High-affinity five/six-letter DNA aptamers with superior specificity enabling the detection of dengue NS1 protein variants beyond the serotype identification

Ken-ichiro Matsunaga, Michiko Kimoto, Vanessa Weixun Lim, Hui Pen Tan, Yu Qian Wong, William Sun, Shawn Vasoo, Yee Sin Leo, and Ichiro Hirao

Nucleic Acids Research, gkab515, doi:10.1093/nar/gkab515

Introducing unnatural bases (UBs) to expand the genetic alphabet of DNA beyond its four base letters, A, T, G, and C, dramatically augments the affinities of DNA aptamers that bind to target proteins. By generating a series of UB-containing DNA (UB-DNA) aptamers (KD: 27−182 pM) targeting each of four dengue non-structural protein 1 (DEN-NS1) serotypes, the authors demonstrate that UB-DNA aptamers obtained by affinity selection could spontaneously achieve high specificity. The extraordinary selectivity of each aptamer allows it to precisely recognize subtle variants of DEN-NS1 with at least 96.9% amino acid sequence identity, far beyond the capability of serotype identification (69‒80% sequence identities). Detection methods incorporating the UB-DNA aptamers will facilitate rapid and accurate diagnoses of viral infections and other diseases.

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