Browsing by Author "Göhringer, Daniela"

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Open Access
Acid‐stable nucleobase protection for a strongly pairing pyridone C‐nucleoside suitable for solid‐phase synthesis of oligonucleotides
(2022) Eyberg, Juri; Göhringer, Daniela; Salihovic, Amila; Richert, Clemens
Oligonucleotides are indispensable tools in diagnostics, therapeutic applications and molecular biology. The low base pairing strength of thymine with adenine complicates their use. Ethynylpyridone C‐nucleosides are analogs of thymidine that pair more strongly and with improved base selectivity, and sequences containing these analogs show improved target affinity and selectivity, but their routine use is hampered by diminished yields of solid‐phase syntheses with the known building blocks. A partial loss of base protecting groups during the acidic deblocking step of chain extension cycles was identified as the cause of lower yields. Here we report the synthesis of an improved phosphoramidite building block featuring a pivaloyloxymethyl (POM) base protecting group. This building block gives oligonucleotides containing the strongly pairing ethynylmethylpyridone C‐nucleoside in high yield and purity via solid‐phase synthesis.
Open Access
Determining the diastereoselectivity of the formation of dipeptidonucleotides by NMR spectroscopy
(2021) Doppleb, Olivia; Bremer, Jennifer; Bechthold, Maren; Sánchez Rico, Carolina; Göhringer, Daniela; Griesser, Helmut; Richert, Clemens
Proteins are composed of l‐amino acids, but nucleic acids and most oligosaccharides contain d‐sugars as building blocks. It is interesting to ask whether this is a coincidence or a consequence of the functional interplay of these biomolecules. One reaction that provides an opportunity to study this interplay is the formation of phosphoramidate‐linked peptido RNA from amino acids and ribonucleotides in aqueous condensation buffer. Here we report how the diastereoselectivity of the first peptide coupling of the peptido RNA pathway can be determined in situ by NMR spectroscopy. When a racemic mixture of an amino acid ester was allowed to react with an 5′‐aminoacidyl nucleotide, diastereomeric ratios of up to 72 : 28 of the resulting dipeptido nucleotides were found by integration of 31P‐ or 1H‐NMR peaks. The highest diastereomeric excess was found for the homochiral coupling product d‐Ser‐d‐Trp, phosphoramidate‐linked to adenosine 5′‐monophosphate with its d‐ribose ring. When control reactions with an N‐acetyl amino acid and valine methyl ester were run in organic solvent, the diastereoselectivity was found to be lower, with diastereomeric ratios≤62 : 38. The results from the exploratory study thus indicate that the ribonucleotide residue not only facilitates the coupling of lipophilic amino acids in aqueous medium but also the formation of a homochiral dipeptide. The methodology described here may be used to search for other stereoselective reactions that shed light on the origin of homochirality.
Open Access
Prolinyl phosphoramidates of nucleotides with increased reactivity
(2024) Humboldt, Adrian; Rami, Fabian; Topp, Franka M.; Arnold, Dejana; Göhringer, Daniela; Pallan, Pradeep S.; Egli, Martin; Richert, Clemens
Nucleoside monophosphates (NMPs) are the subunits of RNA. They are incorporated into growing complementary strands when sequences are copied in enzyme‐free reactions using organic leaving groups at the phosphates. Amino acids are rarely considered as leaving groups, but proline can act as a leaving group when N‐linked to NMPs, so that prolinyl NMPs hydrolyze in aqueous buffer at 37 °C, with half‐life times as short as 2.4 h, and they act as monomers in enzyme‐free primer extension. Still, their level of reactivity is insufficient for practical purposes, requiring months for some extensions. Herein we report the synthesis of eight substituted prolinyl AMPs together with seven related compounds and the results of a study of their reactivity. A δ‐carboxy prolinyl NMP was found to be converted with a half‐life time of just 11 min in magnesium‐free buffer, and a δ‐isopropyl prolinyl NMP was shown to react sevenfold faster than its prolinyl counterpart in enzyme‐free genetic copying of RNA. Our results indicate that both anchimeric and steric effects can be employed to increase the reactivity of aminoacidyl nucleotides, i.e. compounds that combine two fundamental classes of biomolecules in one functional entity.