GC 함량 계산

DNA 템플릿의 GC 함량은 원하는 백본에 타겟 유전자 클로닝의 성공 여부를 결정하는 중요한 요소입니다. GC 함량이 높은 유전자 템플릿은 종종 self-dimers 또는2차 구조를 형성할 가능성이 높고, 더 높은 annealing 온도가 필요합니다.

이 도구를 사용하면 유전자 내의 특정 영역 뿐만 아니라 전체 유전자 서열의 GC 함량을 결정할 수 있습니다. DNA 또는 RNA 서열을 입력하면 각 염기 유형의 수와 퍼센트가 계산됩니다. 윈도우 크기를 조정하면 서열 내의 작거나 큰 부위의 GC 함량을 그래픽 판독값으로 시각화할 수 있습니다.

GC 함량 계산 Crash Course in GC Content

Nucleotide bonds

In DNA and RNA, the distribution of bases has a significant impact on our ability to study and manipulate genes. Within the double helix, adenine always binds to thymine (or uracil in RNA) using two hydrogen bonds, while guanine binds to cytosine using three hydrogen bonds (Figure 1). The higher the number of hydrogen bonds, the more energy required to separate the two nucleotide bases. Therefore, GC pairs will have higher stability than AT pairs. The percentage of GC base pairs in genomes is highly variable, but most species range from 30-60%, with humans averaging 41%.

Nucleotide bonds

Figure 1. Binding of nucleotides across DNA strands (A), with highlighted hydrogen bonds for thymine-adenine pairs (B) and cytosine-guanine pairs (C).

Applications of GC content

When considering a fragment of DNA, for primer design or cloning of an entire gene, it is important to note GC content given the higher amount of energy required to break the three hydrogen bonds. Polymerase chain reaction (PCR) is a widely utilized tool where GC content is of high importance. DNA strands must be broken apart (denatured), and primers must be able to bind to the correct position on the DNA strand (annealing) for amplification. The distribution of nucleotides can influence both processes: DNA templates with high GC content may require higher denaturation temperatures, and high GC content in primers necessitates higher annealing temperatures. The optimal GC content for primers is around 50-55%, but high amplification can be achieved with GC content between 40 and 60%.

Determining the GC content of an entire sequence as well as distribution within a sequence is a valuable tool when designing and troubleshooting experiments. In addition to performing GC content analysis here, a GC content calculator is also built into our Codon Optimization and shRNA Design tools. Both applications can be explored on our Tools page and can be applied to directly to your cloning experiment in the Vector Design Studio.

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