A GC base pair has three intermolecular hydrogen bonds whereas an AT base pair has just two intermolecular hydrogen bonds. Consequently, molecular regions with higher GC content have a more stable secondary structure, which, in turn, can have an impact on PCR. Higher GC content results in higher melting temperatures or specific reagents such as DMSO to break up this secondary GC structure and as a result, GC-rich regions of a sample might be underrepresented during data analysis. You use the NextGENe GC Percentage Calculation tool to determine the GC content of regions in a sample data file.