Representative Publications

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  • Stracy M, Kapanidis AN, Probing Single-molecule and super-resolution imaging of transcription in living bacteria. Methods. 2017;1;120:103-114. doi:10.1016/j.ymeth.2017.04.001. Link.
  • Garza de Leon F, Sellars L, Stracy M, Busby SJ, Kapanidis AN, Tracking Low-Copy Transcription Factors in Living Bacteria: The Case of the lac Repressor. Biophys J. 2017;112(7):1316-1327. doi: 10.1016/j.bpj.2017.02.028. Link
  • Lamberte LE, Baniulyte G, Singh SS, Stringer AM, Bonocora RP, Stracy M, Kapanidis AN, Wade JT, Grainger DC, Horizontally acquired AT-rich genes in Escherichia coli cause toxicity by sequestering RNA polymerase. Nat Microbiol. 2017;9;2:16249. doi: 10.1038/nmicrobiol.2016.249. Link


  • Hohlbein J, Kapanidis AN, Probing the Conformational Landscape of DNA Polymerases Using Diffusion-Based Single-Molecule FRET. Methods Enzymol. 2016;581:353-378. doi: 10.1016/bs.mie.2016.08.023. Link.
  • Robb NC, Te Velthuis AJ, Wieneke R, Tampé R, Cordes T, Fodor E, Kapanidis AN, Single-molecule FRET reveals the pre-initiation and initiation conformations of influenza virus promoter RNA. Nucleic Acids Res. 2016 Dec 1;44(21):10304-10315. Link
  • Plochowietz A, Farrell I, Smilansky Z, Cooperman BS, Kapanidis AN, In vivo single-RNA tracking shows that most tRNA diffuses freely in live bacteria. Nucleic Acids Res. 2016 Sep 12. pii: gkw787. Link
  • Duchi D, Bauer DL, Fernandez L, Evans G, Robb N, Hwang LC, Gryte K, Tomescu A, Zawadzki P, Morichaud Z, Brodolin K, Kapanidis AN, RNA Polymerase Pausing during Initial Transcription. Mol Cell. 2016 Sep 15;63(6):939-50. doi: 10.1016/j.molcel.2016.08.011.Link
  • Te Velthuis AJ, Robb NC, Kapanidis AN, Fodor E, The role of the priming loop in influenza A virus RNA synthesis. Nat Microbiol. 2016 Mar 21;1:16029. doi: 10.1038/nmicrobiol.2016.29.Link
  • Stracy M, Jaciuk M, Uphoff S, Kapanidis AN, Nowotny M, Sherratt DJ, Zawadzki P, Single-molecule imaging of UvrA and UvrB recruitment to DNA lesions in living Escherichia coli. Nat Commun. 2016 Aug 26;7:12568. doi: 10.1038/ncomms12568.Link
  • Sadler EE, Kapanidis AN, Tucker SJ, Solution-Based Single-Molecule FRET Studies of K(+) Channel Gating in a Lipid Bilayer. Biophys J. 2016 Jun 21;110(12):2663-70. doi: 10.1016/j.bpj.2016.05.020.Link
  • Meli M, Sustarsic M, Craggs TD, Kapanidis AN, Colombo G., DNA Polymerase Conformational Dynamics and the Role of Fidelity-Conferring Residues: Insights from Computational Simulations. Front Mol Biosci. 2016 May 27;3:20. doi: 10.3389/fmolb.2016.00020. Link


