Publication

Publication

  • Confinement-Free Wide-Field Ratiometric Tracking of Single Fluorescent Molecules.

    Gilboa, B, Jing, B, Cui, TJ, Sow, M, Plochowietz, A, Mazumder, A, Kapanidis, AN
  • Substrate conformational dynamics facilitate structure-specific recognition of gapped DNA by DNA polymerase.

    Craggs, TD, Sustarsic, M, Plochowietz, A, Mosayebi, M, Kaju, H, Cuthbert, A, Hohlbein, J, Domicevica, L, Biggin, PC, Doye, JPK, Kapanidis, AN
  • Real-time analysis of single influenza virus replication complexes reveals large promoter-dependent differences in initiation dynamics.

    Robb, NC, Te Velthuis, AJW, Fodor, E, Kapanidis, AN
  • Recent Advances in Understanding σ70-Dependent Transcription Initiation Mechanisms.

    Mazumder, A, Kapanidis, AN
  • Tracking antibiotic mechanisms.

    Pambos, OJ, Kapanidis, AN
  • Single Nitrogen-Vacancy Imaging in Nanodiamonds for Multimodal Sensing

    Sow, M, Steuer, H, Gilboa, B, Gines, L, Mandal, S, Adekanye, S, Smith, JM, Williams, OA, Kapanidis, AN
  • Guidelines for DNA recombination and repair studies: Mechanistic assays of DNA repair processes.

    Klein, HL, Ang, KKH, Arkin, MR, Beckwitt, EC, Chang, Y-H, Fan, J, Kwon, Y, Morten, MJ, Mukherjee, S, Pambos, OJ, El Sayyed, H, Thrall, ES
    ,
    et al
  • Publisher Correction: Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study.

    Hellenkamp, B, Schmid, S, Doroshenko, O, Opanasyuk, O, Kühnemuth, R, Adariani, SR, Ambrose, B, Aznauryan, M, Barth, A, Birkedal, V, Bowen, ME, Chen, H
    ,
    et al
  • Understanding Protein Mobility in Bacteria by Tracking Single Molecules.

    Kapanidis, AN, Uphoff, S, Stracy, M
  • Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study.

    Hellenkamp, B, Schmid, S, Doroshenko, O, Opanasyuk, O, Kühnemuth, R, Rezaei Adariani, S, Ambrose, B, Aznauryan, M, Barth, A, Birkedal, V, Bowen, ME, Chen, H
    ,
    et al
  • The RNA polymerase clamp interconverts dynamically among three states and is stabilized in a partly closed state by ppGpp.

    Duchi, D, Mazumder, A, Malinen, AM, Ebright, RH, Kapanidis, AN
  • Tracking tRNA packages.

    Kapanidis, AN, Stracy, M
  • Pausing controls branching between productive and non-productive pathways during initial transcription in bacteria.

    Dulin, D, Bauer, DLV, Malinen, AM, Bakermans, JJW, Kaller, M, Morichaud, Z, Petushkov, I, Depken, M, Brodolin, K, Kulbachinskiy, A, Kapanidis, AN
  • Structural Basis of Transcription Inhibition by Fidaxomicin (Lipiarmycin A3).

    Lin, W, Das, K, Degen, D, Mazumder, A, Duchi, D, Wang, D, Ebright, YW, Ebright, RY, Sineva, E, Gigliotti, M, Srivastava, A, Mandal, S
    ,
    et al
  • Short-Read Single-Molecule DNA Sequencing for Highly Parallel Analysis of Protein-DNA Interactions

    Andrews, R, Steuer, H, Shivalingam, A, El-Sagheer, AH, Brown, T, Kapanidis, AN
  • Single-Molecule Analysis of the Influenza Virus Replication Initiation Mechanism

    Robb, NC, te Velthuis, AJW, Fodor, E, Kapanidis, AN
  • Wide-Field Monitoring of Single Fluorescent Molecules and Nanoparticles without Immobilization

    Gilboa, B, Jing, B, Sow, M, Cui, TJ, Plochowietz, A, Kapanidis, AN
  • Conformational heterogeneity and bubble dynamics in single bacterial transcription initiation complexes

    Duchi, D, Gryte, K, Robb, NC, Morichaud, Z, Sheppard, C, Brodolin, K, Wigneshweraraj, S, Kapanidis, AN
  • Single-molecule and super-resolution imaging of transcription in living bacteria.

