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Achillefs Kapanidis

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TOP 3
Stephan Uphoff; Federico Garza de Leon; Rodrigo Reyes-Lamothe; David J Sherratt; Achillefs N Kapanidis
Single-molecule DNA repair in live bacteria.
Nicole C Robb; Yusdi Santoso; Shimon Weiss; Thorben Cordes; Timothy D Craggs; Diego Duchi; Richard H Ebright; Kristofer Gryte; Ling Chin Hwang; Achillefs N Kapanidis
The transcription bubble of the RNA polymerase-promoter open complex exhibits conformational heterogeneity and millisecond-scale dynamics: implications for transcription start-site selection.
Robert Crawford; Christoph M Erben; Lucy M Hall; Javier Periz; Andrew J Turberfield; Tom Brown; Achillefs N Kapanidis
Non-covalent single transcription factor encapsulation inside a DNA cage.

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All Publications

2013: Stephan Uphoff; Federico Garza de Leon; Rodrigo Reyes-Lamothe; David J Sherratt; Achillefs N Kapanidis
Single-molecule DNA repair in live bacteria.
Proceedings of the National Academy of Sciences of the United States of America 2013;110(20):8063-8.
2013: Nicole C Robb; Yusdi Santoso; Shimon Weiss; Thorben Cordes; Timothy D Craggs; Diego Duchi; Richard H Ebright; Kristofer Gryte; Ling Chin Hwang; Achillefs N Kapanidis
The transcription bubble of the RNA polymerase-promoter open complex exhibits conformational heterogeneity and millisecond-scale dynamics: implications for transcription start-site selection.
Journal of molecular biology 2013;425(5):875-85.
2013: Robert Crawford; Christoph M Erben; Lucy M Hall; Javier Periz; Andrew J Turberfield; Tom Brown; Achillefs N Kapanidis
Non-covalent single transcription factor encapsulation inside a DNA cage.
Angewandte Chemie (International ed. in English) 2013;52(8):2284-8.
2012: Justin N M Pinkney; David J Sherratt; Pawel Zawadzki; Lidia K Arciszewska; Jaroslaw Mazuryk; Achillefs N Kapanidis
Capturing reaction paths and intermediates in Cre-loxP recombination using single-molecule fluorescence.
Proceedings of the National Academy of Sciences of the United States of America 2012;109(51):20871-6.
2012: Timothy D Craggs; Achillefs N Kapanidis
Six steps closer to FRET-driven structural biology.
Nature methods 2012;9(12):1157-8.
2012: Ludovic Le Reste; Kristofer Gryte; Johannes Hohlbein; Achillefs N Kapanidis
Characterization of dark quencher chromophores as nonfluorescent acceptors for single-molecule FRET.
Biophysical journal 2012;102(11):2658-68.
2012: Achillefs N Kapanidis; Robert Crawford
Colorful molecular diagnostics.
Clinical chemistry 2012;58(4):659-60.
2012: Robert Crawford; Douglas J Kelly; Achillefs N Kapanidis
A protein biosensor that relies on bending of single DNA molecules.
Chemphyschem : a European journal of chemical physics and physical chemistry 2012;13(4):918-22.
2012: Kieran Finan; Achillefs N Kapanidis; Joseph P Torella; Peter R Cook
T7 RNA polymerase functions in vitro without clustering.
PloS one 2012;7(7):e40207.
2011: Seamus J Holden; Stephan Uphoff; Achillefs N Kapanidis
DAOSTORM: an algorithm for high- density super-resolution microscopy.
Nature methods 2011;8(4):279-80.
2011: Joseph P Torella; Seamus J Holden; Yusdi Santoso; Johannes Hohlbein; Achillefs N Kapanidis
Identifying molecular dynamics in single-molecule FRET experiments with burst variance analysis.
Biophysical journal 2011;100(6):1568-77.
2011: Stephan Uphoff; Kristofer Gryte; Geraint Evans; Achillefs N Kapanidis
Improved temporal resolution and linked hidden Markov modeling for switchable single-molecule FRET.
Chemphyschem : a European journal of chemical physics and physical chemistry 2011;12(3):571-9.
2010: Seamus J Holden; Stephan Uphoff; Johannes Hohlbein; David Yadin; Ludovic Le Reste; Oliver J Britton; Achillefs N Kapanidis
Defining the limits of single-molecule FRET resolution in TIRF microscopy.
Biophysical journal 2010;99(9):3102-11.
