Intact genomic DNA runs as a single tight, high-molecular-weight band near the top of an agarose gel; degraded DNA shows up as a smear trailing down the lane. A quick gel is the simplest way to check gDNA before long-read sequencing, restriction digests or PCR of long amplicons, because absorbance ratios cannot see fragmentation.
How to run a gDNA integrity gel
- Gel: 0.7–1% agarose, so very large fragments enter the gel and stay distinguishable.
- Load: about 50–200 ng gDNA alongside a ladder that includes high-molecular-weight markers.
- Run: lower voltage (about 3–5 V/cm) for sharper high-molecular-weight bands.
- Handle gently: wide-bore tips and minimal vortexing prevent shearing during loading.
Reading the lane
- Intact: one compact band above the top ladder band; little signal below.
- Partially degraded: high band present but with a smear tailing downward.
- Heavily degraded: no distinct high band, a smear concentrated at lower sizes.
- RNA contamination: a diffuse cloud at the bottom of the lane.
- Protein or salt problems: material stuck in the well or distorted, “smiling” lanes.
Clean vs messy PCR products
- Clean: one sharp band at the expected size.
- Primer-dimer: a fuzzy band below about 100 bp.
- Non-specific products: extra discrete bands — raise annealing temperature or redesign primers.
- Smear: too much template, too many cycles, or degraded template.
When you need to recover a band, a gel extraction kit purifies DNA fragments from agarose for cloning or sequencing.
What a gel cannot tell you
Agarose gels give approximate size and semi-quantitative amount. Use fluorescence for accurate concentration, absorbance ratios for chemical purity (A260/A280 guide), and pulsed-field or capillary methods for precise sizing of very long DNA.
Common questions
What does intact genomic DNA look like on an agarose gel?
A single tight, high-molecular-weight band near the top of the gel, above the largest ladder band, with little or no smear below it.
What does degraded genomic DNA look like?
A smear running down the lane toward lower sizes, with a weak or missing high-molecular-weight band.
What is the faint band at the bottom of my gDNA lane?
Usually RNA carried over from extraction. Treat with RNase A if downstream applications need RNA-free DNA.
How accurate is agarose gel electrophoresis for size and amount?
It gives approximate sizes and semi-quantitative amounts by comparison with a ladder. For precise concentration use fluorescence; for very large DNA sizing, use pulsed-field or capillary methods.
What should a clean PCR product look like on a gel?
One sharp band at the expected size, with no primer-dimer band below ~100 bp, no extra bands and no smear. Non-specific bands or smears suggest annealing or template problems.
Need cleaner RNA to start with? Changyu Biotech supplies silica-column RNA extraction kits such as the CYRN28 Plus RNA Mini Kit and a full range of RNA/DNA extraction kits for research labs worldwide. Request a quote.