors and Bioelectronics 26: 3121–3126.
  2. Cheng Y, Stakenborg T, Van Dorpe P, Lagae L, Wang M, Chen H, Borghs G. (2011)
    Fluorescence Near Gold Nanoparticles for DNA Sensing.
    Anal. Chem. 83: 1307–1314.
  3. Erdmann M, David R, Fornof A, Gaub HE. (2010)
    Electrically controlled DNA adhesion.
    Nature Nanotechnology 5(2):154-9.
  4. Kaiser W, Rant U. (2010)
    Conformations of end-tethered DNA molecules on gold surfaces: influences of applied electric potential, electrolyte screening, and temperature.
    Journal of the American Chemical Society 132(23):7935-45.
  5. Spuhler PS, Knezevic J, Yalçin A, Bao Q, Pringsheim E, Dröge P, Rant U, Unlü MS. (2010)
    Platform for in situ real-time measurement of protein-induced conformational changes of DNA.
    PNAS 107(4):1397-401.
  6. Cattani-Scholz A, Pedone D, Blobner F, Abstreiter G, Schwartz J, Tornow M, Andruzzi L. (2009)
    PNA-PEG modified silicon platforms as functional bio-interfaces for applications in DNA microarrays and biosensors.
    Biomacromolecules 10(3):489-96.
  7. Ho D, Falter K, Severin P, Gaub HE. (2009)
    DNA as a force sensor in an aptamer-based biochip for adenosine.
    Analytical Chemistry 81(8):3159-64.
  8. Moreno M, Rincon E, Pérez JM, González VM, Domingo A, Dominguez E. (2009)
    Selective immobilization of oligonucleotide-modified gold nanoparticles by electrodeposition on screen-printed electrodes.
    Biosensors & Bioelectronics 25(4):778-83.
  9. Rant U, Pringsheim E, Kaiser W, Arinaga K, Knezevic J, Tornow M, Fujita S, Yokoyama N, Abstreiter G. (2009)
    Detection and size analysis of proteins with switchable DNA layers.
    Nano Letters 9(4):1290-5.
  10. Yamazaki S, Famulok M. (2009)
    Screening of novel inhibitors of HIV-1 reverse transcriptase with a reporter ribozyme assay.
    Methods in Molecular Biology 535:187-99.
  11. Cattani-Scholz A, Pedone D, Dubey M, Neppl S, Nickel B, Feulner P, Schwartz J, Abstreiter G, Tornow M. (2008)
    Organophosphonate-based PNA-functionalization of silicon nanowires for label-free DNA detection.
    ACS Nano 2(8):1653-60.
  12. Kuciak M, Gabus C, Ivanyi-Nagy R, Semrad K, Storchak R, Chaloin O, Muller S, Mély Y, Darlix JL. (2008)
    The HIV-1 transcriptional activator Tat has potent nucleic acid chaperoning activities in vitro.
    Nucleic Acids Research 36(10):3389-400.
  13. Naiser T, Ehler O, Kayser J, Mai T, Michel W, Ott A. (2008)
    Impact of point-mutations on the hybridization affinity of surface-bound DNA/DNA and RNA/DNA oligonucleotide-duplexes: comparison of single base mismatches and base bulges.
    BMC Biotechnology 8:48.
  14. Steinbock LJ, Helm M. (2008)
    Wavelength Dependence of Photoinduced Microcantilever Bending in the UV-VIS Range.
    Sensors 8:23-24.
  15. Kühner F, Morfill J, Neher RA, Blank K, Gaub HE. (2007)
    Force-induced DNA slippage.
    Biophysical Journal 92(7):2491-7.
  16. Rant U, Arinaga K, Scherer S, Pringsheim E, Fujita S, Yokoyama N, Tornow M, Abstreiter G. (2007)
    Switchable DNA interfaces for the highly sensitive detection of label-free DNA targets.
    PNAS 104(44):17364-9.
  17. Arinaga K, Rant U, Tornow M, Fujita S, Abstreiter G, Yokoyama N. (2006)
    The role of surface charging during the coadsorption of mercaptohexanol to DNA layers on gold: direct observation of desorption and layer reorientation.