    Stracy, M, Kapanidis, AN
  • Tracking Low-Copy Transcription Factors in Living Bacteria: The Case of the lac Repressor.

    Garza de Leon, F, Sellars, L, Stracy, M, Busby, SJW, Kapanidis, AN
  • In vivosingle-RNA tracking shows that most tRNA diffuses freely in live bacteria

    Plochowietz, A, Farrell, I, Smilansky, Z, Cooperman, BS, Kapanidis, AN
  • Horizontally acquired AT-rich genes in Escherichia coli cause toxicity by sequestering RNA polymerase.

    Lamberte, LE, Baniulyte, G, Singh, SS, Stringer, AM, Bonocora, RP, Stracy, M, Kapanidis, AN, Wade, JT, Grainger, DC
  • Single-molecule FRET reveals the pre-initiation and initiation conformations of influenza virus promoter RNA.

    Robb, NC, Te Velthuis, AJW, Wieneke, R, Tampé, R, Cordes, T, Fodor, E, Kapanidis, AN
  • RNA Polymerase Pausing during Initial Transcription.

    Duchi, D, Bauer, DLV, Fernandez, L, Evans, G, Robb, N, Hwang, LC, Gryte, K, Tomescu, A, Zawadzki, P, Morichaud, Z, Brodolin, K, Kapanidis, AN
  • Single-molecule imaging of UvrA and UvrB recruitment to DNA lesions in living Escherichia coli.

    Stracy, M, Jaciuk, M, Uphoff, S, Kapanidis, AN, Nowotny, M, Sherratt, DJ, Zawadzki, P
  • Stable end-sealed DNA as robust nano-rulers for in vivo single-molecule fluorescence.

    Plochowietz, A, El-Sagheer, AH, Brown, T, Kapanidis, AN
  • Solution-Based Single-Molecule FRET Studies of K(+) Channel Gating in a Lipid Bilayer.

    Sadler, EE, Kapanidis, AN, Tucker, SJ
  • New technologies for DNA analysis--a review of the READNA Project.

    McGinn, S, Bauer, D, Brefort, T, Dong, L, El-Sagheer, A, Elsharawy, A, Evans, G, Falk-Sörqvist, E, Forster, M, Fredriksson, S, Freeman, P, Freitag, C
    ,
    et al
  • The role of the priming loop in Influenza A virus RNA synthesis.

    Te Velthuis, AJW, Robb, NC, Kapanidis, AN, Fodor, E
  • The role of the priming loop in influenza A virus RNA synthesis.

    Te Velthuis, AJW, Robb, NC, Kapanidis, AN, Fodor, E
  • How Structure-Specific DNA-Binding Proteins Recognise their Substrates

    Craggs, TD, Sustarsic, M, Mosayebi, M, Kaju, H, Hohlbein, J, Biggin, PC, Doye, JPK, Kapanidis, AN
  • Single-Molecule Fluorescence Studies of Nucleic-Acid Transactions in Living Bacteria

    Kapanidis, A
  • Single-Molecule Imaging of Transcription, Chromosome Organization, and DNA Repair in Live Bacteria

    Stracy, M, Lesterlin, C, Uphoff, S, Zawadzki, P, Kapanidis, AN
  • DNA Polymerase Conformational Dynamics and the Role of Fidelity-Conferring Residues: Insights from Computational Simulations.

    Meli, M, Sustarsic, M, Craggs, TD, Kapanidis, AN, Colombo, G
  • Probing the Conformational Landscape of DNA Polymerases Using Diffusion-Based Single-Molecule FRET.

    Hohlbein, J, Kapanidis, AN
  • The Localization and Action of Topoisomerase IV in Escherichia coli Chromosome Segregation Is Coordinated by the SMC Complex, MukBEF.

    Zawadzki, P, Stracy, M, Ginda, K, Zawadzka, K, Lesterlin, C, Kapanidis, AN, Sherratt, DJ
  • Aligning the μs-ALEX Setup.