  • Pawel Zawadzki, Mathew Stracy, Katarzyna Ginda, Katarzyna Zawadzka, Christian Lesterlin, Achillefs N. Kapanidis, David J. Sherratt, The Localization and Action of Topoisomerase IV in Escherichia coli Chromosome Segregation Is Coordinated by the SMC Complex, MukBEF, Cell Reports, Volume 13, Issue 11, 22 December 2015, Pages 2587-2596, ISSN 2211-1247. Link
  • May PF, Zawadzki P, Sherratt DJ, Kapanidis AN, Arciszewska LK. Assembly, translocation, and activation of XerCD-dif recombination by FtsK translocase analyzed in real-time by FRET and two-color tethered fluorophore motion. PNAS, 2015 doi: 10.1073/pnas.1510814112 Link
  • Sustarsic M, Kapanidis AN. Taking the ruler to the jungle: single-molecule FRET for understanding biomolecular structure and dynamics in live cells. Current Opinion in Structural Biology, 2015 Aug 18;34:52-59. doi: 10.1016/ Link
  • Plochowietz A, Kapanidis AN. Single in the (Cell) City: a protein-folding story. Nature Methods, 2015 Jul 30;12(8):715-6. doi: 10.1038/nmeth.3491. Link
  • Stracy M, Lesterlin C, Garza de Leon F, Uphoff S, Zawadzki P, Kapanidis AN. Live-cell superresolution microscopy reveals the organization of RNA polymerase in the bacterial nucleoid. PNAS, 2015 Aug 11;112(32):E4390-9. doi: 10.1073/pnas.1507592112. Link
  • Evans GW, Hohlbein J, Craggs T, Aigrain L, Kapanidis AN. Real-time single-molecule studies of the motions of DNA polymerase fingers illuminate DNA synthesis mechanisms. Nucleic Acids Research, 2015. gkv547 (Advanced Access) Link
  • Aigrain L, Sustarsic M, Crawford R, Plochowietz A, Kapanidis AN. Internalization and observation of fluorescent biomolecules in living microorganisms via electroporation. J Vis Exp, 2015 Feb 8; (96). doi: 10.3791/52208. Open Access Video


  • May PFJ, Pinkney JNM, Zawadzki P, Evans GW, Sherratt DJ, and Kapanidis AN. Tethered Fluorophore Motion: Studying Large DNA Conformational Changes by Single-fluorophore Imaging. Biophys J, 2014; 107, 1205-1216. Link
  • Tomescu AI, Robb NC, Hengrung N, Fodor E, Kapanidis AN. Single-molecule FRET reveals a corkscrew RNA structure for the polymerase-bound influenza virus promoter. PNAS, 2014; 111, E3335-E3342. Link
  • Stracy M, Uphoff S, Garza de Leon F, Kapanidis AN. In vivo single-molecule imaging of bacterial DNA replication, transcription, and repair. FEBS Lett., 2014, in press Corrected Proof
  • Plochowietz A, Crawford R, Kapanidis AN. Characterization of organic fluorophores for in vivo FRET studies based on electroporated molecules. Phys Chem Chem Phys, 2014, 16, 12688-12694. Link. Also highlighted in RSC Blogs.
  • Sustarsic M, Plochowietz A, Aigrain L, Yuzenkova Y, Zenkin N, Kapanidis A. Optimized delivery of fluorescently labeled proteins in live bacteria using electroporation. Histochem Cell Biol, 2014; 142, 113-124. Link
  • Uphoff S, Sherratt D, Kapanidis AN. Visualizing protein-DNA interactions in live bacterial cells using photoactivated single-molecule tracking. J of Vis Exp, 2014, 85 Watch the Video Article
  • Uphoff S, Sherratt D, Kapanidis AN. Studying the organization of DNA repair by single-cell and single-molecule imaging. DNA Repair, 2014; 20, 32-40. Link.


