Publications

Publications

Search PubMed and Google Scholar for our latest publications

2025

Kümmerlin M, et al. Tunable fluorogenic DNA probes drive fast and high-resolution single-molecule fluorescence imaging. bioRxiv (2025): 2025-01. doi: https://doi.org/10.1101/2025.01.21.634148
Hepp C, et al. High-throughput Single-Virion DNA-PAINT Reveals Structural Diversity, Cooperativity and Flexibility during Selective Packaging in Influenza. bioRxiv (2025): 2025-02. doi: https://doi.org/10.1101/2025.02.11.637713

2024

Driesen S, Leirs K, Kümmerlin M, Pinheiro C, Hendrix A, Kapanidis AN, Lammertyn J. DNA nanosensors–smart implementation of nucleic acid enzymes on DNA origami for single-molecule biosensing. In Single-Molecule Sensors and NanoSystems International Conference (S3IC), Date: 2024/10/28-2024/10/30, Location: Paris, France 2024 Oct 30.
Farrar, A, Turner P, Sayyed HE., Feehily C, Chatzimichail S, Crook D, Andersson M, Oakley S, Barrett L, Nellåker C, Stoesser N, Kapanidis AN. Ribosome Phenotypes Enable Rapid Antibiotic Susceptibility Testing in Escherichia coli. https://doi.org/10.1101/2024.06.18.24309111.
El Sayyed H, Pambos O, Stracy M, Gottesman M, Kapanidis AN. Single-molecule tracking reveals the functional allocation, in vivo interactions and spatial organization of universal transcription factor NusG. Molecular Cell 2024. doi: https://doi.org/10.1016/j.molcel.2024.01.025

2023

Ploetz E, Ambrose B, Barth A, Börner R, Erichson F, Kapanidis AN, Kim HD, Levitus M, Lohman TM, Mazumder A, Rueda D, Steffeni FD, Cordes T, Magennis SW, Lerner E. A new twist on PIFE: photoisomerisation-related fluorescence enhancement. Methods and Applications of Fluorescence 2023, 12, 012001. doi:10.1088/2050-6120/acfb58.
Hickman SJ, Miller H, Bukys A, Kapanidis AN, Berks BC. Aberrant Topologies of Bacterial Membrane Proteins Revealed by High Sensitivity Fluorescence Labelling. J Mol Bio 2023, Nov 15;436(2):168368. doi: 10.1016/j.jmb.2023.168368.
Farrar A, Feehily C, Turner P, Zagajewski A, Chatzimichail S, Crook D, Andersson M, Oakley S, Barrett L, El Sayyed H, Fowler PW, Nellåker C, Kapanidis AN, Stoesser N. Infection Inspection: Using the power of citizen science to help with image-based prediction of antibiotic resistance in Escherichia coli. merRxiv 2023, doi: https://doi.org/10.1101/2023.12.11.23299807
Lepore A, Thédié D, McLaren L, Azeroglu B, Pambos OJ, Kapanidis AN, El Karoui M. In vivo single-molecule imaging of RecB reveals efficient repair of DNA damage in Escherichia coli. bioRxiv 2023 doi: https://doi.org/10.1101/2023.12.22.573010
Wang, Mazumder, Kapanidis AN. Single-molecule conformational analysis of the RNAP sigma-finger reveals its real-time displacement and relation to promoter escape. bioRxiv 2023 https://www.biorxiv.org/content/10.1101/2023.06.10.544452v1
Chatzimichail S, Turner P, Feehily C, Farrar A, El Sayyed H, Crook D, Andersson M, Oakley S, Barrett L, Kyropoulos J, Nellåker C, Stoesser N, Kapanidis AN. Rapid Identification of Bacteria From Clinical Isolates Using Microfluidic Adaptive Channels and Multiplexed Fluorescence Microscopy. medRxiv 2023, doi: https://doi.org/10.1101/2023.07.16.23292615.
Fan, Jun et al. RNA polymerase redistribution supports growth in E. coli strains with a minimal number of rRNA operons. Nucleic acids research vol. 51,15 (2023): 8085-8101. doi:10.1093/nar/gkad511
McMahon, Andrew et al. High-throughput super-resolution analysis of influenza virus pleomorphism reveals insights into viral spatial organization. PLoS pathogens vol. 19,6 e1011484. 30 Jun. 2023, doi:10.1371/journal.ppat.1011484
Zagajewski, Alexander et al. Deep learning and single-cell phenotyping for rapid antimicrobial susceptibility detection in Escherichia coli. Communications biology vol. 6,1 1164. 14 Nov. 2023, doi:10.1038/s42003-023-05524-4
Kümmerlin, Mirjam et al. Bleaching-resistant, Near-continuous Single-molecule Fluorescence and FRET Based on Fluorogenic and Transient DNA Binding. Chemphyschem : a European journal of chemical physics and physical chemistry vol. 24,12 (2023): e202300175. doi:10.1002/cphc.202300175
Agam, Ganesh et al. Reliability and accuracy of single-molecule FRET studies for characterization of structural dynamics and distances in proteins. Nature methods vol. 20,4 (2023): 523-535. doi:10.1038/s41592-023-01807-0
Shiaelis N, Tometzki A, Peto L, McMahon A, Hepp C, Bickerton E, Favard C, Muriaux D, Andersson M, Oakley S, Vaughan A, Matthews PC, Stoesser N, Crook DW, Kapanidis AN, Robb NC. Virus Detection and Identification in Minutes Using Single-Particle Imaging and Deep Learning. ACS Nano. 2023 doi:10.1021/acsnano.2c10159

