Oligonucleotide-directed mutagenesis is a widely used method for studying e
nzymes and improving their properties. The number of mutants that can be ob
tained with this method is limited by the number of synthetic 25-30mer olig
onucleotides containing the mutation mismatch, becoming impracticably large
with increasing size of a mutant Library. To make this approach more pract
ical, shorter mismatching oligonucleotides (7-12mer) might be employed. How
ever, the introduction of these oligonucleotides in dsDNA poses the problem
of sealing a DNA nick containing 5'-terminal base pair mismatches. In the
present work we studied the ability of T4 DNA ligase to catalyze this react
ion. It was found that T4 DNA ligase effectively joins short oligonucleotid
es, yielding dsDNA containing up to five adjacent mismatches. The end-joini
ng rate of mismatching oligonucleotides is limited by the formation of the
phosphodiester bond, decreasing with an increase in the number of mismatchi
ng base pahs at the 5'-end of the oligonucleotide substrate, However, in th
e case of a 3 bp mismatch, the rate is higher than that obtained with a 2 b
p mismatch. Increasing the matching length with the number of mismatching b
ase pairs fixed, or moving the mismatching motif downstream with respect to
the joining site increases the rate of ligation, The ligation rate increas
es with the molar ratio [oligonucleotide:dsDNA]; however, at high excess of
the oligonucleotide, inhibition of joining was observed. In conclusion, 9m
er oligonucleotides containing a 3 bp mismatch are found optimal substrates
to introduce mutations in dsDNA, opening perspectives for the application
of T4 DNA Ligase in mutagenesis protocols.