Elucidating the Role of Topological Constraint on the Structure of Overstretched DNA Using Fluorescence Polarization Microscopy

Backer, Adam S.; King, Graeme A.; Biebricher, Andreas S.; Shepherd, Jack W.; Noy, Agnes; Leake, Mark C.; Heller, Iddo; Wuite, Gijs J. L.; Peterman, Erwin J. G.

doi:10.1021/acs.jpcb.1c02708

Title: Elucidating the Role of Topological Constraint on the Structure of Overstretched DNA Using Fluorescence Polarization Microscopy

Journal Article · 25 July 2021 · Journal of Physical Chemistry. B

DOI: https://doi.org/10.1021/acs.jpcb.1c02708 · OSTI ID:1810206

^[1]; King, Graeme A. ^[2]; Biebricher, Andreas S. ^[3]; Shepherd, Jack W. ^[4];

^[5];

^[4];

^[3]; Wuite, Gijs J. L. ^[3];

^[3]

Apple Inc, 1 Apple Park Way, Cupertino, California 95014, United States
Institute of Structural and Molecular Biology, University College London, Gower Street, London WC1E 6BT, U.K.
Department of Physics and Astronomy, LaserLaB Amsterdam, Vrije Universiteit Amsterdam, De Boelelaan 1081, Amsterdam 1081 HV, The Netherlands
Department of Physics, University of York, York YO10 5DD, U.K., Department of Biology, University of York, York YO10 5DD, U.K.
Department of Physics, University of York, York YO10 5DD, U.K.

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Sponsoring Organization:: USDOE

OSTI ID:: 1810206

Journal Information:: Journal of Physical Chemistry. B, Journal Name: Journal of Physical Chemistry. B Journal Issue: 30 Vol. 125; ISSN 1520-6106

Publisher:: American Chemical SocietyCopyright Statement

Country of Publication:: United States

Language:: English

References (51)

