Design and fabrication of DNA origami mechanisms and machines

Advances in Reconfigurable Mechanisms and Robots I

Volumn , Issue , 2012, Pages 487-500

  Su, Hai Jun ^a   Castro, Carlos Ernesto ^a   Marras, Alexander Edison ^a   Hudoba, Michael ^a  

^a The Ohio State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DOUBLE-STRANDED DNA (DS-DNA); ENVIRONMENTAL SENSING; MECHANICAL STIFFNESS; MOLECULAR SELF ASSEMBLY; NANO-SCALE MECHANISM; SINGLE STRAND DNA (SS-DNA); SQUARE CROSS-SECTION; STRUCTURAL CONFORMATIONS;

DESIGN; DRUG DELIVERY; KINEMATICS; MANUFACTURE; MECHANISMS; NANOROBOTICS; REPAIR; ROBOTS; TISSUE; TRANSMISSION ELECTRON MICROSCOPY;

DNA;

EID: 84875669725     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1007/978-1-4471-4141-9_44     Document Type: Conference Paper

References (36)

1. McCarthy JM (2000) Geometric design of linkages. Springer, New York
2. Erdman AG, Sandor GN, Kota S (2001) Mechanism design analysis and synthesis, 4th edn. Prentice Hall, Upper Saddle River
3. Chirikjian GS, Kazerounian K, Mavroidis C (2005) Analysis and design of protein based nanodevices: challenges and opportunities in mechanical design. J Mech Des 127(4):695-698 (Pubitemid 41064226)
4. Chirikjian GS (2001) Conformational statistics of macromolecules using generalized convolution. Comput Theor Polym Sci 11(2):143-153
5. Kazerounian K (2004) From mechanisms and robotics to protein conformation and drug design. J Mech Des 126(1):40-45
6. Kazerounian K, Latif K, Alvarado C (2005) Protofold: a successive kinetostatic compliance method for protein conformation prediction. J Mech Des 127(4):712-717 (Pubitemid 41064228)
7. Mavroidis C, Dubey A (2004) Bio-Nanorobotics: state of the art and future challenges. In: Yarmush ML (ed) The Biomedical Engineering Handbook, 3rd edn. CRC Press LLC
8. Hamdi M, Ferreira A (2009) Multiscale design and modeling of protein-based nanomechanisms for nanorobotics. Int J Robot Res 28(4):436-449
9. Sharma G, Mavroidis C, Rege K, Yarmush ML, Budil D (2009) Computational studies of a protein-based nanoactuator for nanogripping applications. Int J Robot Res 28(4):421-435
10. Dill KA, Ozkan SB, Shell MS, Weikl TR (2008) The protein folding problem. Ann Rev Biophys 37:289-316
11. Kuhlman B, Dantas G, Ireton G, Varani G, Stoddard B, Baker D (2003) Design of a novel globular protein fold with atomic-level accuracy. Science 302(5649):1364-1368 (Pubitemid 37452172)
12. Baker D (2006) Prediction and design of macromolecular structures and interactions. Philos Trans R Soc B Biol Sci 361(1467):459-463
13. Leaver-Fay A, Jacak R, Stranges PB, Kuhlman B (2011) A generic program for multistate protein design. PLos ONE 6(7):e20937
14. Watson J, Crick F (1953) Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid. Nature 171(4356):737-738
15. Yakovchuk P, Protozanova E, Frank-Kamenetskii MD (2006) Base-stacking and base-pairing contributions into thermal stability of the DNA double helix. Nucleic Acids Res 34(2):564-574 (Pubitemid 43240244)
16. Seeman NC (1982) Nucleic acid junctions and lattices. J Theor Biol 99(2):237-247
17. Chen JH, Seeman NC (1991) Synthesis from DNA of a molecule with the connectivity of a cube. Nature 350(6319):631-633
18. Li X, Yang X, Qi J, Seeman NC (1996) Antiparallel DNA double crossover molecules as components for nanoconstruction. J Am Chem Soc 118(26):6131-6140 (Pubitemid 26236848)
19. Seeman NC (2003) DNA in a material world. Nature 421(6921):427-431
20. Rothemund PWK (2006) Folding DNA to create nanoscale shapes and patterns. Nature 440(7082):297-302
21. Douglas SM, Dietz H, Liedl T, Hogberg B, Graf F, Shih WM (2009) Self-assembly of DNA into nanoscale three-dimensional shapes. Nature 459(7245):414-418
22. Castro CE, Kilchherr F, Kim D-N, Shiao EL, Wauer T, Wortmann P, Bathe M, Dietz H (2011) A primer to scaffolded DNA origami. Nat Methods 8(3):221-229
23. Ke Y, Sharma J, Liu M, Jahn K, Liu Y, Yan H (2009) Scaffolded DNA origami of a DNA tetrahedron molecular container. Nano Lett 9(6):2445-2447 (PMID: 19419184)
24. Jungmann R, Scheible M, Kuzyk A, Pardatscher G, Castro CE, Simmel FC (2011) DNA origami-based nanoribbons: assembly, length distribution, and twist. Nanotechnology 22(27):275-301
25. Maune HT, Han S-P, Barish RD, Bockrath M, Iii WAG, Rothemund PWK, Winfree E (2010) Self-assembly of carbon nanotubes into two-dimensional geometries using DNA origami templates. Nat Nanotechnol 5(1):61-66
26. Liedl T, Hogberg B, Tytell J, Ingber DE, Shih WM (2010) Self-assembly of three-dimensional prestressed tensegrity structures from DNA. Nat Nanotechnol 5(7):520-524
27. Dietz H, Douglas SM, Shih WM (2009) Folding DNA into twisted and curved nanoscale shapes. Science 325(5941):725-730
28. Andersen ES, Dong M, Nielsen MM, Jahn K, Lind-Thomsen A, Mamdouh W, Gothelf KV, Besenbacher F, Kjems J (2008) DNA origami design of dolphin-shaped structures with flexible tails. ACS Nano 2(6):1213-1218
29. 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(15):5001-5006
30. Bennett GT (1914) The skew isogram mechanism. Proc London Math Soc s2-13(1):151-173
31. Chen Y (2009) Design of Structural Mechanisms. D.Phil. Dissertation, University of Oxford, UK
32. Ke Y, Douglas SM, Liu M, Sharma J, Cheng A, Leung A, Liu Y, Shih WM, Yan H (2009) Multilayer DNA origami packed on a square lattice. J Am Chem Soc 131(43):15903-15908
33. Lilley D (1997) All change at holliday junction. Proc Natl Acad Sci U S A 94(18):9513-9515
34. Perez A, McCarthy J (2002) Bennett's linkage and the cylindroid. Mech Mach Theor 37(11):1245-1260 (Pubitemid 34991861)
35. Chen Y, You Z (2006) Square deployable frames for space applications. Part 1: Theory. Proc Inst Mech Eng [G] 220(4):347-354. (Pubitemid 46478065)
36. Chen Y, You Z (2007) Square deployable frames for space applications. Part 2: Realization. Proc Inst Mech Eng [G] 221(1):37-45 (Pubitemid 46481524)