AutoDimer

AutoDimer screens PCR primers for primer-dimer and hairpin interactions in short DNA oligomers (fewer than 30 nucleotides) to support the design and optimization of multiplex PCR assays probing STR and SNP markers for forensic applications.

Key Features:

• Primer interaction screening: Detects primer-dimer and hairpin interactions in short DNA oligomers to identify unwanted intramolecular and intermolecular bindings.
• Multiplex assay analysis: Simultaneously evaluates numerous primer pairs for multiplex PCR assays involving typically 5–20 loci, exemplified by a 10-plex assay with 20 primers producing 210 potential interactions.
• Sliding overlap algorithm: Employs a sliding algorithm to compare multiple DNA strands in an overlapping manner for pairwise interaction detection.
• Scoring system: Assigns scores to potential duplex interactions and flags those that exceed a user-defined threshold.
• Thermodynamic predictions: Calculates predicted melting temperature (Tm) and free energy of melting (ΔG) for detected interactions.
• Adjustable parameters: Uses adjustable parameters including sodium counterion concentration and total strand concentration in thermodynamic calculations.
• Text output: Writes analysis results, including scores and thermodynamic predictions, to a text file.

Scientific Applications:

• Forensic marker analysis: Supports development of multiplex PCR assays to probe STR and SNP markers for forensic applications.
• Multiplex PCR optimization: Facilitates evaluation and optimization of primer sets for assays spanning multiple loci (5–20 loci).
• Primer design specificity: Improves primer design by identifying and mitigating interactions that reduce PCR efficiency and specificity.

Methodology:

Compares DNA strands using a sliding overlap algorithm, assigns interaction scores against a user-defined threshold, computes Tm and ΔG using adjustable sodium counterion and total strand concentrations, and outputs results to a text file.