Adjustable ellipsoid nanoparticles assembled from re-engineered connectors of the bacteriophage Phi29 DNA packaging motor

ACS Nano

Volumn 3, Issue 8, 2009, Pages 2163-2170

  Xiao, Feng ^a   Cai, Ying ^a,d   Wang, Joseph Che Yen ^b   Green, Dominik ^b   Cheng, R Holland ^b   Demeler, Borries ^c   Guo, Peixuan ^a  

^a 705 Engineering Research Center   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c University of Texas Health Science Center   (United States)

^d VGX Pharmaceuticals Inc   (United States)

Author keywords

Bacteriophage phi29 connector; Bionanotechnology; Nanobiotechnology; Phi29 DNA packaging motor; Protein nanoparticles; Viral DNA packaging; Virus assemble

Indexed keywords

ANALYTICAL ULTRACENTRIFUGATION; BACTERIOPHAGE PHI29; BACTERIOPHAGE PHI29 CONNECTOR; BINDING PEPTIDE; BIONANOTECHNOLOGY; CORE PROTEINS; DISEASE DIAGNOSIS; DNA-PACKAGING MOTOR; DODECAMER; HOMOGENEOUS NANOPARTICLES; N-TERMINALS; ONE-STEP PURIFICATION; PACKAGING MOTORS; PATHOGEN DETECTION; PHI29 DNA PACKAGING MOTOR; SIGNAL ENHANCEMENT; STREPTAVIDIN; VIRAL DNA PACKAGING;

AMINES; BACTERIOPHAGES; CENTRIFUGATION; DIAGNOSIS; DNA; GENES; MOTORS; NANOBIOTECHNOLOGY; NUCLEIC ACIDS; PEPTIDES;

NANOPARTICLES;

NANOPARTICLE; PEPTIDE; PEPTIDE HYDROLASE; VIRUS DNA;

ALGORITHM; ARTICLE; BACTERIOPHAGE; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; DNA PACKAGING; GENETICS; MONTE CARLO METHOD; TRANSMISSION ELECTRON MICROSCOPY; ULTRASTRUCTURE;

ALGORITHMS; BACTERIOPHAGES; DNA PACKAGING; DNA, VIRAL; MICROSCOPY, ELECTRON, TRANSMISSION; MODELS, MOLECULAR; MONTE CARLO METHOD; NANOPARTICLES; NUCLEIC ACID CONFORMATION; PEPTIDE HYDROLASES; PEPTIDES;

EID: 69549108609     PISSN: 19360851     EISSN: 1936086X     Source Type: Journal    
DOI: 10.1021/nn900187k     Document Type: Article

References (42)

