Achillefs Kapanidis - Publications

1999 Rutgers University, New Brunswick, New Brunswick, NJ, United States 

59 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Lerner E, Barth A, Hendrix J, Ambrose B, Birkedal V, Blanchard SC, Börner R, Sung Jung H, Cordes T, Craggs TD, Deniz AA, Diao J, Fei J, Gonzalez RL, Gopich IV, ... ... Kapanidis AN, et al. FRET-based dynamic structural biology: Challenges, perspectives and an appeal for open-science practices. Elife. 10. PMID 33779550 DOI: 10.7554/eLife.60416  0.8
2021 Mazumder A, Wang A, Uhm H, Ebright RH, Kapanidis AN. RNA polymerase clamp conformational dynamics: long-lived states and modulation by crowding, cations, and nonspecific DNA binding. Nucleic Acids Research. PMID 33589919 DOI: 10.1093/nar/gkab074  1
2020 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. PMID 33103692 DOI: 10.1039/d0nr05931e  0.44
2020 Mazumder A, Lin M, Kapanidis AN, Ebright RH. Closing and opening of the RNA polymerase trigger loop. Proceedings of the National Academy of Sciences of the United States of America. PMID 32571927 DOI: 10.1073/Pnas.1920427117  1
2019 Gilboa B, Jing B, Cui TJ, Sow M, Plochowietz A, Mazumder A, Kapanidis AN. Confinement-Free Wide-Field Ratiometric Tracking of Single Fluorescent Molecules. Biophysical Journal. PMID 31711608 DOI: 10.1016/J.Bpj.2019.10.033  1
2019 Robb NC, Taylor JM, Kent A, Pambos OJ, Gilboa B, Evangelidou M, Mentis AA, Kapanidis AN. Rapid functionalisation and detection of viruses via a novel Ca-mediated virus-DNA interaction. Scientific Reports. 9: 16219. PMID 31700064 DOI: 10.1038/s41598-019-52759-5  0.44
2019 Mazumder A, Kapanidis AN. Recent Advances in Understanding σ70-Dependent Transcription Initiation Mechanisms. Journal of Molecular Biology. PMID 31082441 DOI: 10.1016/J.Jmb.2019.04.046  1
2018 Hellenkamp B, Schmid S, Doroshenko O, Opanasyuk O, Kühnemuth R, Adariani SR, Ambrose B, Aznauryan M, Barth A, Birkedal V, Bowen ME, Chen H, Cordes T, Eilert T, Fijen C, ... ... Kapanidis AN, et al. Publisher Correction: Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study. Nature Methods. PMID 30327572 DOI: 10.1038/S41592-018-0193-X  0.56
2018 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, Cordes T, Eilert T, Fijen C, ... ... Kapanidis AN, et al. Precision and accuracy of single-molecule FRET measurements-a multi-laboratory benchmark study. Nature Methods. 15: 669-676. PMID 30171252 DOI: 10.1038/S41592-018-0085-0  0.56
2018 Duchi D, Mazumder A, Malinen AM, Ebright RH, Kapanidis AN. The RNA polymerase clamp interconverts dynamically among three states and is stabilized in a partly closed state by ppGpp. Nucleic Acids Research. PMID 29878276 DOI: 10.1093/Nar/Gky482  1
2018 Dulin D, Bauer DLV, Malinen AM, Bakermans JJW, Kaller M, Morichaud Z, Petushkov I, Depken M, Brodolin K, Kulbachinskiy A, Kapanidis AN. Pausing controls branching between productive and non-productive pathways during initial transcription in bacteria. Nature Communications. 9: 1478. PMID 29662062 DOI: 10.1038/S41467-018-03902-9  0.6
2018 Lin W, Das K, Degen D, Mazumder A, Duchi D, Wang D, Ebright YW, Ebright RY, Sineva E, Gigliotti M, Srivastava A, Mandal S, Jiang Y, Liu Y, Yin R, ... ... Kapanidis AN, et al. Structural Basis of Transcription Inhibition by Fidaxomicin (Lipiarmycin A3). Molecular Cell. PMID 29606590 DOI: 10.1016/J.Molcel.2018.02.026  1
2018 Duchi D, Gryte K, Robb NC, Morichaud Z, Sheppard C, Brodolin K, Wigneshweraraj S, Kapanidis AN. Conformational heterogeneity and bubble dynamics in single bacterial transcription initiation complexes. Nucleic Acids Research. 46: 677-688. PMID 29177430 DOI: 10.1093/nar/gkx1146  0.6
