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Juliette M. Stenz, Jack M. Sullivan; A Hammerhead Ribozyme Database. Invest. Ophthalmol. Vis. Sci. 2012;53(14):5126.
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A bioinformatics study was conducted to develop a database (DB) of hammerhead ribozymes (hhRz) from published literature.
A PubMed query with keyword "hhRz" was performed. Criteria for entry in the DB were: (i) efficacy of hhRz was tested in vitro, and/or in cellulo, and/or in vivo; (ii) efficacy of independent hhRz agents targeting NUH sites was quantifiable through extent of RNA cleavage, mRNA and/or protein knockdown, or quantifiable changes in kinetic parameters; (iii) at least 5 target cleavage sights were tested in each mRNA;(iv) at least one control experiment with scrambled, mismatched, or null hhRz sequence;(v) articles were published in the English language which allowed review by the authors. A rational DB was designed and key information was mined from the included articles and entered in the DB.
The PubMed query returned 951 articles, and 10 met the inclusion criteria. An additional 4 articles and one doctoral dissertation recommended by JMS were also included for a total of 15 articles. The title, author, journal, and date of each article are included in the DB. The hhRz sequence and target mRNA information were included. For in vitro or in cellulo studies the extent of target mRNA cleavage and/or protein knockdown was included. When available, Kcat or Km was also included.
The hhRz DB (Version 1) is a bioinformatics tool intended to assist in selection of optimal NUH hhRz cleavage sights for therapeutic development. Surprisingly, only a small percentage of hhRz studies evaluated cleavage efficacy or knockdown of targets at a substantial number of potential cleavage sites (5) throughout each mRNA. Such information is needed to better assess and refine rules for NUH target site selection. The current data set could be combined with in silico RNA folding or experimental RNA accessibility analysis to correlate with measured knockdown efficacy. The DB can be refined as more studies are conducted and represented in the literature.
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