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Abstract Four new isoorotamide (Io)‐containing PNA nucleobases have been designed for A−U recognition of double helical RNA. New PNA monomers were prepared efficiently and incorporated into PNA nonamers for binding A−U in a PNA:RNA2triplex. Isothermal titration calorimetry and UV thermal melting experiments revealed slightly improved binding affinity for singly modified PNA compared to known A‐binding nucleobases. Molecular dynamics simulations provided further insights into binding ofIobases in the triple helix. Together, the data revealed interesting insights into binding modes including the notion that three Hoogsteen hydrogen bonds are unnecessary for strong selective binding of an extended nucleobase. Cationic monomerIo8additionally gave the highest affinity observed for an A‐binding nucleobase to date. These results will help inform future nucleobase design toward the goal of recognizing any sequence of double helical RNA.
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This content will become publicly available on November 12, 2026
Isoorotamide-based peptide nucleic acid nucleobases with extended linkers aimed at distal base recognition of adenosine in double helical RNA
Non-coding ribonucleic acid (RNA) impacts many biological processes; however, the complexities of its many roles are not completely understood. Therefore, designing tools for molecular recognition is of paramount importance. Peptide nucleic acids (PNA) show promise as a tool for selective recognition of double helical regions of RNA. We herein report the synthesis and binding studies of new isoorotamide-based PNA monomers that target uridine–adenosine base pairs via a distal base recognition strategy. Monomers were designed with an arylisoorotamide core attached to a linker aimed at bypassing the uridine in a U–A pair and ultimately forming Hoogsteen hydrogen bonds with adenosine. Three new monomers were prepared and incorporated into PNAs that were screened against matched RNA hairpins using UV thermal melting and isothermal titration calorimetry experiments. Two of the three PNA oligonucleotides that contained distal binding monomers (Db) demonstrated slightly higher affinity for A–U base pairs while one demonstrated slightly higher affinity for the G–C base pair. These results provide insight into the nature of PNA monomer design particularly around linker design and rigidity.
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- PAR ID:
- 10696149
- Editor(s):
- Allen, Karen N
- Publisher / Repository:
- Beilstein Publishing System
- Date Published:
- Journal Name:
- Beilstein Journal of Organic Chemistry
- Volume:
- 21
- ISSN:
- 1860-5397
- Page Range / eLocation ID:
- 2513 to 2523
- Subject(s) / Keyword(s):
- Hoogsteen hydrogen bonding modified nucleobases peptide nucleic acids PNA–RNA triplexes RNA recognition
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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