sense and antisense?

[Kathleen Anderson]

Dr. Chihara (chihara at noc.usfca.edu) wrote:
: I have seen so many different ways of calling DNA strands sense and 
: antisense that I begin to think it is all nonsense. 
: If antisense RNA is comp. to mRNA, shouldn't the template strand in the 
: DNA be antisense?  This makes the complement (the 5' end we normally see 
: displayed) the sense strand. Hartl's book defines things the other way 
: round, which makes no sense to me. Is there  consensus out there?

I also ran across this discrepancy in the Griffiths text, regarding 
the nomenclature of sense / coding / template naming of DNA strands.  
I've never liked the terminology, since using the words in the 
English way leads to confusion, so I did a mini-survey of the 
genetics books at hand, and it seems that the Griffiths text is 
indeed in the minority (I haven't looked at the Hartl text):

Using as a model:   5'- C A T -3'  = "A" strand DNA
                    3'- G T A -5'  = "B" strand DNA
                    5'- C A U -3'  =  mRNA

The strands are defined in the following terms by the references 
given:

"A" strand = coding strand (3,5,8,9)
           = sense strand (3,5,7,8)
           = non-template strand (1,6,10)
       >>> = anti-sense strand (2)

"B" strand = anti-coding strand (3,9)
           = anti-sense strand (3,5,8)
           = nonsense strand (7)
           = template strand (1,2,5,6,7,8,9,10)
       >>> = coding strand (4)
       >>> = sense strand (2)

>>> denotes minority position; note King & Stansfield go both ways!

(1) Alberts et al., _Molecular Biology of the Cell_, p.205
(2) Griffiths et al., _An Introduction to Genetic Analysis_ 
    (5th), p.378
(3) King & Stansfield, _A Dictionary of Genetics_ (4th), p.66
(4) King & Stansfield, _A Dictionary of Genetics_ (4th), p.316
(5) Lewin, _Genes V_, p.163, 377
(6) Russell, _Genetics_ (3rd), p.364
(7) Singer & Berg, _Genes and Genomes_, p.135
(8) Stryer, _Biochemistry_ (3rd), p.705
(9) Tamarin, _Principles of Genetics_ (4th), p.240
(10)Watson et al., _Molecular Biology of the Gene_ (4th), p.376

The instructor I work for (as a TA/grader) explained to me that the 
confusion arose when the terminology was reversed 10 or so years ago, and 
some have been slower than others to catch on, I guess.

No wonder this has always confused me...personally, I like the 
template/non-template nomenclature best, since it seems to be the 
hardest to screw up.

--
Kathleen Anderson
vstr18a at sfsu.edu