Antisense and sensibilities

Mikhail Alexeyev malexeyev at biost1.thi.tmc.edu
Tue Jan 9 15:09:55 EST 1996


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).

> > > > 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.

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.

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



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