A general theory of DNA-mediated and other valence-limited colloidal interactions

Journal of Chemical Physics

Volumn 137, Issue 9, 2012, Pages

  Varilly, Patrick ^a   Angioletti Uberti, Stefano ^a   Mognetti, Bortolo M ^a   Frenkel, Daan ^a  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

COLLOIDAL INTERACTION; EXTENSIBLE FRAMEWORK; GENERAL THEORY; INTERACTION POTENTIALS; LIGAND-RECEPTOR BINDING; MONTE CARLO CALCULATION; SELF-CONSISTENCY;

PHYSICAL CHEMISTRY; PHYSICS;

LIGANDS;

DNA; SINGLE STRANDED DNA;

ARTICLE; CHEMISTRY; COLLOID; MONTE CARLO METHOD;

COLLOIDS; DNA; DNA, SINGLE-STRANDED; MONTE CARLO METHOD;

EID: 84866109399     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4748100     Document Type: Article

References (43)

1. C. A. Mirkin, R. L. Letsinger, R. C. Mucic, and J. J. Storhoff, A DNA-based method for rationally assembling nanoparticles into macroscopic materials., Nature (London) 382, 607-609 (1996). 10.1038/382607a0 (Pubitemid 26268949)
2. A. P. Alivisatos, K. P. Johnsson, X. G. Peng, T. E. Wilson, C. J. Loweth, M. P. Bruchez, and P. G. Schultz, Organization of nanocrystal molecules using DNA., Nature (London) 382, 609-611 (1996). 10.1038/382609a0 (Pubitemid 26268950)
3. P. L. Biancaniello, A. J. Kim, and J. C. Crocker, Colloidal interactions and self-assembly using DNA hybridization., Phys. Rev. Lett. 94, 58302 (2005). 10.1103/PhysRevLett.94.058302 (Pubitemid 40620897)
4. N. Geerts and E. Eiser, DNA-functionalized colloids: Physical properties and applications., Soft Matter 6, 4647-4660 (2010). 10.1039/c001603a
5. N. L. Rosi and C. A. Mirkin, Nanostructures in biodiagnostics., Chem. Rev. 105, 1547-1562 (2005). 10.1021/cr030067f (Pubitemid 40596871)
6. D. Nykypanchuk, M. M. Maye, D. van der Lelie, and O. Gang, DNA-guided crystallization of colloidal nanoparticles., Nature (London) 451, 549-552 (2008). 10.1038/nature06560 (Pubitemid 351186275)
7. S. Y. Park, A. K. R. Lytton-Jean, B. Lee, S. Weigand, G. C. Schatz, and C. A. Mirkin, DNA-programmable nanoparticle crystallization., Nature (London) 451, 553-556 (2008). 10.1038/nature06508 (Pubitemid 351186267)
8. M. M. Maye, M. T. Kumara, D. Nykypanchuk, W. B. Sherman, and O. Gang, Switching binary states of nanoparticle superlattices and dimer clusters by DNA strands., Nat. Nanotechnol. 5, 116-120 (2010). 10.1038/nnano.2009.378
9. R. J. Macfarlane, B. Lee, M. R. Jones, N. Harris, G. C. Schatz, and C. A. Mirkin, Nanoparticle superlattice engineering with DNA., Science 334, 204-8 (2011). 10.1126/science.1210493
10. N. A. Licata and A. V. Tkachenko, Statistical mechanics of DNA-mediated colloidal aggregation., Phys. Rev. E 74, 41408 (2006). 10.1103/PhysRevE.74. 041408 (Pubitemid 44672757)
11. D. Nykypanchuk, M. M. Maye, D. van der Lelie, and O. Gang, DNA-based approach for interparticle interaction control., Langmuir 23, 6305-14 (2007). 10.1021/la0637566 (Pubitemid 46868705)
12. R. Dreyfus, M. E. Leunissen, R. Sha, A. V. Tkachenko, N. C. Seeman, D. J. Pine, and P. M. Chaikin, Simple quantitative model for the reversible association of DNA coated colloids., Phys. Rev. Lett. 102, 48301 (2009). 10.1103/PhysRevLett.102.048301
13. R. Dreyfus, M. E. Leunissen, R. Sha, A. V. Tkachenko, N. C. Seeman, D. J. Pine, and P. M. Chaikin, Aggregation-disaggregation transition of DNA-coated colloids: Experiments and theory., Phys. Rev. E 81, 41404 (2010). 10.1103/PhysRevE.81.041404
14. M. E. Leunissen, R. Dreyfus, R. Sha, N. C. Seeman, and P. M. Chaikin, Quantitative study of the association thermodynamics and kinetics of DNA-coated particles for different functionalization schemes., J. Am. Chem. Soc. 132, 1903-1913 (2010). 10.1021/ja907919j
15. M. E. Leunissen and D. Frenkel, Numerical study of DNA-functionalized microparticles and nanoparticles: Explicit pair potentials and their implications for phase behavior., J. Chem. Phys. 134, 84702 (2011). 10.1063/1.3557794
16. B. M. Mognetti, M. E. Leunissen, and D. Frenkel, Controlling the temperature sensitivity of DNA-mediated colloidal interactions through competing linkages., Soft Matter 8, 2213-2221 (2012). 10.1039/c2sm06635a
17. W. B. Rogers and J. C. Crocker, Direct measurements of DNA-mediated colloidal interactions and their quantitative modeling., Proc. Natl. Acad. Sci. U.S.A. 108, 15687-15692 (2011). 10.1073/pnas.1109853108
18. B. M. Mognetti, P. Varilly, S. Angioletti-Uberti, F. J. Martinez-Veracoechea, J. Dobnikar, M. E. Leunissen, and D. Frenkel, Predicting DNA-mediated colloidal pair interactions., Proc. Natl. Acad. Sci. U.S.A. 109, E378-E379 (2012). 10.1073/pnas.1119991109