Single-molecule manipulation of double-stranded DNA using optical tweezers: Interaction studies of DNA with RecA and YOYO-1 Bennink, Martin L.; Sch�rer, Orlando D.; Kanaar, Roland Cytometry, Vol. 36, Issue 3 https://doi.org/10.1002/(sici)1097-0320(19990701)36:3<200::aid-cyto9>3.0.co;2-t	journal	July 1999
Single‐Molecule 3D Orientation Imaging Reveals Nanoscale Compositional Heterogeneity in Lipid Membranes Lu, Jin; Mazidi, Hesam; Ding, Tianben Angewandte Chemie International Edition, Vol. 59, Issue 40 https://doi.org/10.1002/anie.202006207	journal	August 2020
A toolbox for generating single-stranded DNA in optical tweezers experiments: Single-Stranded DNA Candelli, Andrea; Hoekstra, Tjalle P.; Farge, Geraldine Biopolymers, Vol. 99, Issue 9 https://doi.org/10.1002/bip.22225	journal	June 2013
Deforming DNA: From Physics to Biology Prévost, Chantal; Takahashi, Masayuki; Lavery, Richard ChemPhysChem, Vol. 10, Issue 9-10 https://doi.org/10.1002/cphc.200900253	journal	July 2009
DNA stretching and compression: large-scale simulations of double helical structures 1 1Edited by I. Tinoco Kosikov, Konstantin M.; Gorin, Andrey A.; Zhurkin, Victor B. Journal of Molecular Biology, Vol. 289, Issue 5 https://doi.org/10.1006/jmbi.1999.2798	journal	June 1999
Nucleotide sequence of bacteriophage λ DNA Sanger, F.; Coulson, A. R.; Hong, G. F. Journal of Molecular Biology, Vol. 162, Issue 4 https://doi.org/10.1016/0022-2836(82)90546-0	journal	December 1982
Polarized Fluorescence Microscopy of Individual and Many Kinesin Motors Bound to Axonemal Microtubules Peterman, Erwin J. G.; Sosa, Hernando; Goldstein, Lawrence S. B. Biophysical Journal, Vol. 81, Issue 5 https://doi.org/10.1016/s0006-3495(01)75926-7	journal	November 2001
Carbocyanine dye orientation in red cell membrane studied by microscopic fluorescence polarization Axelrod, D. Biophysical Journal, Vol. 26, Issue 3 https://doi.org/10.1016/s0006-3495(79)85271-6	journal	June 1979
Steady-state polarization from cylindrically symmetric fluorophores undergoing rapid restricted motion Irving, M. Biophysical Journal, Vol. 70, Issue 4 https://doi.org/10.1016/s0006-3495(96)79748-5	journal	April 1996
Structural considerations in the interaction of DNA and acridines Lerman, L. S. Journal of Molecular Biology, Vol. 3, Issue 1 https://doi.org/10.1016/s0022-2836(61)80004-1	journal	February 1961
A stretched conformation of DNA with a biological role? Bosaeus, Niklas; Reymer, Anna; Beke-Somfai, Tamás Quarterly Reviews of Biophysics, Vol. 50 https://doi.org/10.1017/s0033583517000099	journal	January 2017
Optical and Photophysical Properties of the Oxazole Yellow DNA Probes YO and YOYO Carlsson, Christina; Larsson, Anette; Jonsson, Mats The Journal of Physical Chemistry, Vol. 98, Issue 40 https://doi.org/10.1021/j100091a055	journal	October 1994
Characterization of the Binding of the Fluorescent Dyes YO and YOYO to DNA by Polarized Light Spectroscopy Larsson, Anette; Carlsson, Christina; Jonsson, Mats Journal of the American Chemical Society, Vol. 116, Issue 19 https://doi.org/10.1021/ja00098a004	journal	September 1994
Molecular Dynamics Simulation of DNA Stretching Is Consistent with the Tension Observed for Extension and Strand Separation and Predicts a Novel Ladder Structure Konrad, Michael W.; Bolonick, Joel I. Journal of the American Chemical Society, Vol. 118, Issue 45 https://doi.org/10.1021/ja961751x	journal	January 1996
Extending Single-Molecule Microscopy Using Optical Fourier Processing Backer, Adam S.; Moerner, W. E. The Journal of Physical Chemistry B, Vol. 118, Issue 28 https://doi.org/10.1021/jp501778z	journal	May 2014
Stable dye–DNA intercalation complexes as reagents for high-sensitivity fluorescence detection Glazer, Alexander N.; Rye, Hays S. Nature, Vol. 359, Issue 6398 https://doi.org/10.1038/359859a0	journal	October 1992
Unravelling the structural plasticity of stretched DNA under torsional constraint King, Graeme A.; Peterman, Erwin J. G.; Wuite, Gijs J. L. Nature Communications, Vol. 7, Issue 1 https://doi.org/10.1038/ncomms11810	journal	June 2016
