Losing our SENSEs

Ken Howe howe at DARWIN.UCSC.EDU
Thu Jan 4 19:29:43 EST 1996

Hi all,

I don't believe too many people are confused about which DNA strand acts 
as the template strand during transcription or even about the whole 
process of RNA polymerisation, which strand is read in which direction, 
etc.  It's clear that the confusion exists primarily from the discordant 
usage of the term "SENSE" with respect to a DNA strand.  Both usages are 
manifest from both the literature and the dialogue here.  What is 
unfortunate is that we've been arguing about whose usage is correct and 
whose isn't, rather than concentrating on what a few (myself excluded) have 
been offering as understandable alternatives: terms which are clear and 
undeniable in their meanings.

In this regard, I have never been an advocate of the terms "sense" and 
"antisense" as applied to DNA in any form, nor does it make sense to 
refer to either strand as "coding" or "non-coding".  Again, these terms 
go back to times when less was understood about the mechanism of 
information transfer from DNA to RNA.  In the simplest terms, one strand 
acts as the "template" and the other does not.  The RNA which is produced 
by transcription is understood be have the "sense" orientation because 
it is functional- either as a structural or catalytic molecule, or as 
containing a translatable sequence resulting in the production of a 
polypeptide (also, presumably, functional).  Refering to an RNA as 
"sense" is either redundant or a mechanism to demonstrate functionality 
when an "antisense" RNA molecule is pertinent to the discussion.  To 
reiterate, an "antisense" RNA only has meaning in the context of a 
(sense) RNA, and in the context of a scientific experiment (RPA, 
probing, etc) or an observation of some biological event (eg.,antisense 
regulation of gene expression).

A DNA oligonucleotide having the sequence complementary to the RNA 
sequence (often refered to as the "antisense oligo") should be the only 
usage acceptable for application of the term to DNA, unless there is a 
better terminology.  I think what has occured over time is that, with the 
advent of antisense oligodeoxynucleotide probing, oblation, S1 mapping, etc, 
application of the term "sense" to mean the DNA strand having the same 
sequence as the RNA (as opposed to the "antisense" oligo having 
complementarity to that RNA)  has evolved.  This has occured despite its 
application otherwise.  

An awareness of this controversey and useful dialogue for the 
clarification and restriction of the utilization of these terms in 
question would be more useful than all of the reference flinging we've 
been doing (my deference to those who've been trying to 
address these points and their suggestions, some of which I've adopted).

Finally, in answer to the following statement:
> My problem is, what to do with all the EXISTING textbooks? I fear a great 
> confusion when various sources continue to conflict and the textbooks we 
> all currently have on our shelves become officially wrong.
I must admit that it seems a shame that textbooks can become confusing, 
contradictory or just plain wrong.  The reality of the matter is that the 
printed word, in science, is often never the final word.  That's why we 
have updated versions, corrections, and retractions, not to mention 
paradigm shifts).  It's our responsibility to discuss these matters when 
they come up, how the confusion might have arisen, and suggest 
alternatives which might eliminate the conflict.

Thank you for your time.

Ken Howe
"The onions expressed here are my own"

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