%0 Journal Article
%A Karnik, Abhijit
%A Karnik, Rucha
%A Grefen, Christopher
%D 2013
%J BMC Bioinformatics
%N 1
%M doi:10.1186/1471-2105-14-105
%P 105
%T SDM-assist software to design site-directed mutagenesis primers introducing "silent" restriction sites
%U http://www.biomedcentral.com/1471-2105/14/105
%V 14
%@ 1471-2105
%X BACKGROUND: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.RESULTS: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.CONCLUSIONS: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.