Design and Synthesis of Novel Peptide Nucleic Acid Monomers

All of the four nucleobases in DNA have replaced the 4‐hydroxy group of N‐[2‐(tert‐butoxycarbonylaminomethyl)‐trans‐4‐hydroxy] tetrahydropyrrole acetic acid methyl ester with cis ‐stereochemistry. An efficient route for the synthesis of N‐[2‐(tert‐butoxycarbonylaminomethyl)‐trans‐4‐hydroxy]‐tetrahydropyrrole acetic acid methyl ester has been developed. Starting with this intermediate, the protected monomers were synthesized by the Mitsunobu reaction or via its tosylate.     

Total Synthesis of the Hypermodified RNA Bases Wybutosine and Hydroxywybutosine and Their Quantification Together with Other Modified RNA Bases in Plant Materials

We report an efficient synthesis of the hypermodified natural tRNA modifications wybutosine (yW) and hydroxywybutosine (OHyW). We also describe the preparation of isotopically labeled analogues for precise quantification of yW and OHyW in different tissues including plant materials. The synthesis involved the formation of the unusual tricyclic ring structure of the bases by using a catalytic, intramolecular hydroamination reaction. The basis for the synthesis is also a stereoselective coupling reaction that allows the introduction of the fully substituted side chains to the tricyclic core structure. The isotopologues of yW and OHyW, together with other isotopically labeled tRNA modifications, were ultimately used in LC‐MS quantification experiments to investigate the role of the modified bases in the translational process. Quantification was performed in the plant species Arabidopsis thaliana.     

Development of Red-Shifted and Fluorogenic Nucleoside and Oligonucleotide Diarylethene Photoswitches

The reversible modulation of fluorescence signals by light is of high interest for applications in super-resolution microscopy, especially on the DNA level. In this article we describe the systematic variation of the core structure in nucleoside-based diarylethenes (DAEs), in order to generate intrinsically fluorescent photochromes. The introduction of aromatic bridging units resulted in a bathochromic shift of the visible absorption maximum of the closed-ring form, but caused reduced thermal stability and switching efficiency. The replacement of the thiophene aryl unit by thiazol improved the thermal stability, whereas the introduction of a benzothiophene unit led to inherent and modulatable turn-off fluorescence. This feature was further optimized by introducing a fluorescent indole nucleobase into the DAE core, resulting in an effective photoswitch with a fluorescence quantum yield of 0.0166 and a fluorescence turn-off factor of 3.2. The site-specific incorporation into an oligonucleotide resulted in fluorescence-switchable DNA with high cyclization quantum yields and switching efficiency, which may facilitate future applications.     

From Peptide Nucleic Acids to Supramolecular Structures of Nucleic Acid Derivatives

Nucleic acids play a pivotal role in life processes. The endeavours to shed light on the essential properties of these intriguing building blocks led us to the synthesis of different analogues and the investigation of their properties. First various peptide nucleic acid monomers and oligomers have been synthesized, using an Fmoc/acyl protecting group strategy, and their properties studied. The serendipitous discovery of a side reaction of coupling agents led us to the elaboration of a peptide sequencing method. The capricious behaviour of guanine derivatives spurred the determination of their substitution pattern using ¹³C, ¹⁵N NMR, and mass spectrometric methods. The properties of guanines initiated the logical transition to the study of supramolecular systems composed of purine analogues. Thus, xanthine and uracil derivatives have been obtained and their supramolecular self-assembly properties scrutinized in gas, solid, and liquid states and at solid-liquid interfaces.     

Reversible Photoswitching of RNA Hybridization at Room Temperature with an Azobenzene C‐Nucleoside

Photoregulation of RNA remains a challenging task as the introduction of a photoswitch entails changes in the shape and the stability of the duplex that strongly depend on the chosen linker strategy. Herein, the influence of a novel nucleosidic linker moiety on the photoregulation efficiency of azobenzene is investigated. To this purpose, two azobenzene C‐nucleosides were stereoselectively synthesized, characterized, and incorporated into RNA oligonucleotides. Spectroscopic characterization revealed a reversible and fast switching process, even at 20 °C, and a high thermal stability of the respective cis isomers. The photoregulation efficiency of RNA duplexes upon trans‐to‐cis isomerization was investigated by using melting point studies and compared with the known D ‐threoninol‐based azobenzene system, revealing a photoswitching amplitude of the new residues exceeding 90 % even at room temperature. Structural changes in the duplexes upon photoisomerization were investigated by using MM/MD calculations. The excellent photoswitching performance at room temperature and the high thermal stability make these new azobenzene residues promising candidates for in‐vivo and nanoarchitecture photoregulation applications of RNA.