Format

Send to

Choose Destination
BMC Bioinformatics. 2013 Mar 22;14:105. doi: 10.1186/1471-2105-14-105.

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

Author information

1
Department of Computer Science, University of Bristol, Bristol, UK.

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.

PMID:
23522286
PMCID:
PMC3644487
DOI:
10.1186/1471-2105-14-105
[Indexed for MEDLINE]
Free PMC Article

Supplemental Content

Full text links

Icon for BioMed Central Icon for PubMed Central
Loading ...
Support Center