Synthesis of HBC fluorophores with an electrophilic handle for covalent attachment to Pepper RNA

• Raphael Bereiter and
• Ronald Micura

Beilstein J. Org. Chem. 2025, 21, 727–735, doi:10.3762/bjoc.21.56

• have shown that this feature can be exploited to construct a covalent bond between the fluorophore and the RNA by replacing the N-hydroxyethyl group of the dye with an electrophilic handle, resulting in efficient RNA alkylation at the N7 of G41 [11]. Synthesis and evaluation of Pepper dyes with an

• electrophilic handle In analogy to the reported synthesis of HBC [7], we first developed a route to generate a series of HBC derivatives with N-(bromoalkyl) handles of different lengths (Scheme 2), with the intention of optimizing the RNA alkylation reaction for high yields. The synthesis starts with a

• containing potassium and magnesium ions at a physiological pH of 7.0 for 5 hours. Analysis of the reaction mixture by anion-exchange HPLC revealed that the bromopropyl handle (C3 homolog 8) gave the highest yield of covalently tethered HBC-RNA complex (50%). Significantly less RNA alkylation yield was

Synthesis of electrophile-tethered preQ₁ analogs for covalent attachment to preQ₁ RNA

• Laurin Flemmich and
• Ronald Micura

Beilstein J. Org. Chem. 2025, 21, 483–489, doi:10.3762/bjoc.21.35

• novel compound DPQ1. Keywords: deazapurines; heterocycles; pyrrolopyrimidines; queuosine; riboswitches; ribozymes; RNA alkylation; RNA labelling; Introduction Pre-queuosine 1 (preQ1) is a biosynthetic precursor of the hypermodified nucleoside queuosine (Q) that is found in the wobble position of

Synthesis of O⁶-alkylated preQ₁ derivatives

• Laurin Flemmich,
• Sarah Moreno and
• Ronald Micura

Beilstein J. Org. Chem. 2021, 17, 2295–2301, doi:10.3762/bjoc.17.147

• (preQ1) [1]. Thus far, present-day riboswitches have only been known to bind – but not to be able to react – with their ligands [2][3]. This new finding now opens exciting avenues for the development of RNA labeling tools [4], in particular, for RNA methylation, and more generally, for RNA alkylation. To