DNA GC Content Calculator

DNA GC content

The GC content is the percentage of nitrogenous bases guanine (G) and cytosine (C) in a DNA sequence: %GC = (G + C) / (A + T + G + C) · 100%. Example: in ATGCGTACGTAC (12 bases), there are 3 G + 3 C = 6 → %GC = 50%. A G-C pair holds together with three hydrogen bonds, against only two for A-T, which is why GC-rich DNA is more thermally stable and has a higher melting temperature (Tm). Genomes vary widely. Thermophilic bacteria such as Thermus thermophilus reach ~70% GC, the human genome averages ~41%, and the malaria parasite Plasmodium falciparum sits unusually low at ~19%.

Applications

It comes up in bioinformatics (gene and CpG island annotation), in PCR (primer design, where 40-60% GC is the target), in phylogeny as a taxonomic marker, in oligonucleotide design for qPCR and sequencing, and in molecular biology when studying nucleic-acid stability and gene expression.

FAQ

Why does GC content affect Tm? Because G-C makes three hydrogen bonds against two for A-T, so denaturing the double helix takes more energy. For short oligos, the Wallace rule estimates Tm = 2(A+T) + 4(G+C).

Is high GC always good for PCR? No. Above 60% GC you start seeing secondary structures and primer-dimers; below 40% the primers turn unstable. The safe zone is 40-60%.

Why does Plasmodium have such low GC? It comes down to mutational bias and selection on metabolism. The parasite favours AT in coding regions, and that in turn shapes codon usage and the evolution of resistance genes.