2022

Andrews, R, Steuer H, El-Sagheer AH, Mazumder A, el Sayyed H, Shivalingam A, Brown T, Kapanidis AN. Transient DNA binding to gapped DNA substrates links DNA sequence to the single-molecule kinetics of protein-DNA interactions. bioRxiv 2022, doi:https://doi.org/10.1101/2022.02.27.482175
Evans, Geraint W et al. The Rate-limiting Step of DNA Synthesis by DNA Polymerase Occurs in the Fingers-closed Conformation. Journal of molecular biology vol. 434,2 (2022): 167410. doi:10.1016/j.jmb.2021.167410
Malinen, Anssi M et al. Real-Time Single-Molecule Studies of RNA Polymerase-Promoter Open Complex Formation Reveal Substantial Heterogeneity Along the Promoter-Opening Pathway. Journal of molecular biology vol. 434,2 (2022): 167383. doi:10.1016/j.jmb.2021.167383

2021

Mazumder, Abhishek et al. Transcription initiation at a consensus bacterial promoter proceeds via a 'bind-unwind-load-and-lock' mechanism. eLife vol. 10 e70090. 11 Oct. 2021, doi:10.7554/eLife.70090
Hepp, Christof et al. Viral detection and identification in 20 min by rapid single-particle fluorescence in-situ hybridization of viral RNA. Scientific reports vol. 11,1 19579. 1 Oct. 2021, doi:10.1038/s41598-021-98972-z
Lerner, Eitan et al. FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices. eLife vol. 10 e60416. 29 Mar. 2021, doi:10.7554/eLife.60416
Stracy, Mathew et al. Transient non-specific DNA binding dominates the target search of bacterial DNA-binding proteins. Molecular cell vol. 81,7 (2021): 1499-1514.e6. doi:10.1016/j.molcel.2021.01.039
Afanzar, Oshri et al. The switching mechanism of the bacterial rotary motor combines tight regulation with inherent flexibility. The EMBO journal vol. 40,6 (2021): e104683. doi:10.15252/embj.2020104683
Mazumder, Abhishek et al. RNA polymerase clamp conformational dynamics: long-lived states and modulation by crowding, cations, and nonspecific DNA binding. Nucleic acids research vol. 49,5 (2021): 2790-2802. doi:10.1093/nar/gkab074

2020

Mazumder, Abhishek et al. Closing and opening of the RNA polymerase trigger loop. Proceedings of the National Academy of Sciences of the United States of America vol. 117,27 (2020): 15642-15649. doi:10.1073/pnas.1920427117
Sow M, Steuer H, Adekanye S, Ginés L, Mandal S, Gilboa B, Williams OA, Smith JM , Kapanidis AN. High-throughput nitrogen-vacancy center imaging for nanodiamond photophysical characterization and pH nanosensing. Nanoscale. 2020 Nov 5;12(42):21821-21831. doi: 10.1039/d0nr05931e

