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

Karnik, Abhijit and Karnik, Rucha and Grefen, Christopher (2013) SDM-assist software to design site-directed mutagenesis primers introducing "silent" restriction sites. BMC Bioinformatics, 14: 105. ISSN 1471-2105

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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.

Item Type:
Journal Article
Journal or Publication Title:
BMC Bioinformatics
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© 2013 Karnik et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Uncontrolled Keywords:
?? site-directed mutagenesissdmpcrcloningrestriction endonucleasesoligonucleotidessoftwarebiochemistrymolecular biologycomputer science applications ??
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Deposited On:
28 Nov 2013 10:30
Last Modified:
16 Jan 2024 00:12