Using DNAWorks in designing oligonucleotides for PCR-based gene synthesis

Methods in Molecular Biology

Volumn 852, Issue , 2012, Pages 215-223

  Hoover, David ^a  

^a NATIONAL INSTITUTES OF HEALTH   (United States)

Author keywords

Cloning; Codon optimization; Gene expression; Gene synthesis; Oligonucleotide design; Polymerase chain reaction; Simulated annealing

Indexed keywords

OLIGODEOXYRIBONUCLEOTIDE; SYNTHETIC DNA;

ARTICLE; BIOSYNTHESIS; COMPUTER INTERFACE; COMPUTER PROGRAM; GENETIC ENGINEERING; GENETICS; METHODOLOGY; MUTATION; NUCLEOTIDE SEQUENCE; POLYMERASE CHAIN REACTION;

BASE SEQUENCE; GENES, SYNTHETIC; GENETIC ENGINEERING; MUTATION; OLIGODEOXYRIBONUCLEOTIDES; POLYMERASE CHAIN REACTION; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 84858437097     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-564-0_16     Document Type: Article

References (12)

1. Cox JC, Lape J, Sayed MA and Hellinga HW (2007) Protein fabrication automation. Protein Sci 16:379-390.
2. Sprinzak D, and Elowitz MB (2005) Reconstruction of genetic circuits. Nature 438:443-448.
3. Au LC, Yang FY, Yang WJ, Lo SH and Kao CF (1998) Gene synthesis by a LCR-based approach: High-level production of leptin-L54 using synthetic gene in Escherichia coli . Biochem Biophys Res Commun . 248:200-203.
4. Prodromou C and Pearl L (1992) Recursive PCR: A novel technique for total gene synthesis. Protein Eng 5:827-829.
5. Hoover DM and Lubkowski J (2002) DNAWorks: An automated method for designing oligonucleotides for PCR-based gene synthesis. Nucleic Acids Res 30:e43.
6. Rouillard J-M, Lee W, Truan G, Gao X, Zhou X and Gulari E (2004) Gene2oligo: Oligonucleotide design for in vitro gene synthesis. Nucleic Acids Res 32:W176-W180.
7. Rydzanicz R, Zhao XS and Johnson PE (2005) Assembly PCR oligo maker: A tool for designing oligodeoxynucleotides for constructing long DNA molecules for RNA production. Nucleic Acids Res 33:W521-W525.
8. Richardson SM, Wheelan SJ, Yarrington RM and Boeke JD (2006) GeneDesign: Rapid, automated design of multikilobase synthetic genes. Genome Res 16:550-556.
9. Jayaraj S, Reid R and Santi DV (2005) GeMS: An advanced software package for designing synthetic genes. Nucleic Acids Res 33: 3011-3016.
10. Bode M, Khor S, Ye H, Li,M-H and Ying JY (2009) TmPrime: Fast, fl exible oligonucleotide design software for gene synthesis. Nucleic Acids Res 37:W214-W221.
11. Shevchuk NA, Bryksin AV, Nusinovich YA, Cabello FC, Sutherland, M and Ladisch S (2004) Construction of long DNA molecules using long PCR-based fusion of several fragments simultaneously. Nucleic Acids Res 32:e19.
12. Cheong WC, Lim LS, Huang MC, Bode M and Li M-H (2010) New Insights into the de novo Gene Synthesis Using the Automatic Kinetics Switch Approach. Anal Biochem. 406: 51-60.