2019

Craggs, Timothy D et al. Substrate conformational dynamics facilitate structure-specific recognition of gapped DNA by DNA polymerase. Nucleic acids research vol. 47,20 (2019): 10788-10800. doi:10.1093/nar/gkz797
Robb, Nicole C et al. Rapid functionalisation and detection of viruses via a novel Ca2+-mediated virus-DNA interaction. Scientific reports vol. 9,1 16219. 7 Nov. 2019, doi:10.1038/s41598-019-52759-5
Gilboa, Barak et al. Confinement-Free Wide-Field Ratiometric Tracking of Single Fluorescent Molecules. Biophysical journal vol. 117,11 (2019): 2141-2153. doi:10.1016/j.bpj.2019.10.033
Craggs, Timothy D et al. Substrate conformational dynamics facilitate structure-specific recognition of gapped DNA by DNA polymerase. Nucleic acids research vol. 47,20 (2019): 10788-10800. doi:10.1093/nar/gkz797
Mazumder, Abhishek, and Achillefs N Kapanidis. Recent Advances in Understanding σ70-Dependent Transcription Initiation Mechanisms. Journal of molecular biology vol. 431,20 (2019): 3947-3959. doi:10.1016/j.jmb.2019.04.046
Robb, Nicole C et al. Real-time analysis of single influenza virus replication complexes reveals large promoter-dependent differences in initiation dynamics. Nucleic acids research vol. 47,12 (2019): 6466-6477. doi:10.1093/nar/gkz313
Pambos, Oliver J, and Achillefs N Kapanidis. Tracking antibiotic mechanisms. Nature reviews. Microbiology vol. 17,4 (2019): 201. doi:10.1038/s41579-019-0167-8
Klein, Hannah L et al. Guidelines for DNA recombination and repair studies: Mechanistic assays of DNA repair processes. Microbial cell (Graz, Austria) vol. 6,1 65-101. 7 Jan. 2019, doi:10.15698/mic2019.01.665

2018

Hellenkamp, Björn et al. Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study. Nature methods vol. 15,9 (2018): 669-676. doi:10.1038/s41592-018-0085-0
Duchi, Diego et al. The RNA polymerase clamp interconverts dynamically among three states and is stabilized in a partly closed state by ppGpp. Nucleic acids research vol. 46,14 (2018): 7284-7295. doi:10.1093/nar/gky482
Kapanidis, Achillefs N, and Mathew Stracy. Tracking tRNA packages. Nature chemical biology vol. 14,6 (2018): 528-529. doi:10.1038/s41589-018-0066-8
Kapanidis, Achillefs N et al. Understanding Protein Mobility in Bacteria by Tracking Single Molecules. Journal of molecular biology vol. 430,22 (2018): 4443-4455. doi:10.1016/j.jmb.2018.05.002
Dulin, David et al. Pausing controls branching between productive and non-productive pathways during initial transcription in bacteria. Nature communications vol. 9,1 1478. 16 Apr. 2018, doi:10.1038/s41467-018-03902-9
Kapanidis, Achillefs N et al. Rediscovering Bacteria through Single-Molecule Imaging in Living Cells. Biophysical journal vol. 115,2 (2018): 190-202. doi:10.1016/j.bpj.2018.03.028
Lin, Wei et al. Structural Basis of Transcription Inhibition by Fidaxomicin (Lipiarmycin A3). Molecular cell vol. 70,1 (2018): 60-71.e15. doi:10.1016/j.molcel.2018.02.026
Duchi, Diego et al. Conformational heterogeneity and bubble dynamics in single bacterial transcription initiation complexes. Nucleic acids research vol. 46,2 (2018): 677-688. doi:10.1093/nar/gkx1146

