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Hi Chris!
This looks interesting. I know what a nick is in DNA. I haven’t heard about them in RNA before, so I’m not sure I understand what they are. However it looks like GU’s being at a nick, more than the others.
Could you explain a bit of the terminology? Like insert too.
This seems to be taken from Table 3 of New information content in RNA base pairing deduced from quantitative analysis of high-resolution structures
Eli—the paper is the one above referenced by Omei. It will better explain terms than I could. Worth the read, IMO.
And yes, GU seems favored at ‘nicks’ which is one of the reasons I posted this.
Thx, Chris!
I’ve read the article now. Not carefully enough to fully understand it, but enough that I think I have the gist of it. Although I do think it is interesting, I have to wonder how relevant it is to the labs.
The RNA terms “base pairs” and “helix” are defined much more broadly than usual. The authors started with the X-ray data for a small collection of RNA that seems focused on, if not completely made up of, RNA/protein complexes containing more than one RNA molecule. Then they defined “base pairs” for this experiment in a very general way, intending to include two bases that might be interacting with each other. Then they defined a “helix” as being any collection of three or more “base pairs” that at least sort of resembled the relative positions associated with the normal meaning of the term. See the article for the exact criteria they used, but here’s an informative quote. “Since there are also no restrictions on the angles between neighboring base-pair planes, both curved and straight double-helical stretches are identified.” (I find “straight double helix” to be an oxymoron.) In summary, up to this point, there was no consideration at all of the RNA backbone which might or might not connect bases in one of their “double helixes”.
In the table Chris posted, an “interior intact” base pair is one that had a base pair in both directions of the “helix” and there was a backbone sequentially connecting the three on each side. (The backbone for the two sides might or might not be from the same RNA molecule.) A “terminus intact” base pair had only one neighbor, and both bases of the pair were directly connected to their neighbor by a backbone. An “insert” corresponds to a pair which is not directly connected to either neighbor, but the two neighbors are directly connected. Anything else is called a “nick”.
So the table summarizes some stats on the specific bases that they are going to use in their analysis, which is to characterize the range of geometric relations that occur between proximal bases including, but not limited to, paired bases as we usually think of them.
Eli-
“Like a nick in a regular DNA duplex, a ‘nick’ in the RNA helices corresponds to a break in the covalent link between stacked base pairs. The RNA backbone, however, is ‘broken’ in the sense that the stacked bases occur in sequentially distant nucleotides.”
As to it utility or relevance, each must make their own judgment.