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Volumn 4, Issue 3, 2008, Pages 324-336

Computationally optimised DNA assembly of synthetic genes

Author keywords

Bioinformatics; CODA; Computational biology; Computationally optimised DNA assembly; DNA self assembly; Gene synthesis; Synthetic biology

Indexed keywords

DNA FRAGMENT; OLIGONUCLEOTIDE; PROTEIN TY3 INTEGRASE; SYNTHETIC DNA;

EID: 47749113643     PISSN: 17445485     EISSN: 17445493     Source Type: Journal    
DOI: 10.1504/IJBRA.2008.019578     Document Type: Article
Times cited : (17)

References (25)
  • 1
    • 0038620436 scopus 로고    scopus 로고
    • Codon pairs in the genome of Escherichia coli
    • Boycheva, S., Chkodrov, G. and Ivanov, I. (2003) 'Codon pairs in the genome of Escherichia coli', Bioinformatics, Vol. 19, pp.987-998.
    • (2003) Bioinformatics , vol.19 , pp. 987-998
    • Boycheva, S.1    Chkodrov, G.2    Ivanov, I.3
  • 3
    • 0031573461 scopus 로고    scopus 로고
    • PCR-based gene synthesis and protein NMR spectroscopy
    • Casimiro, D.R., Wright, P.E. and Dyson, H.J. (1997) 'PCR-based gene synthesis and protein NMR spectroscopy', Structure, Vol. 5, pp.1407-1412.
    • (1997) Structure , vol.5 , pp. 1407-1412
    • Casimiro, D.R.1    Wright, P.E.2    Dyson, H.J.3
  • 4
    • 0020363515 scopus 로고
    • Preferential codon usage in prokaryotic genes: The optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes
    • Grosjean, H. and Fiers, W. (1982) 'Preferential codon usage in prokaryotic genes: the optimal codon-anticodon interaction energy and the selective codon usage in efficiently expressed genes', Gene, Vol. 18, pp.199-209.
    • (1982) Gene , vol.18 , pp. 199-209
    • Grosjean, H.1    Fiers, W.2
  • 5
    • 0024673103 scopus 로고
    • Nonrandom utilization of codon pairs in Escherichia coli
    • Gutman, G.A. and Hatfield, G.W. (1989) 'Nonrandom utilization of codon pairs in Escherichia coli', Proc. Natl. Acad. Sci. U.S.A., Vol. 86, pp.3699-3703.
    • (1989) Proc. Natl. Acad. Sci. U.S.A , vol.86 , pp. 3699-3703
    • Gutman, G.A.1    Hatfield, G.W.2
  • 6
    • 0000263398 scopus 로고
    • Codon pair utilization bias in bacteria, yeast and mammals
    • CRC Press, Boca Raton, FL, pp
    • Hatfield, D.L., Lee, B.J. and Pirtle, R.M. (1993) 'Codon pair utilization bias in bacteria, yeast and mammals', Transfer RNA in Protein Synthesis, CRC Press, Boca Raton, FL, pp.157-190.
    • (1993) Transfer RNA in Protein Synthesis , pp. 157-190
    • Hatfield, D.L.1    Lee, B.J.2    Pirtle, R.M.3
  • 7
    • 0029162727 scopus 로고
    • Codon pair utilization biases influence translational elongation step times
    • Irwin, B., Heck, J.D. and Hatfield, G.W. (1995) 'Codon pair utilization biases influence translational elongation step times', J. Biol. Chem., Vol. 270, pp.22801-22806.
    • (1995) J. Biol. Chem , vol.270 , pp. 22801-22806
    • Irwin, B.1    Heck, J.D.2    Hatfield, G.W.3
  • 8
  • 9
    • 0036277249 scopus 로고    scopus 로고
    • Investigating the relationship between genome structure, composition, and ecology in prokaryotes
    • Lio, P. (2002) 'Investigating the relationship between genome structure, composition, and ecology in prokaryotes', Mol. Biol. E, Vol. 19, pp.789-800.
    • (2002) Mol. Biol. E , vol.19 , pp. 789-800
    • Lio, P.1
  • 10
    • 0023737075 scopus 로고
    • FokI method of gene synthesis
    • Mandecki, W. and Bolling, T.J. (1988) 'FokI method of gene synthesis', Gene, Vol. 68, pp.101-107.
    • (1988) Gene , vol.68 , pp. 101-107
    • Mandecki, W.1    Bolling, T.J.2
  • 11
    • 0033591465 scopus 로고    scopus 로고
    • Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure
    • Mathews, D.H., Sabina, J., Zuker, M. and Turner, D.H. (1999) 'Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure', J. Mol. Biol., Vol. 288, pp.911-940.
    • (1999) J. Mol. Biol , vol.288 , pp. 911-940
    • Mathews, D.H.1    Sabina, J.2    Zuker, M.3    Turner, D.H.4
  • 12
    • 0036606766 scopus 로고    scopus 로고
    • eCodonOpt: A systematic computational framework for optimizing codon usage in directed evolution experiments
    • Moore, G.L. and Maranas, C.D. (2002) 'eCodonOpt: a systematic computational framework for optimizing codon usage in directed evolution experiments', Nucleic Acids Res., Vol. 30, pp.2407-2416.
    • (2002) Nucleic Acids Res , vol.30 , pp. 2407-2416
    • Moore, G.L.1    Maranas, C.D.2
  • 13
    • 0027050148 scopus 로고
    • Recursive PCR: A novel technique for total gene synthesis
    • Prodromou, C. and Pearl, L.H. (1992) 'Recursive PCR: a novel technique for total gene synthesis', Protein Eng., Vol. 5, pp.827-829.
    • (1992) Protein Eng , vol.5 , pp. 827-829
    • Prodromou, C.1    Pearl, L.H.2
  • 14
    • 0032539693 scopus 로고    scopus 로고
