The book "Understanding bioinformatics", says that "RNA polymerase transcribes the anticoding strand in the direction from 3' to 5', so that the mRNA strand is produced from the 5' to the 3' end".

But from Khan Academy's article, I got "RNA polymerase builds an RNA strand in the 5' to 3' direction, adding each new nucleotide to the 3' end of the strand". Also "the codons of an mRNA are read in order (from the 5' end to the 3' end)". Which one is correct?


2 Answers 2


They're both correct. The confusion stems from the book talking about the anticoding strand as well as the newly-formed coding RNA strand, whereas Khan Academy talks only about the coding strand.

From the book:

The anticoding strand is transcribed from 3' to 5'. Therefore the coding strand is produced from 5' to 3', meaning the very first nucleotide added by the RNA polymerase is the 5' end, and you add to it in the 3' direction.

From Khan Academy:

The RNA polymerase produces a strand of RNA from 5' to 3'.


@Thymine's answer is correct. I just thought I'd post a more graphic answer for clarity.

                  <==(RNA Pol)3'------------------------- 5'
5' ------------------------------------------------------ 3'  
3' ------------------------------------------------------ 5'

The RNA Polymerase is synthesizing on the 3' to 5' strand, but nucleic acids are always added in reverse direction to the template strand (this goes for DNA replication as well as RNA synthesis).

The confusion arrises, of course, because there are several different ways of looking at it. If you're looking at the polymerase's template strand, you would (like the book) that the RNA Pol is synthesizing 3' to 5'.

On the other hand, if you're looking at the strand being synthesized, you'd say (like Kahn Achademy) that it's being synthesized 5' to 3'. This is why Kahn says

[...] adding each new nucleotide to the 3' end of the strand.

There is an incomplete mRNA fragment with the RNA Pol sitting on the 3' end. That's where it adds each new nucleotide.


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