Selected Publications for ATTO 550:
B. Agrawalla, T. Wang, A. Riegger, M. Domogalla, K. Steinbrink, T. Dörfler, X. Chen, F. Boldt, M. Lamla, J. Michaelis, S. Kuan, T. Weil, Chemoselective Dual Labeling of Native and Recombinant Proteins, Bioconjugate Chemistry 29, 29 (2018).
H. Bagheri, H. Friedman, H. Shao, Y. Chong, C.-A. Lo, F. Emran, I. Kays, X.-J. Yang, E. Cooper, B. Chen, K. Siminovitch, A. Peterson, TIE, The CRISPR journal 1, 223 (2018).
S. Baliga, C. Murphy, L. Sharon, S. Shenoy, D. Biranthabail, H. Weltman, S. Miller, R. Ramasamy, J. Shah, Rapid method for detecting and differentiating Mycobacterium tuberculosis complex and non-tuberculous mycobacteria in sputum by fluorescence in situ hybridization with DNA probes, International Journal of Infectious Diseases 75, 1 (2018).
A. Borgia, M. Borgia, K. Bugge, V. Kissling, P. Heidarsson, C. Fernandes, A. Sottini, A. Soranno, K. Buholzer, D. Nettels, B. Kragelund, R. Best, B. Schuler, Extreme disorder in an ultrahigh-affinity protein complex, Nature 555, 61 (2018).
D. Bracha, M. Walls, M.-T. Wei, L. Zhu, M. Kurian, J. Avalos, J. Toettcher, C. Brangwynne, Mapping Local and Global Liquid Phase Behavior in Living Cells Using Photo-Oligomerizable Seeds, Cell 175, 1467-1480.e13 (2018).
J. Churko, P. Garg, B. Treutlein, M. Venkatasubramanian, H. Wu, J. Lee, Q. Wessells, S.-Y. Chen, W.-Y. Chen, K. Chetal, G. Mantalas, N. Neff, E. Jabart, A. Sharma, G. Nolan, N. Salomonis, J. Wu, Defining human cardiac transcription factor hierarchies using integrated single-cell heterogeneity analysis, Nature Communications 9, 4906 (2018).
D. Daems, W. Pfeifer, I. Rutten, B. Saccà, D. Spasic, J. Lammertyn, Three-Dimensional DNA Origami as Programmable Anchoring Points for Bioreceptors in Fiber Optic Surface Plasmon Resonance Biosensing, ACS Applied Materials & Interfaces 10, 23539 (2018).
F. Dake, Y. Taki, Time-domain fluorescence lifetime imaging by nonlinear fluorescence microscopy constructed of a pump-probe setup with two-wavelength laser pulses, Applied Optics 57, 757 (2018).
L. Dirix, K. Kennes, E. Fron, Z. Debyser, M. van der Auweraer, J. Hofkens, S. Rocha, Photoconversion of Far-Red Organic Dyes, ChemPhotoChem 2, 433 (2018).
B. Hellenkamp, S. Schmid, O. Doroshenko, O. Opanasyuk, R. Kühnemuth, S. Rezaei Adariani, B. Ambrose, M. Aznauryan, A. Barth, V. Birkedal, M. Bowen, H. Chen, T. Cordes, T. Eilert, C. Fijen, C. Gebhardt, M. Götz, G. Gouridis, E. Gratton, T. Ha, P. Hao, C. Hanke, A. Hartmann, J. Hendrix, L. Hildebrandt, V. Hirschfeld, J. Hohlbein, B. Hua, C. Hübner, E. Kallis, A. Kapanidis, J.-Y. Kim, G. Krainer, D. Lamb, N. Lee, E. Lemke, B. Levesque, M. Levitus, J. McCann, N. Naredi-Rainer, D. Nettels, T. Ngo, R. Qiu, N. Robb, C. Röcker, H. Sanabria, M. Schlierf, T. Schröder, B. Schuler, H. Seidel, L. Streit, J. Thurn, P. Tinnefeld, S. Tyagi, N. Vandenberk, A. Vera, K. Weninger, B. Wünsch, I. Yanez-Orozco, J. Michaelis, C. Seidel, T. Craggs, T. Hugel, Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study, Nature Methods 15, 669 (2018).