2016 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. Molecular Cell. PMID 27618490 DOI: 10.1016/J.Molcel.2016.08.011  0.6
2015 Kapanidis A, Majumdar D, Heilemann M, Nir E, Weiss S. Alternating Laser Excitation for Solution-Based Single-Molecule FRET. Cold Spring Harbor Protocols. 2015: pdb.top086405. PMID 26527772 DOI: 10.1101/Pdb.Top086405  0.84
2015 Kapanidis A, Majumdar D, Heilemann M, Nir E, Weiss S. Sample Preparation and Data Acquisition for μs-ALEX. Cold Spring Harbor Protocols. 2015: pdb.prot086439. PMID 26527767 DOI: 10.1101/Pdb.Prot086439  0.84
2015 Kapanidis A, Majumdar D, Heilemann M, Nir E, Weiss S. Aligning the μs-ALEX Setup. Cold Spring Harbor Protocols. 2015: pdb.prot086421. PMID 26527766 DOI: 10.1101/Pdb.Prot086421  0.84
2015 Kapanidis A, Majumdar D, Heilemann M, Nir E, Weiss S. Assembling the μs-ALEX Setup. Cold Spring Harbor Protocols. 2015: pdb.prot086413. PMID 26527765 DOI: 10.1101/Pdb.Prot086413  0.84
2015 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, Fritzsche J, Gibson S, Gullberg M, ... ... Kapanidis AN, et al. New technologies for DNA analysis - a review of the READNA Project. New Biotechnology. PMID 26514324 DOI: 10.1016/J.Nbt.2015.10.003  0.84
2015 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. 43: 5998-6008. PMID 26013816 DOI: 10.1093/Nar/Gkv547  0.84
2015 Aigrain L, Sustarsic M, Crawford R, Plochowietz A, Kapanidis AN. Internalization and observation of fluorescent biomolecules in living microorganisms via electroporation. Journal of Visualized Experiments : Jove. PMID 25741968 DOI: 10.3791/52208  0.84
2015 Stracy M, Lesterlin C, De Leon FG, Uphoff S, Zawadzki P, Kapanidis AN, Ha T. 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. 112: E4390-E4399. DOI: 10.1073/pnas.1507592112  0.84
2014 May PF, Pinkney JN, Zawadzki P, Evans GW, Sherratt DJ, Kapanidis AN. Tethered fluorophore motion: studying large DNA conformational changes by single-fluorophore imaging. Biophysical Journal. 107: 1205-16. PMID 25185556 DOI: 10.1016/j.bpj.2014.07.024  0.84
2014 Plochowietz A, Crawford R, Kapanidis AN. Characterization of organic fluorophores for in vivo FRET studies based on electroporated molecules. Physical Chemistry Chemical Physics : Pccp. 16: 12688-94. PMID 24837080 DOI: 10.1039/c4cp00995a  0.84
2013 Hohlbein J, Aigrain L, Craggs TD, Bermek O, Potapova O, Shoolizadeh P, Grindley ND, Joyce CM, Kapanidis AN. Conformational landscapes of DNA polymerase I and mutator derivatives establish fidelity checkpoints for nucleotide insertion. Nature Communications. 4: 2131. PMID 23831915 DOI: 10.1038/Ncomms3131  0.84
2013 Endesfelder U, Finan K, Holden SJ, Cook PR, Kapanidis AN, Heilemann M. Multiscale spatial organization of RNA polymerase in escherichia coli Biophysical Journal. 105: 172-181. PMID 23823236 DOI: 10.1016/J.Bpj.2013.05.048  0.84
2013 Crawford R, Erben CM, Periz J, Hall LM, Brown T, Turberfield AJ, Kapanidis AN. Non-covalent single transcription factor encapsulation inside a DNA cage. Angewandte Chemie (International Ed. in English). 52: 2284-8. PMID 23325751 DOI: 10.1002/Anie.201207914  0.84
2013 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 Journal of Molecular Biology. 425: 875-885. PMID 23274143 DOI: 10.1016/J.Jmb.2012.12.015  0.84
2012 Craggs TD, Kapanidis AN. Six steps closer to FRET-driven structural biology Nature Methods. 9: 1157-1159. PMID 23223168 DOI: 10.1038/Nmeth.2257  0.84
2011 Holden SJ, Uphoff S, Kapanidis AN. DAOSTORM: An algorithm for high-density super-resolution microscopy Nature Methods. 8: 279-280. PMID 21451515 DOI: 10.1038/nmeth0411-279  0.84
