Antisense and sensibilities

Ferland Louis H. ferlandl at ERE.UMontreal.CA
Wed Jan 10 01:26:42 EST 1996


On 9 Jan 1996, Mikhail Alexeyev wrote:

> Date: 9 Jan 1996 20:09:55 GMT
> From: Mikhail Alexeyev <malexeyev at biost1.thi.tmc.edu>
> To: methods at net.bio.net
> Subject: Re: Antisense and sensibilities
> 
> In article <Stephen_Lasky-0901961015170001 at cis-ts1-slip11.cis.brown.edu>,
> Stephen_Lasky at brown.edu (Stephen R. Lasky) wrote:
> 
>   
> > One problem with "Template strand" is that during replication, both
> > strands are templates.  If we are going to set some intuitive standard for
> > naming strands, why introduce ambiguity into it by using a term that may
> > be perfectly all right for one process, but is also used in another
> > process.
> 
> Let's put it into another prospective. Everything is (obviously) relative.
> The black colour does make sense only in comparison to other colours. If
> every thing in a world was black, we would never use the word "black" to
> define anything since it would not be descriptive. Same goes for
> "template".  I think that term "template" is rearly used to describe
> replication for exactly same reason.  It is being used mainly as opposed
> to newly synthesised strain (and in this case term "template" sometimes is
> being interchanged with "parental"). Therefore, I think that contradiction
> is not too profound here.  However, I also think that term "template"
> should be avoided in description of DNA strands (for consistency's sake).

FERLAND
So, we seem to agree to not use "template", because of this confusion 
risk with replication. In a previous posting, you proposed "anti-sense", 
"for consistency's sake". Lasky and I dislike "anti-sense" because we 
find confusion risks there too (for historical reasons). Could we all 
live with Moldwin's "transcribed" (and the mRNA-like strand as 
"non-transcribed")?


> 
> > > > > If one needs to know which strand of DNA has sequence identical to RNA,
> > > > > there is no need for any operation:
> > > > > 
> > > > >  antisense DNA = antisense RNA
> > > > >  sense DNA     = sense RNA 
> > > > > 
> > > > FERLAND
> > > > I follow you but if the strand similar to RNA is going to become the
> sense 
> > > > strand, I think the simple statement that it is should be sufficient. The 
> > > > rest follows from the knowledge that transcription is anti-parallel.
> > > 
> > > Exactly. That's the beuaty of it. I intentionally made my message 
> > > redundant (and probably annoying).
> > 
> > The problem of naming strands probably arose initially from the
> > anthropomorphization of the central dogma:  Harking back to the original
> > definitions (in which the DNA sense strand hybridized to the mRNA), if the
> > RNA pol "read" and transcribed that strand it made an mRNA that made sense
> > to the ribosomes when they went to translate it. I believe that this is
> > the opposite of  the description above (sense DNA = sense RNA (mRNA) which
> > seems to be in current usage.  But I think that our goal should be to get
> > away from using sense and anti-sense to describe strands in the DNA.
> 
FERLAND
This would be my first priority, too. I don't think I can ever be 
reconciled with changing the definition of an existing term. It would be 
*much* easier to declare them obsolete and adopt new ones around which a 
consensus would crystallize.


> Indeed, it does contradict to description that I prefer. However, I think
> this contradiction arose due to "inverse" logics used to make definition
> 'DNA sense strand hybridized to the mRNA' in which two ANTIPARALLEL
> strands are being called "sense". Therefore, I tend to agree with Joanne
> Tornow in her attempt to straighten the logics used to make definition. 
> 
> Definition 'sense DNA = sense RNA' is mathematically correct and makes a
> lot of sense to me personally. I beg your pardon for quoting myself:
> 
> As a result of transcription  sense DNA produces  antisense RNAand
> antisense DNA produces) sense RNA. Just like math:
> 
> + x - = -
> - x - = +
> 
> with transcription process being equivalent to multiplication by negative
> (BTW, transcription IS multiplication in biological sense of the word).
> 
> If one needs to figure out what DNA strand is being used as a template to
> produce, say, anisense RNA (s)he has to divide: -/- = +. In this example
> first "-" means "anti" in anisense RNA and the second "-" means
> ANTIparallel copying.
> Division is used insted of multiplication since we deduce nature DNA
> sequence from RNA, the process reverse to transcription (and in math
> division is operation reverse  to multiplication).  
> 
> > 
> > Why not define the strands based on the action that is taken on them:  the
> > transcribed strand (T-Strand) (for the anti-parallel complementary strand
> > to the mRNA), and the non-transcirbed stand (N-Strand) for the strand with
> > the same sequence as the mRNA? The name of the gene that is transcribed
> > can be added if it has not already been defined (as suggested by Dr.
> > Moldwin).   mRNA should be mRNA or sense-RNA, and anti-Sense RNA should be
> > the anti-parallel complement to the message.  I don't see any ambiguity in
> > this system.
> 
> This system of definitions is non-controversial and I have no major
> problems with it (as opposed to 'sense DNA strand used to produce RNA').
> The Dr. Moldwin's suggestion would be very valuable in introduction
> addictional clarity (however, it would complicate things to an extent by
> making definitions longer). The potential complication is difficulty to
> describe the strand in question in cases when BOTH strands of the SAME
> gene are being simultaneously transcribed (one resulting in sense and
> another in antisense RNA). Example: transcripts from Pin and Pout in
> IS10R. In those cases Joane's definition is more versatile.
> 
FERLAND
No, I don't think it adds any length to the definitions, for if you have 
two antiparallel transcription units overlapping each other, you still 
have to specify the name of the gene when using Tornow's "sense/template" 
(or any other) nomenclature.


> Another advantage of Joane's definition is that it uses Just two terms
> (instead of four) to describe both DNA and RNA (and I don't see 
> controversy in it). 
> 
> The disadvantage of her definition (as I can see it now) is that
> antiparallelity of DNA synthesis has to be always kept in mind. Your
> definition does not put such pressure on the novice and therefore should
> be easier to learn.
> 
> In any event, I am not going to teach anyone how it should be. This is
> just my opinion if you are interested in it. 
> 
> M. Alexeyev
> 

Dr. Louis H. Ferland
Centre de Recherche, Hotel-Dieu de Montreal
Dept de Nutrition, Universite de Montreal
Phone: (514) 843-2757     FAX: (514) 843-2719





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