Self-assembling RNA square

Proceedings of the National Academy of Sciences of the United States of America

Volumn 108, Issue 16, 2011, Pages 6405-6408

  Dibrov, Sergey M ^a   McLean, Jaime ^a   Parsons, Jerod ^a   Hermann, Thomas ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Crystallography; Fluorescence; RNA structure

Indexed keywords

DOUBLE STRANDED RNA; NANOMATERIAL; OLIGONUCLEOTIDE; UNTRANSLATED RNA; VIRUS RNA;

ARTICLE; CRYSTAL STRUCTURE; CRYSTALLIZATION; HEPATITIS C VIRUS; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HYBRIDIZATION; PRIORITY JOURNAL; PROTEIN ASSEMBLY; PROTEIN SECONDARY STRUCTURE; PROTEIN SYNTHESIS; RNA STRUCTURE; THREE DIMENSIONAL IMAGING;

CRYSTALLOGRAPHY, X-RAY; NUCLEIC ACID CONFORMATION; RNA;

EID: 79955591460     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.1017999108     Document Type: Article

References (23)

1. Holbrook SR, Cheong C, Tinoco I, Jr, Kim SH (1991) Crystal structure of an RNA double helix incorporating a track of non-Watson-Crick base pairs. Nature 353:579-581. (Pubitemid 21912562)
2. Woodson SA (2010) Compact intermediates in RNA folding. Annu Rev Biophys 39:61-77.
3. Jaeger L, Westhof E, Leontis NB (2001) TectoRNA: Modular assembly units for the construction of RNA nano-objects. Nucleic Acids Res 29:455-463. (Pubitemid 32060932)
4. Guo P (2005) RNA nanotechnology: Engineering, assembly and applications in detection, gene delivery and therapy. J Nanosci Nanotechnol 5:1964-1982.
5. Jaeger L, Chworos A (2006) The architectonics of programmable RNA and DNA nanostructures. Curr Opin Struct Biol 16:531-543. (Pubitemid 44149075)
6. Smalley MK, Silverman SK (2006) Fluorescence of covalently attached pyrene as a general RNA folding probe. Nucleic Acids Res 34:152-166. (Pubitemid 43160040)
7. Chworos A, et al. (2004) Building programmable jigsaw puzzles with RNA. Science 306:2068-2072. (Pubitemid 40007653)
8. Win MN, Liang JC, Smolke CD (2009) Frameworks for programming biological function through RNA parts and devices. Chem Biol 16:298-310.
9. Rothemund PW (2006) Folding DNA to create nanoscale shapes and patterns. Nature 440:297-302.
10. Seeman NC (2010) Nanomaterials based on DNA. Annu Rev Biochem 79:65-87.
11. Shapiro BA, Bindewald E, Kasprzak W, Yingling Y (2008) Protocols for the in silico design of RNA nanostructures. Methods Mol Biol 474:93-115.
12. Jaeger L (2009) Defining the syntax for self-assembling RNA tertiary architectures. Nucleic Acids Symp Ser (Oxf) 53:83-84.
13. Severcan I, Geary C, Verzemnieks E, Chworos A, Jaeger L (2009) Square-shaped RNA particles from different RNA folds. Nano Lett 9:1270-1277.
14. Afonin KA, et al. (2010) In vitro assembly of cubic RNA-based scaffolds designed in silico. Nat Nanotechnol 5:676-682.
15. Dibrov SM, Johnston-Cox H, Weng YH, Hermann T (2007) Functional architecture of HCV IRES domain II stabilized by divalent metal ions in the crystal and in solution. Angew Chem Int Ed Engl 46:226-229. (Pubitemid 46071706)
16. Parsons J, et al. (2009) Conformational inhibition of the hepatitis C virus internal ribosome entry site RNA. Nat Chem Biol 5:823-825.
17. Lukavsky PJ, Kim I, Otto GA, Puglisi JD (2003) Structure of HCV IRES domain II determined by NMR. Nat Struct Biol 10:1033-1038. (Pubitemid 37500496)
18. Spahn CM, et al. (2001) Hepatitis C virus IRES RNA-induced changes in the conformation of the 40s ribosomal subunit. Science 291:1959-1962. (Pubitemid 32216995)
19. Otwinowski Z, Minor W (1997) Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol 276:307-326. (Pubitemid 27085611)
20. Adams PD, et al. (2002) PHENIX: Building new software for automated crystallographic structure determination. Acta Crystallogr D Biol Crystallogr 58:1948-1954. (Pubitemid 35337293)
21. Murshudov GN, Vagin AA, Dodson EJ (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr D Biol Crystallogr 53:240-255. (Pubitemid 27235885)
22. Collaborative Computational Project, N (1994) The CCP4 suite: Programs for protein crystallography. Acta Crystallogr D Biol Crystallogr 50:760-763.
23. Emsley P, Cowtan K (2004) Coot: Model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60:2126-2132. (Pubitemid 41742764)