Large scale purification of RNA nanoparticles by preparative ultracentrifugation

Methods in Molecular Biology

Volumn 1297, Issue , 2015, Pages 67-82

  Jasinski, Daniel L ^a   Schwartz, Chad T ^a   Haque, Farzin ^a   Guo, Peixuan ^a  

^a NONE

Author keywords

Large scale purification; Nanobiotechnology; Nanoparticles; Nanotechnology; RNA; RNA nanotechnology; RNA therapeutics; Ultracentrifugation

Indexed keywords

BACTERIOPHAGE DNA; CESIUM CHLORIDE; NANOPARTICLE; RNA; RNA NANOPARTICLE; RNA POLYMERASE; UNCLASSIFIED DRUG; BACTERIOPHAGE T7 RNA POLYMERASE; CESIUM; CHLORIDE; DNA DIRECTED RNA POLYMERASE; VIRUS PROTEIN;

AGAR GEL ELECTROPHORESIS; ANALYTIC METHOD; ARTICLE; DENSITY GRADIENT CENTRIFUGATION; DNA PACKAGING; EQUILIBRIUM CONSTANT; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; IN VITRO STUDY; IN VIVO STUDY; MOLECULAR BIOLOGY; MOLECULAR INTERACTION; POLYACRYLAMIDE GEL ELECTROPHORESIS; PRIORITY JOURNAL; RNA PURIFICATION; RNA STRUCTURE; RNA TRANSCRIPTION; SUCROSE GRADIENT; SYNTHESIS; ULTRACENTRIFUGATION; CHEMISTRY; GENETICS; ISOLATION AND PURIFICATION; PROCEDURES; SIZE EXCLUSION CHROMATOGRAPHY;

CENTRIFUGATION, DENSITY GRADIENT; CESIUM; CHLORIDES; CHROMATOGRAPHY, GEL; CHROMATOGRAPHY, HIGH PRESSURE LIQUID; DNA-DIRECTED RNA POLYMERASES; NANOPARTICLES; RNA; ULTRACENTRIFUGATION; VIRAL PROTEINS;

EID: 84928485094     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-2562-9_5     Document Type: Article

References (29)

1. Guo P, Zhang C, Chen C et al (1998) Inter-RNA interaction of phage phi29 pRNA to form a hexameric complex for viral DNA transportation. Mol Cell 2:149–155
2. Mitra S, Shcherbakova IV, Altman RB et al (2008) High-throughput single-nucleotide structural mapping by capillary automated footprinting analysis. Nucleic Acids Res 36:e63
3. Guo P, Haque F, Hallahan B et al (2012) Uniqueness, advantages, challenges, solutions, and perspectives in therapeutics applying RNA nanotechnology. Nucleic Acid Ther 22: 226–245
4. Khisamutdinov EF, Jasinski DL, Guo P (2014) RNA as a boiling-resistant anionic polymer material to build robust structures with defined shape and stoichiometry. ACS Nano 8:4771–4781
5. Khisamutdinov E, Li H, Jasinski D et al (2014) Enhancing immunomodulation on innate immunity by shape transition among RNA triangle, square, and pentagon nanovehicles. Nucleic Acids Res 42:9996–10004
6. Jasinski D, Khisamutdinov EF, Lyubchenko YL et al (2014) Physicochemically tunable poly-functionalized RNA square architecture with fluorogenic and ribozymatic properties. ACS Nano 8:7620–7629
7. Shu Y, Haque F, Shu D et al (2013) Fabrication of 14 different rna nanoparticles for specific tumor targeting without accumulation in normal organs. RNA 19:766–777
8. Shu Y, Shu D, Haque F et al (2013) Fabrication of pRNA nanoparticles to deliver therapeutic RNAs and bioactive compounds into tumor cells. Nat Protoc 8:1635–1659
9. Shu Y, Cinier M, Shu D et al (2011) Assembly of multifunctional phi29 pRNA nanoparticles for specific delivery of siRNA and other therapeutics to targeted cells. Methods 54: 204–214
10. Liu J, Guo S, Cinier M et al (2010) Fabrication of stable and RNase-resistant RNA nanoparticles active in gearing the nanomotors for viral DNA packaging. ACS Nano 5:237–246
11. Haque F, Shu D, Shu Y et al (2012) Ultrastable synergistic tetravalent RNA nanoparticles for targeting to cancers. Nano Today 7:245–257
12. Shukla GC, Haque F, Tor Y et al (2011) A boost for the emerging field of RNA nanotechnology. ACS Nano 5:3405–3418
13. Shu Y, Pi F, Sharma A et al (2014) Stable RNA nanoparticles as potential new generation drugs for cancer therapy. Adv Drug Deliv Rev 66C:74–89
14. Leontis N, Sweeney B, Haque F et al (2013) Conference scene: advances in RNA nanotechnology promise to transform medicine. Nanomedicine 8:1051–1054
15. Trautmann L, Janbazian L, Chomont N et al (2006) Upregulation of PD-1 expression on HIV-specific CD8+ T cells leads to reversible immune dysfunction. Nat Med 12: 1198–1202
16. Guo P (2010) The emerging field of RNA nanotechnology. Nat Nanotechnol 5:833–842
17. Zassenhaus HP, Butow RA, Hannon YP (1982) Rapid electroelution of nucleic-acids from agarose and acrylamide gels. Anal Biochem 125:125–130
18. Anderson AC, Scaringe SA, Earp BE et al (1996) HPLC purification of RNA for crystallography and NMR. RNA 2:110–117
19. Glisin V, Crkvenjar R, Byus C (1974) Ribonucleic-acid isolated by cesium-chloride centrifugation. Biochemistry 13:2633–2637
20. Ali A, Roossinck MJ (2007) Rapid and efficient purification of Cowpea chlorotic mottle virus by sucrose cushion ultracentrifugation. J Virol Methods 141:84–86
21. Higashi K, Narayana KS, Adams HR et al (1966) Utilization of citric acid procedure and zonal ultracentrifugation for mass isolation of nuclear RNA from Walker 256 carcinosarcoma. Cancer Res 26:1582–1590
22. Lin CX, Perrault SD, Kwak M et al (2013) Purification of DNA-origami nanostructures by rate-zonal centrifugation. Nucleic Acids Res 41:e40
23. Eikenber EF, Bickle TA, Traut RR et al (1970) Separation of large quantities of ribosomal subunits by zonal ultracentrifugation. Eur J Biochem 12:113–116
24. Patsch JR, Sailer S, Kostner G et al (1974) Separation of main lipoprotein density classes from human plasma by rate-zonal ultracentrifugation. J Lipid Res 15:356–366
25. Guo P, Erickson S, Anderson D (1987) A small viral RNA is required for in vitro packaging of bacteriophage phi29 DNA. Science 236: 690–694
26. Guo P, Shu Y, Binzel D et al (2012) Synthesis, conjugation, and labeling of multifunctional pRNA nanoparticles for specific delivery of siRNA, drugs and other therapeutics to target cells. Methods Mol Biol 928:197–219
27. Shu D, Moll WD, Deng Z et al (2004) Bottom-up assembly of RNA arrays and superstructures as potential parts in nanotechnology. Nano Lett 4:1717–1723
28. Shu D, Huang L, Hoeprich S et al (2003) Construction of phi29 DNA-packaging RNA (pRNA) monomers, dimers and trimers with variable sizes and shapes as potential parts for nanodevices. J Nanosci Nanotechnol 3:295–302
29. Ando H, Watanabe S, Ohwaki T, Miyake Y (1985) Crystallization of excipients in tablets. J Pharm Sci 74:128–131