Deciphering the structural properties that confer stability to a DNA nanocage

ACS Nano

Volumn 3, Issue 7, 2009, Pages 1813-1822

  Falconi, Mattia ^a   Oteri, Francesco ^a   Chillemi, Giovanni ^b   Andersen, Felicie F ^c   Tordrup, David ^c   Oliveira, Cristiano L P ^c   Pedersen, Jan S ^c   Knudsen, Birgitta R ^c   Desideri, Alessandro ^a  

^a UNIVERSITY OF ROME TOR VERGATA   (Italy)

^b CASPUR   (Italy)

^c AARHUS UNIVERSITY   (Denmark)

Author keywords

DNA flexibility and geometrical parameters; DNA nanocage structure; Molecular dynamics simulation; Principal component analysis; SAXS spectroscopy

Indexed keywords

AVERAGE STRUCTURE; CLASSICAL MOLECULAR DYNAMICS; CRYO-TRANSMISSION ELECTRON MICROSCOPY; DNA CONFORMATIONS; DNA DOUBLE HELICES; EXPERIMENTAL DATA; GEOMETRICAL PARAMETERS; GLOBAL PROPERTIES; IN-SILICO; MOLECULAR DYNAMICS SIMULATION; NANOCAGES; SAXS SPECTROSCOPY; SIMULATION TIME; SMALL ANGLE X-RAY SCATTERING;

DNA; GENES; MOLECULAR DYNAMICS; MOLECULAR MECHANICS; NUCLEIC ACIDS; X RAY SCATTERING;

PRINCIPAL COMPONENT ANALYSIS;

EID: 68649106698     PISSN: 19360851     EISSN: 1936086X     Source Type: Journal    
DOI: 10.1021/nn900468y     Document Type: Article

References (45)