    Langmuir 22(13):5560-2.
  18. Rant U, Arinaga K, Fujita S, Yokoyama N, Abstreiter G, Tornow M. (2006)
    Electrical manipulation of oligonucleotides grafted to charged surfaces.
    Organic & Biomolecular Chemistry 4(18):3448-55.
  19. Rant U, Arinaga K, Tornow M, Kim YW, Netz RR, Fujita S, Yokoyama N, Abstreiter G. (2006)
    Dissimilar kinetic behavior of electrically manipulated single- and double-stranded DNA tethered to a gold surface.
    Biophysical Journal 90(10):3666-71.
  20. Rant U, Arinaga K, Fujita S, Yokoyama N, Abstreiter G, Tornow M. (2004)
    Structural properties of oligonucleotide monolayers on gold surfaces probed by fluorescence investigations
    Langmuir 20(23):10086-92.
  21. Rant U, Arinaga K, Fujita S, Yokoyama N, Abstreiter G, Tornow M. (2004)
    Dynamic Electrical Switching of DNA Layers on a Metal Surface.
    Nano letters 4(12):2441–2445.
  22. Lange SA, Benes V, Kern DP, Hörber JK, Bernard A. (2004)
    Microcontact printing of DNA molecules.
    Analytical Chemistry 76(6):1641-7.
  23. Kühn U, Nemeth A, Meyer S, Wahle E. (2003)
    The RNA binding domains of the nuclear poly(A)-binding protein.
    The Journal of Biological Chemistry 278(19):16916-25.
  24. Penchovsky R, Birch-Hirschfeld E, McCaskill JS. (2000)
    End-specific covalent photo-dependent immobilisation of synthetic DNA to paramagnetic beads.
    Nucleic Acids Research 28(22):E98.

Others

PNAs, TINAs
  1. Laufer SD, Recke AL, Veldhoen S, Trampe A, Restle T. (2009)
    Noncovalent peptide-mediated delivery of chemically modified steric block oligonucleotides promotes splice correction: quantitative analysis of uptake and biological effect.
    Oligonucleotides 19(1):63-80.
  2. Gruegelsiepe H, Brandt O, Hartmann RK. (2006)
    Antisense inhibition of RNase P: mechanistic aspects and application to live bacteria.
    The Journal of Biological Chemistry 281(41):30613-20.
  3. Pröll F, Möhrle B, Kumpf M, Gauglitz G. (2005)
    Label-free characterisation of oligonucleotide hybridisation using reflectometric interference spectroscopy. Analytical and Bioanalytical Chemistry 382(8):1889-94.
DNA, DNase work
  1. TerMaat JR, Mamedov TG, Pienaar E, Whitney SE, Subramanian A. (2010)
    Automated two-column purification of iminobiotin and BrdU-labeled PCR products for rapid cloning: application to genes synthesized by polymerase chain assembly.
    Journal of Chromatographic Science 48(2):120-4.
  2. Barbosa JS, Costa RR, Testera AM, Alonso M, Rodríguez-Cabello JC, Mano JF. (2009)
    Multi-Layered Films Containing a Biomimetic Stimuli-Responsive Recombinant Protein.
    Nanoscale Research Letters 4(10):1247-1253.
  3. Petermeier M, Jäschke A. (2009)
    New theophylline-activated Diels-Alderase ribozymes by molecular engineering.
    Organic & Biomolecular Chemistry 7(2):288-92.
  4. Albrecht CH, Neuert G, Lugmaier RA, Gaub HE. (2008)
    Molecular force balance measurements reveal that double-stranded DNA unbinds under force in rate-dependent pathways.
    Biophysical Journal 94(12):4766-74.
  5. Di Pasquale F, Fischer D, Grohmann D, Restle T, Geyer A, Marx A. (2008)
    Opposed steric constraints in human DNA polymerase beta and E. coli DNA polymerase I.
    Journal of the American Chemical Society 130(32):10748-57.
  6. Rospigliosi A, Ehlich R, Hoerber H, Middelberg A, Moggridge G. (2007)
    Electron transfer of plurimodified DNA SAMs.
    Langmuir 23(15):8264-71.
