Publications

2019

  • Valero, J., Centola, M., Ma, Y., Skugor, M., Yu, Z., Haydell, MW., Keppner, D. and Famulok, M.
    Design, assembly, characterization and operation of double-stranded interlocked DNA nanostructures.
    Nat. Protoc.  2019, doi: 10.1038/s41596-019-0198-7
  • Skugor, M., Valero, J., Murayama, K., Centola, M., Asanuma, H. and Famulok, M.
    Orthogonally Photocontrolled Non-Autonomous DNA Walker.
    Angew. Chem. Int. Ed Engl. 2019, doi: 10.1002/anie.201901272

2018

  • Kerzhner, M., Matsuoka, H., Wübben, C., Famulok, M. and Schiemann, O.
    High-Yield Spin Labeling of Long RNAs for Electron Paramagnetic Resonance Spectroscopy.
    Biochemistry. 2018, doi: 10.1021/acs.biochem.8b00040
  • Valero, J., Pal, N., Dhakal, S., Walter, NG. and Famulok, M.
    A bio-hybrid DNA rotor-stator nanoengine that moves along predefined tracks.
    Nat. Nanotechnol. 2018, doi: 10.1038/s41565-018-0109-z
  • Domenyuk, V., Gatalica, Z., Santhanam, R., Wei, X., Stark, A., Kennedy, P., Toussaint, B., Levenberg, S., Wang, J., Xiao, N., Greil, R., Rinnerthaler, G., Gampenrieder, SP., Heimberger, AB., Berry, DA., Barker, A., Quackenbush, J., Marshall, JL., Poste, G., Vacirca, JL., Vidal, GA., Schwartzberg, LS., Halbert, DD., Voss, A., Magee, D., Miglarese, MR., Famulok, M., Mayer, G. and Spetzler, D.
    Poly-ligand profiling differentiates trastuzumab-treated breast cancer patients according to their outcomes. 
    Nat. Commun. 2018, doi: 10.10138/s41467-018-03631-z
  • Prusty, DK., Adam, V., Zadegan, RM., Irsen, S. and Famulok, M.
    Supramolecular aptamer nano-constructs for receptor-mediated targeting and light-triggered release of chemotherapeutics into cancer cells.
    Nat. Commun. 2018, doi: 10.1038/s41467-018-02929-2
  • Adam, V., Prusty, DK., Centola, M., Skugor, M., Hannam, JS., Valero, J., Klöckner, B. and Famulok, M.
    Expanding the Tollbox of Photoswitches for DNA Nanotechnology Using Arylazopyrazoles.
    Chemistry. 2018, doi: 10.1002/chem.201705500

2017

  • Centola, M., Valero, J. and Famulok, M.
    Allosteric Control of Oxidative Catalysis by a DNA Rotaxane Nanostructure.
    J Am Chem. Soc. 2017, doi: 10.1021/jacs.7b08839
  • Yin, DM., Hannam, JS., Schmitz, A., Schiemann, O., Hagelücken, G. and Famulok, M.
    Studying the Conformation of a Receptor Tyrosine Kinase in Solution by Inhibitor-Based Spin.
    Angew. Chem. Int. Ed. Engl. 2017, doi: 10.1002/anie.201703154
  • Valero, J., Lohmann, F. and Famulok, M.
    Interlocked DNA topologies for nanotechnology.
    Curr. Opin Biotechnol. 2017, doi: 10.1016/j.copbio.2017.04.002
  • Domenyuk, V., Zhong, Z., Stark, A., Xiao, N., O'Neill, HA., Wei, X., Wang, J., Tinder, TT., Tonapi, S., Duncan, J., Hornung, T., Hunter, A., Miglarese, MR., Schorr, J., Halbert, DD., Quackenbush, J., Poste, G., Berry, DA., Mayer, G., Famulok, M. and Spetzler, D.
    Plasma Exosome Profiling of Cancer Patiens by a Next Generation Systems Biology Approach.
    Sci. Rep. 2017, doi: 10.1038/srep42741

