Microbial Cell (Jan 2019)
Guidelines for DNA recombination and repair studies: Mechanistic assays of DNA repair processes
- 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,
- Eli Rothenberg
Affiliations
- Hannah L Klein
- New York University School of Medicine, Department of Biochemistry and Molecular Pharmacology, New York, NY 10016, USA.
- Kenny K.H. Ang
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA.
- Michelle R. Arkin
- Small Molecule Discovery Center and Department of Pharmaceutical Chemistry, University of California, San Francisco, California 94143, USA.
- Emily C. Beckwitt
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.
- Yi-Hsuan Chang
- Institute of Biochemical Sciences, National Taiwan University, NO. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan.
- Jun Fan
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK.
- Youngho Kwon
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA.
- Michael J. Morten
- New York University School of Medicine, Department of Biochemistry and Molecular Pharmacology, New York, NY 10016, USA.
- Sucheta Mukherjee
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA.
- Oliver J. Pambos
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK.
- Hafez el Sayyed
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK.
- Elizabeth S. Thrall
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA.
- João P. Vieira-da-Rocha
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA.
- Quan Wang
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA.
- Shuang Wang
- Ecole Normale Supérieure, Institut de Biologie de l’Ecole Normale Supérieure (IBENS), CNRS, INSERM, PSL Research University, 75005 Paris, France.
- Hsin-Yi Yeh
- Institute of Biochemical Sciences, National Taiwan University, NO. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan.
- Julie S. Biteen
- Departments of Chemistry and Biophysics, University of Michigan, Ann Arbor, MI 48109, USA.
- Peter Chi
- Institute of Biochemical Sciences, National Taiwan University, NO. 1, Section 4, Roosevelt Road, Taipei 10617, Taiwan.
- Wolf-Dietrich Heyer
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA.
- Achillefs N. Kapanidis
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics, University of Oxford, Oxford, OX1 3PU, UK.
- Joseph J. Loparo
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, Boston, MA 02115, USA.
- Terence R. Strick
- Ecole Normale Supérieure, Institut de Biologie de l’Ecole Normale Supérieure (IBENS), CNRS, INSERM, PSL Research University, 75005 Paris, France.
- Patrick Sung
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT 06520, USA.
- Bennett Van Houten
- Program in Molecular Biophysics and Structural Biology, University of Pittsburgh, Pittsburgh, PA 15261, USA.
- Hengyao Niu
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, IN 47405, USA.
- Eli Rothenberg
- New York University School of Medicine, Department of Biochemistry and Molecular Pharmacology, New York, NY 10016, USA.
- DOI
- https://doi.org/10.15698/mic2019.01.665
- Journal volume & issue
-
Vol. 6,
no. 1
pp. 65 – 101
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.
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
