Reliable PCR Purification Kit

October 05, 2026

BlueskyReddit
Stanford University
Biochemistry
Senior Research Scientist

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Company:

Zymo Research

Product Name:

DNA Clean & Concentrator-25

Catalog Number:

D4033

WNT signaling is essential for embryonic development and adult tissue homeostasis, and its aberrant activation drives several cancers, most notably colorectal cancer. My lab studies the molecular mechanisms of oncogenic WNT signal transduction, with the goal of identifying therapeutic vulnerabilities in colorectal cancer. To generate precise point mutations in endogenous pathway genes, we introduce edits with Cas9 RNP electroporation and single-stranded donor templates (ssODNs), which we produce in-house. I use the Zymo Research DNA Clean & Concentrator-25 (Cat# D4033) to purify the PCR products used as substrates in that workflow.

Experimental Design and Results Summary

Application

Molecular Biology

Starting Material

PCR product

Tips

None

Results Summary

I used this kit to purify short dsDNA amplicons (86 and 92 bp) generated by Phusion PCR, which served as substrates for lambda exonuclease digestion to produce long single-stranded donor templates for homology-directed repair at the AXIN1 locus. Pooled reactions were loaded at one column per 100 µL of PCR reaction. Recovery was excellent for fragments of this size: purified dsDNA came off at 50–60 ng/µL, giving roughly 5–6 µg per column, which was enough to proceed directly to exonuclease treatment. The purified DNA worked well as an enzymatic substrate, and the resulting ssODNs supported successful Cas9 RNP-mediated editing in HAP1 cells.

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Summary

The Good

Two things stood out. First, recovery of very short fragments: at 86–92 bp, many clean-up columns lose substantial material, but this kit returned 5–6 µg per column, consistent with Zymo's stated size range down to about 50 bp. Second, the eluate was clean enough for direct downstream enzymology, with lambda exonuclease digestion working without any additional clean-up step. The 25 µg capacity accommodates pooled PCR reactions, so I could consolidate eight reactions onto a small number of columns, and the small elution volume gave a concentrated product, which mattered because the downstream exonuclease reaction had a fixed volume.

The Bad

None

The Bottom Line

The Zymo DNA Clean & Concentrator-25 delivers high recovery of short PCR products and eluate clean enough to feed directly into enzymatic reactions.

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