A. Ingargiola, S. Weiss, E. Lerner, Monte Carlo Diffusion-Enhanced Photon Inference, The Journal of Physical Chemistry B 122, 11598 (2018).
J. Nikolic, L. Belot, H. Raux, P. Legrand, Y. Gaudin, A. Albertini, Structural basis for the recognition of LDL-receptor family members by VSV glycoprotein, Nature Communications 9, 1029 (2018).
M. Pazos, K. Peters, M. Casanova, P. Palacios, M. VanNieuwenhze, E. Breukink, M. Vicente, W. Vollmer, Z-ring membrane anchors associate with cell wall synthases to initiate bacterial cell division, Nature Communications 9, 5090 (2018).
W. Ren, S. Wen, S. Tawfik, Q. Su, G. Lin, L. Ju, M. Ford, H. Ghodke, A. van Oijen, D. Jin, Anisotropic functionalization of upconversion nanoparticles, Chemical Science 9, 4352 (2018).
D. Roth, M. Nasir, P. Ginzburg, P. Wang, A. Le Marois, K. Suhling, D. Richards, A. Zayats, Förster Resonance Energy Transfer inside Hyperbolic Metamaterials, ACS Photonics 5, 4594 (2018).
D. Rutz, Q. Luo, L. Freiburger, T. Madl, V. Kaila, M. Sattler, J. Buchner, A switch point in the molecular chaperone Hsp90 responding to client interaction, Nature Communications 9, 1472 (2018).
R. Schoch, I. Barel, F. Brown, G. Haran, Lipid diffusion in the distal and proximal leaflets of supported lipid bilayer membranes studied by single particle tracking, The Journal of Chemical Physics 148, 123333 (2018).
M. Urban, S. Both, C. Zhou, A. Kuzyk, K. Lindfors, T. Weiss, N. Liu, Gold nanocrystal-mediated sliding of doublet DNA origami filaments, Nature Communications 9, 1454 (2018).
W. Ye, M. Götz, S. Celiksoy, L. Tüting, C. Ratzke, J. Prasad, J. Ricken, S. Wegner, R. Ahijado-Guzmán, T. Hugel, C. Sönnichsen, Conformational Dynamics of a Single Protein Monitored for 24 h at Video Rate, Nano letters 18, 6633 (2018).
U. Chio, S. Chung, S. Weiss, S.-O. Shan, A protean clamp guides membrane targeting of tail-anchored proteins, Proceedings of the National Academy of Sciences 114, E8585-E8594 (2017).
H. Mönck, D. Toppe, E. Michael, S. Sigrist, V. Richter, D. Hilpert, D. Raccuglia, M. Efetova, M. Schwärzel, A new method to characterize function of the Drosophila heart by means of optical flow, The Journal of experimental biology 220, 4644 (2017).
J. Shah, A. Poruri, O. Mark, U. Khadilka, F. Mohring, R. Moon, R. Ramasamy, A dual colour fluorescence in situ hybridization (FISH) assay for identifying the zoonotic malaria parasite Plasmodium knowlesi with a potential application for the specific diagnosis of knowlesi malaria in peripheral-level laboratories of Southeast Asia, Parasites & vectors 10, 342 (2017).
J. Shah, H. Weltman, P. Narciso, C. Murphy, A. Poruri, S. Baliga, L. Sharon, M. York, G. Cunningham, S. Miller, L. Caviedes, R. Gilman, E. Desmond, R. Ramasamy, Dual color fluorescence in situ hybridization (FISH) assays for detecting Mycobacterium tuberculosis and Mycobacterium avium complexes and related pathogens in cultures, PLOS ONE 12, e0174989 (2017).
O. Afolabi, A. Roeder, A. Iyengar, S. Hadi,
>Evaluation of genetic markers for forensic identification of human body fluids>, Forensic Science International: Genetics Supplement Series
6, e241-e243 (2017).
P. Comba, A. Eisenschmidt, L. Gahan, D.‐P. Herten, G. Nette, G. Schenk, M. Seefeld,
Is CuII Coordinated to Patellamides inside Prochloron Cells?, Chemistry - A European Journal (2017).
