Measurements of Real-Time Replication Kinetics of DNA Polymerases on ssDNA Templates Coated with Single-Stranded DNA-Binding Proteins.
DNA replication
Optical tweezers
Protein-protein interactions
Real-time kinetics
Single-molecule manipulation
Journal
Methods in molecular biology (Clifton, N.J.)
ISSN: 1940-6029
Titre abrégé: Methods Mol Biol
Pays: United States
ID NLM: 9214969
Informations de publication
Date de publication:
2021
2021
Historique:
entrez:
13
4
2021
pubmed:
14
4
2021
medline:
22
6
2021
Statut:
ppublish
Résumé
Optical tweezers can monitor and control the activity of individual DNA polymerase molecules in real time, providing in this way unprecedented insight into the complex dynamics and mechanochemical processes that govern their operation. Here, we describe an optical tweezers-based assay to determine at the single-molecule level the effect of single-stranded DNA-binding proteins (SSB) on the real-time replication kinetics of the human mitochondrial DNA polymerase during the synthesis of the lagging strand.
Identifiants
pubmed: 33847966
doi: 10.1007/978-1-0716-1290-3_18
doi:
Substances chimiques
DNA, Single-Stranded
0
DNA-Binding Proteins
0
DNA-Directed DNA Polymerase
EC 2.7.7.7
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
289-301Références
Wuite GJL, Smith SB, Young M, Keller D, Bustamante C (2000) Single-molecule studies of the effect of template tension on T7 DNA polymerase activity. Nature 404:103–106
doi: 10.1038/35003614
Maier B, Bensimon D, Croquette V (2000) Replication by a single DNA polymerase of a stretched single-stranded DNA. Proc Natl Acad Sci U S A 97:12002–12007
doi: 10.1073/pnas.97.22.12002
Ibarra B, Chemla YR, Plyasunov S, Smith SB, Lázaro JM, Salas BC (2009) Proofreading dynamics of a processive DNA polymerase. EMBO J 28:2794–2802
doi: 10.1038/emboj.2009.219
Kim S, Schroeder CM, Xie XS (2010) Single-molecule study of DNA polymerization activity of HIV-1 reverse transcriptase on DNA templates. J Mol Biol 395:995–1006
doi: 10.1016/j.jmb.2009.11.072
Morin JA, Cao FJ, Lázaro JM, Arias-Gonzalez JR, Valpuesta JM, Carrascosa JL, Salas M, Ibarra B (2012) Active DNA unwinding dynamics during processive DNA replication. Proc Natl Acad Sci U S A 109:8115–8120
doi: 10.1073/pnas.1204759109
Manosas M, Spiering MM, Ding F, Bensimon D, Allemand JF, Benkovic SJ, Croquette V (2012) Mechanism of strand displacement synthesis by DNA replicative polymerases. Nucleic Acids Res 40:6174–6186
doi: 10.1093/nar/gks253
Naufer MN, Murison DA, Rouzina I, Beuning PJ, Williams MC (2017) Single-molecule mechanochemical characterization of E. coli pol III core catalytic activity. Protein Sci 26:1413–1426
doi: 10.1002/pro.3152
Hoekstra TP, Depken M, Lin SN, Cabanas-Danés J, Gross P, Dame RT, Peterman EJG, Wuite GJL (2017) Switching between exonucleolysis and replication by T7 DNA polymerase ensures high fidelity. Biophys J 112:575–583
doi: 10.1016/j.bpj.2016.12.044
Bustamante C, Smith SB, Liphardt J, Smith D (2000) Single-molecule studies of DNA mechanics. Curr Opin Struct Biol 10:279–285
doi: 10.1016/S0959-440X(00)00085-3
Moffitt JR, Chemla YR, Smith SB, Bustamante C (2008) Recent advances in optical tweezers. Annu Rev Biochem 77:205–228
doi: 10.1146/annurev.biochem.77.043007.090225
Shereda RD, Kozlov AG, Lohman TM, Cox MM, Keck JL (2008) SSB as an organizer/mobilizer of genome maintenance complexes. Crit Rev Biochem Mol Biol 43:289–318
doi: 10.1080/10409230802341296
Oliveira MT, Kaguni LS (2011) Reduced stimulation of recombinant DNA polymerase γ and mitochondrial DNA (mtDNA) helicase by variants of mitochondrial single-stranded DNA-binding protein (mtSSB) correlates with defects in mtDNA replication in animal cells. J Biol Chem 286(47):40649–40658
doi: 10.1074/jbc.M111.289983
Cerrón F, de Lorenzo S, Lemishko KM, Ciesielski GL, Kaguni LS, Cao FJ, Ibarra B (2019) Replicative DNA polymerases promote active displacement of SSB proteins during lagging strand synthesis. Nucleic Acids Res 47(11):5723–5734
doi: 10.1093/nar/gkz249
Kaguni LS (2004) DNA polymerase gamma, the mitochondrial replicase. Annu Rev Biochem 73:293–320
doi: 10.1146/annurev.biochem.72.121801.161455
Morin JA, Cerrón F, Jarillo J, Beltran-Heredia E, Ciesielski GL, Arias-Gonzalez JR, Kaguni LS, Cao FJ, Ibarra B (2017) DNA synthesis determines the binding mode of the human mitochondrial single-stranded DNA-binding protein. Nucleic Acids Res 45(12):7237–7248
doi: 10.1093/nar/gkx395
Suksombat S, Khafizov R, Kozlov AG, Lohman TM, Chemla YR (2015) Structural dynamics of E. coli single-stranded DNA binding protein reveal DNA wrapping and unwrapping pathways. elife 4:e08193
doi: 10.7554/eLife.08193
Smith SB, Finzi L, Bustamante C (1992) Direct mechanical measurements of the elasticity of single DNA molecules using magnetic beads. Science 258(5085):1122–1126
doi: 10.1126/science.1439819
Ibarra B, Chemla YR, Plyasunov S, Smith SB, Lázaro JM, Salas M, Bustamante C (2009) Proofreading dynamics of a processive DNA polymerase. EMBO J 28(18):2794–2802
doi: 10.1038/emboj.2009.219
Bouchiat C, Wang MD, Allemand JF, Strick T, Block SM, Croquette V (1999) Estimating the persistence length of a worm-like chain molecule from force-extension measurements. Biophys J 76(1):409–413
doi: 10.1016/S0006-3495(99)77207-3