  7. Shu W, Liu D, Watari M, Riener CK, Strunz T, Welland ME, Balasubramanian S, McKendry RA. (2005)
    DNA molecular motor driven micromechanical cantilever arrays.
    Journal of the American Chemical Society 127(48):17054-60.
  8. Zaborowska Z, Schubert S, Kurreck J, Erdmann VA. (2005)
    Deletion analysis in the catalytic region of the 10-23 DNA enzyme.
    FEBS Letters 579(2):554-8.
  9. Schubert S, Gül DC, Grunert HP, Zeichhardt H, Erdmann VA, Kurreck J. (2003)
    RNA cleaving '10-23' DNAzymes with enhanced stability and activity.
    Nucleic Acids Research 31(20):5982-92.
  10. Zaborowska Z, Fürste JP, Erdmann VA, Kurreck J. (2002)
    Sequence requirements in the catalytic core of the "10-23" DNA enzyme.
    The Journal of Biological Chemistry 277(43):40617-22.
TLR (Toll-like receptors)
  1. Haas T, Metzger J, Schmitz F, Heit A, Müller T, Latz E, Wagner H. (2008)
    The DNA sugar backbone 2' deoxyribose determines toll-like receptor 9 activation.
    Immunity 28(3):315-23.
  2. Peter M, Bode K, Lipford GB, Eberle F, Heeg K, Dalpke AH. (2008)
    Characterization of suppressive oligodeoxynucleotides that inhibit Toll-like receptor-9-mediated activation of innate immunity.
    Immunology 123(1):118-28.
  3. Doyle SL, Jefferies CA, Feighery C, O'Neill LA. (2007)
    Signaling by Toll-like receptors 8 and 9 requires Bruton's tyrosine kinase.
    The Journal of Biological Chemistry 282(51):36953-60.
  4. Heil F, Hemmi H, Hochrein H, Ampenberger F, Kirschning C, Akira S, Lipford G, Wagner H, Bauer S. (2004)
    Species-specific recognition of single-stranded RNA via toll-like receptor 7 and 8.
    Science 303(5663):1526-9.
Other user applications
  1. Kufer SK, Strackharn M, Stahl SW, Gumpp H, Puchner EM, Gaub HE. (2009)
    Optically monitoring the mechanical assembly of single molecules.
    Nature Nanotechnology 4(1):45-9.
  2. Schneider J, Fricke C, Overwin H, Hofmann B, Hofer B. (2009)
    Generation of amylosucrase variants that terminate catalysis of acceptor elongation at the di- or trisaccharide stage.
    Applied and Environmental Microbiology 75(23):7453-60.
  3. Hartl MJ, Kretzschmar B, Frohn A, Nowrouzi A, Rethwilm A, Wöhrl BM. (2008)
    AZT resistance of simian foamy virus reverse transcriptase is based on the excision of AZTMP in the presence of ATP.
    Nucleic Acids Research 36(3):1009-16.
  4. Lunn FA, MacDonnell JE, Bearne SL. (2008)
    Structural requirements for the activation of Escherichia coli CTP synthase by the allosteric effector GTP are stringent, but requirements for inhibition are lax.
    The Journal of Biological Chemistry 283(4):2010-20.
  5. Christoph T, Gillen C, Mika J, Grünweller A, Schäfer MK, Schiene K, Frank R, Jostock R, Bahrenberg G, Weihe E, Erdmann VA, Kurreck J. (2007)
    Antinociceptive effect of antisense oligonucleotides against the vanilloid receptor VR1/TRPV1
    Neurochemistry International 50(1):281-90.
  6. Philibert P, Stoessel A, Wang W, Sibler AP, Bec N, Larroque C, Saven JG, Courtête J, Weiss E, Martineau P. (2007)
    A focused antibody library for selecting scFvs expressed at high levels in the cytoplasm.
    BMC Biotechnology 7:81.
  7. Mescalchin A, Wünsche W, Laufer SD, Grohmann D, Restle T, Sczakiel G. (2006)
    Specific binding of a hexanucleotide to HIV-1 reverse transcriptase: a novel class of bioactive molecules
    Nucleic Acids Research 34(19):5631-7.