2010: Thorben Cordes; Yusdi Santoso; Alexandra I Tomescu; Kristofer Gryte; Ling Chin Hwang; Beatriz Camará; Sivaramesh Wigneshweraraj; Achillefs N Kapanidis
Sensing DNA opening in transcription using quenchable Förster resonance energy transfer.
Biochemistry 2010;49(43):9171-80.
2010: Stephan Uphoff; Seamus J Holden; Ludovic Le Reste; Javier Periz; Sebastian van de Linde; Mike Heilemann; Achillefs N Kapanidis
Monitoring multiple distances within a single molecule using switchable FRET.
Nature methods 2010;7(10):831-6.
2010: Yusdi Santoso; Joseph P Torella; Achillefs N Kapanidis
Characterizing single-molecule FRET dynamics with probability distribution analysis.
Chemphyschem : a European journal of chemical physics and physical chemistry 2010;11(10):2209-19.
2010: Konstantinos Lymperopoulos; Robert Crawford; Joseph P Torella; Mike Heilemann; Ling Chin Hwang; Seamus J Holden; Achillefs N Kapanidis
Single-molecule DNA biosensors for protein and ligand detection.
Angewandte Chemie (International ed. in English) 2010;49(7):1316-20.
2010: Yusdi Santoso; Catherine M Joyce; Olga Potapova; Ludovic Le Reste; Johannes Hohlbein; Joseph P Torella; Nigel D F Grindley; Achillefs N Kapanidis
Conformational transitions in DNA polymerase I revealed by single-molecule FRET.
Proceedings of the National Academy of Sciences of the United States of America 2010;107(2):715-20.
2010: Johannes Hohlbein; Kristofer Gryte; Mike Heilemann; Achillefs N Kapanidis
Surfing on a new wave of single-molecule fluorescence methods.
Physical biology 2010;7(3):031001.
2009: Yusdi Santoso; Achillefs N Kapanidis
Probing biomolecular structures and dynamics of single molecules using in-gel alternating-laser excitation.
Analytical chemistry 2009;81(23):9561-70.
2009: Helen M J Carstairs; Kostas Lymperopoulos; Achillefs N Kapanidis; Jonathan Bath; Andrew J Turberfield
DNA monofunctionalization of quantum dots.
Chembiochem : a European journal of chemical biology 2009;10(11):1781-3.
2009: Russell P Goodman; Christoph M Erben; Jonathan Malo; Wei M Ho; Mireya L McKee; Achillefs N Kapanidis; Andrew J Turberfield
A facile method for reversibly linking a recombinant protein to DNA.
Chembiochem : a European journal of chemical biology 2009;10(9):1551-7.
2009: Achillefs N Kapanidis; Terence Strick
Biology, one molecule at a time.
Trends in biochemical sciences 2009;34(5):234-43.
2009: Mike Heilemann; Ling Chin Hwang; Konstantinos Lymperopoulos; Achillefs N Kapanidis
Single-molecule FRET analysis of protein-DNA complexes.
Methods in molecular biology (Clifton, N.J.) 2009;543():503-21.
2008: Yusdi Santoso; Ling Chin Hwang; Ludovic Le Reste; Achillefs N Kapanidis
Red light, green light: probing single molecules using alternating-laser excitation.
Biochemical Society transactions 2008;36(Pt 4):738-44.
2008: Russell P Goodman; Mike Heilemann; Sören Doose; Christoph M Erben; Achillefs N Kapanidis; Andrew J Turberfield
Reconfigurable, braced, three-dimensional DNA nanostructures.
Nature nanotechnology 2008;3(2):93-6.
2007: P J Harding; H Attrill; S Ross; J R Koeppe; Achillefs N Kapanidis; Anthony Watts
Neurotensin receptor type 1: Escherichia coli expression, purification, characterization and biophysical study.
Biochemical Society transactions 2007;35(Pt 4):760-3.
2007: Sören Doose; Mike Heilemann; Xavier Michalet; Shimon Weiss; Achillefs N Kapanidis
Periodic acceptor excitation spectroscopy of single molecules.
European biophysics journal : EBJ 2007;36(6):669-74.
2007: Nam Ki Lee; Achillefs N Kapanidis; Hye Ran Koh; You Korlann; Sam On Ho; Younggyu Kim; Natalie Gassman; Seong Keun Kim; Shimon Weiss
Three-color alternating-laser excitation of single molecules: monitoring multiple interactions and distances.
Biophysical journal 2007;92(1):303-12.
