Topological interaction by entangled DNA loops

Physical Review Letters

Volumn 109, Issue 18, 2012, Pages

  Feng, Lang ^a   Sha, Ruojie ^a   Seeman, Nadrian C ^a   Chaikin, Paul M ^a  

^a NEW YORK UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA LOOPS; INTER-PARTICLE INTERACTION; NANOSCALE PARTICLES; NON EQUILIBRIUM; OLYMPICS; PARTICLE ASSEMBLIES; TOPOLOGICAL INTERACTIONS;

ASSOCIATION REACTIONS;

TOPOLOGY;

EID: 84868335498     PISSN: 00319007     EISSN: 10797114     Source Type: Journal    
DOI: 10.1103/PhysRevLett.109.188301     Document Type: Article

References (21)

1. C.A. Mirkin, R.L. Letsinger, R.C. Mucic, and J.J. Storhoff, Nature (London) 382, 607 (1996). NATUAS 0028-0836 10.1038/382607a0 (Pubitemid 26268949)
2. R.J. Macfarlane, B. Lee, M.R. Jones, N. Harris, G.C. Schatz, and C.A. Mirkin, Science 334, 204 (2011). SCIEAS 0036-8075 10.1126/science.1210493
3. M.P. Valignat, O. Theodoly, J.C. Crocker, W.B. Russel, and P.M. Chaikin, Proc. Natl. Acad. Sci. U.S.A. 102, 4225 (2005). PNASA6 0027-8424 10.1073/pnas.0500507102 (Pubitemid 40397093)
4. P.L. Biancaniello, A.J. Kim, and J.C. Crocker, Phys. Rev. Lett. 94, 058302 (2005). PRLTAO 0031-9007 10.1103/PhysRevLett.94.058302 (Pubitemid 40620897)
5. D. Nykypanchuk, M.M. Maye, D. van der Lelie, and O. Gang, Nature (London) 451, 549 (2008). NATUAS 0028-0836 10.1038/nature06560 (Pubitemid 351186275)
6. T. Wang, R.J. Sha, R. Dreyfus, M.E. Leunissen, C. Maass, D.J. Pine, P.M. Chaikin, and N.C. Seeman, Nature (London) 478, 225 (2011). NATUAS 0028-0836 10.1038/nature10500
7. R. Dreyfus, M.E. Leunissen, R.J. Sha, A.V. Tkachenko, N.C. Seeman, D.J. Pine, and P.M. Chaikin, Phys. Rev. Lett. 102, 048301 (2009). PRLTAO 0031-9007 10.1103/PhysRevLett.102.048301
8. R. Dreyfus, M.E. Leunissen, R. Sha, A. Tkachenko, N.C. Seeman, D.J. Pine, and P.M. Chaikin, Phys. Rev. E 81, 041404 (2010). PLEEE8 1539-3755 10.1103/PhysRevE.81.041404
9. W.B. Rogers and J.C. Crocker, Proc. Natl. Acad. Sci. U.S.A. 108, 15687 (2011). PNASA6 0027-8424 10.1073/pnas.1109853108
10. L.F. Liu, R.E. Depew, and J.C. Wang, J. Mol. Biol. 106, 439 (1976). JMOBAK 0022-2836 10.1016/0022-2836(76)90095-4
11. A.D. Bates, A. Maxwell, DNA Topology (Oxford University Press, New York, 2005).
12. J.H. Chen, C.A. Rauch, J.H. White, P.T. Englund, and N.R. Cozzarelli, Cell 80, 61 (1995). CELLB5 0092-8674 10.1016/0092-8674(95)90451-4
13. J.H. Chen, P.T. Englund, and N.R. Cozzarelli, EMBO J. 14, 6339 (1995). EMJODG 0261-4189
14. Q. Xu, L. Feng, R. Sha, N.C. Seeman, and P.M. Chaikin, Phys. Rev. Lett. 106, 228102 (2011). PRLTAO 0031-9007 10.1103/PhysRevLett.106.228102
15. M.E. Leunissen, R. Dreyfus, F.C. Cheong, D.G. Grier, R. Sha, N.C. Seeman, and P.M. Chaikin, Nature Mater. 8, 590 (2009). NMAACR 1476-1122 10.1038/nmat2471
16. M.E. Leunissen, R. Dreyfus, R.J. Sha, T. Wang, N.C. Seeman, D.J. Pine, and P.M. Chaikin, Soft Matter 5, 2422 (2009). SMOABF 1744-683X 10.1039/b817679e
17. See Supplemental Material at http://link.aps.org/supplemental/10.1103/ PhysRevLett.109.188301 for videos of experimental measurements, enzymatic unwinding of topological links between particles, details of the model calculation, and discussion of covalent binding of DNA loops with a UV cross-linker.
18. Topoisomerase I (E.coli) from New England BioLabs, http://www.neb.com/ nebecomm/products/productM0301.asp
19. A.V. Tkachenko, Phys. Rev. Lett. 106, 255501 (2011). PRLTAO 0031-9007 10.1103/PhysRevLett.106.255501
20. F.J. Martinez-Veracoechea, B.M. Mladek, A.V. Tkachenko, and D. Frenkel, Phys. Rev. Lett. 107, 045902 (2011). PRLTAO 0031-9007 10.1103/PhysRevLett.107. 045902
21. K. Fujimoto, Y. Yoshimura, T. Ikemoto, A. Nakazawa, M. Hayashi, and I. Saito, Chem. Commun. (Cambridge) 25, 3177 (2005). CHCOFS 1359-7345 10.1039/b504162g (Pubitemid 41002387)