PRISE

PRISE designs sequence-selective PCR primers to distinguish target from non-target DNA sequences for selective amplification.

Key Features:

• Automated Mismatch Placement: Automates placement of primer-template mismatches at the 3' end to increase sequence selectivity.
• Two-Step Design Process: First identifies target and non-target DNA sequences and then crafts primers to amplify targets while minimizing amplification of non-targets.
• Sorting Tools: Organizes candidate primers by properties such as amplicon length, GC content, and sequence selectivity.
• Versatile Specificity: Supports design of primers with varying specificities to target individual sequences or broader gene assemblies.
• User-Defined Primer Analysis: Analyzes user-provided primers against target and non-target sequences to report relevant properties.

Scientific Applications:

• Genomics: Design sequence-selective PCR primers for genomic analyses and sequence discrimination.
• Microbiology: Discriminate closely related microbial sequences for identification and detection.
• Molecular Diagnostics: Develop PCR assays that selectively amplify target pathogen or biomarker sequences while avoiding non-targets.
• Demonstrated Utility: Applied to design sequence-selective PCR primers for the rRNA gene of the fungus Pochonia chlamydosporia.

Methodology:

Identification of target and non-target sequences; automated placement of primer-template mismatches at the 3' end; primer design to minimize non-target amplification; analysis and sorting of candidate primers by amplicon length, GC content, and sequence selectivity.