A DNA ladder is only useful if its bands bracket your fragment on the gel you are running. This guide matches ladder ranges to agarose percentages and covers loading, staining and quantification.
Range: Molecular biology reagents4 minute readUpdated
DNA fragments move through an agarose gel at a speed set mainly by their length, so fragments of known size run in the next lane give you a ruler. Comparing your band with the ladder tells you its approximate size. Because most ladders also state how much DNA is in each band, comparing brightness gives a rough estimate of quantity too. Ladders are also called DNA markers or DNA molecular weight standards.
| Ladder | Typical range | Use it for |
|---|---|---|
| Low range (10, 25 or 50 bp steps) | About 10–700 bp | Primers, small PCR products, small RNA work |
| 100 bp ladder | About 100–1,500 bp | Most PCR and RT-PCR products |
| 1 kb ladder | About 250 bp–10 kb | Plasmids, restriction digests, large PCR products |
| Broad range | About 100 bp–10 kb | Mixed samples on one gel |
| High molecular weight | Above 10 kb | Genomic DNA integrity checks |
Agarose percentage decides which sizes separate well. Too dilute a gel and small fragments run off the end; too concentrated and large fragments barely move.
| Agarose | Separates linear DNA of about |
|---|---|
| 0.5% | 1–30 kb |
| 0.7% | 0.8–12 kb |
| 1.0% | 0.5–10 kb |
| 1.2% | 0.4–7 kb |
| 1.5% | 0.2–3 kb |
| 2.0% | 0.05–2 kb |
Compare the brightness of your band with ladder bands of known mass. If a ladder band of 50 ng looks as bright as your band, your band holds roughly 50 ng. It is a quick estimate, good to about a factor of two, and useful when you are checking a PCR product before cloning. For accurate quantities use a fluorometric assay.
Protein ladders, such as prestained ladders spanning about 5–245 kDa, are a different product. They size proteins in kilodaltons on SDS-PAGE gels and western blots, and the prestained bands show transfer to the membrane. If you are blotting, see the lysis buffer guide and the antibody range.
You will use a ladder at several points in a cloning project: checking the PCR insert, confirming a restriction digest and screening colonies. The cloning workflow guide walks through each step, and the molecular biology range includes DNA ladders alongside polymerases and cloning systems.
For most PCR products under about 1.5 kb, a 100 bp ladder on a 1.5–2% agarose gel. For larger products, a 1 kb ladder on a 0.8–1% gel.
Common causes are a supercoiled plasmid running faster than linear DNA, very different salt concentrations between sample and ladder, overloading, or a gel that was run too fast. Linearise plasmids and keep loading buffers consistent.
Yes, for example by digesting lambda DNA with a restriction enzyme, but a commercial ladder gives evenly spaced, accurately sized bands with known masses, which matters for sizing and quantification.
Follow the datasheet. Ready-to-load ladders are often stable at 4 °C for a few months and at -20 °C long term. Avoid repeated freeze-thaw cycles.
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
Cloning systems, DNA molecular weight standards and DNA polymerases for cloning, PCR and gel analysis.
Molecular biology
Cloning is a chain of small steps, and most failures trace back to one of them. Here is the whole chain, the reagent each step needs, and how to check you have the right clone before you build on it.
4 minute read
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.
4 minute read
Molecular biology
Read the gel first. No band, a smear, extra bands and a fuzzy band under 100 bp each point to a different change, and the positive control tells you whether to trust the mix.
3 minute read
Send the product names or catalogue numbers, quantities and delivery country. We'll confirm availability, lead time and the documents for molecular biology reagents.