[DIYbio] What are common basepair mismatches?

I'm working on a protocol involving DNA hybridization and ligation of
short sticky-ends (about 3 bp), and I'm concerned with the
possibility of sticky-end mismatches. Using nucleotide kinase and
phosphatase I can prevent mismatches from ligating, but if the risk is
low, leaving these steps out decreases the reagent bill and time cost
significantly.... but I need to evaluate the risk so I can choose if
the level is acceptable or not.

So of the possible mismatches, which are most prevalent/likely (even
if statistically the probability is low)?

Basepair mismatch possibilities:
GA, GT, GG, CA, CT, CC,TT, AA

--
Nathan McCorkle
Rochester Institute of Technology
College of Science, Biotechnology/Bioinformatics

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