User:ElNando888/Blog/A minor glitch?

(work in progress)

 

I recently presented the Adenine as a nucleotide a little out of the ordinary, an "outsider" of sorts. Well, there's more to it...

 

Adenine is known to form motifs known as "A-motif". Apparently, the nucleotide fits beautifully on the minor groove side of the GC pair. In contrast, the purines are too small to match well, and the Guanine has a disturbing bulky NH group on its Watson-Crick edge, that makes things difficult locally.

 

 

http://dasher.wustl.edu/bio5357/reading/accchemres-44-xxx-11.pdf

"A Universal Packing Strategy for RNA"

 

http://www.pnas.org/content/98/9/4899.full

"A-Minor Motifs Are Common in All Large RNAs"

"A-Minor Motifs Are More Abundant than Tertiary Base Pairs"

"A-Minor Motifs Often Cluster"

http://www.pnas.org/content/98/9/4899/F1.expansion.html

 

 

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Our designs are first "denatured" (another way to put it is to say that they are melted, but it isn't a proper way to describe the procedure), by bringing them to a temperature of 90°C. In the case of this specific design, it is actually questionable whether the main long stacks actually break apart even at that temperature. In any case, they certainly nucleate (form a helix) at very high temperatures. The barcode hairpin though, probably cannot nucleate before the temperature goes down a lot more. So, for a very long time (specially at atomic scales), the secondary structure looks like the picture above.

 

Now let's review:

1. We have long and very stable stacks, exclusively composed of canonical base pairs, making the helix as rigid as it can be, and with a fair number of GC pairs.
2. And we have a bunch of Adenine doublets freely roaming...

 

Maybe, preventing a stack from forming is as simple as making sure that the nucleotides are far away from each other...

 

In this quick look at the lab results of the Semicircle lab, I mentioned about some exceptions to the barcode "debacle". Turns out that GU pairs or noncanonical pairs:

• do not provide a potential "grip" for an A-motif type I
• and do make the helix that contains them more flexible locally, creating instabilities and variations in the intervals between minor grooves

 

 

So, these recent strange barcodes... a minor glitch? or possibly, an A-minor glitch?