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. ISSN 1471-2105

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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.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
Additional Information:
© 2013 Karnik et al.; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Uncontrolled Keywords:
/dk/atira/pure/subjectarea/asjc/1700/1706
Subjects:
ID Code:
67747
Deposited By:
Deposited On:
28 Nov 2013 10:30
Refereed?:
Yes
Published?:
Published
Last Modified:
02 Jul 2020 01:18