May 12, 2026

Chelex DNA Extraction

DOI
https://dx.doi.org/10.17504/protocols.io.261geymw7v47/v1
  • Jordan Sims1,
  • Scott Burgess2
  • 1UC Berkeley;
  • 2Florida State University
  • Cryptic Pocillopora FP
Jordan Sims
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DOI: https://dx.doi.org/10.17504/protocols.io.261geymw7v47/v1
Protocol Citation: Jordan Sims, Scott Burgess 2026. Chelex DNA Extraction. protocols.io https://dx.doi.org/10.17504/protocols.io.261geymw7v47/v1
License: This is an open access  protocol  distributed under the terms of the  Creative Commons Attribution License,  which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited
Protocol status: Working
We use this protocol and it's working
Created: April 28, 2026
Last Modified: May 12, 2026
Protocol  Integer ID: 315906
Keywords: chelex dna extraction extract dna, using chelex, chelex 100 resin, dna
Abstract
Extract DNA from 112 samples (swabs stored in DNA/RNA Shield) using Chelex 100 Resin
Active time: ~2 hour
Incubation time: 1 hour, 20 minutes
Total time: ~3 hours, 20 minutes
Materials
Equipment required
  • Heat block(s) with 112 slots for 1.5mL tubes
  • Fine point Sharpie
  • Vortex with 1.5mL tube attachment
  • 1.5mL tube rack(s)
  • Mini spinner with 1.5mL tube attachment
  • Microcentrifuge
  • 20µL pipette
  • 200µL pipette
  • One 200µL pipette tip (for aliquoting Chelex solution to all tubes in Step 4)
  • Freezer
 
Consumable materials (per sample)
  • One 1.5mL microcentrifuge tube
  • 100µL 10% Chelex solution (Bio-Rad, cat. #1421253)
  • One 20µL pipette tip
  • One 200µL pipette tip
  • One 2mL cryovial


Before start
This protocol describes a fast and cost-effective method for extracting DNA from swabs of coral tissue stored in DNA/RNA Shield, but any extracted DNA can be used with the subsequent steps of the workflow.
Turn on heat block and set to 55ºC
Prepare one 1.5mL microcentrifuge tube per sample and label with SampleID by writing on the tube lid directly with a fine point Sharpie
Vortex the stock 10% Chelex solution for 60 seconds
Add 100µL 10% Chelex solution to each tube. Vortex Chelex solution every few samples to keep it suspended, as it falls out of solution very quickly
Vortex 24 sample tubes with swab in DNA/RNA Shield on max speed for 5 minutes
Transfer 10µL of DNA/RNA Shield from the sample tube into a pre-filled, labeled 1.5mL microcentrifuge tube containing 100µL 10% Chelex solution
Repeat Steps 5–6 four more times until all 112 samples are processed
Note: To save time, the next batch of samples can be vortexing while the current batch is being transferred into tubes with Chelex
Note: The final batch will only have 16 tubes
Vortex 24 microcentrifuge tubes on max speed for 30 seconds. Tap the tube on the bench to send most of the liquid to the bottom of the tube, or spin it in mini spinner, if necessary
Repeat Step 8 four more times until all 112 samples are processed
Incubate microcentrifuge tubes in the heat block at 55ºC for 60 minutes, then 95ºC for 20 minutes
Return tubes with swabs back to the fridge
During the incubation, label 2mL cryovials with SampleIDs, “DNA”, and date using a fine point Sharpie
After the incubation, centrifuge 24 microcentrifuge tubes at 14,000 rpm for 3 minutes to pellet the Chelex solution
Transfer ~80µL supernatant to a clean, labeled 2mL cryovial for long-term storage. Do not transfer *any* of the pelleted Chelex, as this will inhibit downstream PCR reactions
Repeat Steps 13–14 four more times until all 112 samples are processed
Note: To save time, the next batch of samples can be centrifuging while the current batch is being transferred into cryovial
Note: The final batch will only have 16 tubes
Store extracted DNA in the freezer