Efficient Synthesis and Functional Replication of 3'-Deoxyapionucleic Acid (ApioNA): An RNA-Selective XNA with Conformational Flexibility
Abstract
The development of xeno‑nucleic acids (XNAs) has largely focused on two extremes: polymers that pair with both DNA and RNA, and those that avoid cross‑pairing entirely. In this study, we bridge this divide by comprehensively characterizing 3'-deoxyapionucleic acid (ApioNA), which exhibits a distinct RNA‑selective hybridization profile. By employing an efficient asymmetric synthesis of ApioNA building blocks, we achieved large-scale production of ApioNA oligomers and performed systematic characterization of them. Thermal melting and circular dichroism analyses reveal that ApioNA forms moderately stable duplexes with RNA but only weak duplexes with DNA and minimal self‑pairing. We further establish a complete enzymatic replication cycle (DNA→ApioNA→DNA) using commercial Therminator and Bst 3.0 polymerases, achieving ~98% fidelity. Quantum mechanical calculations reveal that the apiofuranose ring adopts two low‑energy puckering states, while the backbone, featuring an extra methylene group, displays enhanced conformational flexibility that favors A‑form RNA geometry and requires a higher‑energy state to pair with B‑form DNA. This work establishes ApioNA as a practical, RNA-selective genetic polymer and demonstrates how backbone sugar chemistry can be harnessed to program the interaction specificity of synthetic genetic polymers with natural DNA and RNA.
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