19. W. B. Rogers and J. C. Crocker, Reply to Mognetti: DNA handshaking interaction data are well described by mean-field and molecular models., Proc. Natl. Acad. Sci. U.S.A. 109, E380-E380 (2012). 10.1073/pnas.1121102109
20. E. Zaccarelli, I. Saika-Voivod, S. V. Buldyrev, A. J. Moreno, P. Tartaglia, and F. Sciortino, Gel to glass transition in simulation of a valence-limited colloidal system., J. Chem. Phys. 124, 124908 (2006). 10.1063/1.2177241
21. F. J. Martinez-Veracoechea and D. Frenkel, Designing super selectivity in multivalent nano-particle binding., Proc. Natl. Acad. Sci. U.S.A. 108, 10963-10968 (2011). 10.1073/pnas.1105351108
22. V. M. Krishnamurthy, L. A. Estroff, and G. M. Whitesides, Multivalency in ligand design., in Fragment-Based Approaches in Drug Discovery, Methods and Principles in Medicinal Chemistry, edited by, W. Jahnke, and, D. A. Erlanson, (Wiley-VCH, Weinheim, FRG, 2006), Chap. 2, pp. 11-53.
23. J. D. Badjić, A. Nelson, S. J. Cantrill, W. B. Turnbull, and J. F. Stoddart, Multivalency and cooperativity in supramolecular chemistry., Acc. Chem. Res. 38, 723-32 (2005). 10.1021/ar040223k (Pubitemid 41442455)
24. M. Mammen, S.-K. Choi, and G. M. Whitesides, Polyvalent interactions in biological systems: Implications for design and use of multivalent ligands and inhibitors., Angew. Chem., Int. Ed. 37, 2754-2794 (1998). 10.1002/(SICI)1521- 3773(19981102)37:202754::AID-ANIE2754>3.0.CO;2-3 (Pubitemid 29008561)
25. S. Angioletti-Uberti, B. M. Mognetti, and D. Frenkel, Re-entrant melting as a design principle for DNA-coated colloids., Nature Mater. 11, 518-522 (2012). 10.1038/nmat3314
26. See supplementary material at http://dx.doi.org/10.1063/1.4748100 E-JCPSA6-137-034233 for an alternate derivation of the mean-field approximation to our theory using a saddle-point analysis.
27. M. P. Valignat, O. Theodoly, J. C. Crocker, W. B. Russel, and P. M. Chaikin, Reversible self-assembly and directed assembly of DNA-linked micrometer-sized colloids., Proc. Natl. Acad. Sci. U.S.A. 102, 4225-4229 (2005). 10.1073/pnas.0500507102 (Pubitemid 40397093)
28. Z. Tan, E. Gallicchio, M. Lapelosa, and R. M. Levy, Theory of binless multi-state free energy estimation with applications to protein-ligand binding., J. Chem. Phys. 136, 144102 (2012). 10.1063/1.3701175
29. F. Zhu and G. Hummer, Convergence and error estimation in free energy calculations using the weighted histogram analysis method., J. Comput. Chem. 33, 453-465 (2012). 10.1002/jcc.21989
30. O. Taussky, A recurring theorem on determinants., Am. Math. Monthly 56, 672-676 (1949). 10.2307/2305561
31. J. SantaLucia Jr. and D. Hicks, The thermodynamics of DNA structural motifs., Annu. Rev. Biophys. Bioeng. 33, 415-440 (2004). 10.1146/annurev. biophys.32.110601.141800 (Pubitemid 38829966)
32. R. J. Hunter, Foundations of Colloid Science (Oxford University Press, 2000).
33. N. Kern and D. Frenkel, Fluidfluid coexistence in colloidal systems with short-ranged strongly directional attraction., J. Chem. Phys. 118, 9882 (2003). 10.1063/1.1569473
34. P. W. K. Rothemund, Folding DNA to create nanoscale shapes and patterns., Nature (London) 440, 297-302 (2006). 10.1038/nature04586
35. Q. Chen, S. C. Bae, and S. Granick, Directed self-assembly of a colloidal kagome lattice., Nature (London) 469, 381-384 (2011). 10.1038/nature09713
36. N. R. Markham and M. Zuker, DINAMelt web server for nucleic acid melting prediction. Nucleic Acids Res. 33, W577-81 (2005). 10.1093/nar/gki591 (Pubitemid 44529988)
37. D. Frenkel and B. Smit, Understanding Molecular Simulation: From Algorithms to Applications (Computational Science) (Academic, 2001).
38. S. Torquato, Inverse optimization techniques for targeted self-assembly., Soft Matter 5, 1157 (2009). 10.1039/b814211b
39. G. I. Bell, M. Dembo, and P. Bongrand, Cell adhesion: Competition between nonspecific repulsion and specific bonding. Biophys. J. 45, 1051-64 (1984). 10.1016/S0006-3495(84)84252-6 (Pubitemid 14099481)
40. T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model., J. Chem. Phys. 134, 085101 (2011). 10.1063/1.3552946
41. L. R. G. Treloar, The statistical length of long-chain molecules., Trans. Faraday Soc. 42, 77 (1946). 10.1039/tf9464200077
42. H. Yamakawa, Modern Theory of Polymer Solutions (Harper, 1971).
43. J. S. Liu, Monte Carlo Strategies in Scientific Computing (Springer Series in Statistics) (Springer, 2002).