Primerize

Primerize designs primers for PCR assembly of DNA templates to enable synthesis of RNA molecules for in vitro transcription (e.g., with T7 RNA polymerase).

Key Features:

• Optimized Primer Design: Minimizes mispriming at primer boundaries to improve specificity and efficiency during PCR assembly.
• Fixed-Sequence Compatibility: Targets primer design for fixed RNA sequences used in custom RNA synthesis workflows.
• Cost and Performance Optimization: Designs template primers to balance reagent cost and assembly performance.
• Scalable Target Lengths: Capable of handling RNA domains up to 300 nucleotides in length.
• Validated Algorithm: Algorithm has been extensively tested under wide-ranging conditions.

Scientific Applications:

• Custom RNA synthesis for in vitro transcription: Designs DNA templates for production of RNA molecules for downstream in vitro transcription with T7 RNA polymerase.
• Assembly of longer sequences: Facilitates PCR-based assembly of sequences longer than tens of nucleotides as an alternative to chemical synthesis or gel/chromatographic purification.

Methodology:

Computational algorithm optimizes primer boundaries to minimize mispriming for fixed input sequences and has been extensively tested.