Article Summary: Anil Kumar, B.N. Mishra, “Primer Premier 4”, Biotechnology Software and Internet Journal, May-June 1997
Automatically selects primers that have the highest probability of success.
Allows conversions from DNA to RNA or protein and back.
Recognizes standard formats and load sequences automatically.
- Restriction Endonuclease Analysis:
Program comes with a list of approximately 300 enzymes.
Enzyme filtration window allows selection of enzymes with specific properties.
Allows selection of enzymes that will leave specific enzymes.
Presents results as table, sequence or restriction maps and provides a list of non-cutters.
- Hybridization, Sequencing and PCR Primers:
Primers to be used for PCR, sequencing and hybridization are selected by Primer Premier.
Search criteria for primer length, melting temperature, percent GC, 3’ end stability, GC clamp, annealing temperature, degeneracy etc. can be defined.
Secondary structures of primers, hairpin loops, dimers, false priming sites and cross dimers are analyzed.
Search parameters can be adjusted manually, or the search may be run in automatic mode.
The automatic search finds primers using stringent criteria, then gradually relaxing the stringency, until the best primers are located.
- Site-Directed Mutagenesis:
Primers can be edited base by base.
As each base is changed, the program instantly calculates all relevant properties including secondary structures, melting temperature, restriction enzyme sites and amino acid translation, allowing easy addition or deletion of restriction enzyme sites and design of mutagenic primers.
- Degenerate Primers:
Primer Premier has the ability to search and select primers for a protein sequence without having the corresponding DNA sequence.
The protein sequence can be reverse-translated using any codon table to a degenerate DNA sequence.
Program can automatically search for primers in the region of lowest degeneracy.
Separate controls for the total percent of ambiguous bases and 3’ end degeneracy maximize the amplification efficiency.
Multiplex / nested window allows primers to be tested for cross compatibility, permitting the selection of two set of primers for nested PCR.
- Primer Database / Synthesis Form:
Database provides ability to import or export primers and save selected primers to file on the disk.
Database also generates easily customized forms for oligo synthesis.
Primer Premier is accompanied by a well-written and self explanatory manual.