Dave Halitsky replied to my query as follows:
From dhalitsky@www.cumulativeinquiry.com Mon Jan 17 11:02:21 2005 To: <propp@math.wisc.edu> Subject: In regard the symmetries of the bases, please note
that (t,g) vs (a,c) is determined by the keto vs amino distinction which is sufficiently well-known to be enshrined in IUPAC notation as
E = keto = t,g M = amino = a,c
You may be interested in references discussion at
http://www.cumulativeinquiry.com/Problems http://www.cumulativeinquiry.com/Forums
Best regards Dave Halitsky 256-426-6243
I responded:
Thanks! May I forward your reply to others?
Also: I looked at the links you gave me, but couldn't find the relevant thread.
He replied:
From dhalitsky@www.cumulativeinquiry.com Mon Jan 17 11:40:27 2005 To: "'James Propp'" <propp@math.wisc.edu> Subject: 1) by all means; 2) relevant thread
Jim -
Please feel free to do whatever you like with the information. It is good to see the question arising independently of the CumulativeInquiry research team's investigations.
Also, at the link:
http://www.cumulativeinquiry.com/Problems
under the heading:
The "oDAG/Bioinformatic Sequence" Problem
the following set of links appears:
Original CI Posting to sci.math Re Ordered Bioinformatic Sequences G. Sterten's Questions Concerning Above sci.math Posting CI's Responses to G. Sterten's Questions Note from C. Brown re building of oDAGs from sequences over {s,p,d,t} (or {++,-+,--,+-}) Bill Mann's PERL program "problist" for expected probabilities of sequences building half-turn invariant oDAGs Notes from Bill Mann on problist program 1994 Halitsky MathBioSci paper; relevant only for a characterization of the four D(mR)NA bases via 2 binary biochemical features)
The last link is to a 1994 paper which builds specifically on the pyrimidine:purine and keto:amino distinction; the other links can be read in order as a discussion of the more general issue in which you are interested.
You may also wish to see the somewhat obscure development of some related ideas at the URL:
http://www.cumulativeinquiry.com/services_products/index.html
under the link:
Technical documentation (PDF format) of the PABP protocol.
Finally, please note that the (t,a) vs (c,g) opposition is often referred to as:
W(eak) = t,a S(trong) = c,g
because c,g pair canonically with three hydrogen bonds and a,t pair canonically with two hydrogen bonds, respectively "strongly" and "weakly". My co-researcher Jacques Fresco at Princeton will be more than happy to discuss the details of this classification.
Dave
Jim