PL EN


Preferences help
enabled [disable] Abstract
Number of results
2016 | 63 | 4 | 785-787
Article title

RNA dactyloscopy

Content
Title variants
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.
Year
Volume
63
Issue
4
Pages
785-787
Physical description
Dates
published
2016
received
2016-05-31
revised
2016-06-21
accepted
2016-08-05
(unknown)
2016-12-01
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.
Document Type
Publication order reference
YADDA identifier
bwmeta1.element.bwnjournal-article-abpv63p785kz
Identifiers
JavaScript is turned off in your web browser. Turn it on to take full advantage of this site, then refresh the page.