Bio-Rad CHEF Mapper® XA System User Manual

Page 62

Problem

Solution

Applications:

Bands smeary or fuzzy

1. Excessive heating. Lower the voltage or ionic

strength of the buffer

2. Improper switch interval (see Section 9.1)
3. Gel percentage too low; increase
4. Sample degraded; impure enzymes, or wash

cycles too short (agarose blocks)

5. Agarose impurities; consult Bio-Rad
6. Sample overload; adjust sample concentration

Large DNAs not resolved

1. Lower the voltage gradient to below 2 V/cm
2. Increase switch time
3. Agarose impurities

High background in lanes

1. Insufficient washing of samples
2. Sample may be contaminated with RNA or

other material

3. DNA concentration too high

Distorted bands

1. Sample contains too high salt or detergent

concentration

2. Buffer breakdown; change every 24 hours
3. Wells were distorted; recast gel
4. Sample plugs were crushed when placed in

wells

5. Pump flow rate too low; check for kink along

tubing

Thick bands

1. Use thinner wells
2. Load less sample