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Author Notes:

To whom correspondence should be addressed. Tel: +1 404 727 7766; Email: jen.heemstra@emory.edu

The authors would like to thank Prof. John Chaput and his laboratory for the generous gift of KOD RI plasmids and technical advice.

We would also like to thank Dr. Mike Hanson from the University of Utah DNA/peptide core facility for chemical synthesis of the TNA polymers and Dr. Thomas Schubert from 2bind GmbH for performing the MST experiments.

Conflict of interest statement. None declared.

Subjects:

Research Funding:

DARPA Folded Non-Natural Polymers with Biological Function (Fold F(x)) Program [N66001-14-2-4054].

Any opinions, findings and conclusions or recommendations expressed in this publication are those of the authors and do not necessarily reflect the views of DARPA.

Funding for open access charge: DARPA Folded Non-Natural Polymers with Biological Function (Fold F(x)) Program [N66001-14-2-4054]; National Science Foundation [CBET 1818476 to J.M.H.].

Keywords:

  • In vitro
  • XNA aptamer
  • small-molecule recognition
  • threose nucleic acid
  • ochratoxin A
  • experiment

In vitro selection of an XNA aptamer capable of small-molecule recognition.

Journal Title:

Nucleic Acids Research

Volume:

Volume 46, Number 16

Publisher:

, Pages 8057-8068

Type of Work:

Article | Final Publisher PDF

Abstract:

Despite advances in XNA evolution, the binding capabilities of artificial genetic polymers are currently limited to protein targets. Here, we describe the expansion of in vitro evolution techniques to enable selection of threose nucleic acid (TNA) aptamers to ochratoxin A (OTA). This research establishes the first example of an XNA aptamer of any kind to be evolved having affinity to a small-molecule target. Selection experiments against OTA yielded aptamers having affinities in the mid nanomolar range; with the best binders possessing KD values comparable to or better than those of the best previously reported DNA aptamer to OTA. Importantly, the TNA can be incubated in 50% human blood serum for seven days and retain binding to OTA with only a minor change in affinity, while the DNA aptamer is completely degraded and loses all capacity to bind the target. This not only establishes the remarkable biostability of the TNA aptamer, but also its high level of selectivity, as it is capable of binding OTA in a large background of competing biomolecules. Together, this research demonstrates that refining methods for in vitro evolution of XNA can enable the selection of aptamers to a broad range of increasingly challenging target molecules.

Copyright information:

C The Author(s) 2018. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access work distributed under the terms of the Creative Commons Attribution-NonCommercial 4.0 International License (http://creativecommons.org/licenses/by-nc/4.0/).

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