De novo gene synthesis design using TmPrime software.
This chapter presents TmPrime, a computer program to design oligonucleotide for both ligase chain reaction (LCR)- and polymerase chain reaction (PCR)-based de novo gene synthesis. The program divides a long input DNA sequence based on user-specified melting temperatures and assembly conditions, and dynamically optimizes the length of oligonucleotides to achieve homologous melting temperatures. The output reports the melting temperatures, oligonucleotide sequences, and potential formation of secondary structures in a PDF file, which will be sent to the user via e-mail. The program also provides functions on sequence pooling to separate long genes into smaller pieces for multipool assembly and codon optimization for expression based on the highest organism-specific codon frequency. This software has been successfully used in the design and synthesis of various genes with total length >20 kbp. This program is freely available at http://prime.ibn.a-star.edu.sg.
Institute of Bioengineering and Nanotechnology, The Nanos, Singapore. mhli@ibn.a-star.edu.sg
Mo-Huang
MH
Li
Marcus
M
Bode
Mo Chao
MC
Huang
Wai Chye
WC
Cheong
Li Shi
LS
Lim
D001483:Base Sequence; D003062:Codon / Q000235:genetics; D019295:Computational Biology; D006801:Humans; D022521:Ligase Chain Reaction; D008969:Molecular Sequence Data; D009691:Nucleic Acid Denaturation; D009838:Oligodeoxyribonucleotides / Q000096:biosynthesis* / Q000737:chemistry / Q000235:genetics*; D016133:Polymerase Chain Reaction; D012984:Software
D003062:Codon; D009838:Oligodeoxyribonucleotides