Is DNA helicase or RNA polymerase responsible for breaking the hydrogen bond between the 2 strands during transcription for eukaryotic cells? My textbook (WJEC Biology for AS level) says it is DNA helicase that breaks the hydrogen bonds while RNA polymerase catalyses the formation of bonds between RNA nucleotides.

The enzyme DNA helicase breaks the hydrogen bonds between the bases in a specific region of the DNA molecule. This causes the two strands to separate and unwind, exposing nucleotide bases. The enzyme RNA polymerase binds to the template strand of DNA at the beginning of the sequence to be copied.

However, when I searched online, for example on https://en.wikiversity.org/wiki/Effect_of_hydrogen_bond_on_RNA

Transcription can be explained easily in 4 or 5 simple steps, each moving like a wave along the DNA. RNA polymerase unwinds/"unzips" the DNA by breaking the hydrogen bonds between complementary nucleotides. RNA nucleotides are paired with complementary DNA bases. RNA sugar-phosphate backbone forms with assistance from RNA polymerase.

Then do RNA polymerase break hydrogen bonds? If RNA polymerase can break hydrogen bonds between strands then what is the role of DNA helicase in the transcription process?

  • 1
    $\begingroup$ Good. I was answering the question while you were updating your answer, but I hope it clarifies things. Read the section of Berg et al. carefully. Successful text books are big earners for publishers, who put a great deal of effort checking each new edition. So you are likely to get a clearer account from such texts. The only problem is fast-moving fields where the material goes out of date. Wikipedia entries can be a dog's breakfast. $\endgroup$
    – David
    May 24, 2018 at 19:06

1 Answer 1



As I have pointed out in my comment, it is not clear whether the sources mentioned relate to eukaryotes or prokaryotes, assuming they are correct. I am a translation man, rather than a transcription man, and so am answering this from the 2002 edition of Berg et al. ‘Biochemistry’, as I happen to have a copy of my own (a freebie from when I was still teaching) and this edition is freely available online. List members with more expertise in this area are encouraged to post comments to correct any errors in my answer or supply updates.


  1. in neither prokaryotes nor eukaryotes is the DNA helicase that operates during DNA replication involved in transcription although other proteins necessary for transcription have DNA helicase activity.

  2. In prokaryotes it appears that the RNA polymerase holoenzyme (made up of just four subunits) is responsible for unwinding about 17 base-pairs of template DNA. Quoting from Section 28.1.3:

    Each bound polymerase molecule unwinds a 17-bp segment of DNA, which corresponds to 1.6 turns of B-DNA helix

    There may be some ambiguity caused by the description of how this value was determined experimentally as it involved addition of topoisomerase II. However it is clear from discussion elsewhere that this is an enzyme of DNA replication and is not involved in transcription.

  3. In eukaryotes transcription is much more complex, involving separate polymerases for different classes of RNA product and a variety of auxiliary transcription factors in the case of RNA polymerase II, which transcribes mRNA. According to Section 28.2.4:

    The TATA box of DNA binds to the concave surface of TBP [the TATA-box-binding protein]. This binding induces large conformational changes in the bound DNA. The double helix is substantially unwound to widen its minor groove, enabling it to make extensive contact with the antiparallel β strands on the concave side of TBP.

    So the initial recognition of the TATA box causes some unwinding. However the major player appears to be transcription factor TFIIF:

    an ATP-dependent helicase that initially separates the DNA duplex for the polymerase


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