TY - JOUR
T1 - Thermostability Trends of TNA:DNA Duplexes Reveal Strong Purine Dependence
AU - Lackey, Hershel H.
AU - Peterson, Eric M.
AU - Chen, Zhe
AU - Harris, Joel M.
AU - Heemstra, Jennifer M.
N1 - Funding Information:
HHL was supported by the Air Force Institute of Technology Civilian Institute Program. This work was supported by the 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. This work was also supported by the National Science Foundation (DMR 1822262 and CHE 1818781 to J. Heemstra and CHE 1608949 to J. Harris). The authors would like to thank Dr. Peter Flynn for his review of the manuscript.
Publisher Copyright:
© 2019 American Chemical Society.
PY - 2019/5/17
Y1 - 2019/5/17
N2 - The development of high fidelity polymerases and streamlined synthesis of threose nucleic acid (TNA) triphosphates and phosphoramidites has made TNA accessible as a motif for generating nuclease-resistant high-affinity aptamers, antisense oligos, and synthetic genetic biopolymers. Little is known, however, about the thermostability trends of TNA:DNA duplexes. Here we investigate the thermostability of 14 TNA:DNA duplexes with the goal of elucidating the fundamental factors governing TNA:DNA duplex stability. We find that purine content in TNA significantly influences the stability and conformation of TNA:DNA duplexes. Low TNA purine content destabilizes duplexes, with Tm values often 5 °C lower than analogous DNA:DNA and RNA:DNA duplexes. By contrast, TNA:DNA duplexes having high TNA purine content display greater stability than DNA:DNA or RNA:DNA duplexes having the same sequences. High TNA purine content leads TNA:DNA duplexes to adopt conformations similar to RNA:RNA (A-form) configuration, whereas duplexes with low TNA purine content have conformations more similar to DNA:DNA (B-form) configuration. These insights provide a basis for understanding and predicting TNA:DNA duplex stability, which is anticipated to guide the practical use of TNA in biotechnology applications.
AB - The development of high fidelity polymerases and streamlined synthesis of threose nucleic acid (TNA) triphosphates and phosphoramidites has made TNA accessible as a motif for generating nuclease-resistant high-affinity aptamers, antisense oligos, and synthetic genetic biopolymers. Little is known, however, about the thermostability trends of TNA:DNA duplexes. Here we investigate the thermostability of 14 TNA:DNA duplexes with the goal of elucidating the fundamental factors governing TNA:DNA duplex stability. We find that purine content in TNA significantly influences the stability and conformation of TNA:DNA duplexes. Low TNA purine content destabilizes duplexes, with Tm values often 5 °C lower than analogous DNA:DNA and RNA:DNA duplexes. By contrast, TNA:DNA duplexes having high TNA purine content display greater stability than DNA:DNA or RNA:DNA duplexes having the same sequences. High TNA purine content leads TNA:DNA duplexes to adopt conformations similar to RNA:RNA (A-form) configuration, whereas duplexes with low TNA purine content have conformations more similar to DNA:DNA (B-form) configuration. These insights provide a basis for understanding and predicting TNA:DNA duplex stability, which is anticipated to guide the practical use of TNA in biotechnology applications.
KW - nearest neighbor
KW - nucleic acid dynamics
KW - preorganization
KW - purine
KW - TNA
KW - XNA
UR - http://www.scopus.com/inward/record.url?scp=85065102229&partnerID=8YFLogxK
U2 - 10.1021/acssynbio.9b00028
DO - 10.1021/acssynbio.9b00028
M3 - Article
C2 - 30964657
AN - SCOPUS:85065102229
SN - 2161-5063
VL - 8
SP - 1144
EP - 1152
JO - ACS Synthetic Biology
JF - ACS Synthetic Biology
IS - 5
ER -