    Kapanidis, A, Majumdar, D, Heilemann, M, Nir, E, Weiss, S
  • Alternating Laser Excitation for Solution-Based Single-Molecule FRET.

    Kapanidis, A, Majumdar, D, Heilemann, M, Nir, E, Weiss, S
  • Assembling the μs-ALEX Setup.

    Kapanidis, A, Majumdar, D, Heilemann, M, Nir, E, Weiss, S
  • Sample Preparation and Data Acquisition for μs-ALEX.

    Kapanidis, A, Majumdar, D, Heilemann, M, Nir, E, Weiss, S
  • Taking the ruler to the jungle: single-molecule FRET for understanding biomolecular structure and dynamics in live cells.

    Sustarsic, M, Kapanidis, AN
  • Assembly, translocation, and activation of XerCD-dif recombination by FtsK translocase analyzed in real-time by FRET and two-color tethered fluorophore motion.

    May, PFJ, Zawadzki, P, Sherratt, DJ, Kapanidis, AN, Arciszewska, LK
  • Live-cell superresolution microscopy reveals the organization of RNA polymerase in the bacterial nucleoid.

    Stracy, M, Lesterlin, C, Garza de Leon, F, Uphoff, S, Zawadzki, P, Kapanidis, AN
  • Single in the (Cell) City: a protein-folding story.

    Plochowietz, A, Kapanidis, AN
  • Real-time single-molecule studies of the motions of DNA polymerase fingers illuminate DNA synthesis mechanisms.

    Evans, GW, Hohlbein, J, Craggs, T, Aigrain, L, Kapanidis, AN
  • Correction

  • Correction

  • Corrigendum to "In vivo single-molecule imaging of bacterial DNA replication, transcription, and repair" [FEBS Lett. 588 (19) (2014) 3585-3594].

    Stracy, M, Uphoff, S, Garza de Leon, F, Kapanidis, AN
  • Corrigendum to “In vivo single-molecule imaging of bacterial DNA replication, transcription, and repair” [FEBS Lett. 588 (19) (2014) 3585-3594]

    Stracy, M, Uphoff, S, Garza de Leon, F, Kapanidis, AN
  • Internalization and observation of fluorescent biomolecules in living microorganisms via electroporation.

    Aigrain, L, Sustarsic, M, Crawford, R, Plochowietz, A, Kapanidis, AN
  • Real-Time Transcription Initiation by E. coli RNA Polymerase in vitro and in vivo

    Plochowietz, A, Llumigusin, DD, Zawadzki, P, El-Sagheer, AH, Brown, T, Kapanidis, AN
  • Single-Molecule FRET for Dynamic Structural Biology: DNA Polymerase i Structure and Mechanism with Angstrom Precision

    Sustarsic, M, Craggs, T, Hohlbein, J, Cuthbert, A, Taylor, N, Kaju, H, Mosayebi, M, Doye, J, Kapanidis, AN
  • Studies of the FtsK DNA Translocase using Two-Color Tethered Fluorophore Motion

    May, PFJ, Zawadzki, P, Arciszewska, LK, Sherratt, D, Kapanidis, AN
  • In vivo single-molecule imaging of bacterial DNA replication, transcription, and repair.

    Stracy, M, Uphoff, S, Garza de Leon, F, Kapanidis, AN
  • Tethered fluorophore motion: studying large DNA conformational changes by single-fluorophore imaging.

    May, PFJ, Pinkney, JNM, Zawadzki, P, Evans, GW, Sherratt, DJ, Kapanidis, AN
  • Single-molecule FRET reveals a corkscrew RNA structure for the polymerase-bound influenza virus promoter.

    Tomescu, AI, Robb, NC, Hengrung, N, Fodor, E, Kapanidis, AN
  • Studying the organization of DNA repair by single-cell and single-molecule imaging.

    Uphoff, S, Kapanidis, AN
  • Characterization of organic fluorophores for in vivo FRET studies based on electroporated molecules.

    Plochowietz, A, Crawford, R, Kapanidis, AN
  • Optimized delivery of fluorescently labeled proteins in live bacteria using electroporation.