2016

  • Kerzhner, M., Abdullin, D, Wiecek, J., Matsuoka, H., Hagenlücken, G., Schiemann, O. and Famulok, M.
    Post-synthetic Spin-Labeling of RNA through Click Chemistry for PELDOR Measurements.
    Chemistry. 2016, doi: 10.1002/chem. 201601897
  • Weigandt, J., Chung, C. L., Jester, S. S., and Famulok, M.
    Daisy Chain Rotaxanes Made from Interlocked DNA Nanostructures.
    Angew. Chem. Int. Ed.2016, doi: 10.1002/anie.201601042.
  • Valero, J., Lohmann, F., Keppner, D., and Famulok, M.
    Single-stranded tile stoppers for interlocked DNA architectures.
    Chembiochem. 2016, doi: 10.1002/cbic.201500685

2015

  • Lu, C. H., Cecconello, A., Qi, X. J., Wu, N., Jester, S. S., Famulok, M., Matthies, M., Schmidt, T. L., and Willner, I.
    Switchable Reconfiguration of a Seven-Ring Interlocked DNA Catenane Nanostructure.
    Nano Lett.2015, 15, 7133-7137.

  • Zhai, J., Zhang, L., Mojsilovic-Petrovic, J., Jian, X., Thomas, J., Homma, K., Schmitz, A., Famulok, M., Ichijo, H., Argon, Y., Randazzo, P. A., and Kalb, R. G.
    Inhibition of Cytohesins Protects against Genetic Models of Motor Neuron Disease.
    J. Neurosci. 2015, 35, 9088-9105.
  • Lentz, C. S., Sattler, J. M., Fendler, M., Gottwalt, S., Halls, V. S., Strassel, S., Arriens, S., Hannam, J. S., Specht, S., Famulok, M., Mueller, A. K., Hoerauf, A., and Pfarr, K. M.
    In vitro activity of wALADin-benzimidazoles against different life-cycle stages of Plasmodium parasites.
    Antimicrob. Agents Chemother. 2015, 59, 654-658.

2014

  • Li, T., Lohmann, F., and Famulok, M.
    Interlocked DNA nanostructures controlled by a reversible logic circuit.
    Nat. Commun. 2014, 5, 4940. [PDF]
     
  • Mayer, G. and Famulok, M.
    Aptamer and SELEX in Chemistry & Biology.
    Chem. Biol. 2014, 5, 21:1055-8, doi 10.1016
  • Lohmann, F., Weigandt, J., Valero, J., and Famulok, M.
    Logic gating by macrocycle displacement using a double-stranded DNA [3]rotaxane shuttle.
    Angew. Chem. Int. Ed.2014, 53, 10372-10376. [PDF]
  • Lu, C. H., Qi, X. J., Cecconello, A., Jester, S. S., Famulok, M., and Willner, I.
    Switchable reconfiguration of an interlocked DNA olympiadane nanostructure.
    Angew. Chem. Int. Ed.2014, 53, 7499-7503. [PDF]
  • Lohmann, F., Valero, J., and Famulok, M.
    A novel family of structurally stable double stranded DNA catenanes.
    Chem. Commun. 2014, 50, 6091-6093. [PDF]
     
  • Jester, SS. and Famulok, M.
    Mechanically interlocked DNA nanostructures for functional devices.
    Acc. Chem. Res.. 2014, 47:1700-9, doi:10.1021/ar400321h.
     
  • Lentz, C. S., Halls, V. S., Hannam, J. S., Strassel, S., Lawrence, S. H., Jaffe, E. K., Famulok, M., Hoerauf, A., and Pfarr, K. M.
    wALADin benzimidazoles differentially modulate the function of porphobilinogen synthase orthologs.
    J. Med. Chem. 2014, 57, 2498-2510. [PDF]

2013

  • Hussein, M., Bettio, M., Schmitz, A., Hannam, J.S., Theis, J., Mayer, G., Dosa, S., Gütschow, M., and Famulok, M.
    Cyplecksins are covalent inhibitors of the pleckstrin homology domain of cytohesin.
    Angew. Chem. Int. Ed. 2013, 52, 9529-9533. [PDF]

