During transcription: Which DNA strand does RNA polymerase read?

There are lots of nucleic acid strands to keep track of! During transcription there are three nucleotide strands involved:
- The RNA strand that is being made (transcribed) by RNA polymerase
- The two complementary DNA strands that make up the DNA double helix, only one of which is being “read” by RNA polymerase

How does RNA polymerase know which strand of DNA to bind to so that it goes in the right direction?

The RNA polymerase binds to both strands simultaneously, but the direction it is pointing depends on the strand that the promoter sequence is in. In Figure 4-27 you’ll see that the promoter (gray region) can actually be situated on either strand, with the arrows pointing in the downstream direction indicating the direction that the RNA polymerase would travel. It is a specific DNA sequence in the promoter which helps lock the sigma factor and RNA polymerase in the right direction (Figure 4-26).

Figure 4-26. RNA polymerase (RNAP) can bind to the DNA nucleotides in one way which points the RNA polymerase in the correct direction

The DNA sequence ATCG’s cause the DNA helix to have slightly different shapes that the sigma factor can bind to in a specific orientation. The orientation can help determine which direction the polymerase points.

Whichever strand the promoter sequence is situated in is called the ‘plus’ (+) strand or ‘leading strand’ and the RNA polymerase will be oriented so that it will transcribe downstream of the promoter into the coding region (Figure 4-26).

Here’s where things get a little wacky - ready for a mind bender? Even though our point of reference is the (+) strand, and the RNA polymerase travels from 5’ to 3’ according to the (+) strand, the RNA polymerase actually reads and transcribes from the other strand, the template strand. Another name for this is the ‘minus’ (-) strand. In the next section, we’re going to see why RNA polymerase does this, along with the ‘cipher’ that it uses to transcribe DNA sequences into RNA sequences.

Figure 4-27. The gray segment of each strand represents different non-coding promoters. On the top strand, the RNA polymerase would bind and continue to the right toward the 3’ OH end. On the bottom strand, the RNA polymerase would bind to the gray region and transcribe to the left toward the 3’ OH end of that strand

Bidirectional transcription in a plasmid? Have a look at Figure 4-28. This is an adapted illustration of Figure 4-13 where the twist of the DNA helix was removed to show each DNA strand more clearly.

- Your trait/gene: is designed so the RNA polymerase will bind to the promoter (5’P) and transcribe towards the 3’0H direction of the pink (outer) strand. While this happens, it uses the red (inner) strand as a template to create an RNA molecule version of the pink strand.

- Selection gene: is designed so the RNA polymerase will bind to the promoter (5’P) and transcribe towards the 3’0H direction of the red (inner) strand. While this happens, it uses the pink (outer) strand as a template to create an RNA molecule version of the red strand.

The Ori is not involved in transcription. This bidirectional design is often used so that the RNA polymerase from one gene does not continue into the next gene and transcribe it as well. This could decrease your control of the genetic system!

In the figure on the left, even if the RNA polymerase continues past your trait gene, it will not transcribe the selection gene because that RNA polymerase is reading the wrong strand. On the right it is possible that transcription starting in a gene can run through another gene!