Method used for analysing the structure of RNA

General Science Discussion
1

Hello I’ve enjoyed the game for 4-5 days. I have been wondering what method you use to analyze the secondary structure of the synthesized RNA sequences.

2

Hi exutu!

Welcome in our game. There are some of different approaches on how to analyse the data that we use. I assume you are asking to lab designs.

  • We look at what were succesful in the past labs

  • We look for color patterns/repetition, good and bad

  • We use the inbuild tools in eterna, like dot plot and melt plot

  • We use outside tools like RNAfold, Sfold, Nupack, InfoRNA, mfold and RNALocopt. There is many more.

Some use all of the above approaches, other just some and there are propably other methods I haven’t mentioned.

Here is a page with links to some of them

Here is a guide to on how to use Vienna.

Vienna is propably the RNA sequence analysis tool that is closest to our game, as it is made by the same guys who made the energy model Eterna run on. When you find a new RNA sequence analysis tool, try run some of the good designs and some of the bad designs through it. That way you can get an idea about how reliable the tool is. In my oppinion Vienna is the best there is so far, and it is not good enough. Other players have other favorites. Our best lab designer, Mat, refuses to use the outside tools. He said some time back: I’m getting skeptical of bots, they are like using a GPS with the wrong map data.

Also remember, the most interesting is not if a program says a RNA design is good or bad. The most interesting thing is if you can find a pattern in what is good or bad. But tools like Vienna can be a help in spotting bad sites and design. If you use them be skeptical.

Good luck with your designing!

3

Thank you.
It wasn’t exactly what I was trying to say. English isn’t my first language so I will try to reformulate.
I actually mean what is the method (or methods) by which you analyze the structure of the RNA which physically are synthesized in the laboratory. Hope it makes sense.

4

Hi Exutu!

I’m not quite sure if this is what you are after. But here is a couple of forum posts on how the RNA gets handled in the lab.

This one is on our new and comming lab.

5

Thanks that was perfect :slight_smile:
It was Selective 2’-hydroxyl acylation analyzed by primer extension (SHAPE) I was after :slight_smile:

6

If you’re interested, the wikipedia article on nucleic acid structure determination has a section on SHAPE, as well as some other chemical mapping techniques.

7

Thank you :slight_smile:
Though if anyone is interested in additional reading there is a protocol for doing shapes in one of the threads Eli Fisker refers to:
http://www.chem.unc.edu/rna/pdf-files…

8

Hi Exutu!

A little extra, as I just stumbled on it. On the top of this page is the protocol of Rhiju’s lab. It’s very specific. Have fun. :slight_smile: