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Abstract The notion of using synthetic heterocycles instead of the native bases to interface with DNA and RNA has been explored for nearly 60 years. Unnatural bases compatible with the DNA/RNA coding interface have the potential to expand the genetic code and co‐opt the machinery of biology to access new macromolecular function; accordingly, this body of research is core to synthetic biology. While much of the literature on artificial bases focuses on code expansion, there is a significant and growing effort on docking synthetic heterocycles to noncoding nucleic acid interfaces; this approach seeks to illuminate major processes of nucleic acids, including regulation of transcription, translation, transport, and transcript lifetimes. These major avenues of research at the coding and noncoding interfaces have in common fundamental principles in molecular recognition. Herein, we provide an overview of foundational literature in biophysics of base recognition and unnatural bases in coding to provide context for the developing area of targeting noncoding nucleic acid interfaces with synthetic bases, with a focus on systems developed through iterative design and biophysical study.
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Preparation of Light‐responsive Unnatural RNA Bases via a Chromogenic Morita‐Baylis‐Hillman Adduct Path
Abstract RNA‐based tools for biological and pharmacological research are raising an increasing interest. Among these, RNA aptamers whose biological activity can be controlled via illumination with specific wavelengths represent an important target. Here, we report on a proof‐of‐principle study supporting the viability of a systematic use of Morita‐Baylis‐Hillman adducts (MBHAs) for the synthesis of light‐responsive RNA building blocks. Accordingly, a specific acetylated MBHA derivative was employed in the functionalization of the four natural RNA bases as well as two unnatural bases (5‐aminomethyl uracil and 5‐methylaminomethyl uracil). The results reveal a highly selective functionalization for both unnatural bases. The conjugation products were then investigated spectroscopically, photochemically and computationally. It is shown that when a single light‐responsive unit is present (i. e. when using 5‐methylaminomethyl uracil), the generated unnatural uracil behaves like a cinnamic‐framework‐based photochemical switch that isomerizes upon illumination through a biomimetic light‐induced intramolecular charge transfer mechanism driving a barrierless and, therefore, ultrafast reaction path.
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- Award ID(s):
- 2102619
- PAR ID:
- 10555128
- Publisher / Repository:
- Wiley-VCH
- Date Published:
- Journal Name:
- ChemPhotoChem
- Volume:
- 8
- Issue:
- 9
- ISSN:
- 2367-0932
- Subject(s) / Keyword(s):
- Covalent derivatization Morita-Baylis-Hillman adduct photoswitches photochemistry RNA bases uracil solvent dynamics
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
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- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.1002/cptc.202400093
