密碼子優化（Codon optimization）

Protein production

In order to produce proteins, a cel務她l must first translate t話店he relevant mRNA strand. Following tr對黑anscription, the mRNA exits the nuc科時leus where each group of three nu了白cleotides is matched to a tRN中輛A molecule carrying an amin少鐵o acid (Figure 1A). These groups of 樂鐵3 nucleotides are codons, an拿動d each corresponds to an amino acid. Be放友cause there are only 20 amino acids and這北 many more possible c月件ombinations of nucleotide吃低s, there is redundancy in this co可分de (Figure 1B).

Figure 1. Formation of 但計a protein through transcriptio坐時n and translation (A) of codo舞市ns. Each codon c朋爸orresponds to an amino acid or 自多direction (start/sto作城p).

Codon bias

Although there are multiple options 輛上for making each amino acid,木司 their usage is no又計t based on chance. This is becaus購腦e each species exhibits codon b答微ias, the preference for making 飛舞an amino acid with a certain codon. For農們 instance, alanine (Ala) is coded黃刀 by GCU, GCC, GCA, and GCG (Figure雨子 1B), but in humans, GCC 又間is used about 40% of the time. Di家高fferent organisms have differ多你ent codon preferences, whic新友h influences RNA processing and 下那therefore protein folding an快他d function. This creates complications 是河when expressing one gene in anoth新上er organism, i.e. heterologous gen兵林e expression.

The Codon Adaptat東南ion Index (CAI) is a measure of 如討how well given codons match with 愛自the biases of a員機n organism, rang雜服ing from 0 to 1. A就醫 CAI of 1 reflects a c務子oding sequence wher員老e all amino acids reflect the most 海通frequently used codons in that 村聽organism. Our Codon Optimization tool p畫舞resents a sequence that ba很空lances an optim呢話al CAI with other factor那拿s that can influence molecul了線ar experiments.

Enhancing cloning eff街場iciency

Codon optimization can also aid i舊計n increasing cloning e雜答fficiency based on the distributio到電n of nucleotides across the seq子照uence. GC conten很著t is an important variab朋老le to consider when des些又igning and trouble錢道shooting experiments. If GC conte妹近nt is too high or too low, 少亮stability of the query seq開化uence is negatively affected. 美數 窗山 Our GC Content Calculator tool allows for indepen空知dent GC analysis over an錢去 entire sequence and within segment美兒s of a sequence. However, our Codon計他 Optimization tool incorporates th唱來is analysis to optim哥裡ize this variable by finding微文 synonymous codons that inc他新rease or decrease GC con視相tent as needed.

Additionally, sequences that have市門 a high frequency o慢是f repeats can present complications in 媽身cloning efforts due to the 算有lack of unique primer binding sites報輛, and sequences with recognition 歌司sites for restriction enzymes can pres從船ent challenges in 務視experimental design. Using our Codo林樂n Optimization tool allows for她弟 all of these factors to be optimized i雜現n unison with codon bias to pr分你ovide a sequence that 南公is most likely to efficie白這ntly produce your protein in your s土為ystem.