Chemical Biology

Max Planck Fellow

We focus on the structural analysis of biomolecules and on photo-activatable substances.

Publications

Yin, D.M., Hammler, D., Peter, M.F., Marx, A., Schmitz, A. & Hagelueken, G. (2018) “Inhibitor-directed spin labelling - a high precision and minimally invasive technique to study the conformation of proteins in solution.” Chem. Eur. J. , [Epub ahead of print]

Yin, D.M., Hannam, J.S., Schmitz, A., Schiemann, O., Hagelueken, G. & Famulok, M. (2017) “Studying the Conformation of a Receptor Tyrosine Kinase in Solution by Inhibitor-Based Spin Labeling” Angew. Chem. Int. Ed. Engl. 56, 8417–8421

Domenyuk, V., Zhong, Z., Stark, A., Xiao, N., O'Neill, H.A., Wei, X., Wang, J., Tinder, T.T., Tonapi, S., Duncan, J., Hornung, T., Hunter, A., Miglarese, M.R., Schorr, J., Halbert, D.D., Quackenbusch, J., Poste, G., Berry, D.A., Mayer, G., Famulok, M. & Spetzler, D. (2017) "Plasma exosome profiling of cancer patients by a next generation systems biology approach" Sci. Rep. 7, 42741

Kerzhner, M., Abdullin, D., Wiecek, J., Matsuoka, H., Hagelueken, G., Schiermann, O. & Famulok, M. (2016) "Post-synthetic Spin-Labeling of RNA through Click Chemistry for PELDOR Measurements" Eur. J. Chem. 22, 12113 - 12121

Valero, J., Lohmann, F., Keppner, D. & Famulok, M. (2016) "Single-Stranded Tile Stoppers for Interlocked DNA Architectures" ChemBioChem 17, 1146-1149

Weigandt, J., Chung, C.-L., Jester, S. S. & Famulok, M. (2016) "Daisy Chain Rotaxanes Made from Interlocked DNA Nanostructures" Angew. Chem. Int. Ed. Engl. 55, 5512-5516 

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. & Pfarr, K. (2015) "In vitro activity of wALADin benzimidazoles against different life cycle stages of plasmodium parasites" Antimicrob. Agents Chemother.59, 654 - 658 

Lu, C.-H., Cecconello, A., Oi, X.-J., Wu, N., Jester, S.-S., Famulok, M., Matthies, M., Schmidt, T.-L. & Willner, I. (2015) "Switchable Reconfiguration of a seven-ring interlocked DNA catenane nanostructure" Nano Lett. 15, 7133 – 7137 

Zhai, J., Zhang, L., Mojsilovic-Petrovic, J., Jian, X., Thomas, J., Homma, K., Schmitz, A., Famulok, M., Ichijo, H., Randazzo, P. A. & Kalb, R.G. (2015) "Inhibition of cytohesins protects against genetic models of motor neuron disease" J. Neurosci. 35, 9088 - 9105 

Famulok, M. & Mayer, G. (2014) "Aptamers and SELEX in Chemistry & Biology" Chem. Biol. 21, 1055 - 1058 

Jester, S.S. & Famulok, M. (2014) "Mechanically interlocked DNA nanostructures for functional devices" Acc. Chem. Res. 47, 1700 - 1709 

Lentz, C.S., Halls, V.S., Hannam, J.S., Strassel, S., Lawrence, S.H., Jaffe, E.K., Famulok, M., Hoerauf, A. & Pfarr, K.M. (2014) "wALADin benzimidazoles differentially modulate the function of porphobilinogen synthase orthologs" J. Med. Chem. 57, 2498 – 2510 

Li, T., Lohmann, F. & Famulok, M. (2014) "Interlocked DNA nanostructures controlled by a reversible logic circuit" Nat. Commun. 5, 4940 

Lohmann, F., Valero, J. & Famulok, M. (2014) "A novel family of structurally stable double stranded DNA catenanes" Chem. Commun. (Camb.) 50, 6091 - 6093 

Lohmann, F., Weigandt, J., Valero, J. & Famulok, M. (2014) "Logic Gating by Macrocycle Displacement Using a Double-Stranded DNA 3 Rotaxane Shuttle" Angew. Chem. Int. Ed. Engl. 53, 10372 - 10376 

Lu, C.H., Qi, X.J., Cecconello, A., Jester, S.S., Famulok, M. & Willner, I. (2014) "Switchable reconfiguration of an interlocked DNA olympiadane nanostructure" Angew. Chem. Int. Ed. Engl. 53, 7499 - 7503 

Ackermann, D. & Famulok, M. (2013) "Pseudo-complementary PNA actuators as reversible switches in dynamic DNA nanotechnology" Nucleic Acids Res. 41, 4729 - 4739 

