DNA Fragment Analyzer
Simulate restriction enzyme digests on DNA sequences. Select from 10 common restriction enzymes, run single or double digests, and visualize the resulting fragments on a virtual agarose gel with a 1 kb DNA ladder for size estimation.
Input
Virtual Gel Image
Bands migrate based on log(size). Smaller fragments travel further toward the anode (+).
Reference Guide
Restriction Enzymes
Restriction enzymes (restriction endonucleases) are bacterial proteins that cut DNA at specific recognition sequences. Each enzyme recognizes a unique palindromic sequence, typically 4-8 base pairs long.
EcoRI recognizes the sequence GAATTC and cuts between the G and the first A, producing 5' overhangs (sticky ends).
Gel Electrophoresis
DNA fragments are separated by size using agarose gel electrophoresis. DNA is negatively charged due to its phosphate backbone, so it migrates toward the positive electrode (anode) when an electric field is applied.
Smaller fragments move faster through the gel matrix. A DNA ladder with fragments of known sizes is run alongside samples to estimate unknown fragment sizes.
Fragment Migration
The relationship between fragment size and migration distance is logarithmic. Plotting log(size) versus distance migrated produces a roughly linear standard curve.
where d is the migration distance, m is the slope, and b is the y-intercept. This linear relationship holds well for fragments in the 0.5-10 kb range in standard agarose gels.
Double Digests
A double digest uses two restriction enzymes simultaneously. This produces more fragments than either enzyme alone, which helps map the relative positions of restriction sites on the DNA.
By comparing fragment patterns from single digests (enzyme A alone, enzyme B alone) with the double digest (A + B), scientists can determine the order and spacing of restriction sites on the DNA molecule. This technique was fundamental to early molecular biology before DNA sequencing became routine.