Abstract
Optical tweezers enable the isolation and mechanical manipulation of individual nucleoprotein complexes. Here, we describe how to use this technique to interrogate the mechanical properties of individual protein-DNA complexes and extract information about their overall structural organization.
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References
Neuman KC, Nagy A (2008) Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy. Nat Methods 5(6):491–505
Bustamante C, Cheng W, Mejia YX (2011) Revisiting the central dogma one molecule at a time. Cell 144(4):480–497
Capitanio M, Pavone FS (2013) Interrogating biology with force: single molecule high-resolution measurements with optical tweezers. Biophys J 105(6):1293–1303
Choudhary D, Mossa A, Jadhav M, Cecconi C (2019) Bio-Molecular applications of recent developments in optical tweezers. Biomol Ther 9(1):E23
Perkins TT (2014) Ångström-precision optical traps and applications. Annu Rev Biophys 43:279–302
van Mameren J, Wuite GJ, Heller I (2011) Introduction to optical tweezers: background, system designs, and commercial solutions. Methods Mol Biol 783:1–20
Moffitt JR, Chemla YR, Smith SB, Bustamante C (2008) Recent advances in optical tweezers. Annu Rev Biochem 77:205–228
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
Bell JC, Liu B, Kowalczykowski SC (2015) Imaging and energetics of single SSB-ssDNA molecules reveal intramolecular condensation and insight into RecOR function. elife 4:e08646
Hatch K, Danilowicz C, Coljee V, Prentiss M (2007) Direct measurements of the stabilization of single-stranded DNA under tension by single-stranded binding proteins. Phys Rev E 76:021916
Pant K, Karpel RL, Rouzina I, Williams MC (2005) Salt dependent binding of T4 gene 32 protein to single and double-stranded DNA: single molecule force spectroscopy measurements. J Mol Biol 349:317–330
Shokri L, Marintcheva B, Richardson CC, Rouzina I, Williams MC (2006) Single molecule force spectroscopy of salt-dependent bacteriophage T7 gene 2.5 protein binding to single-stranded DNA. J Biol Chem 281:38689–38696
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
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 47:5723–5734
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
Lohman TM, Ferrari ME (1994) Escherichia coli single-stranded DNA-binding protein: multiple DNA-binding modes and cooperativities. Annu Rev Biochem 63:527–570
Smith S, Cui Y, Bustamante C (2003) Optical-trap force transducer that operates by direct measurement of light momentum. Methods Enzymol 361:134–162
Jarillo J, Morín JA, Beltrán-Heredia E, Villaluenga JP, Ibarra B, Cao FJ (2017) Mechanics, thermodynamics, and kinetics of ligand binding to biopolymers. PLoS One 12(4):e0174830
Smith S, Cui Y, Bustamante C (1996) Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules. Science 271(5250):795–799
Acknowledgments
This work was supported by Spanish Ministry of Science, Innovation and Universities grants BFU2015-63714-R and PGC2018-099341-B-I00 to BI and MINECO/FEDER grants FIS2010-17440, FIS2015-67765-R, and RTI2018-095802-B-I00 to FJCG.
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Morin, J.A., Cerrón, F., Cao-García, F.J., Ibarra, B. (2021). Optical Tweezers to Investigate the Structure and Energetics of Single-Stranded DNA-Binding Protein-DNA Complexes. In: Oliveira, M.T. (eds) Single Stranded DNA Binding Proteins. Methods in Molecular Biology, vol 2281. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1290-3_17
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DOI: https://doi.org/10.1007/978-1-0716-1290-3_17
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