The formula
GC content (%) = (G + C) ÷ (A + T + G + C) × 100
Count only A, C, G and T; ambiguous bases such as N are left out of both numbers. The sequence ATGCGCTAAGCC has 12 bases with 7 G or C, so its GC content is 7 ÷ 12 = 58%. Both strands have the same GC content, because every G pairs with a C.
Why GC matters
- Stability: G-C pairs have three hydrogen bonds and stack more strongly than A-T pairs, so GC-rich DNA melts at a higher temperature.
- Primers: aim for 40 to 60% GC and a melting temperature of 55 to 65 °C. A G or C at the 3' end (a GC clamp) helps the primer bind, but more than three in the last five bases causes mispriming.
- PCR: templates above about 65% GC form secondary structure and need additives (DMSO, betaine) or a higher denaturation temperature.
- Sequencing and cloning: very high or very low GC gives uneven coverage and harder assembly.
Typical values
- Human genome: 41% overall, from 35% to over 60% in different regions.
- E. coli: 51%. Saccharomyces cerevisiae: 38%.
- Plasmodium falciparum: 19%, among the lowest known.
- Streptomyces and other actinomycetes: over 70%.
GC skew
GC skew, (G − C) ÷ (G + C) in a sliding window, measures which strand has more G. In bacterial genomes it flips sign at the origin and terminus of replication, so a skew plot locates the origin.
Tools
DNA Stats gives the GC content, base counts and melting temperature of any sequence, for one record or a whole FASTA file. The Primer Tm Calculator checks GC and Tm for primers, and the CpG Island Finder scans GC-rich regions for CpG islands.