2006: Achillefs N Kapanidis; Emmanuel Margeat; Sam On Ho; Ekaterine Kortkhonjia; Shimon Weiss; Richard H. Ebright
Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism.
Science (New York, N.Y.) 2006;314(5802):1144-7.
2006: Emmanuel Margeat; Achillefs N Kapanidis; Philip Tinnefeld; You Wang; Jayanta Mukhopadhyay; Richard H. Ebright; Shimon Weiss
Direct observation of abortive initiation and promoter escape within single immobilized transcription complexes.
Biophysical journal 2006;90(4):1419-31.
2005: Achillefs N Kapanidis; Emmanuel Margeat; Ted A Laurence; Sören Doose; Sam On Ho; Jayanta Mukhopadhyay; Ekaterine Kortkhonjia; Vladimir Mekler; Richard H. Ebright; Shimon Weiss
Retention of transcription initiation factor sigma70 in transcription elongation: single-molecule analysis.
Molecular cell 2005;20(3):347-56.
2005: Achillefs N Kapanidis; Ted A Laurence; Nam Ki Lee; Emmanuel Margeat; Xiangxu Kong; Shimon Weiss
Alternating-laser excitation of single molecules.
Accounts of chemical research 2005;38(7):523-33.
2005: Nam Ki Lee; Achillefs N Kapanidis; You Wang; Xavier Michalet; Jayanta Mukhopadhyay; Richard H. Ebright; Shimon Weiss
Accurate FRET measurements within single diffusing biomolecules using alternating-laser excitation.
Biophysical journal 2005;88(4):2939-53.
2004: Achillefs N Kapanidis; Nam Ki Lee; Ted A Laurence; Sören Doose; Emmanuel Margeat; Shimon Weiss
Fluorescence-aided molecule sorting: analysis of structure and interactions by alternating-laser excitation of single molecules.
Proceedings of the National Academy of Sciences of the United States of America 2004;101(24):8936-41.
2003: Jayanta Mukhopadhyay; Vladimir Mekler; Ekaterine Kortkhonjia; Achillefs N Kapanidis; Yon W Ebright; Richard H. Ebright
Fluorescence resonance energy transfer (FRET) in analysis of transcription-complex structure and function.
Methods in enzymology 2003;371():144-59.
2003: Xavier Michalet; Achillefs N Kapanidis; Ted A Laurence; Fabien Pinaud; Sören Doose; Malte Pflughoefft; Shimon Weiss
The power and prospects of fluorescence microscopies and spectroscopies.
Annual review of biophysics and biomolecular structure 2003;32():161-82.
2002: Vladimir Mekler; Ekaterine Kortkhonjia; Jayanta Mukhopadhyay; Jennifer Knight; Andrey Revyakin; Achillefs N Kapanidis; Wei Niu; Yon W Ebright; Ronald Levy; Richard H. Ebright
Structural organization of bacterial RNA polymerase holoenzyme and the RNA polymerase-promoter open complex.
Cell 2002;108(5):599-614.
2001: Achillefs N Kapanidis; Yon W Ebright; Richard H. Ebright
Site-specific incorporation of fluorescent probes into protein: hexahistidine-tag-mediated fluorescent labeling with (Ni(2+):nitrilotriacetic Acid (n)-fluorochrome conjugates.
Journal of the American Chemical Society 2001;123(48):12123-5.
2001: Achillefs N Kapanidis; Yon W Ebright; R D Ludescher; S Chan; Richard H. Ebright
Mean DNA bend angle and distribution of DNA bend angles in the CAP-DNA complex in solution.
Journal of molecular biology 2001;312(3):453-68.
2001: Jayanta Mukhopadhyay; Achillefs N Kapanidis; Vladimir Mekler; Ekaterine Kortkhonjia; Yon W Ebright; Richard H. Ebright
Translocation of sigma(70) with RNA polymerase during transcription: fluorescence resonance energy transfer assay for movement relative to DNA.
Cell 2001;106(4):453-63.
1998: Arnold J Berk; Thomas Boyer; Achillefs N Kapanidis; Richard H. Ebright; N N Kobayashi; PJ Horn; SM Sullivan; R Koop; M A Surby; Steven J Triezenberg
Mechanisms of viral activators.
Cold Spring Harbor symposia on quantitative biology 1998;63():243-52.
1998: T Lagrange; Achillefs N Kapanidis; H Tang; Danny Reinberg; Richard H. Ebright
New core promoter element in RNA polymerase II-dependent transcription: sequence-specific DNA binding by transcription factor IIB.
Genes & development 1998;12(1):34-44.