Achillefs N Kapanidis

Summary

Affiliation: University of Oxford
Country: UK

Publications

  1. ncbi request reprint Alternating-laser excitation of single molecules
    Achillefs N Kapanidis
    Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E Young Drive East, Los Angeles, California 90095 1569, USA
    Acc Chem Res 38:523-33. 2005
  2. pmc Studying the organization of DNA repair by single-cell and single-molecule imaging
    Stephan Uphoff
    Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom Electronic address
    DNA Repair (Amst) 20:32-40. 2014
  3. ncbi request reprint Retention of transcription initiation factor sigma70 in transcription elongation: single-molecule analysis
    Achillefs N Kapanidis
    Department of Chemistry and Biochemistry, and California Nanosystems Institute, University of California, Los Angeles, 607 Charles E Young Drive East, Los Angeles, California 90095, USA
    Mol Cell 20:347-56. 2005
  4. doi request reprint Biology, one molecule at a time
    Achillefs N Kapanidis
    Department of Physics and Interdisciplinary Research Collaboration in Bionanotechnology, Clarendon Laboratory, University of Oxford, Oxford, UK
    Trends Biochem Sci 34:234-43. 2009
  5. pmc Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism
    Achillefs N Kapanidis
    Department of Chemistry and Biochemistry and Department of Physiology, University of California, Los Angeles, CA 90095, USA
    Science 314:1144-7. 2006
  6. pmc Conformational landscapes of DNA polymerase I and mutator derivatives establish fidelity checkpoints for nucleotide insertion
    Johannes Hohlbein
    Biological Physics Research Group, Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, UK
    Nat Commun 4:2131. 2013
  7. pmc Accurate FRET measurements within single diffusing biomolecules using alternating-laser excitation
    Nam Ki Lee
    Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095 1569, USA
    Biophys J 88:2939-53. 2005
  8. doi request reprint Monitoring multiple distances within a single molecule using switchable FRET
    Stephan Uphoff
    Biological Physics Research Group, Department of Physics, University of Oxford, Oxford, UK
    Nat Methods 7:831-6. 2010
  9. pmc The transcription bubble of the RNA polymerase-promoter open complex exhibits conformational heterogeneity and millisecond-scale dynamics: implications for transcription start-site selection
    Nicole C Robb
    Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
    J Mol Biol 425:875-85. 2013
  10. pmc Direct observation of abortive initiation and promoter escape within single immobilized transcription complexes
    Emmanuel Margeat
    Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, California 90095, USA
    Biophys J 90:1419-31. 2006

Collaborators

Detail Information

Publications50

  1. ncbi request reprint Alternating-laser excitation of single molecules
    Achillefs N Kapanidis
    Department of Chemistry and Biochemistry, University of California, Los Angeles, 607 Charles E Young Drive East, Los Angeles, California 90095 1569, USA
    Acc Chem Res 38:523-33. 2005
    ..The principle of alternation is compatible with several time scales, allowing monitoring of fast dynamics or simultaneous monitoring of a large number of individual molecules...
  2. pmc Studying the organization of DNA repair by single-cell and single-molecule imaging
    Stephan Uphoff
    Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom Electronic address
    DNA Repair (Amst) 20:32-40. 2014
    ..We expect much can be learned about the organization of DNA repair by linking cell heterogeneity to mechanistic observations at the molecular level. ..
  3. ncbi request reprint Retention of transcription initiation factor sigma70 in transcription elongation: single-molecule analysis
    Achillefs N Kapanidis
    Department of Chemistry and Biochemistry, and California Nanosystems Institute, University of California, Los Angeles, 607 Charles E Young Drive East, Los Angeles, California 90095, USA
    Mol Cell 20:347-56. 2005
    ....
  4. doi request reprint Biology, one molecule at a time
    Achillefs N Kapanidis
    Department of Physics and Interdisciplinary Research Collaboration in Bionanotechnology, Clarendon Laboratory, University of Oxford, Oxford, UK
    Trends Biochem Sci 34:234-43. 2009
    ..These approaches have been instrumental in addressing important biological questions in diverse areas such as protein-DNA interactions, protein folding and the function(s) of membrane proteins...
