Abstract
Atomic force microscopy (AFM) is widely used to image and study biological molecules. As an example, we have utilized AFM to investigate how the mechanical properties of DNA polymers depend on electrostatics and the strength of DNA base stacking by studying double-stranded DNA molecules incorporating several different neutral and charged base modifications. Here, we describe ten complementary approaches for determining DNA persistence length by AFM imaging. The combination of different approaches provides increased confidence and statistical reliability over existing methods utilizing only a single approach.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Rivetti C, Guthold M, Bustamante C (1996) Scanning force microscopy of DNA deposited onto mica: equilibration versus kinetic trapping studied by statistical polymer chain analysis. J Mol Biol 264(5):919–932
Hansma HG (2001) Surface biology of DNA by atomic force microscopy. Annu Rev Phys Chem 52:71–92
Bustamante C, Smith SB, Liphardt J, Smith D (2000) Single-molecule studies of DNA mechanics. Curr Opin Struct Biol 10(3):279–285
Bustamante C, Bryant Z, Smith SB (2003) Ten years of tension: single-molecule DNA mechanics. Nature 421(6921):423–427
Neuman KC, Nagy A (2008) Single-molecule force spectroscopy: optical tweezers, magnetic tweezers and atomic force microscopy. Nat Methods 5(6):491–505
Murugesapillai D, Bouaziz S, Maher LJ 3rd, Israeloff NE, Cameron CE, Williams MC (2017) Accurate nanoscale flexibility measurement of DNA and DNA-protein complexes by atomic force microscopy in liquid. Nanoscale 9(31):11327–11337
Peters JP, Mogil LS, McCauley MJ, Williams MC, Maher LJ 3rd (2014) Mechanical properties of base-modified DNA are not strictly determined by base stacking or electrostatic interactions. Biophys J 107(2):448–459
Peters JP, Yelgaonkar SP, Srivatsan SG, Tor Y, Maher LJ 3rd (2013) Mechanical properties of DNA-like polymers. Nucleic Acids Res 41(22):10593–10604
Vologodskaia MY, Vologodskii AV (2002) Contribution of the intrinsic curvature to measured DNA persistence length. J Mol Biol 317(2):205–213
Wang H, Dodd IB, Dunlap DD, Shearwin KE, Finzi L (2013) Single molecule analysis of DNA wrapping and looping by a circular 14mer wheel of the bacteriophage 186 CI repressor. Nucleic Acids Res 41(11):5746–5756
Rivetti C, Codeluppi S (2001) Accurate length determination of DNA molecules visualized by atomic force microscopy: evidence for a partial B-to A-form transition on mica. Ultramicroscopy 87(1–2):55
Wiggins PA, van der Heijden T, Moreno-Herrero F, Spakowitz AJ, Phillips R, Widom J, Dekker C, Nelson PC (2006) High flexibility of DNA on short length scales probed by atomic force microscopy. Nat Nanotechnol 1(2):137–141
Vologodskii A, Frank-Kamenetskii MD (2013) Survey and Summary strong bending of the DNA double helix. Nucleic Acids Res 41(14):6785–6792
Faas FGA, Rieger B, Van Vliet LJ, Cherny DI (2009) DNA deformations near charged surfaces: electron and atomic force microscopy views. Biophys J 97(4):1148–1157
Moukhtar J, Faivre-Moskalenko C, Milani P, Audit B, Vaillant C, Fontaine E, Mongelard F, Lavorel G, St-Jean P, Bouvet P (2010) Effect of genomic long-range correlations on DNA persistence length: from theory to single molecule experiments. J Phys Chem B 114(15):5125–5143
Joanicot M, Revet B (1987) DNA conformational studies from electron microscopy. I. Excluded volume effect and structure dimensionality. Biopolymers 26(2):315–326
Abels JA, Moreno-Herrero F, van der Heijden T, Dekker C, Dekker NH (2005) Single-molecule measurements of the persistence length of double-stranded RNA. Biophys J 88(4):2737–2744
Acknowledgments
This work was supported by the Mayo Foundation, Mayo Edward C. Kendall Fellowship (JPP), and the National Institutes of Health (GM75965 to LJM).
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Peters, J.P., Maher, L.J. (2018). Approaches for Determining DNA Persistence Length Using Atomic Force Microscopy. In: Dame, R. (eds) Bacterial Chromatin. Methods in Molecular Biology, vol 1837. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8675-0_13
Download citation
DOI: https://doi.org/10.1007/978-1-4939-8675-0_13
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-8674-3
Online ISBN: 978-1-4939-8675-0
eBook Packages: Springer Protocols