  • Crawford R, Torella JP, Aigrain L, Plochowietz A, Gryte K, Uphoff S, and Kapanidis AN, Long-Lived Intracellular Single-Molecule Fluorescence Using Electroporated Molecules, Biophys J, 2013; 105, 2439–2450. Link. PDF
  • Zawadzki P, May PFJ, Baker RA, Pinkney JNM, Kapanidis AN, Sherratt DJ, and Arciszewska LK, Conformational transitions during FtsK translocase activation of individual XerCD-dif recombination complexes, PNAS, 2013 vol. 110 (43) pp. 17302-17307. Link. PDF
  • Hohlbein J, Aigrain L, Craggs TD, Bermek O, Potapova O, Shoolizadeh P, Grindley NDF, Joyce CM, and Kapanidis AN, Conformational landscapes of DNA polymerase I and mutator derivatives establish fidelity checkpoints for nucleotide insertion, Nature Communications, 2013; 4, 2131. Link. PDF
  • Periz J, Celma C, Jing B, Pinkney JN, Roy P, Kapanidis AN, Rotavirus mRNAS are released by transcript-specific channels in the double-layered viral capsid, PNAS, 2013; 110, 12042–12047. Link. PDF
  • Endesfelder U, Finan K, Holden SJ, Cook PR, Kapanidis AN, Heilemann M, Multiscale Spatial Organization of RNA Polymerase in Escherichia coli., Biophys. J., 2013; 52 (8), pp.172-181. Link. PDF
  • Uphoff S, Reyes-Lamothe R, Garza de Leon F, Sherratt DJ, Kapanidis AN, Single-molecule DNA repair in live bacteria, PNAS, 2013; 110 (20), pp. 8063-8068. Link. PDF
  • Crawford R, Erben CM, Periz J, Hall LM, Brown T, Turberfield AJ, Kapanidis AN, Non-covalent Single Transcription Factor Encapsulation Inside a DNA Cage., Angew. Chem., 2013; 52 (8), pp.2284-2288. Link. PDF
  • 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, J Mol Biol, 2013; 425 (5), pp.875-885. Link. PDF


  • Craggs TD and Kapanidis AN, Six steps closer to FRET-driven structural biology, Nature Methods, 2012; 9 (12), pp.1157-1159. Link. PDF
  • Pinkney JNM, Zawadzki P, Mazuryk J, Arciszewska LK, Sherratt DJ, Kapanidis AN, Capturing reaction paths and intermediates in Cre-loxP recombination using single-molecule fluorescence, PNAS, 2012; 109 (51), pp.20871-20876. Link. PDF
  • Finan K, Torella JP, Kapanidis AN, Cook PR, T7 RNA polymerase functions in vitro without clustering, PLoS ONE 2012; 7 (7). Link PDF
  • Le Reste L, Hohlbein J, Gryte K, Kapanidis AN, Characterization of Dark Quencher Chromophores as Nonfluorescent Acceptors for Single-Molecule FRET, Biophysical Journal 2012; 105 (1), pp. 2658-2668. PDF
  • Crawford R, Kelly DJ, Kapanidis AN, A Protein Biosensor That Relies on Bending of Single DNA Molecules, ChemPhysChem 2012; 13 (4), pp. 918-922. PDF
  • Kapanidis AN and Crawford R, Colorful Molecular Diagnostics, Clinical Chemistry 2012; 58 (4). PDF


  • Holden SJ, Uphoff S, Kapanidis AN, DAOSTORM: an algorithm for high-density super-resolution microscopy, Nature Methods 2011; 8, pp. 279–280. PDF
  • Torella JP, Holden SJ, Santoso Y, Hohlbein J, Kapanidis AN, Identifying molecular dynamics in single-molecule FRET experiments with Burst Variance Analysis. Biophysical Journal 2011; 100 (6), pp.1568-1577. PDF
  • Uphoff S, Gryte K, Evans G, Kapanidis AN. High temporal resolution and linked hidden Markov modeling for switchable single-molecule FRET. ChemPhysChem 2011; 12 (1), pp.571-579 PDF


  • Cordes T, Santoso Y, Tomescu AI, Gryte K, Hwang LC, Camara B, Wigneshweraraj S, Kapanidis AN, Sensing DNA opening in transcription using quenchable FRET. Biochemistry, 2010; 49, pp 9171-9180. PDF Supporting Information.
  • Holden SJ, Uphoff S, Hohlbein J, Yadin D, Le Reste L, Britton O J, Kapanidis AN, Defining the limits of single-molecule FRET resolution in TIRF microscopy. Biophysical Journal 2010; 99 (9), pp.3102-3111. PDF Supporting Material.
  • Santoso Y*, Torella JP*, Kapanidis AN, Characterizing single-molecule FRET dynamics with Probability Distribution Analysis. ChemPhysChem 2010; 11 (10), pp 2209-2219. *equal contribution. PDF Supporting Information.
  • Lymperopoulos K*, Crawford R*, Torella JP, Heilemann M, Hwang LC, Holden SJ, and Kapanidis AN, Single-molecule DNA biosensors for protein and ligand detection. Angew. Chem. 2010; 49 (7), pp 1316-1320. *equal contribution. PDF Supporting Information.