  8. Böttcher S, Ritgen M, Brüggemann M, Raff T, Lüschen S, Humpe A, Kneba M, Pott C. (2005)
    Flow cytometric assay for determination of FcgammaRIIIA-158 V/F polymorphism.
    Journal of Immunological Methods 306(1-2):128-36.
  9. Meager A, Das RG. (2005)
    Biological standardization of human interferon beta: establishment of a replacement world health organization international biological standard for human glycosylated interferon beta.
    Journal of Immunological Methods 306(1-2):1-15.
  10. Pfeifer S, Greiner-Stöffele T. (2005)
    A recombinant exonuclease III homologue of the thermophilic archaeon Methanothermobacter thermautotrophicus.
    DNA Repair 4(4):433-44.
  11. Ammon-Treiber S, Grecksch G, Stumm R, Riechert U, Tischmeyer H, Reichenauer A, Höllt V. (2004)
    Rapid, transient, and dose-dependent expression of hsp70 messenger RNA in the rat brain after morphine treatment.
    Cell Stress & Chaperones 9(2):182-97.
  12. Olsen DB, Eldrup AB, Bartholomew L, Bhat B, Bosserman MR, Ceccacci A, Colwell LF, Fay JF, Flores OA, Getty KL, Grobler JA, LaFemina RL, Markel EJ, Migliaccio G, Prhavc M, Stahlhut MW, Tomassini JE, MacCoss M, Hazuda DJ, Carroll SS. (2004)
    A 7-deaza-adenosine analog is a potent and selective inhibitor of hepatitis C virus replication with excellent pharmacokinetic properties.
    Antimicrobial Agents and Chemotherapy 48(10):3944-53.
  13. Brewis ND, Phelan A, Normand N, Choolun E, O'Hare P. (2003)
    Particle assembly incorporating a VP22-BH3 fusion protein, facilitating intracellular delivery, regulated release, and apoptosis.
    Molecular Therapy 7(2):262-70.
  14. Zavaglia D, Normand N, Brewis N, O'Hare P, Favrot MC, Coll JL. (2003)
    VP22-mediated and light-activated delivery of an anti-c-raf1 antisense oligonucleotide improves its activity after intratumoral injection in nude mice.
    Molecular Therapy 8(5):840-5.
  15. Kurreck J, Wyszko E, Gillen C, Erdmann VA. (2002)
    Design of antisense oligonucleotides stabilized by locked nucleic acids.
    Nucleic Acids Research 30(9):1911-8.
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    Hammerhead ribozyme design and application.
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    Inhibition of human immuno-deficiency virus type 1 reverse transcriptase by 3'-blocked oligonucleotide primers.
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    Evaluation of five green fluorescence-emitting streptavidin-conjugated fluorochromes for use in immunofluorescence microscopy.
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    Hammerhead like molecules containing non-nucleoside linkers are active RNA catalysts.
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    Synthesis of C-5 substituted pyrimidine nucleosides via organopalladium intermediates.
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    Exciton interaction in molecular beacons: a sensitive sensor for short range modifications of the nucleic acid structure.
    Nucleic Acid Res, 29, 13 e62.  
  8. Caplen NJ, Parrish S, Imani F, Fire A, Morgan AR, (2001)
    Specific inhibition of gene expression by small double-stranded RNAs in invertebrate and vertebrate systems.
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    Proc Natl Acad Sci U S A Apr;72(4):1286-90.
    Inhibition of protein synthesis in rabbit reticulocyte lysates by double-stranded RNA and oxidized glutathione: indirect mode of action on polypeptide chain initiation.
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    A phosphoramidite reagent for automated solid phase synthesis of 5'-biotinylated oligonucleotides.
    Tetrahedron Lett 30: 6287-6290.
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    Chemical synthesis of oligonucleotides containing a free sulfhydryl group and subsequent attachment of thiol specific probes.
    Nucleic Acids Res 13:4485-502.  
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    Enzymatic synthesis of 2'-modified nucleic acids: identification of important phosphate and ribose moieties in RNase P substrates.
    Nucleic Acids Res 23:1845-1853.  
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    The introduction of reporter groups at multiple and/or specific sites in DNA containing phosphorothioate diesters.
