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

• ), we describe the synthesis of a series of derivatives/analogs that contain reactive handles (see main text and the figures below). In principle, the handles can also be applied at the other members of the HBC family, with the expectation of the same reactivity towards Pepper RNA. Synthesis of

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

Stepwise PEG synthesis featuring deprotection and coupling in one pot

• Logan Mikesell,
• Dhananjani N. A. M. Eriyagama,
• Yipeng Yin,
• Bao-Yuan Lu and
• Shiyue Fang

Beilstein J. Org. Chem. 2021, 17, 2976–2982, doi:10.3762/bjoc.17.207

• frequently adopted. For example, in peptide synthesis, peptides with acid-labile side chain protections can be selectively cleaved from the acid-labile 2-chlorotrityl resin with dilute TFA [34]. In RNA synthesis, the acid-sensitive 2'-TOM protecting groups can survive the acidic conditions for removing the 5

Synthetic strategies toward 1,3-oxathiolane nucleoside analogues

• Umesh P. Aher,
• Dhananjai Srivastava,
• Girij P. Singh and
• Jayashree B. S

Beilstein J. Org. Chem. 2021, 17, 2680–2715, doi:10.3762/bjoc.17.182

• counterparts during DNA or RNA synthesis, a biological role that is crucial for cellular reproduction [2]. Most of the drugs that are incorporated in the viral DNA upon phosphorylation in vivo block the DNA polymerase enzyme. However, DNA polymerase recognizes 2’,3’-dideoxynucleosides as substrates, which are

Beyond ribose and phosphate: Selected nucleic acid modifications for structure–function investigations and therapeutic applications

• Christopher Liczner,
• Kieran Duke,
• Gabrielle Juneau,
• Martin Egli and
• Christopher J. Wilds

Beilstein J. Org. Chem. 2021, 17, 908–931, doi:10.3762/bjoc.17.76

• by way of an HCV polymerase and extended to give a full-length oligonucleotide product, whereas 2',4'-diF-rUTP inhibited RNA synthesis at the early stages of dinucleotide-primed reactions [206]. Standard solid-phase synthesis allowed for the incorporation of this modified nucleoside into both RNA and

DNA with zwitterionic and negatively charged phosphate modifications: Formation of DNA triplexes, duplexes and cell uptake studies

• Yongdong Su,
• Maitsetseg Bayarjargal,
• Tracy K. Hale and
• Vyacheslav V. Filichev

Beilstein J. Org. Chem. 2021, 17, 749–761, doi:10.3762/bjoc.17.65

• -phase DNA or RNA synthesis, the introduction of SaRNA monomers into an RNA backbone involved a 14-step preparation of the phosphoramidite for the SaRNA-TT dinucleotide. Similarly, the incorporation of BCNS groups on a DNA backbone requires the synthesis of thymidine and 2’-OMe-uridine phosphoramidites

Changed reactivity of secondary hydroxy groups in C8-modified adenosine – lessons learned from silylation

• Jennifer Frommer and
• Sabine Müller

Beilstein J. Org. Chem. 2020, 16, 2854–2861, doi:10.3762/bjoc.16.234

• being preferentially formed. Optimization of the protection scheme lead to a new and economic route to the desired C8-alkynylated building block and its incorporation in RNA. Keywords: nucleoside chemistry; protecting groups; RNA synthesis; Sonogashira reaction; Introduction Oligoribonucleotides

• synthesis strategy was re-designed, allowing the preparation of building block 9 (Scheme 2) ready for use in solid-phase RNA synthesis with excellent yield. Here, we report on the selectivity problem in 2’-O-silylation of adenosine derivative 7 (Scheme 1) and the optimized synthesis strategy for the

• Sonogashira coupling following a previously established protocol [13], resulting in nucleoside derivative 7 with 44 % yield over these two steps, corresponding to an overall yield of 17% over six reaction steps. Further functionalization of 7 for RNA synthesis required selective 2’-O-silylation to deliver

Phosphoramidite building blocks with protected nitroxides for the synthesis of spin-labeled DNA and RNA

• Timo Weinrich,
• Eva A. Jaumann,
• Ute M. Scheffer,
• Thomas F. Prisner and
• Michael W. Göbel

Beilstein J. Org. Chem. 2018, 14, 1563–1569, doi:10.3762/bjoc.14.133

• therefore developed a third strategy based on photolabile protective groups [41][42][43] finally leading to phosphoramidite 6. This building block behaves in solid-phase RNA synthesis as any normal TOM protected amidite. It is completely stable against the conditions used for strand assembly, RNA

