Every extraction does the same four things: lyse, separate, wash, elute. The chemistry you use for each step decides yield, purity and how many samples you can run a day.
Range: Nucleic acid extraction and purification4 minute readUpdated
In the presence of chaotropic salts such as guanidine and ethanol, DNA and RNA bind to a silica membrane while proteins and other contaminants pass through. Ethanol washes remove the rest, and a low-salt buffer, typically 10 mM Tris at pH 8 to 8.5, releases the nucleic acid.
Columns are quick, need only a microcentrifuge and give reproducible purity, which makes them the format of most extraction kits. Their limits are throughput and the membrane’s binding capacity.
Paramagnetic particles coated with silica or carboxyl groups bind nucleic acid in the same way, but are collected with a magnet instead of a centrifuge. Without spins, beads handle 96 samples at once on a magnetic stand or a liquid-handling robot, and the protocol scales to different input volumes. They are the standard for high-throughput and automated extraction.
Plant tissue is full of polysaccharides and polyphenols that co-purify with DNA and inhibit PCR. The cationic detergent CTAB (cetyltrimethylammonium bromide) forms complexes that separate them from DNA at high salt.
| Component | Concentration | Role |
|---|---|---|
| CTAB | 2% (w/v) | Lyses membranes; separates polysaccharides |
| Tris-HCl, pH 8.0 | 100 mM | Buffer |
| EDTA | 20 mM | Chelates Mg²⁺ to inhibit nucleases |
| NaCl | 1.4 M | High salt keeps polysaccharides out of the DNA fraction |
| PVP | 1–2% (optional) | Binds polyphenols |
| β-mercaptoethanol | 0.2%, added just before use | Prevents polyphenol oxidation |
Organic extraction partitions proteins into a phenol phase and leaves nucleic acids in the aqueous phase, followed by alcohol precipitation. Acid guanidinium thiocyanate-phenol reagents (TRIzol-type) do the same for RNA while inactivating RNases. These methods give high yields from many sample types, but they are slow, hard to scale and use toxic solvents. Most labs now reserve them for samples that columns handle poorly.
| Method | Speed | Throughput | Purity | Hazards | Best for |
|---|---|---|---|---|---|
| Spin column | Fast | Low to medium | High | Low | Most routine extractions |
| Magnetic beads | Fast | High, automatable | High | Low | 96-well and automated workflows |
| CTAB | Slow | Low | Good for plants | Chloroform, β-ME | Polysaccharide-rich plant tissue |
| Phenol-chloroform | Slow | Low | Good with care | Phenol, chloroform | High yield from difficult samples |
| Salting out | Medium | Low to medium | Moderate | Low | Genomic DNA from blood |
Different samples bring different contaminants. The extraction by sample type guide covers blood, tissue, plant, stool, viral samples and plasmids one by one, and the PCR vs qPCR guide covers what happens next.
For most samples, a silica spin-column kit gives the best balance of speed, purity and safety. Magnetic beads are better for high throughput and automation. CTAB suits plant tissue rich in polysaccharides, and organic extraction suits difficult samples where yield matters most.
It is used to extract DNA from plant tissue. The detergent CTAB lyses cells and, at high salt, separates DNA from the polysaccharides and polyphenols that plants contain, which would otherwise inhibit PCR.
Spin columns suit a few to a few dozen samples with simple equipment. Magnetic beads suit 96-well plates and automation, and adapt more easily to different sample volumes.
Common causes are incomplete lysis, too much starting material overloading the column, ethanol left on the membrane before elution, or eluting in too small a volume. Pre-warming the elution buffer and a second elution can also help.
For research use only. Protocols here are general outlines: follow your kit manual and your institution’s safety rules. See our editorial policy.
Products for this workflow
DNA, RNA and plasmid kits, with sample-specific kits for blood, tissue, plant, fecal and viral RNA samples.
DNA and RNA extraction
Blood brings heme, plants bring polysaccharides, stool brings humic acids and tough bacteria, viral samples bring almost no RNA. Here is what each sample needs from an extraction kit.
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qPCR / RT-PCR
End-point PCR tells you whether a sequence is there, qPCR tells you how much, and RT-qPCR does the same for RNA. Here is what changes between them and the reagent list for each.
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DNA and RNA extraction
A poor A260/230 usually means salt or phenol carry-over rather than bad RNA. Low yield usually starts at lysis. Here is how to read the numbers and what to change.
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