1. Niemeyer, C. M. Nanoparticles, Proteins, and Nucleic Acids: Biotechnology Meets Materials Science. Angew. Chem., Int. Ed. 2001, 40, 4128-4158.
2. Seeman, N. C. DNA In A Material World. Nature 2003, 421, 427-431.
3. Guo, P. RNA Nanotechnology: Engineering, Assembly, and Applications in Detection, Gene Delivery, and Therapy. J. Nanosci. Nanotechnol. 2005, 5, 1964-1982.
4. Rothemund, P. W. K. Folding DNA to Create Nanoscale Shapes and Patterns. Nature 2006, 440, 297-302.
5. Shu, D.; Moll, D.; Deng, Z.; Mao, C.; Guo, P. Bottom-Up Assembly of RNA Arrays and Superstructures as Potential Parts in Nanotechnology. Nano Lett. 2004, 4, 1717-1724.
6. Chworos, A.; Severcan, I.; Koyfman, A. Y.; Weinkam, P.; Oroudjev, E.; Hansma, H. G.; Jaeger, L. Building Programmable Jigsaw Puzzles with RNA. Science 2004, 306, 2068-2072.
7. Shu, D.; Huang, L.; Hoeprich, S.; Guo, P. Construction of Phi29 DNA-Packaging RNA (pRNA) Monomers, Dimers, and Trimers with Variable Sizes and Shapes as Potential Parts for Nano-Devices. J. Nanosci. Nanotechnol. 2003, 3, 295-302.
8. Zhang, F.; Lemieux, S.; Wu, X.; St.-Arnaud, S.; McMurray, C. T.; Major, F.; Anderson, D. Function of Hexameric RNA in Packaging of Bacteriophage Phi29 DNA in vitro. Mol. Cell. 1998, 2, 141-147. (Pubitemid 128378976)
9. Guo, P.; Zhang, C.; Chen, C.; Trottier, M.; Garver, K. Inter- RNA Interaction of Phage Phi29 pRNA to Form a Hexameric Complex for Viral DNA Transportation. Mol. Cell 1998, 2, 149-155.
10. Perez, J. M.; Simeone, F. J.; Saeki, Y.; Josephson, L.; Weissleder, R. Viral-Induced Self-Assembly of Magnetic Nanoparticles Allows the Detection of Viral Particles in Biological Media. J. Am. Chem. Soc. 2003, 125, 10192-10193.
11. Mao, C.; Flynn, C. E.; Hayhurst, A.; Sweeney, R.; Qi, J.; Georgiou, G.; Iverson, B.; Belcher, A. M. Viral Assembly of Oriented Quantum Dot Nanowires. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 6946-6951.
12. Guo, Y.; Blocker, F.; Xiao, F.; Guo, P. Construction and 3-D Computer Modeling of Connector Arrays with Tetragonal to Decagonal Transition Induced by pRNA of Phi29 DNA Packaging Motor. J. Nanosci. Nanotechnol. 2005, 5, 856-863.
13. Xiao, F.; Sun, J.; Coban, O.; Schoen, P.; Wang, J. C.; Cheng, R. H.; Guo, P. Fabrication of Massive Sheets of Single Layer Patterned Arrays Using Re-engineered Phi29 Motor Dodecamer. ACS Nano 2009, 3, 100-107.
14. Moll, D.; Huber, C.; Schlegel, B.; Pum, D.; Sleytr, U. B.; Sara, M. S-Layer-Streptavidin Fusion Proteins as Template for Nanopatterned Molecular Arrays. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 14646-14651.
15. Sára, M.; Pum, D.; Schuster, B.; Sleytr, U. B. S-Layers as Patterning Elements for Application in Nanobiotechnology. J. Nanosci. Nanotechnol. 2005, 5, 1939-1953.
16. Sleytr, U. B.; Sara, M. Bacterial and Archaeal S-Layer Proteins: Structure-Function Relationships and Their Biotechnological Applications. Trends Biotechnol. 1997, 15, 20-26.
17. Gentilucci, L.; Tolomelli, A.; Squassabia, F. Peptides and Peptidomimetics in Medicine, Surgery and Biotechnology. Curr. Med. Chem. 2006, 13, 2449-2466.
18. Guo, P.; Grimes, S.; Anderson, D. A Defined System for in Vitro Packaging of DNA-gp3 of the Bacillus Subtilis Bacteriophage Phi29. Proc. Natl. Acad. Sci. U.S.A. 1986, 83, 3505-3509.
19. Simpson, A. A.; Leiman, P. G.; Tao, Y.; He, Y.; Badasso, M. O.; Jardine, P. J.; Anderson, D. L.; Rossman, M. G. Structure Determination of the Head-Tail Connector of Bacteriophage Phi29. Acta Crystallogr. 2001, D57, 1260-1269.
20. Guasch, A.; Pous, J.; Ibarra, B.; Gomis-Ruth, F. X.; Valpuesta, J. M.; Sousa, N.; Carrascosa, J. L.; Coll, M. Detailed Architecture of a DNA Translocating Machine: The High- Resolution Structure of the Bacteriophage Phi29 Connector Particle. J. Mol. Biol. 2002, 315, 663-676.
