Dedicated softwares for DNA origami designs
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1 Dedicated softwares for DNA origami designs DAEDALUS ( à independent to M13 ssdna à generates dedicated DNA scaffolds (450-3,400 bases) NANOANDES 2017, November 22-29, Buenos Aires, Argentina 61
2 Dedicated softwares for DNA origami designs DAEDALUS ( à independent to M13 ssdna à generates dedicated DNA scaffolds (450-3,400 bases) Cite as: R. Veneziano et al., Science /science.aaf4388 (2016). mmed from the NANOANDES 2017, November 22-29, Buenos Aires, Argentina 62
3 DNA origami decorated with nanoparticles 2D nanostructures Q. Liu et al., Methods (2013), NANOANDES 2017, November 22-29, Buenos Aires, Argentina 63
4 DNA origami decorated with nanoparticles 3D nanostructures Q. Liu et al., Methods (2013), NANOANDES 2017, November 22-29, Buenos Aires, Argentina 64
5 DNA nanostructures decorated with nanoparticles and vice-versa! Nature Chemistry 8, (2016) doi: /nchem.2420 NANOANDES 2017, November 22-29, Buenos Aires, Argentina 65
6 DNA origami decorated with proteins ChemBioChem 2016, 17, NANOANDES 2017, November 22-29, Buenos Aires, Argentina 66
7 DNA nanocage decorated with proteins Central cavity of the tetrahedron could accommodate a sphere of radius of approximately 2.6nm,corresponding to a globular protein with a molecular weight of 60 kda. DOI: /anie Single-Molecule Protein Encapsulation in a Rigid DNA Cage** Christoph M. Erben, Russell P. Goodman, and Andrew J. Turberfield* cytochrome c (12.4 kda) NANOANDES 2017, November 22-29, Buenos Aires, Argentina 67
8 DNA-based drug delivery «Particles below 25 nm are subject to filtration in the kidney or uptake in the liver, and particles above 150 nm experience increased filtration in the spleen and phagocytosis by macrophages» => DNA nanocages are the perfect «nanovehicles» a) The DNA tetrahedron is assembled by annealing of 4 ODNs. It consists of three 20 bp sides and three 30 bp sides making it approximately 7.5 nm or 10.5 nm high b) CpG ODNs attached to the vertices of the tetrahedron c) sirna attached to the sides of the tetrahedron d) Doxorubicin interchelates dsdna of the tetrahedron A.H. Okholm, J. Kjems / Advanced Drug Delivery Reviews 106 (2016) NANOANDES 2017, November 22-29, Buenos Aires, Argentina 68
9 NANOANDES 2017, November 22-29, Buenos Aires, Argentina 69
![standard methods. A [2] binding N. C.of a-thrombin Seeman,to theannu. Rev. Figure 2. Symmetric origami after the Biochem. in the Supporting Inf repair of the methylation in the 79, TBA165.](/docs-images/75/71880927/images/10-0.jpg "(left line). The bottom-right and purified as previ 2010, panel shows the 3D profile of an origami with all its binding positions [3] a) R. Chhabra, J. Sharma, Y. Ke, Y.")
10 standard methods. A [2] binding N. C.of a-thrombin Seeman,to theannu. Rev. Figure 2. Symmetric origami after the Biochem. in the Supporting Inf repair of the methylation in the 79, TBA165. (left line). The bottom-right and purified as previ 2010, panel shows the 3D profile of an origami with all its binding positions [3] a) R. Chhabra, J. Sharma, Y. Ke, Y.staple Liu,strands contain occupied by a-thrombin. Chemie DNA origami for biosensing Angewandte corresponding AFM images, and their cross-sections. a) TBABA origami complex. c) a-thrombin complex with demethylated S. Rinker, S. Lindsay, H. Yan, J. Am. Chem. Soc. 2007, 129, 10304; b) H. T. Maune, S. P. Han, R. D. Barish, M. Bockrath, W. A. Iii, P. W. Rothemund, E. Winfree, Nat. Nanotechnol. 2010, 5, 61; c) S. Pal, Z. Deng, B. Ding, H. Yan, Y. Liu, Angew. Chem. 2010, 122, 2760; Angew. Chem. Int. Ed. 2010, 49, 2700; d) B. Sacc", R. Meyer, M. Erkelenz, K. Kiko, A. Arndt, H. Schroeder, K. S. Rabe, C. M. Niemeyer, Angew. Chem. 2010, 122, 9568; Angew. Chem. Int. Ed. time the enzymatic activity of 2010, 49, [4] a) H. Gu, J. Chao, S. J. Xiao, N. C. Seeman, Nature 2010, 465, n an origami platform. This study 202; b) S. F. Wickham, J. Bath, Y. Katsuda, M. Endo, K. Hidaka, of the a-thrombin recognition/ H. Sugiyama, A. J. Turberfield, Nat. Nanotechnol. 2012, 7, 169; le-molecule features of the DNA c) N. V. Voigt, T. Torring, A. Rotaru, M. F. Jacobsen, J. B. ction of1. DNA repair.of The systembinding of a-thrombin Scheme a) Representation the asymmetric Ravnsbaek, R. Subramani, W. Mamdouh, J. Kjems, A. Mokhir, to TBAand aptamers of methylated b) Methyl-TBA repair by ctive reliable, anddna theorigami. results F.ofBesenbacher, K. V. Gothelf, Nat. Nanotechnol. 2010, 5, 200. hagt, thus allowing G-quadruplex formation. c) Representation the spatial addressability of DNA origami in M.symmetric Their binding consistency suggests that DNA origami of a-thrombin to the repaired quad[5] A. V. Pinheiro, D. Han, W. M. Shih, H. Yan, Nat. Nanotechnol. combination with the change of ruplexes. evolved to design hagt activity 2011, 6, 763. conformation of a DNA G-quadruplex to visually detect by AFM the change in its Figure 3. Distribution of heights, corresponding AFM images, and their cross-sections. a) TBAability of our design totodiscern between the methylated and!affinity 2013 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim Angew. Chem. Int. Ed. 2013, 52, 1 5 binding a-thrombin. origami. b) a-thrombin methyl-tba origami complex. c) a-thrombin complex with demethylated non-methylated state. TBA origami. To explore the efficiency of our design, we performed ge numbers! a quantitative study of the binding location of a-thrombin. From the 160 well-formed DNA origami studied, around knowledge, this is the first time the enzymatic activity of NANOANDES 2017, November 22-29, Buenos Aires, Argentina 20 % of them contained all five a-thrombin molecules in hagt has been visualized on an origami platform. This study positions coinciding with unmodified TBA and almost none in combines the capabilities of the a-thrombin recognition/ 2010, 70 49, [4] a) H. Gu, J. Ch 202; b) S. F. Wic
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