Hussein, M., Bettio, M., Schmitz, A., Hannam, J.S., Theis, J., Mayer, G., Dosa, S., Gütschow, M. & Famulok, M. (2013) "Cyplecksins are covalent inhibitors of the pleckstrin homology domain of cytohesin" Angew. Chem. Int. Ed. Engl. 52, 9529 - 9533 

Lentz, C.S., Halls, V., Hannam, J.S., Niebel, B., Strübing, U., Mayer, G., Hoerauf, A., Famulok, M. & Pfarr, K.M. (2013) "A selective inhibitor of heme biosynthesis in endosymbiotic bacteria elicits antifilarial activity in vitro" Chem. Biol. 20, 177 - 187 

Lentz, C.S., Stumpfe, D., Bajorath, J., Famulok, M., Hoerauf, A. & Pfarr, K. M (2015) "New chemotypes for wALADin1-like inhibitors of delta-aminolevulinic acid dehydratase from Wolbachia endobacteria" Bioorg. Med. Chem. Lett. 23, 5558 - 5562 

Li, T. & Famulok, M. (2013) "I-motif-programmed functionalization of DNA nanocircles" J. Am. Chem. Soc. 135, 1593 - 1599 

Niebel, B., Wosnitza, C.I. & Famulok, M. (2013) "RNA-aptamers that modulate the RhoGEF activity of Tiam1" Bioorg. Med. Chem. 21, 6239 - 6246  

Ackermann, D., Jester, S.S. & Famulok, M. (2012) "Design strategy for DNA rotaxanes with a mechanically reinforced PX100 axle" Angew. Chem. In.t Ed. Engl. 51, 6771 - 6775 

Albertoni, B., Hannam, J.S., Ackermann, D., Schmitz, A. & Famulok, M. (2012) "A trifluoromethylphenyl diazirine-based SecinH3 photoaffinity probe" Chem. Commun. (Camb.) 48, 1272 - 1274 

Bill, A., Schmitz, A., König, K., Heukamp, L.C., Hannam, J. S. & Famulok, M. (2012) "Anti-proliferative effect of cytohesin inhibition in gefitinib-resistant lung cancer cells" Plos One 7, e41179 

Hons, M., Niebel, B., Karnowski, N., Weiche, B. & Famulok, M. (2012) "Pan-selective aptamers for the family of small GTPases" Chembiochem 13, 1433 - 1437 

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

Li, T., Ackermann, D., Hall, A.M. & Famulok, M. (2012) "Input-dependent induction of oligonucleotide structural motifs for performing molecular logic" J. Am. Chem. Soc. 134, 3508 - 3516 

Lohmann, F., Ackermann, D. & Famulok, M. (2012) "Reversible light switch for macrocycle mobility in a DNA rotaxane" J. Am. Chem. Soc. 134, 11884 - 11887 

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

Rohrbach, F., Karadeniz, H., Erdem, A., Famulok, M. & Mayer, G. (2012) "Label-free impedimetric aptasensor for lysozyme detection based on carbon nanotube-modified screen-printed electrodes" Analytical biochemistry 421, 454 - 459 

Vinkenborg, J.L., Mayer, G. & Famulok, M. (2012) "Aptamer-based affinity labeling of proteins" Angew. Chem. In.t Ed. Engl. 51, 9176 - 9180 

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. & Schultze, J.L. (2011) "Repression of the genome organizer SATB1 in regulatory T cells is required for suppressive function and inhibition of effector differentiation" Nat. Immunol. 12, 898 - 907 

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

Famulok, M. & Mayer, G. (2011) "Aptamer modules as sensors and detectors" Acc. Chem. Res. 44, 1349 - 1358 

Niebel, B., Weiche, B., Mueller, A.L., Li, D.Y., Karnowski, N. & Famulok, M. (2011) "A luminescent oxygen channeling biosensor that measures small GTPase activation" Chem. Commun. 47, 7521 - 7523 

Vinkenborg, J.L., Karnowski, N. & Famulok, M. (2011) "Aptamers for allosteric regulation" Nat. Chem. Biol. 7, 519 - 527 

Ackermann, D., Rasched, G., Verma, S., Schmidt, T.L., Heckel, A. & Famulok, M. (2010) "Assembly of dsDNA nanocircles into dimeric and oligomeric aggregates" Chem. Commun. (Camb.) 46, 4154 - 4156 

Ackermann, D., Schmidt, T.L., Hannam, J.S., Purohit, C.S., Heckel, A. & Famulok, M. (2010) "A double-stranded DNA rotaxane" Nat. Nanotechn. 5, 436 - 442 

