title: SDM-Assist software to design site-directed mutagenesis primers introducing "silent" restriction sites.
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.
authors.affiliation: Department of Computer Science, University of Bristol, Bristol, UK.
authors.forename: Abhijit
authors.initials: A
authors.lastname: Karnik
authors.forename: Rucha
authors.initials: R
authors.lastname: Karnik
authors.forename: Christopher
authors.initials: C
authors.lastname: Grefen
mesh_terms: D000465:Algorithms; D029681:Arabidopsis Proteins / Q000235:genetics; D017931:DNA Primers / Q000737:chemistry*; D004262:DNA Restriction Enzymes; D004926:Escherichia coli / Q000235:genetics; D016297:Mutagenesis, Site-Directed / Q000379:methods*; D016133:Polymerase Chain Reaction / Q000379:methods; D015221:Potassium Channels / Q000235:genetics; D012984:Software
chemical_list: D029681:Arabidopsis Proteins; D017931:DNA Primers; D015221:Potassium Channels; C074500:AKT1 protein, Arabidopsis; D004262:DNA Restriction Enzymes