Gel Compression

Problems due to sequence context are observed. These problems are usually associated with GC-rich sequence that is problematic due to their high melting temperature. The example in Figure 1 is a GC-rich PCR product that has a compression region between bases 220-230. The peaks are broad and unresolved with overall resolution in the 220-230 base region being poor.

Figure 1. Chromatogram illustrating region of sequence results with gel compression.

The problem was solved by adding an extended denaturation step of 95^oC for 5 minutes prior to loading the sample. Notice in Figure 18 that the peaks are now well defined.

Figure 2. Chromatogram illustrating compression region after denaturing step.