DNA and RNA Origami: Methods and Protocols

ISBN-13: 9781071630273 / Angielski / Twarda / 2023 / 296 str.

Juli?n Valero Moreno

Opis

This volume detials diverse methodological approaches on the assembly and applications of DNA origami assemblies. Chapters guide readers through different synthetic and computational methods, isolation and structural characterization of 2D and 3D DNA origami nanoarchitectures,  nanophotonics, drug delivery, biophysics, and synthetic biology.Written in the successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, DNA and RNA Origami: Methods and Protocols aims to serve as a guideline describing the current state-of-the-art assembly methodologies and applications of DNA origami nanostructures.

Spis treści

Part I: Background and design of nucleic acid origami

 

1. DNA Origami: Recent Progress and Applications

Michael Haydell and Yinzhou Ma

 

2. Design, Assembly, and Function of DNA Origami Mechanisms

Peter E. Beshay, Joshua A. Johson, Jenny V. Le, and Carlos E. Castro

 

3. Computer-aided design and Functionalization of ssRNA Origami Structures

Néstor Sampedro Vallina, Cody Geary, Mette Jepsen, and Ebbe Sloth Andersen

 

4. Reconfigurable Two-dimensional DNA Molecular Arrays

Donglei Yang, Fan Xu, and Pengfei Wang

 

5. Two-dimensional DNA origami lattices assembled on lipid bilayer membranes

Yuki Suzuki, Hiroshi Sugiyama, and Masayuki Endo

 

 

Part II: Molecular dynamics and simulations of DNA origami

6. The oxDNA coarse-grained model as a tool to simulate DNA origami

Jonathan P. K. Doye, Hannah Fowler, Domen Prešern, Joakim Bohlin, Lorenzo Rovigatti, Flavio Romano, Petr Šulc, Chak Kui Wong, Ard A. Louis, John S. Schreck, Megan C. Engel, Michael Matthies, Erik Benson, Erik Poppleton and Benedict E. K. Snodin

 

7. All-atom Molecular Dynamics Simulations of Membrane Spanning

DNA Origami Nanopores

Himanshu Joshi, Chen-Yu Li, and Aleksei Aksimentiev

 

Part III: Single-molecule characterization of DNA origami

8. Single molecule imaging of enzymatic reactions on DNA origami

An Yan, Lele Sun, and Di Li

 

9. Single-molecule nanomechanical genotyping with DNA origami-based shape IDs

Qian Li, Jie Chao, Honglu Zhang, and Chunhai Fan

 

10. Using single molecule FRET to evaluate DNA nanodevices at work

Nibedita Pal and Nils G. Walter

 

Part IV: Applications of DNA/RNA origami

 

11. Parallel Functionalization of DNA Origami

Rasmus P. Thomsen, Rasmus S. Sørensen and Jørgen Kjems

 

12. Protein Coating of DNA Origami

 Heini Ijäs, Mauri A. Kostiainen, and Veikko Linko

 

13. Cellular uptake of DNA origami                                              

Maartje M.C. Bastings, EPFL

 

14. Binding and characterization of DNA origami nanostructures on lipid membranes

Alena Khmelinskaia, Petra Schwille, and Henri G. Franquelim

 

15. Electrical actuation of DNA based nanomechanical systems Jonathan List, Enzo Kopperger, Friedrich C. Simmel

 

16. Enzyme cascade reactions on DNA origami scaffold

Eiji Nakata, Huyen Dinh, Lin Peng, and Takashi Morii

 

17. Aptamers as Functional Modules for DNA Nanostructures

Simon Chi-Chin Shiu, Andrew B. Kinghorn, Wei Guo, Liane S. Slaughter, Danyang Ji, Xiaoyong Mo, Lin Wang, Ngoc Chau Tran, Chun Kit Kwok, Anderson Ho Cheung Shum, Edmund Chun Ming Tse, and Julian A. Tanner

 

18. Production and Testing of RNA Origami Anticoagulants

Abhichart Krissanaprasit, Carson Key, Kristen Froehlich, and Thomas H. LaBean