Jul 25, 2025

Public workspaceRapid DNA Extraction from sediment using spin columns (teaching)

DOI
https://dx.doi.org/10.17504/protocols.io.3byl467d8go5/v1
  • Linda Armbrecht1,
  • Sophie Franke1
  • 1Ecology and Biodiversity Center, Institute for Marine and Antarctic Studies, University of Tasmania
Sophie Franke
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DOI: https://dx.doi.org/10.17504/protocols.io.3byl467d8go5/v1
Protocol Citation: Linda Armbrecht, Sophie Franke 2025. Rapid DNA Extraction from sediment using spin columns (teaching). protocols.io https://dx.doi.org/10.17504/protocols.io.3byl467d8go5/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 occasionally for teaching and it's working well.
Created: July 17, 2025
Last Modified: July 25, 2025
Protocol Integer ID: 222689
Keywords: rapid dna extraction from sediment, qiagen soil dna extraction kit, dna extraction, rapid dna extraction, dna from sediment material, extraction method for the rapid extraction, rapid extraction, extraction method, extraction, using spin column, spin column, dna, sediment, sediment material, dna binding, purification component, soil
Abstract
An extraction method for the rapid extraction of DNA from sediment material, using a Lysis Buffer from Rohland et al. (2018) and DNA binding and purification components of a Qiagen Soil DNA extraction kit.
Troubleshooting
DNA Lysis and Isolation
Lysis

Note
General advice

  • Use best practise pipetting techniques (e.g., wear gloves, avoid contamination)


Add 500 µL lysis buffer to your sample (your tutors will do this 24 hrs prior to the prac).Sample0,25 g sediment
AB
Lysis Buffer ComponentsVol. (uL)
0.5M EDTA (pH 8)450
H2037.25
Tween 200.25
Proteinase K12.5
Total500

Vortex briefly to mix sediments with lysis buffer (your tutors will do this 24 hrs prior to the prac).
Incubate over night on rotator (your tutors will do this 24 hrs prior to the prac).
Shaker10 rpm, Room temperature 17 hrs

Wipe the outside of the tubes with 80 % ethanol.
Note
  • wipe especially along the rim of the tubes, as they are the most prone to contamination
  • label your tubes clearly again, in case the labeling has been removed from the ethanol

Centrifuge the tubes for 2 minutes at 16,400 g to separate the lysate from undigested sample material.

Note
Before starting step 1.4:

  • clean the centrifuge rotor surface with a bit of ethanol
  • ensure the centrifuge is balanced (i.e., an even number of tubes, each tube contains the same volume of liquid, tubes are arranged opposite of each other)
  • ensure the lid is on the rotor before closing the centrifuge and turning it on


Transfer the lysate to a fresh 1.7 mL tube. Be careful not to transfer any sediment.


Note
  • it's useful to place the pipette over the lowest point of the pellet while you're taking up the supernatant, do not touch the pellet
  • pipette slowly and continuously

Bind DNA
Add 1200 µL of Solution C4 (50 - 70 % guanidinhydrochlorid + 1 - 10 % isopropylalcohol) to the supernatant and vortex for 5 s.



Loading procedure (3 x) of the spin column
Load the first 675 µL of the supernatant onto an Spin Column and centrifuge. Centrifigation10000 x g , room temperature, 1 min.
Discard the flow-through.

Load the second 675 µL of the supernatant onto an Spin Column and centrifuge.Centrifigation10000 x g , room temperature, 1 min.
Discard the flow-through.
Load the rest of the supernatant onto an Spin Column and centrifuge.Centrifigation10000 x g , room temperature, 1 min.
Discard the flow-through.
Wash
Removing any contaminants / residues from the filter membrane
Add 500 µL of Solution C5 (= 70 % ethanol) to the spin column.
Centrifuge the spin column and discard the flow-through.
Centrifigation10000 x g , 30 s, room temperature

Centrifuge the spin column again and discard the flow-through with the collection tube.
Centrifigation10000 x g , 1 min, room temperature

Carefully place the spin column in a clean 1.7 mL tube. Avoid splashing any Solution C5 onto the spin column.

Note
  • don't touch the spin column itself (risk of contamination), only the rim (top of column where the lid is)

Elute
Elute the bound DNA from the filter membrane.
Add 25 µL of Elution Buffer (EB / C6 buffer) to the center of the white filter membrane, let sit for 2 minutes.

Note
  • It's important to double check whether the membrane filter has fully soaked up all of the 25 µL of C6 buffer. Aim to get the elution buffer into the centre of the filter membrane, but avoid touching the filter membrane with the pipette tip!
  • Stick to the incubation time. Incubating for a bit longer is okay, but you shouldn't incubate for a shorter period of time.

Critical
Centrifuge Centrifigation10000 x g , 30 s
and discard the Spin Column but keep the tube containing your extracted DNA!

Combine the replicate sediment DNA extracts in one tube.
Leave the control extract in a separate tube.
Expected result
  • 1 x tube with ~ 75 µL of transparent DNA extract --> ready for downstream applications

  • 1 x tube with the extraction control

Storage
Store your DNA extract and control (clearly labeled in a rack or cryo box) in the freezer at -20 °C until the next prac.