Exploring the sequence space of a DNA aptamer using microarrays

Evaldas Katilius, Carole Flores, Neal Woodbury

Research output: Contribution to journalArticlepeer-review

106 Scopus citations


The relationship between sequence and binding properties of an aptamer for immunoglobulin E (IgE) was investigated using custom DNA microarrays. Single, double and some triple mutations of the aptamer sequence were created to evaluate the importance of specific base composition on aptamer binding. The majority of the positions in the aptamer sequence were found to be immutable, with changes at these positions resulting in more than a 100-fold decrease in binding affinity. Improvements in binding were observed by altering the stem region of the aptamer, suggesting that it plays a significant role in binding. Results obtained for the various mutations were used to estimate the information content and the probability of finding a functional aptamer sequence by selection from a random library. For the IgE-binding aptamer, this probability is on the order of 10-10 to 10-9. Results obtained for the double and triple mutations also show that there are no compensatory mutations within the space defined by those mutations. Apparently, at least for this particular aptamer, the functional sequence space can be represented as a rugged landscape with sharp peaks defined by highly constrained base compositions. This makes the rational optimization of aptamer sequences using step-wise mutagenesis approaches very challenging.

Original languageEnglish (US)
Pages (from-to)7626-7635
Number of pages10
JournalNucleic acids research
Issue number22
StatePublished - Dec 2007

ASJC Scopus subject areas

  • Genetics


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