  • Niebel, B., Wosnitza, C., and Famulok, M.
    RNA-aptamers that modulate the RhoGEF activity of Tiam1.
    Bioorg. Med. Chem. 2013, 21, 6239-6246. [PDF]

  • Lentz, C. S., Halls, V., Hannam, J. S., Niebel, B., Strübing, U., Mayer, G., Hoerauf, A., Famulok, M.*, and Pfarr, K. M.*
    A selective inhibitor of heme biosynthesis in endosymbiotic bacteria elicits antifilarial activity in vitro.
    Chem. Biol. 2013, 20, 177-187. [PDF]
    *shared PIs

  • Li, T., and Famulok, M.
    I-motif-programmed functionalization of DNA nanocircles.
    J. Am. Chem. Soc. 2013, 135, 1593-1599. [PDF]

  • Ackermann, D., and Famulok, M.
    Pseudo-complementary PNA actuators as reversible switches in dynamic DNA nanotechnology.
    Nucleic Acids Res. 2013, 41, 4729-4739. [PDF]

2012

  • Vinkenborg, J. L., Mayer, G., and Famulok, M.
    Aptamer-based affinity labeling of proteins.
    Angew. Chem. Int. Ed. 2012, 51, 9176-9180. [PDF]

  • Bill, A., Schmitz, A., König, K., Heukamp, L. C., Hannam, J. S., and Famulok, M.
    Anti-proliferative effect of cytohesin inhibition in gefitinib-resistant lung cancer cells.
    PLoS ONE 2012, 7, e41179. [PDF]

  • Lohmann, F., Ackermann, D., and Famulok, M.
    Reversible light switch for macrocycle mobility in a DNA rotaxane.
    J. Am. Chem. Soc. 2012, 134, 11884-11887. [PDF]

  • Ackermann, D., Jester, S. S., and Famulok, M.
    Design strategy for DNA rotaxanes with a mechanically reinforced PX100 axle.
    Angew. Chem. Int. Ed. 2012, 51, 6771-6775.

  • Hons, M., Niebel, B., Karnowski, N., Weiche, B., and Famulok, M.
    Pan-selective aptamers for the family of small GTPases.
    ChemBioChem 2012, 13, 1433-1437. [PDF]

  • Li, J., Malaby, A. W., Famulok, M., Sabe, H., Lambright, D. G., Hsu, V. W.
    Grp1 plays a key role in linking insulin signaling to glut4 recycling.
    Dev. Cell 2012, 22, 1286-1298. [PDF]

  • Li, T., Ackermann, D., Hall, A. M., and Famulok, M.
    Input-dependent induction of oligonucleotide structural motifs for performing molecular logic.
    J. Am. Chem. Soc. 2012, 134, 3508-3516. [PDF]

  • Rohrbach, F., Karadeniz, H., Erdem, A., Famulok, M., and Mayer, G.
    Label-free impedimetric aptasensor for lysozyme detection based on carbon nanotube-modified screen-printed electrodes.
    Anal. Biochem. 2012, 421, 454-459. [PDF]

  • Albertoni, B., Hannam, J. S., Ackermann, D., Schmitz, A., and Famulok, M.
    A trifluoromethylphenyl diazirine-based SecinH3 photoaffinity probe.
    Chem. Commun. 2012, 48, 1272-1274. [PDF]

  • Miao, B., Skidan, I., Yang, J., You, Z., Fu, X., Famulok, M., Schaffhausen, B., Torchilin, V., Yuan, J., and Degterev, A.
    Inhibition of cell migration by PITENINs: the role of ARF6.
    Oncogene 2012, 31, 4317-4332. [PDF]