2011 Torella JP, Holden SJ, Santoso Y, Hohlbein J, Kapanidis AN. Identifying molecular dynamics in single-molecule fret experiments with burst variance analysis Biophysical Journal. 100: 1568-1577. PMID 21402040 DOI: 10.1016/j.bpj.2011.01.066  0.84
2010 Holden SJ, Uphoff S, Hohlbein J, Yadin D, Le Reste L, Britton OJ, Kapanidis AN. Defining the limits of single-molecule FRET resolution in TIRF microscopy Biophysical Journal. 99: 3102-3111. PMID 21044609 DOI: 10.1016/j.bpj.2010.09.005  0.84
2010 Cordes T, Santoso Y, Tomescu AI, Gryte K, Hwang LC, Camará B, Wigneshweraraj S, Kapanidis AN. Sensing DNA opening in transcription using quenchable Förster resonance energy transfer Biochemistry. 49: 9171-9180. PMID 20818825 DOI: 10.1021/Bi101184G  0.84
2010 Uphoff S, Holden SJ, Le Reste L, Periz J, Van De Linde S, Heilemann M, Kapanidis AN. Monitoring multiple distances within a single molecule using switchable FRET Nature Methods. 7: 831-836. PMID 20818380 DOI: 10.1038/nmeth.1502  0.84
2010 Hohlbein J, Gryte K, Heilemann M, Kapanidis AN. Surfing on a new wave of single-molecule fluorescence methods. Physical Biology. 7: 031001. PMID 20686191 DOI: 10.1088/1478-3975/7/3/031001  0.8
2010 Santoso Y, Joyce CM, Potapova O, Le Reste L, Hohlbein J, Torella JP, Grindley ND, Kapanidis AN. Conformational transitions in DNA polymerase I revealed by single-molecule FRET. Proceedings of the National Academy of Sciences of the United States of America. 107: 715-20. PMID 20080740 DOI: 10.1073/Pnas.0910909107  0.84
2010 Lymperopoulos K, Crawford R, Torella JP, Heilemann M, Hwang LC, Holden SJ, Kapanidis AN. Single-molecule DNA biosensors for protein and ligand detection Angewandte Chemie - International Edition. 49: 1316-1320. PMID 20077444 DOI: 10.1002/anie.200904597  0.84
2009 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 : a European Journal of Chemical Biology. 10: 1551-7. PMID 19449345 DOI: 10.1002/cbic.200900165  0.84
2009 Heilemann M, Hwang LC, Lymperopoulos K, Kapanidis AN. Single-molecule FRET analysis of protein-DNA complexes. Methods in Molecular Biology (Clifton, N.J.). 543: 503-21. PMID 19378183 DOI: 10.1007/978-1-60327-015-1_29  0.8
2009 Holden SJ, Kapanidis AN. Alternating-Laser Excitation and Pulsed-Interleaved Excitation of Single Molecules Single Particle Tracking and Single Molecule Energy Transfer. 131-162. DOI: 10.1002/9783527628360.ch6  0.84
2008 Goodman RP, Heilemann M, Doose S, Erben CM, Kapanidis AN, Turberfield AJ. Reconfigurable, braced, three-dimensional DNA nanostructures. Nature Nanotechnology. 3: 93-6. PMID 18654468 DOI: 10.1038/nnano.2008.3  0.8
2007 Harding PJ, Attrill H, Ross S, Koeppe JR, Kapanidis AN, Watts A. Neurotensin receptor type 1: Escherichia coli expression, purification, characterization and biophysical study. Biochemical Society Transactions. 35: 760-3. PMID 17635142 DOI: 10.1042/BST0350760  0.84
2007 Doose S, Heilemann M, Michalet X, Weiss S, Kapanidis AN. Periodic acceptor excitation spectroscopy of single molecules. European Biophysics Journal : Ebj. 36: 669-74. PMID 17279362 DOI: 10.1007/S00249-007-0133-7  0.8
2007 Lee NK, Kapanidis AN, Koh HR, Korlann Y, Ho SO, Kim Y, Gassman N, Kim SK, Weiss S. Three-color alternating-laser excitation of single molecules: monitoring multiple interactions and distances. Biophysical Journal. 92: 303-12. PMID 17040983 DOI: 10.1529/Biophysj.106.093211  0.8
