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. Author manuscript; available in PMC: 2014 Jan 9.
Published in final edited form as: J Am Chem Soc. 2012 Dec 21;135(1):354–366. doi: 10.1021/ja3095558

Scheme 5. Reaction scheme for the simulation.

Scheme 5

Polymerization proceeds along an arbitrary template sequence. Reaction (1) is a possible initiation point for a cascade of errors. If an incorrect nucleotide is incorporated, the fidelity and the speed of the following reactions are reduced. If reaction (2) is followed by a correct incorporation, extension occurs at a reduced reaction rate in reactions (3) and (5) until the normal rate is recovered. More likely, (2) is followed by another error, which leads to an even stronger reduction in the rate of reaction (4) and a slower recovery in reaction (6) and subsequent steps. Yet another error in (4) leads to a slow reaction (7) and so forth.