Gel electrophoresis is the process of using an electrical current to separate charged particles based on molecular weight and structure as they are pulled through a gel medium.

Electrophoresis is commonly used to separate DNA fragments (which carry a negative charge) in a medium of agarose gel. 

As these DNA fragments move through the gel, similarly sized fragments move at a similar rate and form bands that can be visualized when properly stained and viewed using a UV or LED Transilluminator.

Small fragments move faster, large fragments move slower, and a pattern emerges. 

The pattern can be analyzed to reveal insights into the nature of the samples.

A DNA ladder works like a molecular yardstick.

If a researcher is trying to determine the size of a DNA fragment, a DNA ladder, which is composed of a selection of known DNA fragment sizes, can be run alongside the unknown samples as a reference.

Since the DNA ladder is a critical point of reference used to determine the size of unknown DNA fragments, the quality and accuracy of the DNA ladder is paramount.

How are DNA ladders made, and what makes one better than the other?

The ACC-PR4000 series SmartCheck™ DNA ladders are an excellent example of DNA ladders that eliminate most errors commonly associated with sample analysis. 

SmartCheck™ DNA ladders are produced from proprietary plasmids, digested to completion, and then purified in a multi-step chromatography process.

Stellar Scientific’s SmartCheck™ DNA Ladders are supplied in a ready-to-use format to reduce any pipetting errors during gel prep. 

Two visible tracking dyes, bromophenol blue and xylene cyanol are included in the mixture so the electrophoresis progress can be monitored in real-time.

Additionally, glycerol is included to add weight to the ladder mixture so it can be added easily into the gel wells without floating away. 

Each fragment in the ladder also has a relative concentration (0.1 mg/mL) that can be used to compare intensity (brightness) of unknown DNA bands to the ladder to estimate quantity.

SmartCheck DNA Ladders are offered in three sizes: 50bp, 100bp, and 1Kb.

Each lot of SmartCheck™ DNA Ladders is tested with a spectrophotometer to confirm DNA concentration, as well as agarose electrophoresis to confirm band sharpness.

How do DNA stains improve electrophoresis results?

To ensure proper viewing of samples/ladders, a quality DNA stain must be used to see clear, distinct bands.

Stellar Scientific’s SmartGlow™ DNA Stains pair perfectly with the SmartCheck DNA Ladders.

SmartGlow stains are ideal for the excitation of nucleic acids via UV and/or blue light illumination. 

Unlike Ethidium Bromide (EtBr), SmartGlow stains are non-mutagenic and environmentally safe (no special disposal methods).

SmartGlow PS (Pre Stain) can be used as a direct replacement for Ethidium Bromide in agarose and polyacrylamide gel electrophoresis.

SmartGlow™ LD (Loading Dye) is supplied at 6X concentration and is added directly to the samples. No dye needs to be added to the gel or running buffer.

Both stains emit green fluorescence when bound to nucleic acids and can be viewed on a UV or blue light transilluminator.