2017

Stracy, Mathew, and Achillefs N Kapanidis. Single-molecule and super-resolution imaging of transcription in living bacteria. Methods (San Diego, Calif.) vol. 120 (2017): 103-114. doi:10.1016/j.ymeth.2017.04.001
Garza de Leon, Federico et al. Tracking Low-Copy Transcription Factors in Living Bacteria: The Case of the lac Repressor. Biophysical journal vol. 112,7 (2017): 1316-1327. doi:10.1016/j.bpj.2017.02.028
Lamberte, Lisa E et al. Horizontally acquired AT-rich genes in Escherichia coli cause toxicity by sequestering RNA polymerase. Nature microbiology vol. 2 16249. 9 Jan. 2017, doi:10.1038/nmicrobiol.2016.249

2016

Hohlbein, J, and A N Kapanidis. Probing the Conformational Landscape of DNA Polymerases Using Diffusion-Based Single-Molecule FRET. Methods in enzymology vol. 581 (2016): 353-378. doi:10.1016/bs.mie.2016.08.023
Robb, Nicole C et al. Single-molecule FRET reveals the pre-initiation and initiation conformations of influenza virus promoter RNA. Nucleic acids research vol. 44,21 (2016): 10304-10315. doi:10.1093/nar/gkw884
Plochowietz, Anne et al. In vivo single-RNA tracking shows that most tRNA diffuses freely in live bacteria. Nucleic acids research vol. 45,2 (2017): 926-937. doi:10.1093/nar/gkw787
Duchi, Diego et al. RNA Polymerase Pausing during Initial Transcription. Molecular cell vol. 63,6 (2016): 939-50. doi:10.1016/j.molcel.2016.08.011
Te Velthuis, Aartjan J W et al. The role of the priming loop in influenza A virus RNA synthesis. Nature microbiology vol. 1 16029. 21 Mar. 2016, doi:10.1038/nmicrobiol.2016.29
Stracy, Mathew et al. Single-molecule imaging of UvrA and UvrB recruitment to DNA lesions in living Escherichia coli. Nature communications vol. 7 12568. 26 Aug. 2016, doi:10.1038/ncomms12568
Sadler, Emma E et al. Solution-Based Single-Molecule FRET Studies of K(+) Channel Gating in a Lipid Bilayer. Biophysical journal vol. 110,12 (2016): 2663-2670. doi:10.1016/j.bpj.2016.05.020
Meli, Massimiliano et al. DNA Polymerase Conformational Dynamics and the Role of Fidelity-Conferring Residues: Insights from Computational Simulations. Frontiers in molecular biosciences vol. 3 20. 27 May. 2016, doi:10.3389/fmolb.2016.00020

2015

Zawadzki, Pawel et al. The Localization and Action of Topoisomerase IV in Escherichia coli Chromosome Segregation Is Coordinated by the SMC Complex, MukBEF. Cell reports vol. 13,11 (2015): 2587-2596. doi:10.1016/j.celrep.2015.11.034
May, Peter F J et al. Assembly, translocation, and activation of XerCD-dif recombination by FtsK translocase analyzed in real-time by FRET and two-color tethered fluorophore motion. Proceedings of the National Academy of Sciences of the United States of America vol. 112,37 (2015): E5133-41. doi:10.1073/pnas.1510814112
Sustarsic, Marko, and Achillefs N Kapanidis. Taking the ruler to the jungle: single-molecule FRET for understanding biomolecular structure and dynamics in live cells. Current opinion in structural biology vol. 34 (2015): 52-9. doi:10.1016/j.sbi.2015.07.001
Plochowietz, A., Kapanidis, A. Single in the (Cell) City: a protein-folding story. Nat Methods 12, 715–716 (2015). https://doi.org/10.1038/nmeth.3491
Stracy, Mathew et al. Live-cell superresolution microscopy reveals the organization of RNA polymerase in the bacterial nucleoid. Proceedings of the National Academy of Sciences of the United States of America vol. 112,32 (2015): E4390-9. doi:10.1073/pnas.1507592112
Evans, Geraint W et al. Real-time single-molecule studies of the motions of DNA polymerase fingers illuminate DNA synthesis mechanisms. Nucleic acids research vol. 43,12 (2015): 5998-6008. doi:10.1093/nar/gkv547
Aigrain, Louise et al. Internalization and Observation of Fluorescent Biomolecules in Living Microorganisms via Electroporation. Journal of Visualized Experiments : JoVE (2015): n. pag. Open Access Video

Publications before 2015

Disclaimer: All downloads are for non-profit, personal use only.