The impact of DNA intercalators on DNA and DNA-processing enzymes elucidated through force-dependent binding kinetics Biebricher, Andreas S.; Heller, Iddo; Roijmans, Roel F. H. Nature Communications, Vol. 6, Issue 1 https://doi.org/10.1038/ncomms8304	journal	June 2015
Mapping the 3D orientation of piconewton integrin traction forces Brockman, Joshua M.; Blanchard, Aaron T.; Pui-Yan, Victor Nature Methods, Vol. 15, Issue 2 https://doi.org/10.1038/nmeth.4536	journal	December 2017
Quantifying force-dependent and zero-force DNA intercalation by single-molecule stretching Vladescu, Ioana D.; McCauley, Micah J.; Nuñez, Megan E. Nature Methods, Vol. 4, Issue 6 https://doi.org/10.1038/nmeth1044	journal	April 2007
Quantifying how DNA stretches, melts and changes twist under tension Gross, Peter; Laurens, Niels; Oddershede, Lene B. Nature Physics, Vol. 7, Issue 9 https://doi.org/10.1038/nphys2002	journal	May 2011
Hyperstretching DNA Schakenraad, Koen; Biebricher, Andreas S.; Sebregts, Maarten Nature Communications, Vol. 8, Issue 1 https://doi.org/10.1038/s41467-017-02396-1	journal	December 2017
Super-resolution imaging of fluorescent dipoles via polarized structured illumination microscopy Zhanghao, Karl; Chen, Xingye; Liu, Wenhui Nature Communications, Vol. 10, Issue 1 https://doi.org/10.1038/s41467-019-12681-w	journal	October 2019
Birefringent Fourier filtering for single molecule coordinate and height super-resolution imaging with dithering and orientation Curcio, Valentina; Alemán-Castañeda, Luis A.; Brown, Thomas G. Nature Communications, Vol. 11, Issue 1 https://doi.org/10.1038/s41467-020-19064-6	journal	October 2020
Reconstitution of anaphase DNA bridge recognition and disjunction Sarlós, Kata; Biebricher, Andreas S.; Bizard, Anna H. Nature Structural & Molecular Biology, Vol. 25, Issue 9 https://doi.org/10.1038/s41594-018-0123-8	journal	September 2018
A polarized view on DNA under tension van Mameren, Joost; Vermeulen, Karen; Wuite, Gijs J. L. The Journal of Chemical Physics, Vol. 148, Issue 12 https://doi.org/10.1063/1.5004019	journal	March 2018
Unraveling the structure of DNA during overstretching by using multicolor, single-molecule fluorescence imaging van Mameren, J.; Gross, P.; Farge, G. Proceedings of the National Academy of Sciences, Vol. 106, Issue 43 https://doi.org/10.1073/pnas.0904322106	journal	October 2009
The structure of DNA overstretched from the 5'5' ends differs from the structure of DNA overstretched from the 3'3' ends Danilowicz, C.; Limouse, C.; Hatch, K. Proceedings of the National Academy of Sciences, Vol. 106, Issue 32 https://doi.org/10.1073/pnas.0904729106	journal	July 2009
Tension induces a base-paired overstretched DNA conformation Bosaeus, N.; El-Sagheer, A. H.; Brown, T. Proceedings of the National Academy of Sciences, Vol. 109, Issue 38 https://doi.org/10.1073/pnas.1213172109	journal	September 2012
Revealing the competition between peeled ssDNA, melting bubbles, and S-DNA during DNA overstretching using fluorescence microscopy King, G. A.; Gross, P.; Bockelmann, U. Proceedings of the National Academy of Sciences, Vol. 110, Issue 10 https://doi.org/10.1073/pnas.1213676110	journal	February 2013
Revealing the competition between peeled ssDNA, melting bubbles, and S-DNA during DNA overstretching by single-molecule calorimetry Zhang, X.; Chen, H.; Le, S. Proceedings of the National Academy of Sciences, Vol. 110, Issue 10 https://doi.org/10.1073/pnas.1213740110	journal	February 2013
Quantitative nanoscale imaging of orientational order in biological filaments by polarized superresolution microscopy Valades Cruz, Cesar Augusto; Shaban, Haitham Ahmed; Kress, Alla Proceedings of the National Academy of Sciences, Vol. 113, Issue 7 https://doi.org/10.1073/pnas.1516811113	journal	February 2016
Dissection of molecular assembly dynamics by tracking orientation and position of single molecules in live cells Mehta, Shalin B.; McQuilken, Molly; La Riviere, Patrick J. Proceedings of the National Academy of Sciences, Vol. 113, Issue 42 https://doi.org/10.1073/pnas.1607674113	journal	September 2016