    • A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics
    • SantaLucia Jr., J. (1998) 'A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics', Proc. Natl. Acad. Sci. U.S.A., Vol. 95, pp.1460-1465.
    • (1998) Proc. Natl. Acad. Sci. U.S.A , vol.95 , pp. 1460-1465
    • SantaLucia Jr., J.1
  • 15
    • 0031804028 scopus 로고    scopus 로고
    • DNA nanotechnology: Novel DNA constructions
    • Seeman, N.C. (1998) 'DNA nanotechnology: novel DNA constructions', Annu. Rev. Biophys. Biomol. Struct., Vol. 27, pp.225-248.
    • (1998) Annu. Rev. Biophys. Biomol. Struct , vol.27 , pp. 225-248
    • Seeman, N.C.1
  • 16
    • 0032860161 scopus 로고    scopus 로고
    • DNA engineering and its application to nanotechnology
    • Seeman, N.C. (1999) 'DNA engineering and its application to nanotechnology', Trends Biotechnol., Vol. 17, pp.437-443.
    • (1999) Trends Biotechnol , vol.17 , pp. 437-443
    • Seeman, N.C.1
  • 17
    • 0023650543 scopus 로고
    • The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications
    • Sharp, P.M. and Li, W.H. (1987) 'The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications', Nucleic Acids Res., Vol. 15, pp.1281-1295.
    • (1987) Nucleic Acids Res , vol.15 , pp. 1281-1295
    • Sharp, P.M.1    Li, W.H.2
  • 18
    • 0347364647 scopus 로고    scopus 로고
    • Generating a synthetic genome by whole genome assembly: PhiX174 bacteriophage from synthetic oligonucleotides
    • Smith, H.O., Hutchison III, C.A., Pfannkoch, C. and Venter, J.C. (2003) 'Generating a synthetic genome by whole genome assembly: phiX174 bacteriophage from synthetic oligonucleotides', Proc. Natl. Acad. Sci. U.S.A., Vol. 100, pp.15440-15445.
    • (2003) Proc. Natl. Acad. Sci. U.S.A , vol.100 , pp. 15440-15445
    • Smith, H.O.1    Hutchison III, C.A.2    Pfannkoch, C.3    Venter, J.C.4
  • 19
    • 0024405193 scopus 로고
    • Codon usage determines translation rate in Escherichia coli
    • Sorensen, M.A., Kurland, C.G. and Pedersen, S. (1989) 'Codon usage determines translation rate in Escherichia coli', J. Mol. Biol., Vol. 207, pp.365-377.
    • (1989) J. Mol. Biol , vol.207 , pp. 365-377
    • Sorensen, M.A.1    Kurland, C.G.2    Pedersen, S.3
  • 20
    • 0028784138 scopus 로고
    • Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides
    • Stemmer, W.P., Crameri, A., Ha, K.D., Brennan, T.M. and Heyneker, H.L. (1995) 'Single-step assembly of a gene and entire plasmid from large numbers of oligodeoxyribonucleotides', Gene, Vol. 164, pp.49-53.
    • (1995) Gene , vol.164 , pp. 49-53
    • Stemmer, W.P.1    Crameri, A.2    Ha, K.D.3    Brennan, T.M.4    Heyneker, H.L.5
  • 21
    • 0024002906 scopus 로고
    • Optimization of ligation reaction conditions in gene synthesis
    • Theriault, N.Y., Carter, J.B. and Pulaski, S.P. (1988) 'Optimization of ligation reaction conditions in gene synthesis', Biotechniques, Vol. 6, pp.470-474.
    • (1988) Biotechniques , vol.6 , pp. 470-474
    • Theriault, N.Y.1    Carter, J.B.2    Pulaski, S.P.3
  • 22
    • 0031579372 scopus 로고    scopus 로고
    • Splicing by overlap extension by PCR using asymmetric amplification: An improved technique for the generation of hybrid proteins of immunological interest
    • Warrens, A.N., Jones, M.D. and Lechler, R.I. (1997) 'Splicing by overlap extension by PCR using asymmetric amplification: an improved technique for the generation of hybrid proteins of immunological interest', Gene, Vol. 186, pp.29-35.
    • (1997) Gene , vol.186 , pp. 29-35
    • Warrens, A.N.1    Jones, M.D.2    Lechler, R.I.3
  • 23
    • 0024477261 scopus 로고
    • On finding all suboptimal foldings of an RNA molecule
    • Zuker, M. (1989) 'On finding all suboptimal foldings of an RNA molecule', Science, Vol. 244, pp.48-52.
    • (1989) Science , vol.244 , pp. 48-52
    • Zuker, M.1
  • 24
    • 0042121256 scopus 로고    scopus 로고
    • Mfold web server for nucleic acid folding and hybridization prediction
    • Zuker, M. (2003) 'Mfold web server for nucleic acid folding and hybridization prediction', Nucleic Acids Res., Vol. 31, pp.3406-3415.
    • (2003) Nucleic Acids Res , vol.31 , pp. 3406-3415
    • Zuker, M.1
  • 25
    • 0002287019 scopus 로고    scopus 로고
    • Algorithms and thermodynamics for RNA secondary structure prediction: A practical guide
    • Kluwer Academic Publishers, Dordrecht, pp
    • Zuker, M., Mathews, D.H. and Turner, D.H. (1999) 'Algorithms and thermodynamics for RNA secondary structure prediction: a practical guide', RNA Biochemistry and Biotechnology, Kluwer Academic Publishers, Dordrecht, pp.11-43.
    • (1999) RNA Biochemistry and Biotechnology , pp. 11-43
    • Zuker, M.1    Mathews, D.H.2    Turner, D.H.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.