  5. pmc Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism
    Achillefs N Kapanidis
    Department of Chemistry and Biochemistry and Department of Physiology, University of California, Los Angeles, CA 90095, USA
    Science 314:1144-7. 2006
    ....
  6. pmc Conformational landscapes of DNA polymerase I and mutator derivatives establish fidelity checkpoints for nucleotide insertion
    Johannes Hohlbein
    Biological Physics Research Group, Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, UK
    Nat Commun 4:2131. 2013
    ..The mutator phenotype of the low-fidelity derivatives correlates well with reduced affinity for complementary dNTPs and highlights the partially closed conformation as a primary checkpoint for nucleotide selection. ..
  7. pmc Accurate FRET measurements within single diffusing biomolecules using alternating-laser excitation
    Nam Ki Lee
    Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095 1569, USA
    Biophys J 88:2939-53. 2005
    ..ALEX can benefit structural analysis of biomolecules, especially when such molecules are inaccessible to conventional structural methods due to heterogeneity or transient nature...
  8. doi request reprint Monitoring multiple distances within a single molecule using switchable FRET
    Stephan Uphoff
    Biological Physics Research Group, Department of Physics, University of Oxford, Oxford, UK
    Nat Methods 7:831-6. 2010
    ..Our experiments on DNA molecules, a protein-DNA complex and dynamic Holliday junctions demonstrate the potential of switchable FRET for studying dynamic, multicomponent biomolecules...
  9. pmc The transcription bubble of the RNA polymerase-promoter open complex exhibits conformational heterogeneity and millisecond-scale dynamics: implications for transcription start-site selection
    Nicole C Robb
    Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
    J Mol Biol 425:875-85. 2013
    ..Our study marks the first experimental observation of conformational dynamics in the transcription bubble of RP(o) and indicates that DNA dynamics within the bubble affect the search for transcription start sites...
  10. pmc Direct observation of abortive initiation and promoter escape within single immobilized transcription complexes
    Emmanuel Margeat
    Department of Chemistry and Biochemistry, University of California at Los Angeles, Los Angeles, California 90095, USA
    Biophys J 90:1419-31. 2006
    ....
  11. pmc Identifying molecular dynamics in single-molecule FRET experiments with burst variance analysis
    Joseph P Torella
    Department of Physics and Biological Physics Research Group, University of Oxford, Oxford, United Kingdom
    Biophys J 100:1568-77. 2011
    ....
  12. pmc Capturing reaction paths and intermediates in Cre-loxP recombination using single-molecule fluorescence
    Justin N M Pinkney
    Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, United Kingdom
    Proc Natl Acad Sci U S A 109:20871-6. 2012
    ..After recombination, the product synaptic complex was extremely stable and refractory to subsequent rounds of recombination...
  13. pmc Characterization of dark quencher chromophores as nonfluorescent acceptors for single-molecule FRET
    Ludovic Le Reste
    Biological Physics Research Group, Department of Physics, University of Oxford, Oxford, United Kingdom
    Biophys J 102:2658-68. 2012
    ....
  14. doi request reprint Single-molecule FRET analysis of protein-DNA complexes
    Mike Heilemann
    Department of Physics and IRC in Bionanotechnology, Clarendon Laboratory, University of Oxford, Parks Road, Oxford, OX1 3PU, UK
    Methods Mol Biol 543:503-21. 2009
    ..An application of this method to the study of a bacterial transcription initiation complex is presented...
  15. doi request reprint Sensing DNA opening in transcription using quenchable Förster resonance energy transfer
    Thorben Cordes
    Biological Physics Research Group, Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Parks Road, Oxford, United Kingdom
    Biochemistry 49:9171-80. 2010
    ..Our results demonstrate that quFRET should find numerous applications in many processes involving DNA opening and closing, as well as in the development of new antibacterial therapies involving transcription...
