Path: utzoo!utgpu!water!watmath!clyde!att!osu-cis!tut.cis.ohio-state.edu!mailrus!ames!coherent!aimt!weitek!pyramid!prls!philabs!aecom!werner
From: werner@aecom.YU.EDU (Craig Werner)
Newsgroups: sci.bio
Subject: Re: Nature Articles. Anyone read them?
Keywords: amino acid tRNA charging code
Message-ID: <1899@aecom.YU.EDU>
Date: 17 Jul 88 06:08:04 GMT
References: <1628@runx.ips.oz> <6209@bloom-beacon.MIT.EDU>
Organization: Albert Einstein Coll. of Med., NY
Lines: 49

In article <6209@bloom-beacon.MIT.EDU>, ayermish@athena.mit.edu (Aimee Yermish) writes:
> 
> "Second genetic code" is a nice term to latch on to. 
	
	"Second genetic code" was never used by the original authors. It
had its origins in the nature commentary that appeared in the front of the
issue.

> you need a stop codon, too.  mRNA has only four possible bases
> (adenine, cytosine, guanine, and uracil), so it must use three bases
> in each codon to uniquely specify an amino acid (4x4=16, that's not
> enough.  4x4x4=64, wayplenty).  In tRNA, there are one or two more
> kinds of bases (pseudouracil is the only one I can think of offhand),
> letting the cell uniquely specify an amino acid in only two bases
> (sounds like Name that Tune, huh?).

	Actually in another recent paper, it was shown that a tRNA
made completely out of DNA (well,with 1 ribonucleotide at the end
since the 2'0H is needed for charging) was recognized and charged
with the correct tRNA with only slightly different kinetics. It has
been known for some time that native tRNAs (without modified bases)
work just fine.
	Secondly, while a "pair" of bases was cited in the popular 
reporting, it is unclear whether, this means a dinucleotide or
a base-pair. It is important because a dinucleotide has 16 possibilities,
while a base pair only contains 8 (or only 4 unless 3D structure is
important, which it probably is). The structure described by Schimmel
et. al. is a base pair, so basically it turns out that they solved the
Alanine-recognition problem and very little else.

	Consider the following analogy. In Exon shuffling experiments
of the MHC,it was shown that the two outer domains contained all the
information to present antigen and be rejected as foreign in grafts.
The third domain didn't matter in these experiments.  Well, the third
domain is relatively conserved, so the shuffle actually didn't change
anything of importance. It took old-fashioned mutant searches 
(Potter, et. al) to show that the third domain was crucial.
Similarly, changing a base pair in a tRNA turned it into an alanine
tRNA, but there are other cues that are based simply on tRNAness
that get missed in the shuffle, as it were.




-- 
	        Craig Werner   (future MD/PhD, 4 years down, 3 to go)
	     werner@aecom.YU.EDU -- Albert Einstein College of Medicine
              (1935-14E Eastchester Rd., Bronx NY 10461, 212-931-2517)
                                 "But I digress..."