  • Hohlbein J, Gryte K, Heilemann M, Kapanidis AN, Surfing on the third wave of single-molecule fluorescence methods. Physical Biology 2010; 7 (3) PDF.
  • Santoso Y*, Joyce CM*, Potapova O, Le Reste L, Hohlbein J, Torella JP, Grindley NDF, Kapanidis AN, Conformational transitions in DNA polymerase I revealed by single-molecule FRET. PNAS 2010; 107 (2), pp 715-720. *equal contribution. PDF Supporting Information.


  • Hwang LC, Hohlbein J, Holden SJ, Kapanidis AN, Single-Molecule FRET: Methods and Biological Applications. Chapter 5 in Handbook of Single-Molecule Biophysics, Springer New York, 2009. Link.

  • Santoso Y, Kapanidis AN, Probing Biomolecular Structures and Dynamics of Single Molecules Using In-gel Alternating-Laser Excitation. Anal. Chem. 2009; 81 (23), pp 9561–9570. PDF Supporting Information.
  • Holden SJ, Kapanidis AN, Alternating-Laser Excitation and Pulsed-Interleaved Excitation of Single Molecules. Chapter 6 in Single Particle Tracking and Single Molecule Energy Transfer: Applications in the Bio and Nano Sciences, Wiley-VHC, 2009

  • Carstairs HM, Lymperopoulos K, Kapanidis AN, Bath J, Turberfield AJ. DNA monofunctionalization of quantum dots. Chembiochem. 2009 Jul 20;10(11):1781-3.

  • Goodman RP, Erben CM, Malo J, Ho WM, McKee ML, Kapanidis AN, Turberfield AJ. A facile method for reversibly linking a recombinant protein to DNA. Chembiochem. 2009 Jun 15;10(9):1551-7.

  • Kapanidis AN, Strick T. Biology, one molecule at a time. Trends Biochem Sci. 2009 May;34(5):234-43. PDF

  • Heilemann M, Hwang LC, Lymperopoulos K, Kapanidis AN. Single-molecule FRET analysis of protein-DNA complexes. Methods Mol Biol. 2009;543:503-21. Link


  • Santoso Y, Hwang LC, Le Reste L, Kapanidis AN. Red light, green light: probing single molecules using alternating laser excitation. Biochem Soc Transactions, 2008 Aug;36(Pt 4):738-44. PDF

  • Goodman RP, Heilemann M, Doose S, Erben CM, Kapanidis AN, Turberfield AJ. Reconfigurable, braced, three-dimensional DNA nanostructures. Nature Nanotech, 2008, 3, 93-96. PDF Supplementary Information

  • Kapanidis AN, Heilemann M, Margeat E, Kong X, Nir E, Weiss S. Alternating-Laser Excitation of Single Molecules. Chapter in Single-molecule techniques: a laboratory manual, 2008, 85-119.


  • Heilemann M, Lymperopoulos K, Wigneshweraraj SR, Buck M, Kapanidis AN. Studying sigma54-dependent transcription with alternating-laser excitation (ALEX) spectroscopy. Proc SPIE, 2007, 6633. PDF

  • Harding PJ, Attrill H, Ross S, Koeppe JR, Kapanidis AN, Watts A. Neurotensin receptor type 1: Escherichia coli expression, purification, characterization and biophysical study. Bioch Soc Transactions, 2007, 35, 760-763.