  16. pmc Fluorescence-aided molecule sorting: analysis of structure and interactions by alternating-laser excitation of single molecules
    Achillefs N Kapanidis
    Department of Chemistry and Biochemistry, University of California, 607 Charles E Young Drive East, Los Angeles, CA 90095, USA
    Proc Natl Acad Sci U S A 101:8936-41. 2004
    ....
  17. pmc Probing biomolecular structures and dynamics of single molecules using in-gel alternating-laser excitation
    Yusdi Santoso
    Department of Physics and Biological Physics Research Group, Clarendon Laboratory, University of Oxford, Parks Road, Oxford, OX1 3PU, United Kingdom
    Anal Chem 81:9561-70. 2009
    ..In-gel ALEX will be a versatile tool for studying structures and dynamics of complex biomolecules and their assemblies...
  18. pmc Conformational transitions in DNA polymerase I revealed by single-molecule FRET
    Yusdi Santoso
    Biological Physics Research Group, Department of Physics, Clarendon Laboratory, University of Oxford, Oxford OX1 3PU, United Kingdom
    Proc Natl Acad Sci U S A 107:715-20. 2010
    ..Ternary complexes formed in the presence of mismatched dNTPs or complementary ribonucleotides show unique FRET species, which we suggest are relevant to kinetic checkpoints that discriminate against these incorrect substrates...
  19. doi request reprint Characterizing single-molecule FRET dynamics with probability distribution analysis
    Yusdi Santoso
    Department of Physics and Biological Physics Research Group, University of Oxford, Parks Road, Oxford OX1 3PU, UK
    Chemphyschem 11:2209-19. 2010
    ..We expect this method to be useful in extracting rates from processes exhibiting dynamic FRET, and in hypothesis-testing models of conformational dynamics against experimental data...
  20. pmc Single-molecule DNA repair in live bacteria
    Stephan Uphoff
    Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, United Kingdom
    Proc Natl Acad Sci U S A 110:8063-8. 2013
    ..We integrated these single-molecule observations to generate a quantitative, systems-level description of a model repair pathway in vivo...
  21. pmc Long-lived intracellular single-molecule fluorescence using electroporated molecules
    Robert Crawford
    Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, United Kingdom
    Biophys J 105:2439-50. 2013
    ..Our method should broaden the range of biological questions addressable in microbes by single-molecule fluorescence...
  22. pmc Periodic acceptor excitation spectroscopy of single molecules
    Soren Doose
    Clarendon Laboratory, Department of Physics and IRC in Bionanotechnology, Oxford University, Oxford, UK
    Eur Biophys J 36:669-74. 2007
    ....
  23. pmc Defining the limits of single-molecule FRET resolution in TIRF microscopy
    Seamus J Holden
    Biological Physics Research Group, Department of Physics, University of Oxford, Oxford, United Kingdom
    Biophys J 99:3102-11. 2010
    ..the mechanisms of which are often characterized by distance changes on the scale of one DNA basepair...
  24. doi request reprint Improved temporal resolution and linked hidden Markov modeling for switchable single-molecule FRET
    Stephan Uphoff
    Department of Physics and Biological Physics Research Group, University of Oxford, Parks Road, Oxford OX1 3PU, UK
    Chemphyschem 12:571-9. 2011
    ..Improved temporal resolution and novel data analysis make switchable FRET a valuable tool in molecular and structural biology...
  25. pmc Single-molecule imaging of UvrA and UvrB recruitment to DNA lesions in living Escherichia coli
    Mathew Stracy
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
    Nat Commun 7:12568. 2016
    ..Subsequent UvrB recruitment requires ATP hydrolysis in the proximal site. Finally, UvrA dissociates from the lesion complex, allowing UvrB to orchestrate the downstream NER reactions. ..
  26. pmc RNA Polymerase Pausing during Initial Transcription
    Diego Duchi
    Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
    Mol Cell 63:939-50. 2016
    ..We summarized our work in a model for initial transcription, in which pausing is controlled by a complex set of determinants that modulate the transition from a 6- to a 7-nt RNA. ..
