DNA is synthesized in the 5' to 3' direction. The template is antiparallel to the strand being synthesized.
The attacking nucleophile is the 3'-hydroxyl at the end of the growing strand (sometimes called the primer terminus).
The electrophile is the phosphorus atom of the α-phosphoryl group of the incoming nucleotide. A proofreading
exonuclease activity, a separate activity and active site in most DNA polymerases, comes
into play if an incorrect nucleotide is added.
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Click on the attacking nucleophile.
Great—now click on the atom it attacks.
Simulating....
DNA Pol senses the incorrect base pairing, and is stalled. Click on the activity that will proofread the incorrect nucleotide.
Click on the attacking electrophile.
Great! Now click on the molecule it is attacking.
Objective
Create a double-stranded DNA using DNA polymerase, and understand the chemistry behind the polymerization reaction and the polymerase proofreading mechanism.
Reward
Collect the DNA Polymerase token and unlock the DNA Replication simulation marker.