I did my graduate work with Brenda L. Bass, in the Department of Biochemistry at the University of Utah in Salt Lake City.For my doctoral thesis, I characterized the interaction of a zinc finger protein, dsRBP-ZFa, with dsRNA and RNA-DNA hybrids.
Double stranded RNA is much different than DNA, which is nearly always double stranded in cells. The structure of dsRNA is such that proteins have a much more difficult time binding it in a sequence specific manner. This is because most of the atoms in DNA or dsRNA that can be used by a protein to distinguish a G:C base pair from an A:T or A:U base pair are located in the major groove of these polynucleotides. If you would like a graphical illustration comparing DNA and dsRNA take a look at this image. When I speak about dsRNA, I don’t mean the sort of thing you get in stem regions of stem-loops, I’m talking about long regions of 18 base-pairs or more. So, that’s basically what turned my crank during grad school.
In these illustrations, (Min = minor groove, Maj = major groove). The other image (gif) illustrates the different hydrogen bond donors and acceptors found in A:U and G:C base pairs.
The zinc finger is possibly the most common structural motif for binding DNA. As such, there is a lot of information available about them. More information about zinc finger protein structures that have been solved may be found at the NRL 3D database. You can also search from this site if your WWW client allows that sort of thing. The protein database at Brookhaven National Labs is accessible through a gopher connection and allows keyword searches under the ‘access to the entries’ subtopic. Check it out, there are some great gifs and tons of information on nearly all the structures that have been solved to date. There is a WWW page for crystallography if you’re interested in that sort of thing. Here are a couple of other science related WWW servers that you might find interesting. The ExPASy molecular biology server, the Johns Hopkins server and the NCBI server.
Here is an animation I made of a zinc finger structure (using Rasmol) as determined by NMR.
In this illustration, only histidine and cysteine residues are depicted. The pink region is known as an alpha helix and the yellow arrows are two beta strands.
dsRBP-ZFa contains seven zinc finger motifs. It binds dsRNA with a dissociation constant of about 1 x 10-10 M and does not bind to ssRNA or B-form DNA. It also binds RNA-DNA hybrids quite well, with a dissociation constant of 2 x 10-9 M. Currently, the biological function of dsRBP-ZFa is unknown although there are many similar sequences in the database and I obtained some interesting in-situ hybridization results.
I examined the localization of ZFa mRNA in Xenopus embryos using in situ mRNA hybridizations. You can view the embryos here.