Oligonucleotide optimization for DNA synthesis

Tobias M. Louw, Scott E. Whitney, Joel R. Termaat, Elsje Pienaar, Hendrik J Viljoen

Research output: Contribution to journalArticle

2 Citations (Scopus)

Abstract

Large DNA constructs can be synthesized from smaller oligonucleotides using the polymerase chain reaction. The set of oligonucleotides should be designed so that the melting temperature amongst oligonucleotide hybridization pairs do not vary greatly and the length of each oligonucleotide should not exceed 50 nucleotides. A near optimal oligonucleotide set is calculated using reliable gradient optimization methods. This was accomplished by defining a set of discrete arrays that is used to determine the melting temperature of a subset of the larger DNA sequence, depending on the subset start and end positions. These arrays were then incorporated into an objective function, which was optimized using the Broyden-Fletcher-Goldfarb-Shanno method. This method is adjusted slightly to incorporate explicit length and temperature constraints. Experimental results confirmed that the method performs better than similar software programs for the cases investigated and produces suitable oligonucleotide sets for DNA assembly.

Original languageEnglish (US)
Pages (from-to)1912-1918
Number of pages7
JournalAIChE Journal
Volume57
Issue number7
DOIs
StatePublished - Jul 1 2011

Fingerprint

Oligonucleotides
DNA
Freezing
Temperature
Melting point
Polymerase chain reaction
DNA sequences
Nucleotides
Software
Polymerase Chain Reaction

Keywords

  • Bioengineering
  • DNA synthesis
  • Melting temperature
  • Oligonucleotide
  • Optimization

ASJC Scopus subject areas

  • Biotechnology
  • Environmental Engineering
  • Chemical Engineering(all)

Cite this

Louw, T. M., Whitney, S. E., Termaat, J. R., Pienaar, E., & Viljoen, H. J. (2011). Oligonucleotide optimization for DNA synthesis. AIChE Journal, 57(7), 1912-1918. https://doi.org/10.1002/aic.12410

Oligonucleotide optimization for DNA synthesis. / Louw, Tobias M.; Whitney, Scott E.; Termaat, Joel R.; Pienaar, Elsje; Viljoen, Hendrik J.

In: AIChE Journal, Vol. 57, No. 7, 01.07.2011, p. 1912-1918.

Research output: Contribution to journalArticle

Louw, TM, Whitney, SE, Termaat, JR, Pienaar, E & Viljoen, HJ 2011, 'Oligonucleotide optimization for DNA synthesis', AIChE Journal, vol. 57, no. 7, pp. 1912-1918. https://doi.org/10.1002/aic.12410
Louw TM, Whitney SE, Termaat JR, Pienaar E, Viljoen HJ. Oligonucleotide optimization for DNA synthesis. AIChE Journal. 2011 Jul 1;57(7):1912-1918. https://doi.org/10.1002/aic.12410
Louw, Tobias M. ; Whitney, Scott E. ; Termaat, Joel R. ; Pienaar, Elsje ; Viljoen, Hendrik J. / Oligonucleotide optimization for DNA synthesis. In: AIChE Journal. 2011 ; Vol. 57, No. 7. pp. 1912-1918.
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