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SDM-Assist software to design site-directed mutagenesis primers introducing “silent” restriction sites

Abhijit Karnik1, Rucha Karnik2 and Christopher Grefen2*

Author Affiliations

1 Department of Computer Science, University of Bristol, Bristol, UK

2 Molecular, Cell & Systems Biology, University of Glasgow, Glasgow, UK

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BMC Bioinformatics 2013, 14:105  doi:10.1186/1471-2105-14-105

Published: 22 March 2013



Over the past decades site-directed mutagenesis (SDM) has become an indispensable tool for biological structure-function studies. In principle, SDM uses modified primer pairs in a PCR reaction to introduce a mutation in a cDNA insert. DpnI digestion of the reaction mixture is used to eliminate template copies before amplification in E. coli; however, this process is inefficient resulting in un-mutated clones which can only be distinguished from mutant clones by sequencing.


We have developed a program – ‘SDM-Assist’ which creates SDM primers adding a specific identifier: through additional silent mutations a restriction site is included or a previous one removed which allows for highly efficient identification of ‘mutated clones’ by a simple restriction digest.


The direct identification of SDM clones will save time and money for researchers. SDM-Assist also scores the primers based on factors such as Tm, GC content and secondary structure allowing for simplified selection of optimal primer pairs.

Site-directed mutagenesis; SDM; PCR; Cloning; Restriction endonucleases; Oligonucleotides; Software