1. Seeman, N. C. DNA Nanotechnology: Novel DNA Constructions. Annu. Rev. Biophys. Biomol. Struct. 1998, 27, 225-248.
2. Seeman, N. C. DNA in a Material World. Nature 2003, 421, 427-431.
3. Seeman, N. C. DNA Enables Nanoscale Control of the Structure of Matter. Q. Rev. Biophys. 2005, 38, 363-371.
4. Seeman, N. C. From Genes to Machines: DNA Nanomechanical Devices. Trends Biochem. Sci. 2005, 30, 119-125.
5. Ding, B.; Seeman, N. C. Operation of a DNA Robot Arm Inserted into a 2D DNA Crystalline Substrate. Science 2006, 314, 1583-1585.
6. Andersen, F. F.; Andersen, K. E.; Kusk, M.; Frohlich, R. F.; Westergaard, O.; Andersen, A. H.; Knudsen, B. R. Recombinogenic Flap Ligation Mediated by Human Topoisomerase I. J. Mol. Biol. 2003, 330, 235-246.
7. Liao, S.; Mao, C.; Birktoft, J. J.; Shuman, S.; Seeman, N. C. Resolution of Undistorted Symmetric Immobile DNA Junctions by Vaccinia Topoisomerase I. Biochemistry 2004, 43, 1520-1531.
8. Lee, J.; Tonozuka, T.; Jayaram, M. Mechanism of Active Site Exclusion in a Site-Specific Recombinase: Role of the DNA Substrate in Conferring Half-of-the-Sites Activity. Genes Dev. 1997, 11, 3061-3071.
9. Winfree, E.; Liu, F. R.; Wenzler, L. A.; Seeman, N. C. Design and Self-Assembly of Two-Dimensional DNA Crystals. Nature 1998, 394, 539-544.
10. Yan, H.; Park, S. H.; Finkelstein, G.; Reif, J. H.; LaBean, T. H. DNA-Templated Self-Assembly of Protein Arrays and Highly Conductive Nanowires. Science 2003, 301, 1882-1884.
11. Malo, J.; Mitchell, J. C.; Venien-Bryan, C.; Harris, J. R.; Wille, H.; Sherratt, D. J.; Turberfield, A. J. Engineering a 2D Protein-DNA Crystal. Angew. Chem., Int. Ed. 2005, 44, 3057-3061.
12. Rinker, S.; Liu, Y.; Yan, H. Two-Dimensional LNA/DNA Arrays: Estimation the Helicity of LNA/DNA Hybrid Duplex. Chem. Commun. 2006, 25, 2675-2677.
13. Rothemund, P. W. K. Folding DNA to Create Nano-Scale Shapes and Patterns. Nature 2006, 440, 297-302.
14. Chen, J. H.; Seeman, N. C. Synthesis from DNA of a Molecule with the Connectivity of a Cube. Nature 1991, 350, 631-633.
15. Zhang, Y.; Seeman, N. C. The Construction of a DNA Truncated Octahedron. J. Am. Chem. Soc. 1994, 116, 1661-1669.
16. Shih, W. M.; Quispe, J. D.; Joyce, G. F. A 1.7-Kilobase Single- Stranded DNA That Folds into a Nanoscale Octahedron. Nature 2004, 427, 618-621.
17. Goodman, R. P.; Schaap, A. T.; Tardin, C. F.; Erben, C. M.; Berry, R. M.; Schmidt, C. F.; Turberfield, A. J. Rapid Chiral Assembly of Rigid DNA Building Blocks for Molecular Nanofabrication. Science 2005, 310, 1661-1665.
18. Erben, C. M.; Goodman, R. P.; Turberfield, A. J. A Self- Assembled DNA Bipyramid. J. Am. Chem. Soc. 2007, 6, 6992-6993.
19. Aldaye, F. A.; Sleiman, H. F. Modular Access to Structurally Switchable 3D Discrete DNA Assemblies. J. Am. Chem. Soc. 2007, 129, 13376-13377.
20. Andersen, F. F.; Knudsen, B.; Oliveira, C. L.; Frøhlich R.F., Krüger , D.; Bungert, J.; Agbandje-McKenna, M.; McKenna, R.; Juul, S. Assembly and Structural Analysis of a Covalently Closed Nano-Scale DNA Cage. Nucleic Acids Res. 2008, 36, 1113-1119.
21. Maiti, P. K.; Pascal, T. A.; Vaidehi, N.; Goddard, W. A., III. The Stability of Seeman JX DNA Topoisomers of Paranemic Crossover (PX) Molecules as a Function of Crossover Number. Nucleic Acids Res. 2004, 32, 6047-6056.
22. Maiti, P. K.; Pascal, T. A.; Vaidehi, N.; Heo, J.; Goddard, W. A., III. Atomic-Level Simulations of Seeman DNA Nanostructures: the Paranemic Crossover in Salt Solution. Biophys. J. 2006, 90, 1463-1479.
23. Maiti, P. K.; Pascal, T. A.; Goddard, W. A., III. Understanding DNA Based Nanostructures. J. Nanosci. Nanotechnol. 2007, 7, 1712-1720.
