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Complementary Strands
Special, Online Only Articles from IDT

Primer Design Improved, Batch Entry Added: The New PrimerQuest® Design Tool

We are pleased to announce release of a new, improved version of PrimerQuest® software, IDT's foundational design tool for sequencing, endpoint PCR, and qPCR. 

What's new?

Improved Primer and Probe DesignPrimerQuest

  • Significant improvements made to overall parameter criteria for primer/probe size, Tm, and %GC
  • Additional checks added for homodimer, homodimer 3′ end, heterodimer, and heterodimer 3′ end
  • Added checks to ensure the probe does not have a 5′ end G 
  • Improved default parameters for GC Clamp, Poly X, and Pair Max Difference Tm
  • Primer3 engine updated to version 2.2.3 

Design Primers for up to 50 Sequences at a Time

  • Submit up to 50 sequences to PrimerQuest software via Excel upload, a list of GenBank Accession IDs or RefSeq IDs, or manual entry in FASTA format

Simplified and Streamlined User InterfacePrimerQuest Results

  • Design primers for common experiment types with one click
  • Or, easily access customizable design parameter settings

New Design Functions

  • Greater solution variability
  • Added parameters for targeting exon junctions
  • Option to force primers to 3` or 5` ends (for applications like SNP detection)

What is PrimerQuest


PrimerQuest software is IDT’s foundational PCR and qPCR design tool and, hence, one of our most widely used SciTools® applications. As well as serving the primer design needs of customers who perform sequencing and endpoint PCR, it serves customers whose research involves qPCR in species other than human, mouse, and rat (for human, mouse, and rat, use the IDT PrimeTime® Assay Library Selection Tool).