Lünse, C.E., Michlewski, G., Hopp, C.S., Rentmeister, A., Caceres, J.F., Famulok, M. & Mayer, G. (2010) "An aptamer targeting the apical-loop domain modulates pri-miRNA processing" Angew. Chem. Int. Ed. Engl. 49, 4674 - 4677 

Mayer, G., Ahmed, M.S., Dolf, A., Endl, E., Knolle, P.A. & Famulok, M. (2010) "Fluorescence-activated cell sorting for aptamer SELEX with cell mixtures" Nat. Protoc. 5, 1993 - 2004 

Niebel, B., Lentz, C., Pofahl, M., Mayer, G., Hoerauf, A., Pfarr, K.M. & Famulok, M. (2010) "ADLOC: an aptamer-displacement assay based on luminescent oxygen channeling" Chemistry 16, 11100 - 11107 

Stumpfe, D., Bill, A., Novak, N., Loch, G., Blockus, H., Geppert, H., Becker, T., Schmitz, A., Hoch, M., Kolanus, W., Famulok, M. & Bajorath, J. (2010) "Targeting multifunctional proteins by virtual screening: structurally diverse cytohesin inhibitors with differentiated biological functions" ACS Chem. Biol. 5, 839 - 849

Klotz, L., Burgdorf, S., Dani, I., Saijo, K., Flossdorf, J., Hucke, S., Alferink, J., Nowak, N., Beyer, M., Mayer, G., Langhans, B., Klockgether, T., Waisman, A., Eberl, G., Schultze, J., Famulok, M., Kolanus, W., Glass, C., Kurts, C. & Knolle, P.A. (2009) "The nuclear receptor PPAR gamma selectively inhibits Th17 differentiation in a T cell-intrinsic fashion and suppresses CNS autoimmunity" J. Exp. Med. 206, 2079-2089

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, R.K., Famulok, M., Zhang, K., Ginsberg, H.H. & Li, D.Y. (2009) "Slit2-Robo4 signaling promotes vascular stability by blocking Arf6 activity" Nat. Cell Biol. 11, 1325-1331

Gronewold, T.M., Baumgartner, A., Hierer, J., Sierra, S., Blind, M., Schäfer, F., Blümer, J., Tillmann, T., Kiwitz, A., Kaiser, R., Zabe-Kühn, M., Quandt, E. & Famulok, M. (2009) "Kinetic binding analysis of aptamers targeting HIV-1 proteins by a combination of a microbalance array and mass spectrometry (MAMS)" J. Proteome Res. 8, 3568-3577

Beyer, M., Karbach, J., Mallmann, M.R., Zander, T., Eggle, D., Classen, S., Debey-Pascher, S., Famulok, M., Jäger, E. & Schultze, J.L. (2009) "Cancer vaccine enhanced, non-tumor-reactive CD8(+) T cells exhibit a distinct molecular program associated with "division arrest anergy" Cancer Res. 69, 4346-4354

Erdem, A., Karadeniz, H., Mayer, G., Famulok, M. & Caliskan, A. (2009) "Electrochemical sensing of aptamer-protein interactions using magnetic particle assay and single-use sensor technology" Electroanalysis 21, 1278-1284

Famulok, M. (2009) "Exploring chemical space with aptamers" J. Med. Chem. 52, 6951-6957

Bi, X., Schmitz, A., Hayallah, A.M., Song, J.N. & Famulok, M. (2008) "Affinity-based labeling of cytohesins with a bifunctional SecinH3 photoaffinity probe" Angew. Chem. Int. Ed. 47, 9565-9568

Fusz, S., Srivatsan, S.G., Ackermann, D. & Famulok, M. (2008) "Photocleavable initiator nucleotide substrates for an aldolase ribozyme" J. Org. chem. 73, 5069-5077

Hafner, M., Vianini, E., Albertoni, B., Marchetti, L., Grüne, I., Gloeckner, C. & Famulok, M. (2008) "Displacement of protein-bound aptamers with small molecules screened by fluorescence polarization" Nat. Prot. 3, 579-587

Heckel, A. & Famulok, M. (2008) "Building objects from nucleic acids for a nanometer world" Biochimie 90, 1096-1107

Mayer, G., Ackermann, D., Kuhn, N. & Famulok, M. (2008) "Construction of DNA architectures with RNA hairpins" Angew. Chem. Int. Ed. 47, 971-973

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

Rasched, G., Ackermann, D., Schmidt, T.L., Broekmann, P., Heckel, A. & Famulok, M. (2008) "DNA minicircles with gaps for versatile functionalization" Angew. Chem. Int. Ed. 47, 967-970

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