RNA dactyloscopy

• Authors: Marta Gabryelska , Eliza Wyszko , Jan Barciszewski
• Languages of publication: EN

Abstracts

EN

Despite the wealth of data on RNA secondary structure, conformational dynamics and tertiary structure in vitro and in vivo, predicting RNA biological activity in cellular environments remains difficult. Here, we present a comparison between in silico RNA fingerprinting and published experimental data that sheds light on efficient design of the hammerhead ribozyme molecules with a high intracellular efficiency. Our method, which we call RNA dactyloscopy, is a reliable tool for assessing the catalytic properties, modeling and design of RNA.

Keywords

EN

hammerhead ribozyme; RNA tertiary structure; fingerprint

• Journal: Acta Biochimica Polonica
• Year: 2016
• Volume: 63
• Issue: 4
• Pages: 785-787

Dates

published

2016

received

2016-05-31

revised

2016-06-21

accepted

2016-08-05

(unknown)

2016-12-01

Contributors

author

Marta Gabryelska

• Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland
• Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom

author

Eliza Wyszko

• Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland

author

Jan Barciszewski

• Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznań, Poland

References

• Fedoruk-Wyszomirska A, Szymański M, Wyszko E, Barciszewska MZ, Barciszewski J (2009) Highly active low magnesium hammerhead ribozyme. J Biochem 145: 451-459. https://doi.org/10.1093/jb/mvn182.
• Gabryelska MM, Wyszko E, Szymański M, Popenda P, Barciszewski J (2013) Prediction of hammerhead ribozyme intracellular activity with the catalytic core fingerprint. Biochem J 451: 439-451. https://doi.org/10.1042/BJ20121761.
• Kato Y, Kuwabara T, Warashina M, Toda H, Taira K (2001) Relationships between the activities in vitro and in vivo of various kinds of ribozyme and their intracellular localization in mammalian cells. J Biol Chem 276: 15378-15385. https://doi.org/10.1074/jbc.M010570200.
• Kim Y, Cairns MJ, Marouga R, Sun L (2003) E6AP gene suppression and characterization with in vitro selected hammerhead ribozymes. Cancer Gene Ther 10: 707-716. https://doi.org/10.1038/sj.cgt.7700623.
• Lorenz R, Bernhart SH, Honer zu Siederdissen C, Tafer H, Flamm C, Stadler PF, Hofacker IL (2011) ViennaRNA Package 2.0. Algorithms Mol Biol 6: 26. https://doi.org/10.1186/1748-7188-6-26.
• Perreault J, Weinberg Z, Roth A, Popescu O, Chartrand P, Ferbeyre G, Breaker RR (2011) Identification of hammerhead ribozymes in all domains of life reveals novel structural variations. PloS Comput Biol 7: e1002031. https://doi.org/10.1371/journal.pcbi.1002031.
• Popenda M, Szachniuk M, Antczak M, Purzycka KJ, Lukasiak P, Bartol N, Blazewicz J, Adamiak RW (2012) Automated 3D structure composition for large RNAs. Nucleic Acids Res 40: e112. https://doi.org/10.1093/nar/gks339.
• Scherr M, Grez M, Ganser A, Engels JW (1997) Specific hammerhead ribozyme-mediated cleavage of mutant N-ras mRNA in vitro and ex vivo. Oligoribonucleotides as therapeutic agents. J Biol Chem 272: 14304-14313. https://doi.org/10.1074/jbc.272.22.14304.
• Westhof E, Masquida B, Jaeger L (1996) RNA tectonics: towards RNA design. Fold Des 1: R78-R88. https://doi.org/10.1016/S1359-0278(96)00037-5.

Identifiers

DOI

10.18388/abp.2016_1341