    Nucleic Acids Symp Ser 21:43-44.  
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    Bioavailability of antisense oligonucleotides in neuroblastoma cells: comparison of efficacy among different types of molecules.
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    Progress in antisense oligonucleotide therapeutics.
    Annu Rev Pharmacol Toxicol 36:107-129.  
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    Two- and three-color immunofluorescence using aminocoumarin, fluorescein, and phycoerythrin-labelled antibodies and single laser flow cytometry.
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    Synthesis and fluorescence properties of Oregon Green 514 labeled peptides.
    Bioorg Med Chem Lett 9:2989-2994.  
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    Using phosphorothioate-substituted RNA to investigate the thermodynamic role of phosphates in a sequence specific RNA-protein complex.
    Biochemistry 39:55-63.  
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    RNA interference in Trypanosoma brucei: cloning of small interfering RNAs provides evidence for retroposon-derived 24-26-nucleotide RNAs.
    RNA 2001 Nov;7(11):1522-30.  
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    Monitoring conformational dynamics of a single molecule by selective fluorescence spectroscopy.
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    Enhanced down regulation of the p75 nerve growth factor receptor by cholesteryl and bis-cholesteryl antisense oligonucleotides.
    Antisense Nucleic Acid Drug Dev 8:489-498. 
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    Interactions of the EcoRV restriction endonuclease with fluorescent oligodeoxynucleotides.
    Gene 157:153-156.  
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    Oligonucleotide libraries-variatio delectat.
    Curr Opin Chem Biol 2:320-327. 
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    Aptamers as tools in molecular biology and immunology.
    Curr Top Microbiol Immunol 243:123-136.  
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    Simultaneous detection of multiple point mutations using fluorescence-coupled competitive primer extension.
    Biotechnique22:964-968.  
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    Non-canonical substrates of aminoacyl-tRNA synthetases: the tRNA-like structure of brome mosaic virus genomic RNA.
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    Functionalization of oligonucleotides by the incorporation of thio-specific reporter groups.
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    Biotechnol 13;86(3):203-24  
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    2-Iminobiotin-containing reagent and affinity columns.
    Methods Enzymol 184: 167-173 
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    The DNA strand of chimeric RNA/DNA oligonucleotides can direct gene repair/conversion activity in mammalian and plant cell-free extracts.
    Nucleic Acids Res, Nov 1;28(21):4332-9.  
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    Homooligomeric dA.dU and dA.dT sequences in parallel and antiparallel strand orientation: consequence of the 5-methyl groups on stability, structure and interaction with the minor groove binding drug Hoechst 33258.
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    DNA and RNA sequence determination based on phosphorothioate chemistry.
    Science 240:1520-1522.  
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    Tetrahedron 51: 9375-9384. 
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    A species of small antisense RNA in posttranscriptional gene silencing in plants.
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    Fluorescence resonance energy transfer (FRET) to follow ribozyme reactions in real time.
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    Real time quantitative PCR.
    Genome Res 6:986-994. 
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    Quantitative measurements on the duplex stability of 2,6-dia-minopurine and 5-chloro-uracil nucleotides using enzymatically synthesized oligomers.
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    Forks and combs and DNA: the synthesis of branched oligodeoxyribonucleotides
    Nucleic Acids Res 17:6959-6967. 
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    Energy transfer primers with 5- or 6-carboxyrhodamine-6G as acceptor chromophores.
    Anal Biochem 238:165-170.  
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    Optimization of spectroscopic and electrophoretic properties of energy transfer primers.
    Anal Biochem 252:78-88.  
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    The characteristics of inhibition of protein synthesis by double-stranded ribonucleic acid in reticulocyte lysates.
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    Design of leader sequences that improve the efficiency of the enzymatic synthesis of 2'-amino-pyrimidine RNA for in vitro selection.
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    Comparative Study of DNA Enzymes and Ribozymes against the Same Full-length Messenger RNA of the Vanilloid Receptor.
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    Design of antisense oligonucleotides stabilized by locked nucleic acids.
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    In vivo gene repair of point and frameshift mutations directed by chimeric RNA/DNA oligonucleotides and modified single-stranded oligonucleotides.
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