Convergent evolution to an aptamer observed in small populations on DNA microarrays

Phys Biol. 2010 Sep 1;7(3):036007. doi: 10.1088/1478-3975/7/3/036007.


The development of aptamers on custom synthesized DNA microarrays, which has been demonstrated in recent publications, can facilitate detailed analyses of sequence and fitness relationships. Here we use the technique to observe the paths taken through sequence-fitness space by three different evolutionary regimes: asexual reproduction, recombination and model-based evolution. The different evolutionary runs are made on the same array chip in triplicate, each one starting from a small population initialized independently at random. When evolving to a common target protein, glucose-6-phosphate dehydrogenase (G6PD), these nine distinct evolutionary runs are observed to develop aptamers with high affinity and to converge on the same motif not present in any of the starting populations. Regime specific differences in the evolutions, such as speed of convergence, could also be observed.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Aptamers, Nucleotide / chemistry*
  • Aptamers, Nucleotide / genetics
  • Computer Simulation
  • Glucosephosphate Dehydrogenase / chemistry
  • Glucosephosphate Dehydrogenase / metabolism
  • Models, Genetic
  • Oligonucleotide Array Sequence Analysis*


  • Aptamers, Nucleotide
  • Glucosephosphate Dehydrogenase