PCRsetup

PCRsetup facilitates planning and computational analysis of PCR and qPCR primer design and reaction conditions to optimize oligonucleotide selection and predict properties relevant to nucleic acid amplification experiments.

Key Features:

• Primer Design: Supports design of primers for standard, multiplex, long-distance, inverse, real-time, unique, group-specific, bisulphite modification assays, Overlap-Extension PCR Multi-Fragment Assembly, and oligonucleotide sets for ligase chain reaction-based sequence assembly.
• Oligonucleotide Property Prediction: Predicts oligonucleotide properties by analyzing experimental studies of PCR efficiency and computes melting temperatures for standard and degenerate oligonucleotides, including locked nucleic acids (LNA)-modified oligos.
• Comprehensive Analyses: Performs detailed analyses of individual primers and primer pairs, including detection of potential dimer formations and G-quadruplex structures.
• Complexity Assessment: Evaluates linguistic complexity of oligonucleotides to inform sequence selection that minimizes secondary structure formation.
• Dilution and Resuspension Calculator: Provides calculations for dilutions and resuspensions to prepare oligonucleotide solutions.
• Room-temperature PCR setup without hot-start enzymes: Supports planning of PCR reactions intended to be set up at room temperature without the need for hot-start enzymes.

Scientific Applications:

• Molecular biology: Supports primer design and reaction planning for PCR and qPCR experiments in molecular biology research.
• Genetics: Assists in designing and evaluating primers and assays for genetic analyses that rely on nucleic acid amplification.
• Diagnostics: Enables assay development and specificity assessment for diagnostic PCR and qPCR applications.
• Nucleic acid amplification workflows: Aids workflows requiring precise nucleic acid amplification through optimized primer selection and reaction condition prediction.

Methodology:

Analyzes empirical PCR efficiency data to inform predictive calculations of oligonucleotide properties and melting temperatures (including degenerate and LNA-modified oligos) and applies computational analyses to detect primer dimers and G-quadruplex structures.