Cis-Acting 5' Hammerhead ribozyme optimization for in vitro transcription of highly structured RNAs

Methods in Molecular Biology

Volumn 1086, Issue , 2014, Pages 21-40

  Meyer, Mélanie ^a   Masquida, Benoît ^a  

^a UNIVERSITÉ DE STRASBOURG   (France)

Author keywords

In vitro transcription; Lariat capping GIR1 ribozyme; Ribozymes; RNA folding; RNA tertiary interactions

Indexed keywords

HAMMERHEAD RIBOZYME; RNA;

5' UNTRANSLATED REGION; ARTICLE; ENZYME KINETICS; IN VITRO STUDY; PRIORITY JOURNAL; PROTEIN CLEAVAGE; RNA FOLDING; RNA TRANSCRIPTION;

HEPATITIS DELTA VIRUS;

ANIMALS; BASE SEQUENCE; BLOTTING, NORTHERN; CLONING, MOLECULAR; COMPUTER SIMULATION; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; NUCLEIC ACID CONFORMATION; RECOMBINANT FUSION PROTEINS; RNA; RNA, CATALYTIC; RNA, HELMINTH; SCHISTOSOMA; SOFTWARE; TRANSCRIPTION, GENETIC;

EID: 84934436067     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-62703-667-2_2     Document Type: Article

References (22)

1. Fedor MJ, Uhlenbeck OC (1990) Substrate sequence effects on "hammerhead" RNA catalytic effi ciency. Proc Natl Acad Sci USA 87:1668-1672
2. Khvorova A, Lescoute A, Westhof E et al (2003) Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity. Nat Struct Biol 10:708-712
3. Martick M, Scott WG (2006) Tertiary contacts distant from the active site prime a ribozyme for catalysis. Cell 126:309-320
4. Pley HW, Flaherty KM, McKay DB (1994) Three-dimensional structure of a hammerhead ribozyme. Nature 372:68-74
5. Scott WG, Finch JT, Klug A (1995) The crystal structure of an all-RNA hammerhead ribozyme: a proposed mechanism for RNA catalytic cleavage. Cell 81:991-1002
6. Rupert PB, Ferre-D'Amare AR (2001) Crystal structure of a hairpin ribozyme-inhibitor complex with implications for catalysis. Nature 410:780-786
7. Lacroix-Labonte J, Girard N, Lemieux S et al (2012) Helix-length compensation studies reveal the adaptability of the VS ribozyme architecture. Nucleic Acids Res 40: 2284-2293
8. Masquida B, Beckert B, Jossinet F (2010) Exploring RNA structure by integrative molecular modelling. N Biotechnol 27:170-183
9. Helm M, Brule H, Giege R et al (1999) More mistakes by T7 RNA polymerase at the 5 ends of in vitro-transcribed RNAs. RNA 5:618-621
10. Milligan JF, Uhlenbeck OC (1989) Synthesis of small RNAs using T7 RNA polymerase. Methods Enzymol 180:51-62
11. Solomatin S, Herschlag D (2009) Methods of site-specifi c labeling of RNA with fl uorescent dyes. Methods Enzymol 469:47-68
12. Beckert B, Masquida B (2011) Synthesis of RNA by in vitro transcription. Methods Mol Biol 703:29-41
13. Price SR, Ito N, Oubridge C et al (1995) Crystallization of RNA-protein complexes I. Methods for the large-scale preparation of RNA suitable for crystallographic studies. J Mol Biol 249:398-408
14. Fechter P, Rudinger J, Giege R et al (1998) Ribozyme processed tRNA transcripts with unfriendly internal promoter for T7 RNA polymerase: production and activity. FEBS Lett 436:99-103
15. Mörl M, Lizano E, Willkomm DK et al (2005) Production of RNAs with homogenous 5 and 3 ends. In: Hartmann RK, Bindereif A, Westhof E (eds) Handbook of RNA biochemistry, Wiley VCH Verlag Gmbh & Co, Weinheim, Germany, vol 1. pp 22-35
16. Ferré-D'Amaré AR, Doudna JA (1996) Use of cis-and trans-ribozymes to remove 5? and 3? heterogeneities from milligrams of in vitro transcribed RNA. Nucleic Acids Res 24:977-978
17. Nielsen H, Westhof E, Johansen S (2005) An mRNA is capped by a 2?, 5? lariat catalyzed by a group I-like ribozyme. Science 309: 1584-1587
18. Hofacker IL, Fontana W, Stadler PF et al (1994) Fast folding and comparison of RNA secondary structures. Monatshefte für Chemie/Chemical Monthly 125:167-188
19. Canny MD, Jucker FM, Kellogg E et al (2004) Fast cleavage kinetics of a natural hammerhead ribozyme. J Am Chem Soc 126: 10848-10849
20. Ichetovkin IE, Abramochkin G, Shrader TE (1997) Substrate recognition by the leucyl/phenylalanyl-tRNA-protein transferase. Conservation within the enzyme family and localization to the trypsin-resistant domain. J Biol Chem 272:33009-33014
21. Milligan JF, Groebe DR, Witherell GW et al (1987) Oligoribonucleotide synthesis using T7 RNA polymerase and synthetic DNA templates. Nucleic Acids Res 15:8783-8798
22. Jossinet F, Ludwig TE, Westhof E (2010) Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels. Bioinformatics 26:2057-2059