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Mutagenic Primer Design

MutaPrimer designs mutagenic primers for use with Stratagene's QuikChange site directed mutagenesis kits which enable single/multiple base changes, insertions or deletions.

Site-directed mutagenesis has become one of the most important tools in molecular biology. It is a technique to introduce mutations at selected sites in a DNA molecule, usually a circular plasmid molecule. In general, site-directed mutagenesis requires that the wild-type gene sequence be known.

With QuikChange kits offered by Stratagene, you can carry out vector modifications and express resultant mutant proteins for many applications including exploration of protein structure-function relationships, study of gene expression, identification of drug resistant variants, and other drug discovery activities. With these kits, you can mutagenize several sites in double stranded DNA using a single mutagenic oligonucleotide.

The current version of MutaPrimer designs primers to work with Stratagene's QuikChange and QuikChange XL Kits.

Sequence Information

You can start the primer search process by loading either the DNA sequence or the amino acid sequence directly from Entrez or from your local drive. When starting with the peptide sequence, you can use the "Expression System" option to translate it into a non-degenerate DNA sequence. MutaPrimer achieves this by using the codon frequency data for the selected expression system. The translation tool can be used to display the proteins coded by the both wild and mutant DNA sequences.

Mutant Information

After loading the gene or protein of interest simply add the mutation information by specifying the mutation type using easy to use MutaPrimer screens. Launch the search, and voila! You will be presented with the best primers for assured experimental success.

Primer Properties

MutaPrimer designs mutagenic primers that fully comply with the primer design guidelines published by Stratagene for their QuikChange site directed mutagenesis kits. According to the guidelines, the most important parameters are desired Tm and required lengths for the flanking regions.

Primer Rating

In addition to complying with Stratagene's guidelines, MutaPrimer checks all possible secondary structures of the primers such as dimers, hairpin, repeats and runs and displays them graphically. MutaPrimer then rates all available primers using the specified primer properties, and the secondary structure stabilities. It then reports the best mutagenic primers along with the alternates (up to 50). The rating algorithm is based on a proven statistical optimization technique to pick the very best primers for every experiment. We believe that assay success is assured by this innovative algorithm built into MutaPrimer.