Wednesday, April 21, 2010

Love python!

I love python simplicity.

The next code creates a random sequence of RNA of a desired length sooooo easily.

import random
import sys

# Print the script usage info if the user
# doesn't supply the correct number of arguments.
if len(sys.argv) != 2:
print 'Usage: '

# Read the length of the random RNA sequence
# that you want to generate.
arg1 = sys.argv[1]

# Create the random sequence in the output file
outseq = open('rnaseq%s.seq' % arg1, 'w')
rna = ''.join([random.choice('AUGC') for x in range(int (arg1))])

Friday, April 2, 2010

The time is ripe for RNA

Maybe this is one of many posts which insist in the same point, but this time the indicator I'm using is one dear to all U.S.A. based chemists.
Simply, what I want to say is:
In every issue of Chemical and Engineering news there is at least one review per week of a new discovery or advance in RNA understanding, and this has been going on at least for the whole of the last year. Amazing!

This weeks issue mentions a radical mechanism used by enzymes to methylate adenines in the ribosome, and the previous week they talk about the other role of tRNA, that of being an apoptosis (cell-suicide) regulator, and I could go on.

Finally, Sponer's gang has published another article on quantum mechanical calculations of stacked bases. They previously did a study of stacked uracil's, now they are doing a study of stacked adenines. It's interesting to see that they seem not to know the trend on stacking interactions:
purine-purine > pyrimidine-purine > pyrimidine-pyrimidine
They do kind of; "trying to get it out of the way", mention that they are working in vacuo, that the experimental results in vacuo are not comparable, and at the same time they mention that solvation effects are important, explicitly for the B-DNA case, but they seem just to leave it at that.

Perhaps the reason for doing ApA is that someone told them about the NMR and solubility experiments which show the stacking trend?
Also, why don't they use the standard reference frame? It makes it hard to understand their stacked groups and to compare to say RNA geometrical information coming out of curves or 3dna from analysis of x-ray or NMR structures of RNA.