    Sustarsic, M, Plochowietz, A, Aigrain, L, Yuzenkova, Y, Zenkin, N, Kapanidis, A
  • Erratum: Defining the limits of single-molecule FRET resolution in TIRF microscopy (Biophys J. (2010) 99 (3102-3111))

    Holden, SJ, Uphoff, S, Hohlbein, J, Yadin, D, Le Reste, L, Britton, OJ, Kapanidis, AN
  • Visualizing protein-DNA interactions in live bacterial cells using photoactivated single-molecule tracking

    Uphoff, S, Sherratt, DJ, Kapanidis, AN
  • Visualizing protein-DNA interactions in live bacterial cells using photoactivated single-molecule tracking.

    Uphoff, S, Sherratt, DJ, Kapanidis, AN
  • A Novel FRET-Based Structure of DNA Polymerase Complexed with Kinked Gapped-DNA

    Craggs, TD, Sustarsic, M, Hohlbein, J, Cuthbert, A, Taylor, N, Evans, G, Kapanidis, AN
  • Combining Accurate FRET and Tracking of Single Protein and DNA Molecules in Live Bacteria

    Plochowietz, A, Crawford, R, Aigrain, L, Sustarsic, M, Kapanidis, AN
  • New FRET Methods for Studying Processing of Nucleic Acids by Protein Machines

    Kapanidis, A
  • Optimized delivery of fluorescently labeled proteins in live bacteria using electroporation

    Sustarsic, M, Plochowietz, A, Aigrain, L, Yuzenkova, Y, Zenkin, N, Kapanidis, A
  • Optimized Internalization of Fluorescently Labeled Biomolecules into Live Bacteria

    Sustarsic, M, Aigrain, L, Plochowietz, A, Craggs, T, Kapanidis, A
  • Super-Resolution Fluorescence Microscopy of Transcription Sites in E. coli

    Endesfelder, U, Finan, K, Holden, S, Cook, PR, Kapanidis, AN, Heilemann, M
  • Super-Resolution Imaging of Transcription in Live Bacterial Cells

    Stracy, M, Uphoff, S, Garza de Leon, F, Kapanidis, A
  • Long-lived intracellular single-molecule fluorescence using electroporated molecules.

    Crawford, R, Torella, JP, Aigrain, L, Plochowietz, A, Gryte, K, Uphoff, S, Kapanidis, AN
  • Conformational transitions during FtsK translocase activation of individual XerCD-dif recombination complexes.

    Zawadzki, P, May, PFJ, Baker, RA, Pinkney, JNM, Kapanidis, AN, Sherratt, DJ, Arciszewska, LK
  • Rotavirus mRNAS are released by transcript-specific channels in the double-layered viral capsid.

    Periz, J, Celma, C, Jing, B, Pinkney, JNM, Roy, P, Kapanidis, AN
  • Multiscale spatial organization of RNA polymerase in Escherichia coli.

    Endesfelder, U, Finan, K, Holden, SJ, Cook, PR, Kapanidis, AN, Heilemann, M
  • Single-molecule DNA repair in live bacteria.

    Uphoff, S, Reyes-Lamothe, R, Garza de Leon, F, Sherratt, DJ, Kapanidis, AN
  • The transcription bubble of the RNA polymerase-promoter open complex exhibits conformational heterogeneity and millisecond-scale dynamics: Implications for transcription start-site selection

    Robb, NC, Cordes, T, Hwang, LC, Gryte, K, Duchi, D, Craggs, TD, Santoso, Y, Weiss, S, Ebright, RH, Kapanidis, AN
  • The transcription bubble of the RNA polymerase-promoter open complex exhibits conformational heterogeneity and millisecond-scale dynamics: implications for transcription start-site selection.

    Robb, NC, Cordes, T, Hwang, LC, Gryte, K, Duchi, D, Craggs, TD, Santoso, Y, Weiss, S, Ebright, RH, Kapanidis, AN
  • Non-covalent single transcription factor encapsulation inside a DNA cage.

    Crawford, R, Erben, CM, Periz, J, Hall, LM, Brown, T, Turberfield, AJ, Kapanidis, AN
  • Characterizing Influenza a RNA Polymerase - Promoter Interaction using Ensemble Fluorescence Spectroscopy

    Tomescu, AI, Robb, NC, Hengrung, N, Fodor, E, Kapanidis, AN
  • Conformational landscapes of DNA polymerase I and mutator derivatives establish fidelity checkpoints for nucleotide insertion.

