Thermodynamics

Oligonucleotide optimization for DNA synthesis

  1. Tobias M. Louw,
  2. Scott E. Whitney,
  3. Joel R. TerMaat,
  4. Elsje Pienaar,
  5. Hendrik J. Viljoen*

Article first published online: 29 SEP 2010

DOI: 10.1002/aic.12410

Issue

AIChE Journal

AIChE Journal

Volume 57, Issue 7, pages 1912–1918, July 2011

Additional Information

How to Cite

Louw, T. M., Whitney, S. E., TerMaat, J. R., Pienaar, E. and Viljoen, H. J. (2011), Oligonucleotide optimization for DNA synthesis. AIChE J., 57: 1912–1918. doi: 10.1002/aic.12410

Author Information

  1. Dept. of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE, 68588

*Dept. of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, NE, 68588

Publication History

  1. Issue published online: 9 JUN 2011
  2. Article first published online: 29 SEP 2010
  3. Accepted manuscript online: 23 AUG 2010 10:38AM EST
  4. Manuscript Revised: 6 AUG 2010
  5. Manuscript Received: 19 FEB 2010

Funded by

  • National Institutes of Health. Grant Number: R33 RR022860

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Keywords:

  • DNA synthesis;
  • bioengineering;
  • optimization;
  • melting temperature;
  • oligonucleotide

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. © 2010 American Institute of Chemical Engineers AIChE J, 2011

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