  • Doose S, Heilemann M, Michalet X, Weiss S, Kapanidis AN. Periodic acceptor excitation spectroscopy of single molecules. European Biophys J, 2007, 36, 669-674. PDF

  • Lee NK, Kapanidis AN, Koh HR, Wang Y, Ho SO, Kim Y, Gassman N, Kim SK, and Weiss S. Three-color alternating-laser excitation of single molecules: monitoring multiple interactions and distances. Biophys J 2007, 92, 303-12. PDF Supplementary Material


  • Kapanidis AN, Margeat E, Ho SO, Kortkhonjia E, Weiss S, Ebright RH. Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism. Science 2006;314: 1144-7. PDF Supporting Online Material

  • Margeat E, Kapanidis AN, Tinnefeld P, Wang Y, Mukhopadhyay J, Ebright RH, Weiss S. Direct observation of promoter escape and abortive initiation in single immobilized transcription complexes. Biophys J, 2006, 90, 1419-31.PDF


  • Kapanidis AN, Margeat E, Laurence T, Doose S, Ho SO, Mukhopadhyay J, Kortkhonjia E, Ebright RH, Weiss S. Retention of transcription initiation factor σ70 in transcription elongation: single-molecule analysis. Mol Cell, 2005, 20, 347-56. Highlighted in “Single RNA polymerases on the stage”, Nat Meth, 2006, 3, 3. PDF Supplemental Data

  • Kapanidis AN, Laurence T, Lee NK, Margeat E, Kong X, Weiss S. Alternating-laser excitation of single molecules. Acc Chem Res, 2005, 2005, 38, 523-33. PDF.

  • Lee NK, Kapanidis AN, Wang Y, Michalet X, Mukhopadhyay J, Ebright RH, Weiss S. Accurate FRET measurements within single diffusing biomolecules using alternating-laser excitation. Biophys J, 2005, 88, 2939-53. PDF Supplemental Text

2004 and earlier

  • Kapanidis AN, Lee NK, Laurence T, Doose S, Margeat E, Weiss S. Fluorescence-aided molecule sorting: analysis of structure and interactions by alternating-laser excitation of single molecules. Proc Natl Acad Sci. 2004;101: 8936-41. Full text + Supporting Information

  • Laurence T, Kapanidis AN, Kong X, Chemla D, Weiss S. Photon-arrival-time interval distribution (PAID): a novel tool for analyzing molecular interactions. J Phys Chem B, 2004;108: 3051-67.
    PDF Supporting Information

  • Michalet X, Kapanidis AN, Laurence T, Pinaud F, Doose S, Pflughoefft M, Weiss S. The power and prospects of fluorescence microscopies and spectroscopies. Annu Rev Biophys Biomol Struct. 2003;32:161-182. PDF

  • Kapanidis AN, Weiss S. Fluorescent probes and bioconjugation chemistries for single-molecule fluorescence analysis of biomolecules. J Chem Phys. 2002;117:10953-10964. PDF

  • Mekler V, Kortkhonjia E, Mukhopadhyay J, Knight J, Revyakin A, Kapanidis AN, Niu W, Ebright YW, Levy R, Ebright RH. Structural organization of RNA polymerase holoenzyme and the RNA polymerase-promoter open complex: systematic fluorescence resonance energy transfer and distance-constrained docking. Cell. 2002;109:1-20. PDF Supplemental Data

  • Kapanidis AN, Ebright YW, Ludescher RD, Chan S, Ebright RH. Mean DNA Bend Angle and Distribution of DNA Bend Angles in the CAP-DNA Complex in Solution. J Mol Biol. 2001;312:453-468. PDF

  • Kapanidis AN, Ebright YW, Ebright RH. Site-specific incorporation of fluorescent probes into protein: hexahistidine-tag-mediated fluorescent labeling using (Ni2+:Nitrilotriacetic acid)n-fluorochrome conjugates. J Am Chem Soc. 2001;123:12123-12125. PDF Supporting Information

  • Mukhopadhyay J*, Kapanidis AN*, Mekler V, Kortkhonjia E, Ebright YW, Ebright RH. Translocation of s70 with RNA polymerase during transcription: fluorescence resonance energy transfer assay for movement relative to DNA. Cell 2001;106:453-463. *Equal contribution. PDF

  • Lagrange T, Kapanidis AN, Tang H, Reinberg D, Ebright RH. New core promoter element in RNA polymerase II-dependent transcription: sequence-specific DNA binding by transcription factor IIB. Genes Dev. 1998;12:34-44. PDF

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