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Coming from a software engineering standpoint, suppose I have a string of code like so:

... 5'-ATAGAC-3' ...

... 3'-TATCTG-5' ...

Assume the above code is part of a larger segment. Now, reading from 3' to 5', the promoter and operator would be somewhere before the structural gene on the 2nd stand:

(Promoter) (Operator) ... 3'-TATCTG-5' ...

Where would it be on the first strand? From what it looks like, the first strand codes for a completely different protein than the second stand:

... 5'-ATAGAC-3' ... (Operator) (Promoter)

Yet, the two strands are complementary.

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You make one mistake: DNA is always read in 5'->3' direction. So when you promoter is before the gene, it is on its 5' site. So it would be 3'-TATCTG-retomorp-5' or in the right reading direction: 5'promoter-GTCTAT-3'. –  Chris May 27 at 6:24
    
    
DNA is built 5'-3' but the template strand is read 3'-5'. –  arao6 May 27 at 14:44

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In your example, yes the two strands do code for different proteins. However, biologically this generally doesn't occur. I say generally because I don't want to rule it out definitively but I don't know of an instance where both strands at a given locus code for a protein and, where it does occur, it is often used as a criterion for annotating one of the elements as dubious. Along with that, there would be no promoter immediately 5' to one of the strands. Even if it does occur biologically, each strand would code for a different protein and would be a different gene.

In any gene, one of the strands is identical to the RNA transcript (before processing and with T instead of U). This is called the coding or sense strand and runs 5' -> 3'. The other strand is used as a template by RNA polymerase (RNAP) to polymerize the RNA transcript. It runs 3' -> 5' and is called the template or antisense strand.

Also, a note on promoters: promoter consensus sequences by convention are given on the sense strand. However, as far as I know, transcription initiation factors recognize the base pairing between both strands in the major groove of dsDNA because they must bind before promoter melting occurs. Thus, I wouldn't say that a promoter exists only on the template strand.

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So would both DNA stands code for the same protein at a given locus? How is this possible, given that the bases are different when reading one strand vs. the other? –  arao6 May 27 at 14:48
    
No, they would code for two different proteins and in opposite directions… –  canadianer May 27 at 18:37
    
Thanks. How does the cell "know" which strand to read? What I mean is, you mentioned that "transcription initiation factors recognize the base pairing between both strands in the major groove of dsDNA". How does it know which strand to read? The promoter strand? –  arao6 May 27 at 22:57
    
The strand is determined by the promoter location. Since promoters are directional and transcripts are only polymerized 5' -> 3', there is only one choice for sense and antisense strands from a given promoter. –  canadianer May 28 at 0:36

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