Abstract
To study the physical properties of molecules and their reaction processes, direct visualization of target molecules is one of the straightforward methods. Atomic force microscopy (AFM) enables the direct imaging of biomolecules under physiological conditions at nanometer-scale spatial resolution. In addition, using the DNA origami technology, the precise placement of target molecules in a designed nanostructure has been achieved, and the detection of the molecules at the single-molecule level has been realized. DNA origami is applied for visualizing the detailed movement of molecules combining with high-speed AFM (HS-AFM), which enables the analysis of the dynamic movement of biomolecules in a subsecond time resolution.
Here, we describe the combination of the DNA origami system with HS-AFM for the imaging of rotation of dsDNA originated from B–Z transition. The rotation of dsDNA during B–Z transition is directly visualized in a DNA origami using the HS-AFM. These target-oriented observation systems serve to the detailed analysis of DNA structural changes in real time at molecular resolution.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
Torring T, Voigt NV, Nangreave J, Yan H, Gothelf KV (2011) DNA origami: a quantum leap for self-assembly of complex structures. Chem Soc Rev 40:5636–5646
Rajendran A, Endo M, Sugiyama H (2012) Single-molecule analysis using DNA origami. Angew Chem Int Ed 51:874–890
Endo M, Yang Y, Sugiyama H (2013) DNA origami technology for biomaterials applications. Biomater Sci 1:347–360
Rothemund PW (2006) Folding DNA to create nanoscale shapes and patterns. Nature 440:297–302
Ando T, Kodera N, Takai E, Maruyama D, Saito K, Toda A (2001) A high-speed atomic force microscope for studying biological macromolecules. Proc Natl Acad Sci U S A 98:12468–12472
Ando T, Kodera N (2012) Visualization of mobility by atomic force microscopy. Methods Mol Biol 896:57–69
Uchihashi T, Kodera N, Ando T (2012) Guide to video recording of structure dynamics and dynamic processes of proteins by high-speed atomic force microscopy. Nat Protoc 7:1193–1206
Rajendran A, Endo M, Sugiyama H (2014) State-of-the-Art High-Speed Atomic Force Microscopy for Investigation of Single-Molecular Dynamics of Proteins. Chem Rev 114:1493–1520
Endo M, Katsuda Y, Hidaka K, Sugiyama H (2010) Regulation of DNA methylation using different tensions of double strands constructed in a defined DNA nanostructure. J Am Chem Soc 132:1592–1597
Jovin TM, Soumpasis DM, Mcintosh LP (1987) The transition between B-DNA and Z-DNA. Annu Rev Phys Chem 38:521–560
Mao CD, Sun WQ, Shen ZY, Seeman NC (1999) A nanomechanical device based on the B-Z transition of DNA. Nature 397:144–146
Rajendran A, Endo M, Hidaka K, Sugiyama H (2013) Direct and real-time observation of rotary movement of a DNA nanomechanical device. J Am Chem Soc 135:1117–1123
Behe M, Felsenfeld G (1981) Effects of methylation on a synthetic polynucleotide: the B--Z transition in poly(dG-m5dC).poly(dG-m5dC). Proc Natl Acad Sci U S A 78:1619–1623
Douglas SM, Marblestone AH, Teerapittayanon S, Vazquez A, Church GM, Shih WM (2009) Rapid prototyping of 3D DNA-origami shapes with caDNAno. Nucleic Acids Res 37:5001–5006
Author information
Authors and Affiliations
Corresponding authors
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2023 The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Endo, M., Sugiyama, H. (2023). Single-Molecule Visualization of B–Z Transition in DNA Origami Using High-Speed AFM. In: Kim, K.K., Subramani, V.K. (eds) Z-DNA. Methods in Molecular Biology, vol 2651. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-3084-6_17
Download citation
DOI: https://doi.org/10.1007/978-1-0716-3084-6_17
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-3083-9
Online ISBN: 978-1-0716-3084-6
eBook Packages: Springer Protocols