We bumped into bacterial Nudix pyrophosphohydrolase RppH which seems to do the same thing (RNA decapping). Does anyone has experience in using this enzyme for RNA processing for GRO-seq?
According to a recent patent from NEB (https://www.google.com/patents/US20120077230?dq=rpph+cap&hl=en&sa=X&ei=oFHzUbGNDsjmigLP-YH4CA&ved=0CDkQ6AEwAA) RppH should work instead of TAP, however the specific activity is about 100-fold lower, which negates the price advantage per volume. If you don't really care about sequencing the actual 5' end at base-pair resolution, you could use the A-tail/RT/circularization method published in Ingolia et al Science, 2009 for Ribo-Seq, or alternatively the 3' ligation/RT/circularization variant as described in their later paper on NET-Seq (Chruchman and Weissman, 2011, Nature). The former has been used successfully for GRO-Seq (Hah, Cell, 2011; Wang, Nature 2011), and the latter also works similarly well for RNA-Seq.
According to a recent patent from NEB (https://www.google.com/patents/US20120077230?dq=rpph+cap&hl=en&sa=X&ei=oFHzUbGNDsjmigLP-YH4CA&ved=0CDkQ6AEwAA) RppH should work instead of TAP, however the specific activity is about 100-fold lower, which negates the price advantage per volume. If you don't really care about sequencing the actual 5' end at base-pair resolution, you could use the A-tail/RT/circularization method published in Ingolia et al Science, 2009 for Ribo-Seq, or alternatively the 3' ligation/RT/circularization variant as described in their later paper on NET-Seq (Chruchman and Weissman, 2011, Nature). The former has been used successfully for GRO-Seq (Hah, Cell, 2011; Wang, Nature 2011), and the latter also works similarly well for RNA-Seq.
Are you looking for RNA decapping enzymes? Tobacco acid pyrophosphatase is out of the market right now. Here are some other alternatives for Tobacco acid pyrophosphatase . Check the following link for Tobacco Decapping Enzyme, human DCP2, and E.coli RppH
http://www.enzymax.net/mRNA_decapping_enzymes.htm
Many of the nudix family of proteins have been shown to have strong decapping activity. The most important part will be to be certain your enzyme is not contaminated with exonucleases. We have a new enzyme that will be released soon as a product. Contact me if you're interested.
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