21. Tsuprun, V.; Anderson, D.; Egelman, E. H. The Bacteriophage Phi29 Head-Tail Connector Shows 13-Fold Symmetry in Both Hexagonally Packed Arrays and as Single Particles. Biophys. J. 1994, 66, 2139-2150.
22. Garver, K.; Guo, P. Boundary of pRNA Functional Domains and Minimum pRNA Sequence Requirement for Specific Connector Binding and DNA Packaging of Phage Phi29. RNA 1997, 3, 1068-1079.
23. Maier, T.; Drapal, N.; Thanbichler, M.; Bock, A. Strep-Tag II Affinity Purification: An Approach to Study Intermediates of Metalloenzyme Biosynthesis. Anal. Biochem. 1998, 259, 68-73.
24. Voss, S.; Skerra, A. Mutagenesis of a Flexible Loop in Streptavidin Leads to Higher Affinity for the Strep-Tag II Peptide and Improved Performance in Recombinant Protein Purification. Protein Eng. 1997, 10 (8), 975-982.
25. Schmidt, T. G. M.; Skerra, A. The Strep-Tag System for One- Step Purification and High-Affinity Detection or Capturing of Proteins. Nat. Protoc. 2007, 2, 1528-1535.
26. Brookes, E.; Demeler, B. Parallel Computational Techniques for the Analysis of Sedimentation Velocity Experiments in Ultrascan. Colloid Polym. Sci. 2008, 286, 139-148.
27. Demeler, B.; van Holde, K. E. Sedimentation Velocity Analysis of Highly Heterogeneous Systems. Anal. Biochem. 2004, 335, 279-288.
28. Lamm, O. Die Differentialgleichung der Ultrazentrifugierung. Ark. Mat. Astr. Fys. 1929, 21B, 1-4.
29. Brookes, E.; Demeler, B. Parsimonious Regularization Using Genetic Algorithms Applied to the Analysis of Analytical Ultracentrifugation Experiments. In GECCO Proceedings, ACM 978-1-59593-697-1/07/0007, 2007.
30. Demeler, B.; Brookes, E. Monte Carlo Analysis of Sedimentation Experiments. Colloid Polym. Sci. 2008, 286, 129-137.
31. Burley, S. K.; Petsko, G. A. Aromatic-Aromatic Interaction-A Mechanism of Protein-Structure Stabilization. Science 1985, 229, 23-28.
32. Tewari, A. K.; Dubey, R. Emerging Trends in Molecular Recognition: Utility of Weak Aromatic Interactions. Bioorg. Med. Chem. 2008, 16, 126-143.
33. Blakaj, D. M.; McConnell, K. J.; Beveridge, D. L.; Baranger, A. M. Molecular Dynamics and Thermodynamics of Protein-RNA Interactions: Mutation of a Conserved Aromatic Residue Modifies Stacking Interactions and Structural Adaptation in the U1A-Stem Loop 2 RNA Complex. J. Am. Chem. Soc. 2001, 123, 2548-2551.
34. Shiels, J. C.; Tuite, J. B.; Nolan, S. J.; Baranger, A. M. Investigation of a Conserved Stacking Interaction in Target Site Recognition by the U1A Protein. Nucleic Acids Res. 2002, 30, 550-558.
35. Studier, F. W.; Rosenberg, A. H.; Dunn, J. J.; Dubendorff, J. W. Use of T7 RNA Polymerase to Direct the Expression of Cloned Genes. Methods Enzymol. 1990, 185, 60-89.
36. Guo, P.; Moss, B. Interaction and Mutual Stabilization of the Two Subunits of Vaccinia Virus Mrna Capping Enzyme Co-Expressed in Escherichia Coli. Proc. Natl. Acad. Sci. U.S.A. 1990, 87, 4023-4027.
37. Demeler, B. A Comprehensive Data Analysis Software Package for Analytical Ultracentrifugation Experiments. In Modern Analytical Ultracentrifugation: Techniques and Methods; Scott, D. J., Harding, S. E., Rowe, A. J. Eds.; Royal Society of Chemistry: U.K. 2005; pp 210-229.
38. Cao, W. M.; Demeler, B. Modeling Analytical Ultracentrifugation Experiments with an Adaptive Space-Time Finite Element Solution of the Lamm Equation. Biophys. J. 2005, 89, 1589-1602.
39. Durchschlag, H. Thermodynamic Data for Biochemistry and Biotechnology; Springer-Verlag, New York, 1986.
40. Brookes, E.; Boppana, R. V.; Demeler, B. Computing Large Sparse Multivariate Optimization Problems with an Application in Biophysics. Supercomputing '06, ACM 0-7695-2700-0/06 2006.
41. Schuck, P.; Demeler, B. Direct Sedimentation Analysis of Interference Optical Data in Analytical Ultracentrifugation. Biophys. J. 1999, 76, 2288-2296. (Pubitemid 29266382)
42. Brookes, E.; Demeler, B. Analytical Ultracentrifugation VIII. In Progress in Colloid Polymer Science, Wandrey, C., Colfen, H., Eds.: Springer, New York, 2006; pp 78-82.