Computational Sequence Design with R2oDNA Designer

Methods Mol Biol. 2017;1651:249-262. doi: 10.1007/978-1-4939-7223-4_18.


Recently developed DNA assembly methods have enabled the rapid and simultaneous assembly of multiple parts to create complex synthetic gene circuits. A number of groups have proposed the use of computationally designed orthogonal spacer sequences to guide the ordered assembly of parts using overlap-directed or homologous recombination-based methods. This approach is particularly useful for assembling multiple parts with repetitive elements. Orthogonal spacer sequences (sometimes called UNSs-unique nucleotide sequences) also have a number of other potential uses including in the design of synthetic promoters regulated by novel regulatory elements.

Keywords: Biologically neutral sequences; Computational design; DNA assembly; Orthogonal sequences; Spacer sequences; Unique nucleotide sequences (UNSs).

MeSH terms

  • Algorithms
  • Animals
  • DNA / genetics*
  • Escherichia coli / genetics
  • Gene Regulatory Networks*
  • Homologous Recombination
  • Humans
  • Repetitive Sequences, Nucleic Acid*
  • Saccharomyces cerevisiae / genetics
  • Software*
  • Synthetic Biology


  • DNA