Gels of DNA nanostars never crystallize

ACS Nano

Volumn 8, Issue 4, 2014, Pages 3567-3574

  Rovigatti, Lorenzo ^a   Smallenburg, Frank ^a   Romano, Flavio ^b   Sciortino, Francesco ^a  

^a SAPIENZA UNIVERSITY OF ROME   (Italy)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

DNA hydrogels; DNA nanostars; DNA self assembly; physical gels

Indexed keywords

GELS; HYDROGELS;

CRYSTALLINE PHASE; DNA SELF-ASSEMBLY; MOLECULAR NETWORKS; NANOSTAR; NUMERICAL TECHNIQUES; PHYSICAL GEL; REALISTIC MODEL; THERMODYNAMICALLY STABLE;

DNA;

DNA; HYDROGEL;

CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; CRYSTALLIZATION; GENETICS; HYDROGEL; NUCLEOTIDE SEQUENCE; TEMPERATURE;

BASE SEQUENCE; CRYSTALLIZATION; DNA; HYDROGELS; MODELS, MOLECULAR; NUCLEIC ACID CONFORMATION; TEMPERATURE;

EID: 84899437917     PISSN: 19360851     EISSN: 1936086X     Source Type: Journal    
DOI: 10.1021/nn501138w     Document Type: Article

References (50)

