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

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Abstract

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.<br /><br />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.<br /><br />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.

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Karnik, A., Karnik, R., & Grefen, C. (2013). SDM-Assist software to design site-directed mutagenesis primers introducing “ silent” restriction sites. BMC Bioinformatics, 14. https://doi.org/10.1186/1471-2105-14-105

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