Synthesis and Evolution of a Threose Nucleic Acid Aptamer Bearing 7‑Deaza-7-Substituted Guanosine Residues

• Published in: Journal of the American Chemical Society Vol. 140; no. 17; pp. 5706 - 5713
• Main Authors: Mei, Hui, Liao, Jen-Yu, Jimenez, Randi M, Wang, Yajun, Bala, Saikat, McCloskey, Cailen, Switzer, Christopher, Chaput, John C
• Format: Journal Article
• Language: English
• Published: WASHINGTON American Chemical Society 02.05.2018; Amer Chemical Soc
• Subjects: Chemistry; Chemistry, Multidisciplinary; Physical Sciences; Science & Technology; SYSTEM; HALOGEN BONDS; BASE-PAIRS; REPLICATION; GENETIC POLYMERS; RNA; TNA; TRANSCRIPTION; IN-VITRO SELECTION; DNA-POLYMERASE
• DOI: 10.1021/jacs.7b13031
• ISSN: 0002-7863

In vitro selection experiments carried out on artificial genetic polymers require robust and faithful methods for copying genetic information back and forth between DNA and xeno-nucleic acids (XNA). Previously, we have shown that Kod-RI, an engineered polymerase developed to transcribe DNA templates into threose nucleic acid (TNA), can function with high fidelity in the absence of manganese ions. However, the transcriptional efficiency of this enzyme diminishes greatly when individual templates are replaced with libraries of DNA sequences, indicating that manganese ions are still required for in vitro selection. Unfortunately, the presence of manganese ions in the transcription mixture leads to the misincorporation of tGTP nucleotides opposite dG residues in the templating strand, which are detected as G-to-C transversions when the TNA is reverse transcribed back into DNA. Here we report the synthesis and fidelity of TNA replication using 7-deaza-7-modified guanosine base analogues in the DNA template and incoming TNA nucleoside triphosphate. Our findings reveal that tGTP misincorporation occurs via a Hoogsteen base pair in which the incoming tGTP residue adopts a syn conformation with respect to the sugar. Substitution of tGTP for 7-deaza-7-phenyl tGTP enabled the synthesis of TNA polymers with >99% overall fidelity. A TNA library containing the 7-deaza-7-phenyl guanine analogue was used to evolve a biologically stable TNA aptamer that binds to HIV reverse transcriptase with low nanomolar affinity.