Engineering defined motor ensembles with DNA origami

Methods in Enzymology

Volumn 540, Issue , 2014, Pages 169-188

  Goodman, Brian S ^a   Reck Peterson, Samara L ^a  

^a HARVARD MEDICAL SCHOOL   (United States)

Author keywords

Cytoskeleton; DNA origami; Dynein; Ensembles; Kinesin; Multiple motors; Myosin; Synthetic cargo

Indexed keywords

ANALYTIC METHOD; ARTICLE; ASSAY; COVALENT BOND; CYTOSKELETON; DNA STRUCTURE; ENGINEERING; GEOMETRY; PRIORITY JOURNAL;

CYTOSKELETON; DNA ORIGAMI; DYNEIN; ENSEMBLES; KINESIN; MULTIPLE MOTORS; MYOSIN; SYNTHETIC CARGO;

ANIMALS; DNA; DYNEINS; HUMANS; KINESIN; MICROTUBULES; MOLECULAR MOTOR PROTEINS; MYOSINS; NUCLEIC ACID CONFORMATION;

EID: 84896376165     PISSN: 00766879     EISSN: 15577988     Source Type: Book Series    
DOI: 10.1016/B978-0-12-397924-7.00010-8     Document Type: Chapter

References (36)

1. G. Bellot, M.A. McClintock, J.J. Chou, and W.M. Shih DNA nanotubes for NMR structure determination of membrane proteins Nature Protocols 8 4 2013 755 770
2. P. Bieling, I.A. Telley, J. Piehler, and T. Surrey Processive kinesins require loose mechanical coupling for efficient collective motility EMBO Reports 9 11 2008 1121 1127
3. S.M. Block Kinesin motor mechanics: Binding, stepping, tracking, gating, and limping Biophysical Journal 92 9 2007 2986 2995
4. S.A. Bryantseva, and O.N. Zhapparova Bidirectional transport of organelles: Unity and struggle of opposing motors Cell Biology International 36 1 2012 1 6
5. R.B. Case, D.W. Pierce, N. Hom-Booher, C.L. Hart, and R.D. Vale The directional preference of kinesin motors is specified by an element outside of the motor catalytic domain Cell 90 5 1997 959 966
6. C.E. Castro, F. Kilchherr, D.-N. Kim, E.L. Shiao, T. Wauer, and P. Wortmann et al. A primer to scaffolded DNA origami Nature Methods 8 3 2011 221 229
7. N.D. Derr, B.S. Goodman, R. Jungmann, A.E. Leschziner, W.M. Shih, and S.L. Reck-Peterson Tug-of-war in motor protein ensembles revealed with a programmable DNA origami scaffold Science (New York, NY) 338 6107 2012 662 665
8. H. Dietz, S.M. Douglas, and W.M. Shih Folding DNA into twisted and curved nanoscale shapes Science (New York, NY) 325 5941 2009 725 730
9. S.M. Douglas, I. Bachelet, and G.M. Church A logic-gated nanorobot for targeted transport of molecular payloads Science (New York, NY) 335 6070 2012 831 834
10. S.M. Douglas, H. Dietz, T. Liedl, B. Högberg, F. Graf, and W.M. Shih Self-assembly of DNA into nanoscale three-dimensional shapes Nature 459 7245 2009 414 418
11. S.M. Douglas, A.H. Marblestone, S. Teerapittayanon, A. Vazquez, G.M. Church, and W.M. Shih Rapid prototyping of 3D DNA-origami shapes with caDNAno Nucleic Acids Research 37 15 2009 5001 5006
12. R.P. Erickson, Z. Jia, S.P. Gross, and C.C. Yu How molecular motors are arranged on a cargo is important for vesicular transport PLoS Computational Biology 7 5 2011 e1002032
13. A. Gennerich, and S.L. Reck-Peterson Probing the force generation and stepping behavior of cytoplasmic Dynein Methods in Molecular Biology (Clifton, NJ) 783 2011 63 80
14. S.P. Gross Hither and yon: A review of bi-directional microtubule-based transport Physical Biology 1 1-2 2004 R1 R11
15. P. Guo The emerging field of RNA nanotechnology Nature Nanotechnology 5 12 2010 833 842
16. N. Hirokawa, S. Niwa, and Y. Tanaka Molecular motors in neurons: Transport mechanisms and roles in brain function, development, and disease Neuron 68 4 2010 610 638