24. Lankas, F.; Lavery, R.; Maddocks, J. H. Kinking Occurs during Molecular Dynamics Simulations of Small DNA Minicircles. Structure 2006, 14, 1527-1534.
25. Harris, S. A.; Laughton, C. A.; Liverpool, T. B. Mapping the Phase Diagram of the Writhe of DNA Nanocircles Using Atomistic Molecular Dynamics Simulations. Nucleic Acids Res. 2007, 36, 21-29.
26. Garcia, A. E. Large-Amplitude Nonlinear Motions in Proteins. Phys. Rev. Lett. 1992, 68, 2696-2699.
27. Falconi, M.; Oteri, F.; Eliseo, T.; Cicero, D. O.; Desideri, A. MD Simulations of Papillomavirus DNA-E2 Protein Complexes Hints at a Protein Structural Code for DNA Deformation. Biophys. J. 2008, 95, 1108-1117.
28. Chillemi, G.; Falconi, M.; Amadei, A.; Zimatore, G.; Desideri, A.; Di Nola, A. The Essential Dynamics of Cu, Zn Superoxide Dismutase: Suggestion of Inter-Subunit Communication. Biophys. J. 1997, 73, 1007-1018.
29. Arcangeli, C.; Bizzarri, A. R.; Cannistraro, S. Concerted Motions in Copper Plastocyanin and Azurin: An Essential Dynamics Study. Biophys. Chem. 2001, 90, 45-56.
30. Hess, B. Convergence of Sampling in Proteins Simulations. Phys. Rew. E 2002, 65, 31910-31920.
31. McCammon, J. A.; Harvey, S. C. Short Time Dynamics. Dynamics of Proteins and Nucleic Acids; Cambridge University Press: New York, 1987; pp 79-116.
32. Case, D. A.; Cheatham, T. E., III; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M.; Onufriev, A., Jr.; Simmerling, C.; Wang, B.; Woods, R. The AMBER Biomolecular Simulation Programs. J. Comput. Chem. 2005, 26, 1668-1688.
33. Duan, Y.; Wu, C.; Chowdhury, S.; Lee, M. C.; Xiong, G.; Zhang, W.; Yang, R.; Cieplak, P.; Luo, R.; Lee, T. A Point- Charge Force Field for Molecular Mechanics Simulations of Proteins. J. Comput. Chem. 2003, 24, 1999-2012.
34. Ponder, J. W.; Case, D. A. Force Fields for Protein Simulations. Adv. Protein Chem. 2003, 66, 27-85.
35. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. Comparison of Simple Potential Functions for Simulating Liquid Water. J. Chem. Phys. 1983, 79, 926-935.
36. Berendsen, H. J. C.; Postma, J. P. M.; van Gusteren, W. F.; Di Nola, A.; Haak, J. R. Molecular Dynamics with Coupling to an External Bath. J. Comput. Phys. 1984, 81, 3684-3690.
37. Darden, T.; York, D.; Pedersen, L. Particle Mesh Ewald an N · log(n) Method for Ewald Sums in Large Systems. J. Chem. Phys. 1993, 98, 10089-10092.
38. Cheatham, T. E.; Miller, J. L.; Fox, T.; Darden, T. A.; Kollman, P. A. Molecular Dynamics Simulation on Solvated Biomolecular Systems: The Particle Mesh Ewald Method Leads to Stable Trajectories of DNA, RNA and Proteins. J. Am. Chem. Soc. 1995, 117, 4193-4194.
39. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n- Alkanes. J. Comput. Phys. 1977, 23, 327-341.
40. Hess, B.; Kutzner, C.; van der Spoel, D.; Lindahl, E. GROMACS 4: Algorithms for Highly Efficient, Load- Balanced, and Scalable Molecular Simulation. J. Chem. Theory Comput. 2008, 4, 435-447.
41. Lavery, R.; Sklenar, H. Defining the Structure of Irregular Nucleic Acids: Conventions and Principles. J. Biomol. Struct. Dyn. 1989, 6, 655-667.
42. Hubbard, S. J.; Thornton, J. M. NACCESS; Department of Biochemistry and Molecular Biology, University College London, 1993.
43. Pedersen, J. S. A Flux- and Background-Optimized Version of the NanoSTAR Small-Angle X-ray Scattering Camera for Solution Scattering. J. Appl. Crystallogr. 2004, 37, 369-380.
44. Pedersen, J. S. Analysis of Small-Angle Scattering Data from Colloids and Polymer Solutions: Modeling and Least- Squares Fitting. Adv. Colloid Interface Sci. 1997, 70, 171-210.
45. Humphrey, W.; Dalke, A.; Schulten, K. VMDOVisual Molecular Dynamics. J. Mol. Graph. 1996, 14, 33-38.