A New Fast RNA Folding Program Distinguishes mRNAs From Introns

Connectron RNA sources and iRNAs that come in Pareto distributions (i.e. many with short lengths and few with long lengths) must be extracted from larger transcripts.  A new RNA folding program – FastRNA – rapidly makes plausible folds for RNAs of all types (i.e. viruses, introns and mRNAs) and lengths (i.e. 12kb in 2 minutes and 67kb in 80 minutes). 

When introns are freed from a transcript, they fold so that many long stems (i.e. reverse complemented pairs of sequences) form.  Dicer cuts any RNA with stems 20-base pairs or longer into three new RNAs which themselves can refold.  Acting in this fashion, Dicer recursively turns any intron into a collection of short and long fragments.  The short fragments can be the Connectron sources and the iRNAs.

FastRNA shows that mRNAs fold in a way that is different from the way introns fold.  Introns have many Dicer stems that produce three fragments for each dicer clip whereas the mRNAs have fewer Dicer segments and produce fewer fragments per Dicer action.

The folded RNAs can be viewed in 3D with KiNG from Duke University.  The images bring beauty to the eye and plausibility to the mind!

FastRNA is available for download for Macs, PCs and Unix machines on Facebook.  Search for FastRNA and click on TransferBigFiles.