PCR & qPCR · 4 min read

Primer PICKR: from published primers to your qPCR workflow

Find literature-supported primer candidates, review their evidence and connect primer selection with your PCR or qPCR workflow.

What Primer PICKR provides

Primer PICKR helps researchers find primer pairs extracted from published literature. Its ranking combines evidence of use with sequence properties and pair compatibility. Treat the ranking as a starting point for selecting candidates, rather than proof that an assay will perform well in your samples.

Search the right gene and species

Open Primer PICKR, select the organism and enter the official gene symbol. Narrow the results by melting temperature, GC content, primer length, amplicon length and literature evidence. Review forward and reverse sequences together with the linked publications. Combined citations may refer to either individual primer; shared citations indicate that both sequences occur together. Read the original methods to confirm the assay context.

Check specificity before ordering

Use NCBI Primer-BLAST to evaluate an existing primer pair against the relevant organism and database. Both sequences should be entered in the 5′ to 3′ direction. For transcript-focused work, check the intended transcript and exon structure; the RefSeq mRNA options help assess exon-junction or intron-related requirements. A literature ranking does not replace this specificity check.

Compare candidates under consistent conditions

Use the EcoTech Primer Tm Calculator with the same reaction settings for both primers, then review the Primer Pair Compatibility Checker and Primer Dimer Predictor. Differences between tools can reflect different calculation settings. Keep the selected sequences, source publications and analysis conditions in your experiment record. Computational screening is one stage of assay development, not experimental validation.

Choose reagents for the assay format

For a two-step gene-expression workflow, EcoScript 5x First Strand cDNA Synthesis Kit supports the cDNA preparation stage, followed by a suitable qPCR reagent. ClearPeak 2x SYBR Master Mix is the dye-based option; ClearPeak 2x Probe Master Mix requires an appropriate probe as well as primers. For endpoint PCR, review EcoTaq DNA Polymerase or EcoTaq HotStart DNA Polymerase. Consult each linked datasheet for compatibility and reaction conditions; no particular Primer PICKR pair is claimed to be validated with these products.

Plan normalization separately

Finding primers for a commonly used reference gene does not establish that the gene is stable in your experiment. Use the Housekeeping Gene Finder to review context-specific candidates and supporting literature. Validate normalization controls in your own samples and consider multiple reference genes.