B. Dalzon, C. Aude-Garcia, V. Collin-Faure, H. Diemer, D. Béal, F. Dussert, D. Fenel, G. Schoehn, S. Cianférani, M. Carrière, T. Rabilloud,
Differential proteomics highlights macrophage-specific responses to amorphous silica nanoparticles, Nanoscale
9, 9641 (2017).
R. Friedrich, S. Block, M. Alizadehheidari, S. Heider, J. Fritzsche, E. Esbjörner, F. Westerlund, M. Bally,
A nano flow cytometer for single lipid vesicle analysis, Lab on a chip
17, 830 (2017).
V. Müller, F. Westerlund,
Optical DNA mapping in nanofluidic devices, Lab on a chip
17, 579 (2017).
A. Silvestri, D. Di Silvio, I. Llarena, R. Murray, M. Marelli, L. Lay, L. Polito, S. Moya, Influence of surface coating on the intracellular behaviour of gold nanoparticles, Nanoscale 9, 14730 (2017).
A. Andreoni, L. Nardo, R. Rigler,
Time-resolved homo-FRET studies of biotin-streptavidin complexes, Journal of Photochemistry and Photobiology B: Biology
162, 656 (2016).
J. Funke, H. Dietz,
Placing molecules with Bohr radius resolution using DNA origami, Nature Nanotechnology
11, 47 (2016).
X. Hopkins, W. Gill, R. Kringel, G. Wang, J. Hass, S. Acharya, J. Park, I. Jeon, B. An, J. Lee, J. Ryu, R. Hill, D. McIlroy, Y. Kim, D. Choi,
Radio frequency-mediated local thermotherapy for destruction of pancreatic tumors using Ni–Au core–shell nanowires, Nanotechnology
28, 03LT01 (2016).
H. Koh, X. Wang, S. Myong,
Visualizing repetitive diffusion activity of double-strand RNA binding proteins by single molecule fluorescence assays, Methods
105, 109 (2016).
J. Liu, V. Postupalenko, S. Lorcher, D. Wu, M. Chami, W. Meier, C. Palivan,
DNA-Mediated Self-Organization of Polymeric Nanocompartments Leads to Interconnected Artificial Organelles, Nano letters
16, 7128 (2016).
J. Scholefield, R. Henriques, A. Savulescu, E. Fontan, A. Boucharlat, E. Laplantine, A. Smahi, A. Israël, F. Agou, M. Mhlanga,
Super-resolution microscopy reveals a preformed NEMO lattice structure that is collapsed in incontinentia pigmenti, Nature Communications
7, 12629 (2016).
J. de Torres, M. Mivelle, S. Moparthi, H. Rigneault, N. van Hulst, M. Garcia-Parajo, E. Margeat, J. Wenger,
Plasmonic Nanoantennas Enable Forbidden Forster Dipole-Dipole Energy Transfer and Enhance the FRET Efficiency, Nano letters
16, 6222 (2016).
B. Zierer, M. Rübbelke, F. Tippel, T. Madl, F. Schopf, D. Rutz, K. Richter, M. Sattler, J. Buchner,
Importance of cycle timing for the function of the molecular chaperone Hsp90, Nature Structural & Molecular Biology
23, 1020 (2016).
D. Falconnet, J. She, R. Tornay, E. Leimgruber, D. Bernasconi, L. Lagopoulos, P. Renaud, N. Demierre, P. van den Bogaard,
Rapid, sensitive and real-time multiplexing platform for the analysis of protein and nucleic-acid biomarkers, Analytical Chemistry
87, 1582 (2015).
N. Hazan, T. Tomov, R. Tsukanov, M. Liber, Y. Berger, R. Masoud, K. Toth, J. Langowski, E. Nir,
Nucleosome Core Particle Disassembly and Assembly Kinetics Studied Using Single-Molecule Fluorescence, Biophysical Journal
109, 1676 (2015).
C. Kim, O.-c. Lee, J.-Y. Kim, W. Sung, N. Lee,
Dynamic Release of Bending Stress in Short dsDNA by Formation of a Kink and Forks, Angewandte Chemie International Edition
54, 8943 (2015).