17. K. Jaqaman, D. Loerke, M. Mettlen, H. Kuwata, S. Grinstein, and S.L. Schmid et al. Robust single-particle tracking in live-cell time-lapse sequences Nature Methods 5 8 2008 695 702
18. R. Jungmann, C. Steinhauer, M. Scheible, A. Kuzyk, P. Tinnefeld, and F.C. Simmel Single-molecule kinetics and super-resolution microscopy by fluorescence imaging of transient binding on DNA origami Nano Letters 10 11 2010 4756 4761
19. Y. Ke, N.V. Voigt, K.V. Gothelf, and W.M. Shih Multilayer DNA origami packed on hexagonal and hybrid lattices Journal of the American Chemical Society 134 3 2012 1770 1774
20. A. Keppler, S. Gendreizig, T. Gronemeyer, H. Pick, H. Vogel, and K. Johnsson A general method for the covalent labeling of fusion proteins with small molecules in vivo Nature Biotechnology 21 1 2003 86 89
21. M. Langecker, V. Arnaut, T.G. Martin, J. List, S. Renner, and M. Mayer et al. Synthetic lipid membrane channels formed by designed DNA nanostructures Science (New York, NY) 338 6109 2012 932 936
22. C. Lin, S.D. Perrault, M. Kwak, F. Graf, and W.M. Shih Purification of DNA-origami nanostructures by rate-zonal centrifugation Nucleic Acids Research 41 2 2013 e40
23. R. Mallik, D. Petrov, S.A. Lex, S.J. King, and S.P. Gross Building complexity: An in vitro study of cytoplasmic dynein with in vivo implications Current Biology 15 23 2005 2075 2085
24. A.V. Pinheiro, D. Han, W.M. Shih, and H. Yan Challenges and opportunities for structural DNA nanotechnology Nature Nanotechnology 6 12 2011 763 772
25. W. Qiu, N.D. Derr, B.S. Goodman, E. Villa, D. Wu, and W. Shih et al. Dynein achieves processive motion using both stochastic and coordinated stepping Nature Structural & Molecular Biology 19 2 2012 193 200
26. W.B. Redwine, R. Hernández-López, S. Zou, J. Huang, S.L. Reck-Peterson, and A.E. Leschziner Structural basis for microtubule binding and release by dynein Science (New York, NY) 337 6101 2012 1532 1536
27. A.R. Rogers, J.W. Driver, P.E. Constantinou, D. Kenneth Jamison, and M.R. Diehl Negative interference dominates collective transport of kinesin motors in the absence of load Physical Chemistry Chemical Physics 11 24 2009 4882 4889
28. P.W.K. Rothemund Folding DNA to create nanoscale shapes and patterns Nature 440 7082 2006 297 302
29. F. Ruhnow, D. Zwicker, and S. Diez Tracking single particles and elongated filaments with nanometer precision Biophysical Journal 100 11 2011 2820 2828
30. W.M. Shih, and C. Lin Knitting complex weaves with DNA origami Current Opinion in Structural Biology 20 3 2010 276 282
31. J.P.J. Sobczak, T.G. Martin, T. Gerling, and H. Dietz Rapid folding of DNA into nanoscale shapes at constant temperature Science (New York, NY) 338 6113 2012 1458 1461
32. R.D. Vale The molecular motor toolbox for intracellular transport Cell 112 4 2003 467 480
33. R.D. Vale, F. Malik, and D. Brown Directional instability of microtubule transport in the presence of kinesin and dynein, two opposite polarity motor proteins The Journal of Cell Biology 119 6 1992 1589 1596
34. M. Vershinin, B.C. Carter, D.S. Razafsky, S.J. King, and S.P. Gross Multiple-motor based transport and its regulation by Tau Proceedings of the National Academy of Sciences of the United States of America 104 1 2007 87 92
35. M.A. Welte Bidirectional transport along microtubules Current Biology 14 13 2004 R525 R537
36. A. Yildiz, J.N. Forkey, S.A. McKinney, T. Ha, Y.E. Goldman, and P.R. Selvin Myosin V walks hand-over-hand: Single fluorophore imaging with 1.5-nm localization Science (New York, NY) 300 5628 2003 2061 2065