GenScript offers a variety of DNA ladders with sizes ranging from 100 bp to 3 kb for use in agarose gel electrophoresis. All DNA ladders can be supplied in a ready-to-use mix with no need to heat or dilute prior to loading. Because a key to accurate band analysis is using the appropriate DNA ladder for your application, GenScript provides the following table to help you choose the best ladder for your specific needs.
Each ladder contains nucleic acid fragments of specific base pair lengths designed as a size reference for linear PCR products. The 100 bp DNA ladders provide accurate sizing of nucleic acid small fragments from 100 to 1,500 bp for use as molecular weight standards for agarose gel electrophoresis. The 500 base pair bands have increased intensity to serve as reference points. Two formats can be offered as listed:
The 100bp Plus DNA ladder is composed of 8 bands which are 100 bp, 250 bp, 500 bp, 750 bp, 1000 bp, 1500 bp, 2000 bp and 3000 bp. The 500 bp band is more intense and easily distinguishable as a reference point.
The GenScript PCR DNA Ladder is composed of seven bands of 100 bp, 300 bp, 500 bp, 700 bp, 1,000 bp, 1,500 bp, and 2,000 bp. The 500 bp band is more intense and easily distinguishable as a reference point.
Q1. Which process can increase the band sharpness to avoid smeared DNA bands?
1. Use fresh electrophoresis buffers, freshly poured gels, nuclease free vials and tips to minimize nuclease contamination of DNA solutions.
2. Do not allow voltage to exceed ~20 V/cm. Maintain a temperature <30° C during electrophoresis.
3. Samples containing high concentrations of salts may result in smeared band patterns. Washing the pellet with ice cold 75% ethanol and suspending the sample in water or TE buffer will eliminate salts present in the sample.
4. When inserting the comb into the gel, make sure that it is vertical to the gel surface and stable during gel casting and solidification.
1. Electrophoresis buffer should completely cover the entire gel during sample loading and run.
2. The sample volume should be large enough to fill 1/3 of the total capacity of the well. Large wells should not be used with small sample volumes. If needed the sample volume can be adjusted with 1X loading dye.
3. Do not use an excessively high voltage for electrophoresis. Run the gels at 5-8 V/cm. To minimize band curving, use a lower voltage for several minutes at the beginning of electrophoresis.
4. Use pure water, clean flasks and clean equipment for preparation of gels. Pour the gel slowly avoiding formation of bubbles.
1. The correct gel percentage is important for optimal separation of the marker DNA.
When preparing agarose gels always adjust the gel percentage to more than 1.2%. Otherwise, the gel percentage will be too low and result in missing low range DNA bands.
2. The presence of DNA binding proteins in the sample, such as ligases, phosphatases or restriction enzymes may alter DNA migration in the gel or cause the DNA to remain in the gel wells.
3. DNA with long complementary overhangs may anneal resulting in an atypical migration pattern.