  27. pmc The Localization and Action of Topoisomerase IV in Escherichia coli Chromosome Segregation Is Coordinated by the SMC Complex, MukBEF
    Pawel Zawadzki
    Department of Biochemistry, University of Oxford, South Parks Road, Oxford OX1 3QU, UK
    Cell Rep 13:2587-96. 2015
    ..Finally, we show that the MukB-ParC interaction is crucial for timely decatenation and segregation of newly replicated ori DNA...
  28. pmc Assembly, translocation, and activation of XerCD-dif recombination by FtsK translocase analyzed in real-time by FRET and two-color tethered fluorophore motion
    Peter F J May
    Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, United Kingdom
    Proc Natl Acad Sci U S A 112:E5133-41. 2015
    ....
  29. pmc Live-cell superresolution microscopy reveals the organization of RNA polymerase in the bacterial nucleoid
    Mathew Stracy
    Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, United Kingdom
    Proc Natl Acad Sci U S A 112:E4390-9. 2015
    ..This work provides a global view of the organization of RNA polymerase and transcription in living cells. ..
  30. pmc Rotavirus mRNAS are released by transcript-specific channels in the double-layered viral capsid
    Javier Periz
    Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, United Kingdom
    Proc Natl Acad Sci U S A 110:12042-7. 2013
    ..Our approach can be extended to study other viruses and transcription systems. ..
  31. doi request reprint Non-covalent Single Transcription Factor Encapsulation Inside a DNA Cage
    Robert Crawford
    Biological Physics Research Group, Department of Physics, University of Oxford, Clarendon Laboratory, Parks Road, Oxford, OX1 3PU UK
    Angew Chem Int Ed Engl 52:2284-8. 2013
    ..CAP is shown to stably bind inside the DNA cage at a 1:1 ratio by bending one edge to accommodate the protein. Single-molecule fluorescence measurements confirm the orientation of CAP within the cage...
  32. doi request reprint A protein biosensor that relies on bending of single DNA molecules
    Robert Crawford
    Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, UK
    Chemphyschem 13:918-22. 2012
    ..The method should allow detection of a wide range of DNA-bending proteins...
  33. doi request reprint The role of the priming loop in influenza A virus RNA synthesis
    Aartjan J W te Velthuis
    Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK
    Nat Microbiol 1:16029. 2016
    ..Overall, this work advances our understanding of influenza A virus RNA synthesis and identifies the initiation platform of viral replication. ..
  34. pmc The role of the priming loop in Influenza A virus RNA synthesis
    Aartjan J W te Velthuis
    Sir William Dunn School of Pathology, University of Oxford, South Parks Road, OX1 3RE, Oxford, United Kingdom Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, OX1 3PU, United Kingdom
    Nat Microbiol 1:. 2016
    ..Overall, this work advances our understanding of Influenza A virus RNA synthesis and identifies the initiation platform of viral replication...
  35. pmc Single-molecule FRET reveals the pre-initiation and initiation conformations of influenza virus promoter RNA
    Nicole C Robb
    Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford OX1 3PU, UK
    Nucleic Acids Res 44:10304-10315. 2016
    ..Our data provide insights into the dynamic motions of RNA that occur during initial influenza replication and has implications for our understanding of the replication mechanisms of similar pathogenic viruses...
  36. pmc Tethered fluorophore motion: studying large DNA conformational changes by single-fluorophore imaging
    Peter F J May
    Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, Oxford, OX1 3PU, UK
    Biophys J 107:1205-16. 2014
    ..We hope that TFM will be a useful addition to the single-molecule toolkit, providing excellent insight into protein-nucleic acid interactions. ..
  37. pmc Real-time single-molecule studies of the motions of DNA polymerase fingers illuminate DNA synthesis mechanisms
    Geraint W Evans
    Department of Physics and Biological Physics Research Group, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX1 3PU, United Kingdom
    Nucleic Acids Res 43:5998-6008. 2015
    ....
  38. doi request reprint Surfing on a new wave of single-molecule fluorescence methods
    Johannes Hohlbein
    Department of Physics, Biological Physics Research Group, University of Oxford, Oxford, UK
    Phys Biol 7:031001. 2010
    ....
