How to find an RNA –or more precisely, how to tell your computer to find an RNA

Now that I told you that finding a non-coding RNA gene can be difficult…in fact you can find some classes rather easily. It all comes down to computer programming. Computers are great. If you tell them what you want in clear and precise ways they will go out and find it and leave you to have a nice cup of coffee. However, it is up to you to tell them the right directions and that is the tricky part of finding RNAs. When we know what to look for –secondary structure and sequence motifs – we can find them.  Take for example a transfer RNA, the non-coding RNA that delivers amino acids to the ribosome to convert the message in mRNA into proteins. It has a very clear secondary structure (often called the clover-leaf structure because of its shape – see the diagram below).  The fun part is converting the human-readable structure into a code that the computer can look for, we do this using what is called ‘bracket notation’ where the paired nucleotides are represented by brackets and the unpaired by dots. If you go around the tRNA structure from 5’ end (on the right top) to 3’ (left top) the sequence and structure looks like this (with the bases that can change being called N and D stands for any nucleotide that is not a C):

GGACGUGUNGCGCGUAGDCGGDAGCGCNCUCCCUUGGCNNGGGAGAGGNCUCCGGTNCGAUUCCGGACUCGUCCACCA

(((((((..((((..........)))).(((((.......))))).....(((((.......))))))))))))....

You can see there are four regions of pairings (or stacks) represented by the open and closed brackets. These combinations can get very complicated but usually the computer software can work it out. Once you have this structure you are on the way to searching a long piece of DNA to see if that structure is contained within.

For those of you who would like to play a little with RNA structure head to the VARNA software site  http://varna.lri.fr/demo.html  (you will need to have an up to date version of Java installed for this to run). Remember if you change an opening bracket on one side of a stack then you will need to change the corresponding closing bracket. Try dragging the stacks around and have some fun!!!

http://www.wiley.com/college/boyer/0470003790/structure/tRNA/trna_intro.htm