Gibson Assembly Calculator:

This program will take a nucleic acid sequence and return the 60 base oligos you need to perform the Gibson assembly, and calculate the molecular weight and GC content. The Gibson assembly was developed to make very large DNA sequences in a efficient and simple manner, and in the original form involves chemically synthesizing 60 base 5' and 3' oligonucleotides which overlap by 20 bases and cover both strands of the desired final product. These oligonucleotides are treated with a mixture of DNA ligase, exonuclease and polymerase and in 1 hour the desired sequence is generated! The original Gibson et al. paper was published in 2009 and the method has been used to generate functioning synthetic eukaryotic chromosomes and entire mitochondrial and prokaryote genomes. In our simple program sequence should be single letter DNA code, so A, T, G and C, and it does not matter if the input is upper or lower case or mixed. At present the program will not ignore numbers, spaces, characters like B or Z which do not correspond to one of the 4 DNA bases in the DNA sequence. We will fix this problem, but for now enter your sequence without any other characters but A, T, G and C. However it can take FASTA format sequences, and will ignore text following the ">" character, the first item in a FASTA file, until there is a line feed/carriage return character. It will print out the molecular weight of the sequence you entered along with the molecular weight and will then print out a list of the 60 base oligos, each overhanging the next by 20 bases, used to make the upper strand of the desired sequence. It then prints out the corresponding 60 base sequences used to make the lower strands. So all you have to do is paste in your desired sequence, copy and paste the output into a wordprocessor or spreadsheet program and email to whoever makes your oligonucleotides.

Disclaimer: This program was constructed primarily to save time for busy researchers around the world. We hope you find it useful, and we are confident that it is accurate and reliable. However, we cannot be held responsible for any problems which may arise as a result of the use of this program.

©EnCor Biotechnology Inc. . To go to EnCor Homepage Press Here