2011

  • Beyer, M., Thabet, Y., Müller, R. U., Sadlon, T., Classen, S., Lahl, K., Basu, S., Zhou, X., Bailey-Bucktrout, S. L., Krebs, W., Schönfeld, E. A., Böttcher, J., Golovina, T., Mayer, C. T., Hofmann, A., Sommer, D., Debey-Pascher, S., Endl, E., Limmer, A., Hippen, K. L., Blazar, B. R., Balderas, R., Quast, T., Waha, A., Mayer, G., Famulok, M., Knolle, P. A., Wickenhauser, C., Kolanus, W., Schermer, B., Bluestone, J. A., Barry, S. C., Sparwasser, T., Riley, J. L., and Schultze, J. L.
    Repression of the genome organizer SATB1 in regulatory T cells is required for suppressive function and inhibition of effector differentiation.
    Nat. Immunol.2011,12, 898-907. [PDF]

  • Niebel, B., Weiche, B., Mueller, A. L., Li, D. Y., Karnowski, N., and Famulok, M.
    A luminescent oxygen channeling biosensor that measures small GTPase activation.
    Chem. Commun. 2011, 47, 7521-7523. [PDF]

  • Bill, A., Blockus, H., Stumpfe, D., Bajorath, J., Schmitz, A., and Famulok, M.
    A homogeneous fluorescence resonance energy transfer system for monitoring the activation of a protein switch in real time.
    J. Am. Chem. Soc. 2011, 133, 8372-8379. [PDF]

2010

  • Mayer, G., Ahmed, M-S. L., Dolf, A., Endl, E., Knolle, P. A., and Famulok, M.
    Fluorescence-activated cell sorting for aptamer SELEX with cell mixtures.
    Nature Protocols 2010, 5, 1993-2004. [PDF]

  • Bill, A., Schmitz, A., Albertoni, B., Song, J-N., Heukamp, L. C., Walrafen, D., Thorwirth, F., Verveer, J. P., Zimmer, S., Meffert, L., Schreiber, A., Chatterjee, S., Thomas, R. K., Ullrich, R. T., Lang, T., and Famulok, M.
    Cytohesins are cytoplasmic ErbB receptor activators.
    Cell 2010, 143, 201-211. [PDF]

  • Stumpfe, D., Bill, A., Novak, N., Loch, G., Blockus, H., Geppert, H., Becker, T., Schmitz, A., Hoch, M., Kolanus, W., Famulok, M.*, and Bajorath, J.*
    Targeting multifunctional proteins by virtual screening: structurally diverse cytohesin inhibitors with differentiated biological functions.
    ACS Chem. Biol. 2010, 5, 839-849. [PDF]
    *shared PIs
  • Niebel, B., Lentz, C., Pofahl, M., Mayer, G., Hoerauf, A., Pfarr, K. M., and Famulok, M. 
    ADLOC – an aptamer-displacement assay based on luminescent oxygen channeling. 
    Chemistry 2010, 16, 11100-11107. [PDF]
  • Lünse, C. E., Michlewski, G., Hopp, C. S., Rentmeister, A., Cáceres, J. F., Famulok, M.*, and Mayer, G.*
    An aptamer targeting the apical-loop domain modulates pri-miRNA processing.
    Angew. Chem. Int. Ed. 2010, 49, 4674-4677. [PDF]
    *shared PIs

  • Ackermann, D., Rasched, G., Verma, S., Schmidt, T. L., Heckel, A., and Famulok, M.
    Assembly of dsDNA nanocircles into dimeric and oligomeric aggregates. 
    Chem. Commun. 2010, 46, 4154-4156. [PDF]

  • Ackermann, D., Schmidt, T. L., Hannam, J. S., Purohit, C. S., Heckel, A., and Famulok, M.
    A double-stranded DNA rotaxane.
    Nat. Nanotechnol. 2010, 5, 436-442. [PDF]

2009

  • Klotz, L., Burgdorf, S., Dani, I., Saijo, K., Flossdorf, J., Hucke, S., Alferink, J., Novak, N., Beyer, M., Mayer, G., Langhans, B., Klockgether, T., Waisman, A., Eberl, G., Schultze, J., Famulok, M., Kolanus, W., Glass, C., Kurts, C., and Knolle, P. A.
    The nuclear receptor PPARg selectively controls TH17 differentiation in a T cell-intrinsic fashion and suppresses CNS autoimmunity.
    J. Exp. Med. 2009, 206, 2079-2089. [PDF]

