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

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High-affinity five/six-letter DNA aptamers with superior specificity enabling the detection of dengue NS1 protein variants beyond the serotype identification
Title:
High-affinity five/six-letter DNA aptamers with superior specificity enabling the detection of dengue NS1 protein variants beyond the serotype identification
Other Titles:
Nucleic Acids Research
Publication Date:
25 June 2021
Citation:
Matsunaga, K., Kimoto, M., Lim, V. W., Tan, H. P., Wong, Y. Q., Sun, W., … Hirao, I. (2021). High-affinity five/six-letter DNA aptamers with superior specificity enabling the detection of dengue NS1 protein variants beyond the serotype identification. Nucleic Acids Research. doi:10.1093/nar/gkab515
Abstract:
Abstract Genetic alphabet expansion of DNA by introducing unnatural bases (UBs), as a fifth letter, dramatically augments the affinities of DNA aptamers that bind to target proteins. To determine whether UB-containing DNA (UB-DNA) aptamers obtained by affinity selection could spontaneously achieve high specificity, we have generated a series of UB-DNA aptamers (KD: 27−182 pM) targeting each of four dengue non-structural protein 1 (DEN-NS1) serotypes. The specificity of each aptamer is remarkably high, and the aptamers can recognize the subtle variants of DEN-NS1 with at least 96.9% amino acid sequence identity, beyond the capability of serotype identification (69−80% sequence identities). Our UB-DNA aptamers specifically identified two major variants of dengue serotype 1 with 10-amino acid differences in the DEN-NS1 protein (352 aa) in Singaporeans’ clinical samples. These results suggest that the high-affinity UB-DNA aptamers generated by affinity selection also acquire high target specificity. Intriguingly, one of the aptamers contained two different UBs as fifth and sixth letters, which are essential for the tight binding to the target. These two types of unnatural bases with distinct physicochemical properties profoundly expand the potential of DNA aptamers. Detection methods incorporating the UB-DNA aptamers will facilitate precise diagnoses of viral infections and other diseases.
License type:
Attribution 4.0 International (CC BY 4.0)
Funding Info:
This research / project is supported by the National Research Foundation Singapore - Competitive Research Programme
Grant Reference no. : NRF-CRP17-2017-07

This research is supported by core funding from: Institute of Bioengineering and Bioimaging
Grant Reference no. :
Description:
This is a version of record of an article accepted for publication in Nucleic Acids Research following peer review. The version of record Matsunaga, K., Kimoto, M., Lim, V. W., Tan, H. P., Wong, Y. Q., Sun, W., … Hirao, I. (2021). High-affinity five/six-letter DNA aptamers with superior specificity enabling the detection of dengue NS1 protein variants beyond the serotype identification. Nucleic Acids Research. doi:10.1093/nar/gkab515 is also available online at: http://dx.doi.org/10.1093/nar/gkab515
ISSN:
0305-1048
1362-4962