W. Peelaerts, L. Bousset, A. van der Perren, A. Moskalyuk, R. Pulizzi, M. Giugliano, C. van Den Haute, R. Melki, V. Baekelandt,
a-Synuclein strains cause distinct synucleinopathies after local and systemic administration, Nature
522, 340 (2015).
S. Simoncelli, W. de Alwis, C. Fasciani, C. Boddy, P. Aramendía, E. Alarcon, J. Scaiano, Thermoplasmonic ssDNA Dynamic Release from Gold Nanoparticles Examined with Advanced Fluorescence Microscopy, The Journal of Physical Chemistry Letters 6, 1499 (2015).
S. Zirkin, S. Fishman et al.,
Lighting Up Individual DNA Damage Sites by In Vitro Repair Synthesis, J. Am. Chem. Soc.
136, 7771 (2014).
S. Hou, L. Sun et al.,
Fluorescence correlation spectroscopy analysis for accurate determination of proportion of doubly labeled DNA in fluorescent DNA pool for quantitative biochemical assays, Biosens. Bioelectr.
51, 8 (2014).
S. Huo, M. Tabaka,
A flexible fluorescence correlation spectroscopy based method for quantification of the DNA double labeling efficiency with precision control, Laser Phys. Lett.
11, 085602 (2014).
P. Ghenuche, J. de Torres et al.,
Nanophotonic Enhancement of the Förster Resonance Energy-Transfer Rate with Single Nanoapertures, Nano Lett.
14, 4707 (2014).
M. Jahn, A. Rehn et al.,
The charged linker of the molecular chaperone Hsp90 modulates domain contacts and biological function, PNAS
111, 17881 (2014).
A. Reinhardt, M. Horn et al.,
Novel Imidazolium Salt−Peptide Conjugates and Their Antimicrobial Activity, Bioconjugate Chem.
25, 2166 (2014).
J.S. Rinne, T.P. Kaminski et al.,
Light-inducible molecular beacons for spatiotemporally highly defined activation, Chem. Commun.
49, 5375 (2013).
M. Chung, D. Kim, A.E. Herr,
Microchamber Western Blotting Using Poly L Lysine Conjugated Polyacrylamide Gel for Blotting of Sodium Dodecyl Sulfate Coated Proteins, Anal. Chem.
85, 7753 (2013).
M. Ritzefeld, V. Walhorn et al.,
Cooperative Binding of PhoBDBD to Ist Cognate DNA Sequence - A Combined Application of Single-Molecule and Ensemble Methods, Biochemistry
52, 8177 (2013).
E. Ronzitti, B. Harke, A. Diaspro,
Frequency dependent detection in a STED microscope using modulated excitation light, Optics Express
21, 201 (2013).
J.N. Douglas, L.A. Gardner, M.C. Levin,
Antibodies to an Intracellular Antigen Penetrate Neuronal Cells and Cause Deleterious Effects, J. Clin. Cell. Immunol.
4, 1000134 (2013).
M. Mamenko, O. Zaika et al.,
Ca2+ Imaging as a Tool to Assess TRP Channel Function in Murine Distal Nephrons, Methods Mol. Biol.
998, 371 (2013).
R. Tsukanov, T.E. Tomov et al.,
Detailed Study of DNA Hairpin Dynamics Using Single-Molecule Fluorescence Assisted by DNA Origami, J. Phys. Chem. B
117, 11932 (2013).
T.E. Tomov, R. Tsukanov et al.,
Rational Design of DNA Motors: Fuel Optimization through Single-Molecule Fluorescence, J. Am. Chem. Soc.
135, 11935 (2013).
I. Haq, J.A. Irving et al.,
Reactive centre loop mutants of α-1-antitrypsin reveal position-specific effects on intermediate formation along the polymerization pathway, Biosci. Rep.
33, e00046 (2013).
F. Panzeri, A. Ingargiola et al.,
Single-molecule FRET experiments with a red-enhanced custom technology SPAD, Proc. SPIE
8590, 85900D (2013).
H. Mannell, J. Pircher et al.,
Targeted Endothelial Gene Delivery by Ultrasonic Destruction of Magnetic Microbubbles Carrying Lentiviral Vectors, Pharm. Res.
29, 1282 (2012).