Supercoiling DNA optically King, Graeme A.; Burla, Federica; Peterman, Erwin J. G. Proceedings of the National Academy of Sciences, Vol. 116, Issue 52 https://doi.org/10.1073/pnas.1908826116	journal	December 2019
Stretched and overwound DNA forms a Pauling-like structure with exposed bases Allemand, J. F.; Bensimon, D.; Lavery, R. Proceedings of the National Academy of Sciences, Vol. 95, Issue 24 https://doi.org/10.1073/pnas.95.24.14152	journal	November 1998
Single molecule optical measurements of orientation and rotations of biological macromolecules Shroder, Deborah Y.; Lippert, Lisa G.; Goldman, Yale E. Methods and Applications in Fluorescence, Vol. 4, Issue 4 https://doi.org/10.1088/2050-6120/4/4/042004	journal	November 2016
Modelling Extreme Stretching of DNA Lebrun, A.; Lavery, R. Nucleic Acids Research, Vol. 24, Issue 12 https://doi.org/10.1093/nar/24.12.2260	journal	June 1996
Force spectroscopy and fluorescence microscopy of dsDNA-YOYO-1 complexes: implications for the structure of dsDNA in the overstretching region Murade, C. U.; Subramaniam, V.; Otto, C. Nucleic Acids Research, Vol. 38, Issue 10 https://doi.org/10.1093/nar/gkq034	journal	February 2010
The emergence of sequence-dependent structural motifs in stretched, torsionally constrained DNA Shepherd, Jack W.; Greenall, Robert J.; Probert, Matt I. J. Nucleic Acids Research, Vol. 48, Issue 4 https://doi.org/10.1093/nar/gkz1227	journal	January 2020
Single Molecule Dynamics Studied by Polarization Modulation Ha, T.; Enderle, Th.; Chemla, D. S. Physical Review Letters, Vol. 77, Issue 19 https://doi.org/10.1103/PhysRevLett.77.3979	journal	November 1996
Overstretching and force-driven strand separation of double-helix DNA Cocco, Simona; Yan, Jie; Léger, Jean-Francois Physical Review E, Vol. 70, Issue 1 https://doi.org/10.1103/physreve.70.011910	journal	July 2004
Fundamental Limits on Measuring the Rotational Constraint of Single Molecules Using Fluorescence Microscopy Zhang, Oumeng; Lew, Matthew D. Physical Review Letters, Vol. 122, Issue 19 https://doi.org/10.1103/physrevlett.122.198301	journal	May 2019
Simultaneous Imaging of Individual Molecules Aligned Both Parallel and Perpendicular to the Optic Axis Dickson, Robert M.; Norris, D. J.; Moerner, W. E. Physical Review Letters, Vol. 81, Issue 24 https://doi.org/10.1103/physrevlett.81.5322	journal	December 1998
Structural Transitions of a Twisted and Stretched DNA Molecule Léger, J. F.; Romano, G.; Sarkar, A. Physical Review Letters, Vol. 83, Issue 5 https://doi.org/10.1103/physrevlett.83.1066	journal	August 1999
Single-molecule polarization microscopy of DNA intercalators sheds light on the structure of S-DNA Backer, Adam S.; Biebricher, Andreas S.; King, Graeme A. Science Advances, Vol. 5, Issue 3 https://doi.org/10.1126/sciadv.aav1083	journal	March 2019
DNA: An Extensible Molecule Cluzel, P.; Lebrun, A.; Heller, C. Science, Vol. 271, Issue 5250 https://doi.org/10.1126/science.271.5250.792	journal	February 1996
Overstretching B-DNA: The Elastic Response of Individual Double-Stranded and Single-Stranded DNA Molecules Smith, S. B.; Cui, Y.; Bustamante, C. Science, Vol. 271, Issue 5250 https://doi.org/10.1126/science.271.5250.795	journal	February 1996
Spatio-angular fluorescence microscopy I Basic theory Chandler, Talon; Shroff, Hari; Oldenbourg, Rudolf Journal of the Optical Society of America A, Vol. 36, Issue 8 https://doi.org/10.1364/josaa.36.001334	journal	January 2019
Orientation imaging of single molecules by wide-field epifluorescence microscopy Böhmer, Martin; Enderlein, Jörg Journal of the Optical Society of America B, Vol. 20, Issue 3 https://doi.org/10.1364/josab.20.000554	journal	January 2003
Enhanced DNA imaging using super-resolution microscopy and simultaneous single-molecule orientation measurements Backer, Adam S.; Lee, Maurice Y.; Moerner, W. E. Optica, Vol. 3, Issue 6 https://doi.org/10.1364/optica.3.000659	journal	January 2016
Single-molecule orientation localization microscopy for resolving structural heterogeneities between amyloid fibrils Ding, Tianben; Wu, Tingting; Mazidi, Hesam Optica, Vol. 7, Issue 6 https://doi.org/10.1364/optica.388157	journal	January 2020

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