@Article{karnik2013sdm,
AUTHOR = {Karnik, Abhijit and Karnik, Rucha and Grefen, Christopher},
TITLE = {SDM-assist software to design site-directed mutagenesis primers introducing "silent" restriction sites},
JOURNAL = {BMC Bioinformatics},
VOLUME = {14},
YEAR = {2013},
NUMBER = {1},
PAGES = {105},
URL = {http://www.biomedcentral.com/1471-2105/14/105},
DOI = {10.1186/1471-2105-14-105},
ISSN = {1471-2105},
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.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.},
}