DNA and RNA Origami: Methods and Protocols (Methods in Molecular Biology)

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 Nstor 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 PreSern, Joakim Bohlin, Lorenzo Rovigatti, Flavio Romano, Petr sulc, 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. Srensen and Jrgen Kjems 12. Protein Coating of DNA Origami Heini Ijs, 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