Wednesday, March 21, 2007

How RNA Polymerase Works: The Chemical Reaction

During the elongation step in transcription, the transcription complex consisting of RNA polymerase plus various elongation factors moves along the double-stranded DNA copying the template strand to produce a single-stranded RNA. In the example shown below the RNA product is mRNA and the enzyme would be RNA polymerase II in eukaryotes.

The transcription bubble spans about 20 nucleotides of DNA. This corresponds to the opening of two turns of the double helix. During transcription, a transient DNA:RNA double helix forms and this is sufficient to form one turn of the hybrid helix. As the complex moves down the gene from left to right, ribonucleotides are added one at a time to the growing 3′ end of the RNA. This is positioned in the active site of RNA polymerase.

The known structures of the bacterial and eukaryotic RNA polymerases have allowed workers to decipher the details of transcription in a way the wasn't possible before these structures were available. I'm going to describe the steps by which this amazing molecular machine adds nucleotides to make RNA.

Let's begin by looking at the chemical reaction. An incoming ribonucleoside triphosphate (blue) aligns with the DNA template strand to form a base pair. G pairs with C and A pairs with T/U. In the figure we use generic bases B and B′ to represent the real bases. For each addition, a number of different nucleotides need to be tested to see if they match the base on the template strand. Since there are four different ribonucleotides this means that, on average, 25% of the pairing attempts will be successful. The unsuccessful nucleotides have to be allowed to escape from the active site. Since the active site is buried deep within the enzyme, there must be a channel that allows ribonucleotides to diffuse easily to and from the active site.

Once a proper base pair has formed, the chemical reaction takes place. In technical terms this is referred to as a nucleotidyl-group-transfer reaction. It involves a nucleophilic attack by the electron-rich oxygen of the 3′ hydroxyl group on the α-phosphorus of the incoming ribonucleoside triphosphate. The result is the formation of a new phosphodiester linkage and the release of pyrophosphate. The mechanism of the reaction requires a metal ion (Mg2+) at the active site. Subsequent cleavage of pyrophosphate helps drive the reaction in the direction of RNA synthesis.

The rate of the reaction in eukaryotes is on the order of 50 nucleotide additions per second. This means that the precursors (nucleoside triphosphates) have to diffuse into and out of the active site very rapidly.

The stage is now set for the addition of the next ribonucleotide. Before this can happen the transcription complex has to shift by one base pair in the direction of transcription so the 3′ hydroxyl group of the most recently added nucleotide is now positioned in the active site next to the Mg2+ ion. Looking at the top figure you can see that several other things have to happen simultaneously. The DNA helix has to uniwind by one base pair in front of the transcription complex and rewind by one base pair at the back of the the bubble. The short DNA:RNA helix also has to unwind by one base pair. This all happens without the complex falling off the DNA because this is a highly processive reaction. (A processive reaction is one that doesn't release the polymer as it's being synthesized. )

In another post I'll show how these molecules fit into the RNA polymerase structure.


  1. I think there's one small mistake in the post--in the case of RNA Polymerase, A pairs with U, not T.

  2. Matt says,

    I think there's one small mistake in the post--in the case of RNA Polymerase, A pairs with U, not T.

    Okay, thanks. I changed it to A pairs with T/U. It's not a big deal—what's a little methyl group among friends? :-)

  3. Drink some methanol and you'll find out. ;)

  4. This is so helpful! Thank you. I am a little confused about what the Mg2+ ion does. Does it counter the negative charge from the phosphate or the alkoxide nucleophile? Also, what causes the hydroxyl group to get deprotonated? Thanks!

  5. The top Mg2+ interacts with 3’ OH on terminus of RNA, lowers pKa of group allowing deprotonation by some base (last I heard it hadn't been identified, it could be a nearby sidechain or bulk OH-).
    3’O then attacks phosphorous atom.

    The second Mg2+ ion enters bound to incoming NTP. Mg2+ positions and neutralizes charges on β, γ phosphates, possibly a role something akin to stabilizing the transition state.

    Another amino acid (His in RNAPII) on a structure called the trigger loop acts as an acid and donates proton to pyrophosphate leaving group to complete the reaction.