1. Watson, J. D.; Crick, F. H. Molecular Structure of Nucleic Acids Nature 1953, 171, 737-738
2. Seeman, N. DNA in a Material World Nature 2003, 421, 427-431
3. Seeman, N. C. DNA Nanotechnology: Novel DNA Constructions Annu. Rev. Biophys. Biomol. Struct. 1998, 27, 225-248
4. Lee, J. B.; Peng, S.; Yang, D.; Roh, Y. H.; Funabashi, H.; Park, N.; Rice, E. J.; Chen, L.; Long, R.; Wu, M. et al. A Mechanical Metamaterial Made from a DNA Hydrogel Nat. Nanotechnol. 2012, 7, 816-820
5. Ouldridge, T. E.; Hoare, R. L.; Louis, A. A.; Doye, J. P. K.; Bath, J.; Turberfield, A. J. Optimizing DNA Nanotechnology through Coarse-Grained Modeling: A Two-Footed DNA Walker ACS Nano 2013, 7, 2479-2490
6. Wollman, A. J.; Sanchez-Cano, C.; Carstairs, H. M.; Cross, R. A.; Turberfield, A. J. Transport and Self-Organization Across Different Length Scales Powered by Motor Proteins and Programmed by DNA Nat. Nanotechnol. 2013, 9, 44-47
7. Rothemund, P. Folding DNA To Create Nanoscale Shapes and Patterns Nature 2006, 440, 297-302
8. Yang, Y.; Han, D.; Nangreave, J.; Liu, Y.; Yan, H. DNA Origami with Double-Stranded DNA as a Unified Scaffold ACS Nano 2012, 6, 8209-8215
9. Soloveichik, D.; Seelig, G.; Winfree, E. DNA as a Universal Substrate for Chemical Kinetics Proc. Natl. Acad. Sci. U.S.A. 2010, 107, 5393-5398
10. He, Y.; Ye, T.; Su, M.; Zhang, C.; Ribbe, A. E.; Jiang, W.; Mao, C. Hierarchical Self-Assembly of DNA into Symmetric Supramolecular Polyhedra Nature 2008, 452, 198-201
11. Seeman, N. C. Nucleic Acid Junctions and Lattices J. Theor. Biol. 1982, 99, 237-247
12. Roh, Y. H.; Ruiz, R. C. H.; Peng, S.; Lee, J. B.; Luo, D. Engineering DNA-Based Functional Materials Chem. Soc. Rev. 2011, 40, 5730-5744
13. Biffi, S.; Cerbino, R.; Bomboi, F.; Paraboschi, E. M.; Asselta, R.; Sciortino, F.; Bellini, T. Phase Behavior and Critical Activated Dynamics of Limited-Valence DNA Nanostars Proc. Natl. Acad. Sci. U.S.A. 2013, 110, 15633-15637
14. Rovigatti, L.; Bomboi, F.; Sciortino, F. Accurate Phase Diagram of Tetravalent DNA Nanostars. arXiv:1401.2837v1 2014.
15. Bianchi, E.; Largo, J.; Tartaglia, P.; Zaccarelli, E.; Sciortino, F. Phase Diagram of Patchy Colloids: Towards Empty Liquids Phys. Rev. Lett. 2006, 97, 168301-168304
16. Russo, J.; Tartaglia, P.; Sciortino, F. Reversible Gels of Patchy Particles: Role of the Valence J. Chem. Phys. 2009, 131, 014504
17. Rovigatti, L.; Kob, W.; Sciortino, F. The Vibrational Density of States of a Disordered Gel Model J. Chem. Phys. 2011, 135, 104502
18. Smallenburg, F.; Sciortino, F. Liquids More Stable than Crystals in Particles with Limited Valence and Flexible Bonds Nat. Phys. 2013, 9, 554-558
19. Martinez-Veracoechea, F. J.; Mladek, B. M.; Tkachenko, A. V.; Frenkel, D. Design Rule for Colloidal Crystals of DNA-Functionalized Particles Phys. Rev. Lett. 2011, 107, 045902
20. Lu, P. J.; Zaccarelli, E.; Ciulla, F.; Schofield, A. B.; Sciortino, F.; Weitz, D. A. Gelation of Particles with Short-Range Attraction Nature 2008, 453, 499-503
21. Foffi, G.; Sciortino, F.; Tartaglia, P.; Zaccarelli, E.; Verso, F. L.; Reatto, L.; Dawson, K. A.; Likos, C. N. Structural Arrest in Dense Star-Polymer Solutions Phys. Rev. Lett. 2003, 90, 238301
22. Dawson, K. A. The Glass Paradigm for Colloidal Glasses, Gels, and Other Arrested States Driven by Attractive Interactions Curr. Opin. Colloid Interface Sci. 2002, 7, 218-227
23. Starr, F. W.; Sciortino, F. Model for Assembly and Gelation of Four-Armed DNA Dendrimers J. Phys.: Condens. Matter 2006, 18, L347-L353
24. Knotts, T. A.; Rathore, N.; Schwartz, D. C.; de Pablo, J. J. A Coarse Grain Model for DNA J. Chem. Phys. 2007, 126, 4901
25. Knorowski, C.; Burleigh, S.; Travesset, A. Dynamics and Statics of DNA-Programmable Nanoparticle Self-Assembly and Crystallization Phys. Rev. Lett. 2011, 106, 215501
26. Li, T. I.; Sknepnek, R.; Macfarlane, R. J.; Mirkin, C. A.; Olvera de la Cruz, M. Modeling the Crystallization of Spherical Nucleic Acid Nanoparticle Conjugates with Molecular Dynamics Simulations Nano Lett. 2012, 12, 2509-2514
