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From: eddy@boulder.UUCP
Newsgroups: sci.bio
Subject: Re: information content of DNA
Message-ID: <891@sigi.Colorado.EDU>
Date: Wed, 8-Apr-87 10:08:07 EST
Article-I.D.: sigi.891
Posted: Wed Apr  8 10:08:07 1987
Date-Received: Sat, 11-Apr-87 08:40:09 EST
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Reply-To: eddy@beagle.Colorado.EDU (Sean Eddy)
Organization: University of Colorado, Boulder
Lines: 49

>Come now, isn't it a tad early to make such a declaration?  The literature
>has on the order of 100 genomes published, all but a handful being viruses.
>A couple of real cases of overlapping genes have been discovered; both are
>in viruses.  From this you are going to presume to predict that there are
>no cases at all in higher organisms?  You have more chutzpa than I.

No, John, the point Dizzy was making was that while cases of overlap exist,
they are 1)very rare  2)very short and 3)only in two of the three reading
frames. The party line is that these cases have evolved because of the
pressure on viral genomes to be as small as possible (the smaller they
are, the faster they replicate). The difficulties in writing overlapping
codes are enormous even for a human who is doing the writing deliberately;
the difficulties for evolution are incredible.

And remember that your original point was that any given sequence 
potentially represents 6 (!) codings, not just two. Dizzy rightly
replied that this is a good approximation to impossible. 

So what I'm trying to get across is that you're right, in theory;
a given nucleotide sequence is capable of coding for 6 different
proteins. The practical consideration is that DNA sequence length
is not a limiting factor for anything except phage. Thus Dizzy is
also right that there is little reason to expect coding region overlaps
in anything but phage.

(Um, just to be safe, the above applies only to overlaps for the purpose
of information compression. Examples exist, I believe, of overlap
for the purpose of regulation.)

>Also, the literature already contains some descriptions of stretches of
>DNA that have regulatory functions rather than coding for amino acids.
>Also, sometimes DNA (more often RNA) ends up curling around, interacting
>with itself like an enzyme, and modifying its own function.  This could
>easily activate stretches that otherwise appear to be dummies.  It's not 
>well understood yet, but wait a few more years.

I know the RNA literature to some degree (considering some of the big
guns in RNA 'ribozymes' are here at Colorado). But I have never heard
of DNA possessing catalytic activity. My impression was that the 2' OH
on RNA was what enabled it to be reactive; DNA ('deoxy') lacks this
2' OH. Could you provide references for catalytic DNA??  --this is not
a flame, I am really interested; there's too much molecular biology to
hope to know it all.

- Sean Eddy
- Dept. of Molecular, Cellular, Developmental Biology
- Univ. of Colorado, Boulder; Boulder, CO 80309
- 
- "Ph.D.'s are for suckers."  -- from 'Ask Mr. Science'