Primer design

The function of primer design includes not only primer filtration by Tm, but also mispriming and restriction analyses on the primers. DNAMAN can help you to find optimal primers that satisfy your requirements.

• DNAMAN allows you to set numerous control criteria for optimal primer filtration, such as the regions of target DNA, size of PCR products, primer characteristics, reaction conditions and primer configurations.

  

• You can carry out a restriction analysis on the primers in order to select those with or without restriction site(s).
• You can discard the primers that are easy to anneal to secondary sites of target DNA using mispriming analysis.

Melting temperature prediction

DNAMAN calculates and reports the thermodynamic Tm, hybridization Tm, and GC+AT Tm of DNA-DNA hybridization. You can also have the Tm information on the hybridization of DNA-RNA and RNA-RNA. These Tms can be used for PCR primers as well as hybridization probes.

Complementarity of primers

Primer complementarity may affect the performance of PCR primers or hybridization probes. DNAMAN analyzes the following three kinds of primer complementarity.

• Self-complementary
  DNAMAN searches for the most possible self-complementary configuration of primers with the lowest free energy.
• Complementarity with target DNA
  DNAMAN searches for the complementary sequences between the primer and both stands of target DNA.
• Two primer complementarity
  DNAMAN searches for complementary sequences between two primers. It reports the continuous and discontinuous complementary sequences.

Mispriming analysis

With mispriming analysis you can search for all possible annealing sites of a primer on target DNA sequence. DNAMAN allows you to set up Score matrix: perfect match, mismatch and G-T match; Position weight matrix, Gap penalty and Cut-off score. This analysis can eliminate PCR primers that are easy to anneal to secondary sites.

Silent mutation primers

Silent mutation analysis allows you to design a desired mutation site on a DNA sequence. This mutation will result in the modification of restriction property without changing the coding amino acid sequence. This function searches for potential mutation positions to create or destroy restriction enzyme sites. You can use this function to design primers to create a silent muation on target DNA sequence.

Directed mismatch primers

Directed mismatch analysis allows you to create or remove restriction sites on a DNA sequence or its mutants (variants) by incorporating mismatch at a site near the mutation. Using this function you can design PCR primers to create or destroy a restriction site in order to distinguish the wild type allele and a common mutant allele.