    Hohlbein, J, Aigrain, L, Craggs, TD, Bermek, O, Potapova, O, Shoolizadeh, P, Grindley, NDF, Joyce, CM, Kapanidis, AN
  • Internalization of Fluorescent Biomolecules for Long-Lived Single-Molecule Observation in Living Bacteria

    Crawford, R, Aigrain, L, Plochowietz, A, Torella, JP, Uphoff, S, Kapanidis, AN
  • Single-Molecule Fluorescence and FRET Measurements on Internalized Proteins in Living Bacteria

    Aigrain, L, Crawford, R, Torella, JP, Plochowietz, A, Sustarsic, M, Kapanidis, AN
  • Capturing reaction paths and intermediates in Cre-loxP recombination using single-molecule fluorescence.

    Pinkney, JNM, Zawadzki, P, Mazuryk, J, Arciszewska, LK, Sherratt, DJ, Kapanidis, AN
  • Six steps closer to FRET-driven structural biology.

    Craggs, TD, Kapanidis, AN
  • Single-molecule FRET measurements in bacterial cells

    Aigrain, L, Crawford, R, Torella, J, Plochowietz, A, Kapanidis, A
  • Characterization of dark quencher chromophores as nonfluorescent acceptors for single-molecule FRET.

    Le Reste, L, Hohlbein, J, Gryte, K, Kapanidis, AN
  • Colorful molecular diagnostics.

    Kapanidis, AN, Crawford, R
  • A protein biosensor that relies on bending of single DNA molecules.

    Crawford, R, Kelly, DJ, Kapanidis, AN
  • Detection of Specific mRNA Synthesis in Rotavirus using Single Molecule Hybridization

    Periz, J, Celma, C, Pinkney, J, Roy, P, Kapanidis, A
  • Single-Molecule Studies of Transcription Initiation using a Vesicle Approach

    Llumigusin, DD, Robb, N, Gryte, K, Kapanidis, AN
  • Super-Resolution Fluorescence Microscopy of Transcription Sites in E. Coli

    Finan, KR, Heilemann, M, Endesfelder, U, Holden, S, Cook, PR, Kapanidis, A
  • In vivo single-molecule biochemistry of chromosome replication and segregation in bacteria.

    Sherratt, D, Reyes-Lamothe, R, Badrinaryanan, A, Nicolas, E, Henry, O, Kapanidis, A, Uphoff, S, Leake, M
  • Measuring enzyme copy numbers and single-molecule reaction rates in living cells.

    Uphoff, S, Reyes-Lamothe, R, de Leon, FG, Leake, M, Sherratt, D, Kapanidis, A
  • Regime-Changing Hidden Markov Modeling and Statistical Analysis for Complex Single-Molecule Time Series

    Gryte, K, Wardrope, A, Evans, G, Uphoff, S, Le Reste, L, Kapanidis, AN
  • Single-Molecule DNA Repair in Live Bacteria

    Uphoff, S, Reyes-Lamothe, R, Sherratt, DJ, Kapanidis, AN
  • Single-Molecule Fluorescence Studies of Site-Specific DNA Recombination

    Pinkney, J, Zawadzki, P, Sherratt, DJ, Kapanidis, AN
  • Single-Molecule FRET in Living Bacteria

    Crawford, R, Torella, JP, Kapanidis, AN
  • T7 RNA polymerase functions in vitro without clustering.

    Finan, K, Torella, JP, Kapanidis, AN, Cook, PR
  • DAOSTORM: an algorithm for high- density super-resolution microscopy.

    Holden, SJ, Uphoff, S, Kapanidis, AN
  • DAOSTORM: An algorithm for high-density super-resolution microscopy

    Holden, SJ, Uphoff, S, Kapanidis, AN
  • Identifying molecular dynamics in single-molecule FRET experiments with burst variance analysis.

    Torella, JP, Holden, SJ, Santoso, Y, Hohlbein, J, Kapanidis, AN
  • More
List of site pages