Guidelines for DNA recombination and repair studies: Mechanistic assays of DNA repair processes
Authors:Hannah L Klein1, Kenny K.H. Ang2, Michelle R. Arkin2, Emily C. Beckwitt3,4, Yi-Hsuan Chang5, Jun Fan6, Youngho Kwon7,8, Michael J. Morten1, Sucheta Mukherjee9, Oliver J. Pambos6, Hafez el Sayyed6, Elizabeth S. Thrall10, João P. Vieira-da-Rocha9, Quan Wang11, Shuang Wang12,13, Hsin-Yi Yeh5, Julie S. Biteen14, Peter Chi5,15, Wolf-Dietrich Heyer9,16, Achillefs N. Kapanidis6, Joseph J. Loparo10, Terence R. Strick12,13,17, Patrick Sung7,8, Bennett Van Houten3,18,19, Hengyao Niu11 and Eli Rothenberg1
doi: 10.15698/mic2019.01.665
Volume 6, pp. 65 to 101, published 07/01/2019.
1 New York University School of Medicine, Department of Biochemistry and Molecular Pharmacology, New York, NY 10016, USA.
2 Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA.
3 Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.
4 The University of Pittsburgh Cancer Institute, Hillman Cancer Center, Pittsburgh, PA 15213, USA.
5 Institute of Biochemical Sciences, National Taiwan University, NO. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan.
6 Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK.
7 Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA.
8 Department of Biochemistry and Structural Biology, University of Texas Health San Antonio, San Antonio, Texas 78229, USA.
9 Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA.
10 Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA.
11 Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA.
12 Ecole Normale Supérieure, Institut de Biologie de l’Ecole Normale Supérieure (IBENS), CNRS, INSERM, PSL Research University, 75005 Paris, France.
13 Institut Jacques Monod, CNRS, UMR7592, University Paris Diderot, Sorbonne Paris Cité F-75205 Paris, France.
14 Departments of Chemistry and Biophysics, University of Michigan, Ann Arbor, MI 48109, USA.
15 Institute of Biological Chemistry, Academia Sinica, 128 Academia Road, Section 2, Nankang, Taipei 11529, Taiwan.
16 Department of Molecular and Cellular Biology, University of California, Davis, CA 95616, USA.
17 Programme Equipe Labellisées, Ligue Contre le Cancer, 75013 Paris, France.
18 Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.
19 Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.
Keywords:
chromatin dynamics, chromosome rearrangements, crossovers, DNA breaks, DNA helicases, DNA repair centers, DNA repair synthesis, DNA resection, double strand break repair, DSBs, endonuclease protection assay, genome instability, gross chromosome rearrangements, fluorescent proteins, FRET, homologous recombination, mismatch repair, nonhomologous end joining, nucleotide excision repair, PALM, photoactivated fluorescent proteins, recombinase filament assembly, single-molecule, single-particle tracking, super resolution, structure-selective endonucleases, synthesis-dependent strand annealing, transcription coupled repair
Corresponding Author(s):
Conflict of interest statement:
The authors declare no conflict of interest.
Please cite this article as:
Hannah L Klein, Kenny K.H. Ang, Michelle R. Arkin, Emily C. Beckwitt, Yi-Hsuan Chang, Jun Fan, Youngho Kwon, Michael J. Morten, Sucheta Mukherjee, Oliver J. Pambos, Hafez el Sayyed, Elizabeth S. Thrall, João P. Vieira-da-Rocha, Quan Wang, Shuang Wang, Hsin-Yi Yeh, Julie S. Biteen, Peter Chi, Wolf-Dietrich Heyer, Achillefs N. Kapanidis, Joseph J. Loparo, Terence R. Strick, Patrick Sung, Bennett Van Houten, Hengyao Niu and Eli Rothenberg (2018). Guidelines for DNA recombination and repair studies: Mechanistic assays of DNA repair processes. Microbial Cell 6(1): 65-101. doi: 10.15698/mic2019.01.665
© 2018 Klein et al. This is an open-access article released under the terms of the Creative Commons Attribution (CC BY) license, which allows the unrestricted use, distribution, and reproduction in any medium, provided the original author and source are acknowledged.
Abstract:
Genomes are constantly in flux, undergoing changes due to recombination, repair and mutagenesis. In vivo, many of such changes are studies using reporters for specific types of changes, or through cytological studies that detect changes at the single-cell level. Single molecule assays, which are reviewed here, can detect transient intermediates and dynamics of events. Biochemical assays allow detailed investigation of the DNA and protein activities of each step in a repair, recombination or mutagenesis event. Each type of assay is a powerful tool but each comes with its particular advantages and limitations. Here the most commonly used assays are reviewed, discussed, and presented as the guidelines for future studies.