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. 2009 Sep 26;37(22):7603–7611. doi: 10.1093/nar/gkp800

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© The Author(s) 2009. Published by Oxford University Press.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Figure 7. — Idling by Pfu-Pol on encountering a template strand deaminated base. The polymerase (yellow) captures uracil four bases ahead of the primer–template junction using a specific binding pocket (green). Further, extremely slow, polymerization can add two bases to give a strained conformation (indicated by hatched borders) in which the primer–template junction and the uracil binding site are too close, with a separation of two bases. A conformational change restores the spacing to four bases by unwinding the terminal two bases in the primer and, hence, relieves the strain. This conformational change places the single-stranded bases in the 3′–5′ exonuclease site (rose) enabling their removal.