2006 Kapanidis AN, Margeat E, Ho SO, Kortkhonjia E, Weiss S, Ebright RH. Initial transcription by RNA polymerase proceeds through a DNA-scrunching mechanism. Science (New York, N.Y.). 314: 1144-7. PMID 17110578 DOI: 10.1126/Science.1131399  0.84
2006 Margeat E, Kapanidis AN, Tinnefeld P, Wang Y, Mukhopadhyay J, Ebright RH, Weiss S. Direct observation of abortive initiation and promoter escape within single immobilized transcription complexes. Biophysical Journal. 90: 1419-31. PMID 16299085 DOI: 10.1529/Biophysj.105.069252  0.84
2005 Kapanidis AN, Margeat E, Laurence TA, Doose S, Ho SO, Mukhopadhyay J, Kortkhonjia E, Mekler V, Ebright RH, Weiss S. Retention of transcription initiation factor sigma70 in transcription elongation: single-molecule analysis. Molecular Cell. 20: 347-56. PMID 16285917 DOI: 10.1016/J.Molcel.2005.10.012  0.84
2005 Kapanidis AN, Laurence TA, Lee NK, Margeat E, Kong X, Weiss S. Alternating-laser excitation of single molecules. Accounts of Chemical Research. 38: 523-33. PMID 16028886 DOI: 10.1021/Ar0401348  0.84
2005 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. Biophysical Journal. 88: 2939-53. PMID 15653725 DOI: 10.1529/Biophysj.104.054114  0.84
2004 Kapanidis AN, Lee NK, Laurence TA, Doose S, Margeat E, Weiss S. 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. 101: 8936-41. PMID 15175430 DOI: 10.1073/Pnas.0401690101  0.84
2004 Laurence TA, Kapanidis AN, Kong X, Chemla DS, Weiss S. Photon arrival-time interval distribution (PAID): A novel tool for analyzing molecular interactions Journal of Physical Chemistry B. 108: 3051-3067.  0.84
2003 Mukhopadhyay J, Mekler V, Kortkhonjia E, Kapanidis AN, Ebright YW, Ebright RH. Fluorescence resonance energy transfer (FRET) in analysis of transcription-complex structure and function. Methods in Enzymology. 371: 144-59. PMID 14712697 DOI: 10.1016/S0076-6879(03)71010-6  0.84
2003 Michalet X, Kapanidis AN, Laurence T, Pinaud F, Doose S, Pflughoefft M, Weiss S. The power and prospects of fluorescence microscopies and spectroscopies. Annual Review of Biophysics and Biomolecular Structure. 32: 161-82. PMID 12598370 DOI: 10.1146/Annurev.Biophys.32.110601.142525  0.84
2002 Mekler V, Kortkhonjia E, Mukhopadhyay J, Knight J, Revyakin A, Kapanidis AN, Niu W, Ebright YW, Levy R, Ebright RH. Structural organization of bacterial RNA polymerase holoenzyme and the RNA polymerase-promoter open complex. Cell. 108: 599-614. PMID 11893332 DOI: 10.1016/S0092-8674(02)00667-0  0.84
2001 Kapanidis AN, Ebright YW, Ebright RH. Site-specific incorporation of fluorescent probes into protein: Hexahistidine-tag-mediated fluorescent labeling with (Ni2+:Nitrilotriacetic Acid)n - Fluorochrome conjugates [20] Journal of the American Chemical Society. 123: 12123-12125. PMID 11724636 DOI: 10.1021/Ja017074A  0.84
2001 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 Journal of Molecular Biology. 312: 453-468. PMID 11563909 DOI: 10.1006/Jmbi.2001.4976  0.84
2001 Mukhopadhyay J, Kapanidis AN, Mekler V, Kortkhonjia E, Ebright YW, Ebright RH. Translocation of sigma(70) with RNA polymerase during transcription: fluorescence resonance energy transfer assay for movement relative to DNA. Cell. 106: 453-63. PMID 11525731 DOI: 10.1016/S0092-8674(01)00464-0  0.84
1998 Berk AJ, Boyer TG, Kapanidis AN, Ebrighit RH, Kobayashi NN, Horn PJ, Sullivan SM, Koop R, Surby MA, Triezenberg SJ. Mechanisms of viral activators Cold Spring Harbor Symposia On Quantitative Biology. 63: 243-252. PMID 10384288 DOI: 10.1101/Sqb.1998.63.243  0.84
1998 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 and Development. 12: 34-44. PMID 9420329 DOI: 10.1101/Gad.12.1.34  0.84
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