A. Gross, C.R. Grüning et al.,
A molecular toolkit for population genetic investigations of the ash dieback pathogen Hymenoscyphus pseudoalbidus, For. Path.
42, 252 (2012).
R. Masoud, R. Tsukanov et al.,
Studying the Structural Dynamics of Bipedal DNA Motors with Single-Molecule Fluorescence Spectroscopy, ACS Nano
6, 6272 (2012).
S. Bultmann, R. Morbitzer et al.,
Targeted transcriptional activation of silent oct4 pluripotency gene by combining designer TALEs and inhibition of epigenetic modifiers, Nucl. Acids Res.
40, 5368 (2012).
Z. Tang, Q. Wei, A. Wie,
Metal-Mesh Litography, Appl. Mater Interfaces
3, 4812 (2011).
J. Strömqvist, L. Nardo et al.,
Binding of Biotin to Streptavidin: A combined fluorescence correlation spectroscopy and time-resolved fluorescence study, Eur. Phys. J. Special Topics
199, 181 (2011).
E. Favaro, D.R. Sumita, M.R. Whittle,
Use of universal reporter primers in multiplex PCR of autosomal loci, FSI Genetics Suppl.
Series 3, e71 (2011).
D. Kozak, P. Kithva et al.,
Development of encoded particle-polymer arrays for the accelerated screening of antifouling layers, Chem. Commun.
47, 9687 (2011).
R. H. Meltzer, J. R. Krogmeier et al.,
A lab-on-chip biothreat detection using single-molecule DNA mapping, Lab Chip
11, 863 (2011).
S. Braun, C. Humphreys et al.,
Amyloid-Associated Nucleic Acid Hybridisation, PLoS ONE
6, e19125 (2011).
Y. Cheng, T. Stakenborg et al.,
Fluorescence Near Gold Nanoparticles for DNA Sensing, Anal. Chem.
83, 1307 (2011).
M. Busby, L. K. J. Stadler et al.,
Optimisation of a multivalent Strep tag for protein detection, Biophys. Chem.
152, 170 (2010).
Z. Lui, F. Galli et al.,
Stable Single-Walled Carbon Nanotube – Streptavidin Complex for Biorecognition, J. Phys. Chem. C
114, 4345 (2010).
E. J. White, S.V. Fridrikh,
Staphylococcus aureus Strain Typing by Single-Molecule DNA Mapping in Fluidic Microchips with Fluorescent Tags, Clinic. Chem. (2009). [doi: 10.1317/clinchem.2009.128967]
R. Roy, S. Hohng, T. Ha, A practical guide to single-molecule FRET, Nature Methods 5(6), 2008, 507-516.
C. Frauer, H. Leonhard,
A versatile non-radioactive assay for DNA methyltransferase activity and DNA binding, Nucl. Acids Res., 1 (2009).
Y. Jiang, A. Matevossian, H.-S. Huang, J. Straubhaar, Sch. Akbarian,
Isolation of neuronal chromatin from brain tissue, Neuroscience
9, 42 (2009).
P.P.T. Surawski, B.J. Battersby, G.A. Lawrie et al.,
Flow cytometric detection of proteolysis in peptide libraries synthesised on optically encoded supports, Mol. BioSyst.
4, 774 (2008).
S.R. Corrie, R. Vogel, I. Keen, K. Jack et al.,
A structural study of hybrid organosilica materials for colloid-based DNA biosensors, J. Mater. Chem.
18, 523 (2008).
D. Kozak, A. Chen, M. Trau,
Profiling Protein-Surface Interactions of Multicomponent Suspensions via Flow Cytometry, Langmuir
24, 1204 (2008).
M. Pagliaro, R. Ciriminna, M. Wong Chi Man, S. Campestrini,
Better Chemistry through Ceramics: The Physical Bases of the Outstanding Chemistry of ORMOSIL, J. Phys. Chem. B
110, 1976 (2006).
C.R. Miller, R. Vogel, P.P.T. Surawsky, S.R. Corrie, A. Rühmann, M. Trau,
Biomolecular screening with novel organosilica microspheres, Chem. Comm., 4783 (2005).
T. Osanai, K. Magota, M. Tanaka et al.,
Intracellular signaling for vasoconstrictor factor 6, Hypertension
46, 1140 (2005).
