Top Questions

Can you design and synthesize a set of sequencing primers?

Design forward and reverse sequencing primers using our free PrimerQuest® tool (under the SciTools® Tab at www.idtdna.com).  After opening the tool, click "Show Custom Design Parameters", and choose the forward or reverse sequencing parameter set. Primer Position:  The best sequencing data is typically found 80-150 bp out from the primer; it is difficult to get good base calls <50 bp and >300 bp from the primer.  Primer Design: Primers should be between 18-30 nt long with an optimal length of 20-25 nt;  have a G-C content between 40-60%; and a Tm between 55-65°C. Avoid primers that form strong self-dimers or hairpins. Use our free OligoAnalyzer® tool (also found under the SciTools Menu) to check for such structures. Avoid primers which are 90% homologous to other regions within your sample. We recommend running a BLAST search to check for sequence homology; this can be done from within the OligoAnalyzer software.
Tags:
  • Oligoanalyzer
  • primerquest
  • sequencing
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