27. Ouldridge, T. E. Coarse-Grained Modelling of DNA and DNA Self-Assembly. Ph.D. Thesis, University of Oxford, 2011.
28. Hsu, C. W.; Fyta, M.; Lakatos, G.; Melchionna, S.; Kaxiras, E. Ab Initio Determination of Coarse-Grained Interactions in Double-Stranded DNA J. Chem. Phys. 2012, 137, 105102
29. Hinckley, D. M.; Freeman, G. S.; Whitmer, J. K.; de Pablo, J. J. An Experimentally-Informed Coarse-Grained 3-Site-per-Nucleotide Model of DNA: Structure, Thermodynamics, and Dynamics of Hybridization J. Chem. Phys. 2013, 139, 144903
30. Ouldridge, T. E.; Louis, A. A.; Doye, J. P. K. Structural, Mechanical, and Thermodynamic Properties of a Coarse-Grained DNA model J. Chem. Phys. 2011, 134, 085101
31. Ouldridge, T. E.; Louis, A. A.; Doye, J. P. K. DNA Nanotweezers Studied with a Coarse-Grained Model of DNA Phys. Rev. Lett. 2010, 104, 178101
32. Šulc, P.; Romano, F.; Ouldridge, T. E.; Rovigatti, L.; Doye, J. P. K.; Louis, A. A. Sequence-Dependent Thermodynamics of a Coarse-Grained DNA Model J. Chem. Phys. 2012, 137, 135101
33. Doye, J. P. K.; Ouldridge, T. E.; Louis, A. A.; Romano, F.; Sulc, P.; Matek, C.; Snodin, B. E. K.; Rovigatti, L.; Schreck, J. S.; Harrison, R. M. et al. Coarse-Graining DNA for Simulations of DNA Nanotechnology Phys. Chem. Chem. Phys. 2013, 15, 20395-20414
34. Saika-Voivod, I.; Smallenburg, F.; Sciortino, F. Understanding Tetrahedral Liquids through Patchy Colloids J. Chem. Phys. 2013, 139, 234901
35. Maldovan, M.; Thomas, E. Diamond Structured Photonic Crystals Nat. Mater. 2004, 3, 593-600
36. Wegener, M. Metamaterials Beyond Optics Science 2013, 342, 939-940
37. Vega, C.; Monson, P. A. Solid-Fluid Equilibrium for a Molecular Model with Short Ranged Directional Forces J. Chem. Phys. 1998, 109, 9938-9949
38. Romano, F.; Sanz, E.; Sciortino, F. Crystallization of Tetrahedral Patchy Particles in Silico J. Chem. Phys. 2011, 134, 174502
39. Noya, E. G.; Vega, C.; Doye, J. P. K.; Louis, A. A. Phase Diagram of Model Anisotropic Particles with Octahedral Symmetry J. Chem. Phys. 2007, 127, 054501
40. Doye, J. P. K.; Louis, A. A.; Lin, I.-C.; Allen, L. R.; Noya, E. G.; Wilber, A. W.; Kok, H. C.; Lyus, R. Controlling Crystallization and Its Absence: Proteins, Colloids and Patchy Models Phys. Chem. Chem. Phys. 2007, 9, 2197-2205
41. Doppelbauer, G.; Noya, E. G.; Bianchi, E.; Kahl, G. Self-Assembly Scenarios of Patchy Colloidal Particles Soft Matter 2012, 8, 7768-7772
42. Vega, C.; Sanz, E.; Abascal, J. L. F.; Noya, E. G. Determination of Phase Diagrams via Computer Simulation: Methodology and Applications to Water, Electrolytes and Proteins J. Phys.: Condens. Matter 2008, 20, 153101-153139
43. Smith, B.; Frenkel, D. Understanding Molecular Simulations; Academic Press: New York, 1996.
44. Romano, F.; Hudson, A.; Doye, J. P. K.; Ouldridge, T. E.; Louis, A. A. The Effect of Topology on the Structure and Free Energy Landscape of DNA Kissing Complexes J. Chem. Phys. 2012, 136, 215102
45. Romano, F.; Chakraborty, D.; Doye, J. P. K.; Ouldridge, T. E.; Louis, A. A. Coarse-Grained Simulations of DNA Overstretching J. Chem. Phys. 2013, 138, 085101
46. Matek, C.; Ouldridge, T. E.; Levy, A.; Doye, J. P. K.; Louis, A. A. DNA Cruciform Arms Nucleate through a Correlated but Asynchronous Cooperative Mechanism J. Phys. Chem. B 2012, 116, 11616-11625
47. De Michele, C.; Rovigatti, L.; Bellini, T.; Sciortino, F. Self-Assembly of Short DNA Duplexes: From a Coarse-Grained Model to Experiments through a Theoretical Link Soft Matter 2012, 8, 8388
48. Kern, N.; Frenkel, D. Fluid-Fluid Coexistence in Colloidal Systems with Short-Ranged Strongly Directional Attraction J. Chem. Phys. 2003, 118, 9882-9889
49. http://dna.physics.ox.ac.uk.
50. Frenkel, D.; Ladd, A. J. C. New Monte Carlo Method To Compute the Free Energy of Arbitrary Solids. Application to the FCC and HCP Phases of Hard Spheres J. Chem. Phys. 1984, 81, 3188-3193