Binding site mismatch

Figure 9.4 Duplex 3 4 and two duplexes 3 6 and 3 7 containing mismatched-binding sites. The repulsive mismatched binding sites in 3 6 (acceptor-acceptor) and in 3 7 (donor-donor) cause mote than a 40-fold decrease in the stabilities of these duplexes compared to 3 4.

Figure 23.12. Bidirectional mismatch repair in E. coli. MutS binds to mismatches formed by errors made during replication. MutL binds to the MutS-bound complex. MutH incises the newly synthesized strand next to the unmethylated GATC sequence. The green arrows indicate signally between the two sites of activity. DNA helicase II unwinds the DNA and exonucleases excise the DNA from the point of incision up to and including the incorrect base. DNA Pol III synthesizes new DNA to replace the excised DNA. (Reproduced with permission from Iyer, R. R., Pluciennik, A., Burdett, V., and Modrich, P. L. DNA mismatch repair Functions and mechanism. Chem. Rev. 106, 302-323, 2006.)...

However, IUPAC consensus sequences strongly depend on the sequence set used for definition. The final IUPAC consensus sequence remains arbitrary depending on the rules used to determine the consensus. Cavener defined some rules that we have used at GSF for several years now and, in our experience, IUPAC consensus sequences defined that way can be useful [29]. However, IUPAC consensus sequences may reject biologically functional binding sites due to a single mismatch (or an ill-defined IUPAC sequence). 

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