  • Jones, C. A., Nishiya, N., London, N. R., Zhu, W., Sorensen, L. K., Chan, A., Lim, C. J., Chen, H., Zhang, Q., Schultz, P. G., Hayallah, A. M., Thomas, K. R., Famulok, M., Zhang, K., Ginsberg, M. H., and Li, D. Y.
    Slit2-Robo4 signaling promotes vascular stability by blocking Arf6 activity.
    Nat. Cell Biol. 2009, 11, 1325-1331. [PDF]

  • Gronewold, T. M. A., Baumgartner, A., Hierer, J., Huber, C., Blind, M., Schäfer, F., Blümer, J., Tillmann, T., Kiwitz, A., Zabe-Kühn, M., Quandt, E., and Famulok, M.
    Kinetic binding analysis of aptamers targeting HIV-1 proteins by a combination of a microbalance array and mass spectrometry (MAMS).
    J. Proteome Res. 2009, 8, 3568-3577. [PDF]

  • Beyer, M., Karbach, J., Mallmann, M. R., Zander, T., Eggle, D., Classen, S., Debey-Pascher, S., Famulok, M., Jäger, E., and Schultze, J. L.
    Cancer vaccine enhanced, non-tomour-reactive CD8(+) T cells exhibit a distinct molecular program associated with ‘division arrest anergy’.
    Cancer Res. 2009, 69, 4346-4354. [PDF]

  • Erdem, A.*, Karadeniz, H., Mayer, G., Famulok, M.*, and Caliskan, A.
    Electrochemical sensing of aptamer-protein interactions using magnetic particle assay and single-use sensor technology.
    Electroanalysis 2009, 21, 1278-1284. [PDF]
    *shared PIs

2008

  • Bi, X., Schmitz, A., Hayallah, A. M., Song, J.-N., and Famulok, M.
    Affinity-based labelling of cytohesins with a bifunctional SecinH3 photoaffinity probe.
    Angew. Chem. Int. Ed. 2008, 47, 9565-9568. [PDF]

  • Fusz, S., Srivatsan, S. G., Ackermann, D., and Famulok, M.
    Photocleavable initiator nucleotide substrates for an aldolase ribozyme.
    J. Org. Chem. 2008, 73, 5069-5077. [PDF]

  • Raddatz, M. S., Dolf, A., Endl, E., Knolle, P., Famulok, M., and Mayer, G.
    Enrichment of cell-targeting and population-specific aptamers by fluorescence-activated cell sorting.
    Angew. Chem. Int. Ed. 2008, 47, 5190-5193. [PDF]

  • Hafner, M., Vianini, E., Albertoni, B., Marchetti, L., Grüne, I., Gloeckner, C., and Famulok, M.
    Displacement of protein-bound aptamers with small molecules screened by fluorescence polarization.
    Nature Protocols 2008, 3, 579-587. [PDF]
  • Mayer, G., Ackermann, D., Kuhn, N., and Famulok, M.
    Construction of DNA architectures with RNA hairpins.
    Angew. Chem. Int. Ed. 2008, 47, 971-973. [PDF]
  • Rasched, G., Ackermann, D., Schmidt, T. L., Broekmann, P., Heckel, A., and Famulok, M.
    DNA minicircles with gaps for versatile functionalization.
    Angew. Chem. Int. Ed. 2008, 47, 967-970. [PDF]

  • Rentmeister, A., Mayer, G., Kuhn, N., and Famulok, M.
    Secondary structures and functional requirements for thiM riboswitches from Desulfovibrio vulgaris, Erwinia carotovora and Rhodobacter spheroides.
    Biol. Chem. 2008, 389, 127-134. [PDF]

2007

  • Yamazaki, S., Tan, L., Mayer, G., Hartig, J. S., Song, J.-N., Reuter, S., Restle, T., Laufer, S. D., Grohmann, D., Kräusslich, H.-G., Bajorath, J., and Famulok, M.
    Aptamer displacement identifies alternative small-molecule target sites that escape viral resistance.
    Chem. Biol. 2007, 14, 804-812. [PDF]

