Hybriization basic (?) question - (Jan/08/2010 )

Hi guys, something that has been bugging me (even though it sounds simple). Let's assume we have an mRNA strand with the sequence 5'-ACACACACACACGGGGAAAA-3'

Let's also assume we have molecule#1 (reverse complement): 5'-TTTTCCCCGTGTGTGTGTGT-3'

And molecule #2 (complement): 5'-TGTGTGTGTGTGCCCCTTTT-3'

My question.. If we put mRNA together with one of the #1 or #2, in which cases will there be a DNA-RNA hybrid? Will it bind only with #1 or with both? In other words, does the orientation of the complement molecule matter and why?

I used to think both will bind because I was thinking of hydrogen bonds between bases only. But is there more to it?

Only#1. All double stranded molecules are anti-parallel, with both a 5' and 3' base at each end of the double helix.

phage434 on Jan 8 2010, 06:32 PM said:

That's what I thought.. So when we are talking about A-T and C-G interaction through hydrogen bonds that actually includes the free phosphate groups somehow? Or is it a spatial thing (the chains have to allign antiparallel for the phosphate groups to fit or something?)?.

Sorry if I sound naive, it has been a long time since I learned all this and it's kinda forgotten. I used to have the impression that free phosphate groups only come into play for propagation of a chain. And that as long as you have complementary bases they will still form hydrogen bonds cause the reacting bits are separate from the phosphates.

I'm just trying to make it clear how it works on the chemical interaction level.. :/

biobio on Jan 8 2010, 09:42 PM said:

your old impression is correct, the chain propagates through the phosphate group.

hydrogen bonding between chains is through the side groups.

(these are gross oversimplifications but you should get the idea).