Predicting the Genetic Stability of Engineered DNA Sequences with the EFM Calculator

ACS Synth Biol. 2015 Aug 21;4(8):939-43. doi: 10.1021/acssynbio.5b00068. Epub 2015 Jul 1.


Unwanted evolution can rapidly degrade the performance of genetically engineered circuits and metabolic pathways installed in living organisms. We created the Evolutionary Failure Mode (EFM) Calculator to computationally detect common sources of genetic instability in an input DNA sequence. It predicts two types of mutational hotspots: deletions mediated by homologous recombination and indels caused by replication slippage on simple sequence repeats. We tested the performance of our algorithm on genetic circuits that were previously redesigned for greater evolutionary reliability and analyzed the stability of sequences in the iGEM Registry of Standard Biological Parts. More than half of the parts in the Registry are predicted to experience >100-fold elevated mutation rates due to the inclusion of unstable sequence configurations. We anticipate that the EFM Calculator will be a useful negative design tool for avoiding volatile DNA encodings, thereby increasing the evolutionary lifetimes of synthetic biology devices.

Keywords: computer-aided design (CAD); design-build-test cycle; genetic engineering; genetic robustness; hypermutable site; metabolic engineering.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • DNA / genetics*
  • Directed Molecular Evolution*
  • Genetic Engineering*
  • Sequence Analysis, DNA / methods*
  • Software*


  • DNA