Preview on Yamazaki et al. by Fowler, C. C., and Li, Y.
Aptamers and small molecules play tug of war.
Chem. Biol. 2007, 14, 736-738. [PDF]

    • Rentmeister, A., Mayer, G., Kuhn, N., and Famulok, M.
      Thiamine-pyrophosphate induced conformational changes in the expression domain of the thiM riboswitch.
      Nucleic Acids Res. 2007, 35, 3713-3722. [PDF]

    • Knieps, M., Herrmann, S., Lehmann, C., Löer, B., Hoch, M., and Famulok, M.
      Anti-innexin 2 aptamers specifically inhibit the heterologous interaction of the innexin 2 and innexin 3 carboxyl-termini in vitro.
      Biol. Chem. 2007, 388, 561-568. [PDF]

    • Schmidt, T. L., Nandi, C. K., Rasched, G., Parui, P. P., Brutschy, B., Famulok, M., and Heckel, A.
      Polyamide struts for DNA architectures.
      Angew. Chem. Int. Ed. 2007, 46, 4382-4384. [PDF]

    • Mayer, G., Raddatz, M.-S., Grunwald, J. D., and Famulok, M.
      RNA ligands that distinguish metabolite-induced conformations in the TPP riboswitch.
      Angew. Chem. 2007, 119, 563-566. [PDF]

    • Najafi-Shoushtari, S. H., and Famulok, M.
      DNA aptamer-mediated regulation of the hairpin ribozyme by human α-thrombin.
      Blood Cells Mol. Dis.2007, 38, 19-24. [PDF]

    2006

    • Wahle, T., Sastre, M., Thal, D. R., Rentmeister, A., Bogdanovic, N., Famulok, M., Heneka, M. T., and Walter, J.
      GGA1 is expressed in the human brain and affects the generation of amyloid beta-peptide.
      J. Neurosci. 2006, 26, 12838-12846. [PDF]

    • Hafner, M., Schmitz, A., Grüne, I., Srivatsan, S. G., Paul, B., Kolanus, W., Quast, T., Kremmer, E., Bauer I., and Famulok, M.
      Inhibition of cytohesins by SecinH3 leads to hepatic insulin resistance.
      Nature 2006, 444, 941-944. [PDF]

    News and Views on Hafner et al. by Jackson, C. L.
    Diabetes: Kicking off the insulin cascade.
    Nature2006, 444, 833-834. [PDF]

      • Rentmeister, A., Bill, A., Wahle, T., Walter, J., and Famulok, M.
        RNA aptamers selectively modulate protein recruitment to the cytoplasmic domain of ß-secretase BACE1 in vitro.
        RNA 2006, 12, 1650-1660. [PDF] - [Supplementary material]

      • Gronewold, T., Baumgartner, A., Quandt, E., and Famulok, M.
        Discrimination of single mutations in cancer-related gene fragments with a surface acoustic wave sensor.
        Anal. Chem. 2006, 78, 4865-4871. [PDF]

      • Lehmann, C., Lechner, H., Löer, B., Knieps, M., Herrmann, S., Famulok, M., Bauer, R. and Hoch, M.
        Heteromerization of Innexin gap junction proteins regulates epithelial tissue organization in Drosophila.
        Mol. Biol. Cell 2006, 17, 1676-1685. [PDF]

      • Mayer, G., and Famulok, M.
        High-throughput-compatible assay for glmS riboswitch metabolite dependence.
        ChemBioChem 2006, 7, 602-604. [PDF]

      • Kettenberger, H., Eisenführ, A., Brueckner, F., Theis, M., Famulok, M.*, and Cramer, P.*
        Structure of an RNA polymerase II-RNA inhibitor complex elucidates transcription regulation by noncoding RNAs.
        Nat. Struc. Mol. Biol. 2006, 13, 44-48. [PDF]
        *shared PIs