  39. doi request reprint Red light, green light: probing single molecules using alternating-laser excitation
    Yusdi Santoso
    Department of Physics and Interdisciplinary Research Collaboration in Bionanotechnology, Clarendon Laboratory, University of Oxford, Parks Road, Oxford, UK
    Biochem Soc Trans 36:738-44. 2008
    ..We also highlight applications of ALEX to the study of protein-nucleic acid interactions...
  40. pmc Visualizing protein-DNA interactions in live bacterial cells using photoactivated single-molecule tracking
    Stephan Uphoff
    Microbiology Unit, Department of Biochemistry, University of Oxford Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford
    J Vis Exp . 2014
    ..Here, we describe the concept of the method and demonstrate sample preparation, data acquisition, and data analysis procedures. ..
  41. doi request reprint In vivo single-molecule imaging of bacterial DNA replication, transcription, and repair
    Mathew Stracy
    Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, United Kingdom
    FEBS Lett 588:3585-94. 2014
    ..Together, these studies demonstrate how single-molecule imaging is transforming our understanding of DNA-binding proteins in cells. ..
  42. pmc Single-molecule FRET reveals a corkscrew RNA structure for the polymerase-bound influenza virus promoter
    Alexandra I Tomescu
    Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, United Kingdom
    Proc Natl Acad Sci U S A 111:E3335-42. 2014
    ..In addition, the simplicity of this system should translate readily to the study of any virus polymerase-promoter interaction. ..
  43. pmc T7 RNA polymerase functions in vitro without clustering
    Kieran Finan
    Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
    PLoS ONE 7:e40207. 2012
    ..coli chromosome do not associate more frequently when transcribed by T7 RNAP. We conclude that if clustering does occur in vivo, it must be driven by weak interactions, or mediated by a phage-encoded protein...
  44. doi request reprint A facile method for reversibly linking a recombinant protein to DNA
    Russell P Goodman
    Department of Physics, Clarendon Laboratory, University of Oxford, Parks Road, Oxford OX13PU, UK
    Chembiochem 10:1551-7. 2009
    ..We have used this new linker to bind proteins to a variety of DNA motifs commonly used in the fabrication of nanostructures by DNA self-assembly...
  45. ncbi request reprint The power and prospects of fluorescence microscopies and spectroscopies
    Xavier Michalet
    Department of Chemistry and Biochemistry, UCLA, Young Hall, 607 Charles E Young Drive East, Los Angeles, California 90095, USA
    Annu Rev Biophys Biomol Struct 32:161-82. 2003
    ....
  46. ncbi request reprint In vivo single-RNA tracking shows that most tRNA diffuses freely in live bacteria
    Anne Plochowietz
    Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Parks Road, OX1 3PU, Oxford, UK
    Nucleic Acids Res . 2016
    ....
  47. ncbi request reprint Structural organization of bacterial RNA polymerase holoenzyme and the RNA polymerase-promoter open complex
    Vladimir Mekler
    Howard Hughes Medical Institute, Waksman Institute, Rutgers University, Piscataway, NJ 08854, USA
    Cell 108:599-614. 2002
    ..1 is located outside the active center cleft. The approach described here should be applicable to the analysis of other nanometer-scale complexes...
  48. pmc Three-color alternating-laser excitation of single molecules: monitoring multiple interactions and distances
    Nam Ki Lee
    School of Chemistry, Seoul National University, Seoul, Korea
    Biophys J 92:303-12. 2007
    ..This study paves the way for advanced single-molecule analysis of complex mixtures and biomolecular machinery...
  49. ncbi request reprint Fluorescence resonance energy transfer (FRET) in analysis of transcription-complex structure and function
    Jayanta Mukhopadhyay
    Waksman Institute, Howard Hughes Medical Institute, Rutgers University, 190 Frelinghuysen Road, Piscataway, New Jersey 08854, USA
    Methods Enzymol 371:144-59. 2003
  50. doi request reprint Reconfigurable, braced, three-dimensional DNA nanostructures
    Russell P Goodman
    Nat Nanotechnol 3:93-6. 2008
    ..The introduction of shape-changing structural modules opens new avenues for the manipulation of matter on the nanometre scale...