DNA constraints [sf#6]

[srynobio]

Reported by eilbeck on 2007-02-07 16:44 UTC
Submitting another request from Colin, so it does not get lost.

It's all to do with annotating a paper: "Control of macromolecular
structure and function using covalently attached double-stranded DNA
constraints", PMID 17216052.

* Currently I've annotated the paper with SO:0000442 (dsDNA oligos) but
I was wondering whether "DNA constraint" ought to be a new term,

• child of "reagent" (SO:0000695)
• tentative definition "A double-stranded DNA used to control
  macromolecular structure and function."

* Also, what about chemically substituted DNAs and RNAs? The paper
mentions "5'-tethered-aldehyde DNA" and "2'-amino-RNA". Would they fall
within the scope of SO?

* "P4-P6 domain". This is a 160 nucleotide RNA domain in the
Tetrahymena group I intron. It gets 60 hits on PubMed. It looks like a
model domain for people studying folding. Is it within scope?

* "tetraloop". Currently annotated as SO:0000313 "stem_loop". Should
tetraloop be a child of stem_loop?

I think that's it for that paper.