An overview of recent advances in duplex DNA recognition by small molecules

• Sayantan Bhaduri,
• Nihar Ranjan and
• Dev P. Arya

Beilstein J. Org. Chem. 2018, 14, 1051–1086, doi:10.3762/bjoc.14.93

Stimuli-responsive oligonucleotides in prodrug-based approaches for gene silencing

• Françoise Debart,
• Christelle Dupouy and
• Jean-Jacques Vasseur

Beilstein J. Org. Chem. 2018, 14, 436–469, doi:10.3762/bjoc.14.32

• groups at the distal α-carbon or lengthening the proximal ethyl linker to a butyl linker. With such RNN phosphoramidite building blocks >3000, RNN ONs have been synthesized with high yields comparable to those of RNA synthesis, demonstrating the robustness and versatility of the chemical method. Three

Synthetic mRNA capping

• Fabian Muttach,
• Nils Muthmann and
• Andrea Rentmeister

Beilstein J. Org. Chem. 2017, 13, 2819–2832, doi:10.3762/bjoc.13.274

• analogue [50]. The problem of orientation is circumvented when GpppA cap analogues are used in combination with the T7 class II promotor phi2.5 which allows initiating RNA synthesis with ATP. Hence, GpppA- or m7GpppA-capped RNAs can be produced [51]. When the common GTP-initiating T7 class III promoter

• followed by chemical or enzymatic installation of the 5′-cap. The general principle of solid-phase RNA synthesis is beyond the scope of this review and has been described in excellent review articles [101][102][103][104]. The longest RNA synthesized via solid-phase chemistry to date has a length of 170

• of the replicative DNA polymerase from Thermococcus gorgonarius (Tgo) into a DNA-dependent RNA polymerase (termed TGK) enabled production of up to 1,700 nt long RNAs from a ssDNA template and an RNA primer [119]. The primer-dependent RNA synthesis obviates the need to initiate RNA synthesis with pppG

Chemical systems, chemical contiguity and the emergence of life

• Terrence P. Kee and
• Pierre-Alain Monnard

Beilstein J. Org. Chem. 2017, 13, 1551–1563, doi:10.3762/bjoc.13.155

• ], the complexity of de novo RNA synthesis and its functional interconnection with other biopolymers in the cellular context question its early, single-handed role. The polymerization of short RNA chains and peptides has been investigated within aqueous vesicle lumens as well as water/oil emulsions, and

First total synthesis of kipukasin A

• Chuang Li,
• Haixin Ding,
• Zhizhong Ruan,
• Yirong Zhou and
• Qiang Xiao

Beilstein J. Org. Chem. 2017, 13, 855–862, doi:10.3762/bjoc.13.86

• ; Introduction Endogenous nucleosides are involved in DNA and RNA synthesis, cell signalling, enzyme regulation and metabolism etc. [1][2]. Therefore, the synthesis of novel nucleosides to mimic their physiological counterparts has potential therapeutic significance, which has led to the development of a large

Adsorption of RNA on mineral surfaces and mineral precipitates

• Elisa Biondi,
• Yoshihiro Furukawa,
• Jun Kawai and
• Steven A. Benner

Beilstein J. Org. Chem. 2017, 13, 393–404, doi:10.3762/bjoc.13.42

• locale to locale. This is obvious even to an amateur. For example, natural calcium phosphate (apatite), of possible prebiotic interest as a source of the phosphate essential to prebiotic RNA synthesis [13], has different colors that reflect inclusion of different atomic species that are not in the

Solution phase synthesis of short oligoribonucleotides on a precipitative tetrapodal support

• Alejandro Gimenez Molina,
• Amit M. Jabgunde,
• Pasi Virta and
• Harri Lönnberg

Beilstein J. Org. Chem. 2014, 10, 2279–2285, doi:10.3762/bjoc.10.237

• been elaborated. Novel 2'-O-(2-cyanoethyl)-5'-O-(1-methoxy-1-methylethyl) protected ribonucleoside 3'-phosphoramidites have been prepared and their usefulness as building blocks in RNA synthesis on a soluble support has been demonstrated. As a proof of concept, a pentameric oligoribonucleotide, 3

Synthesis of a bifunctional cytidine derivative and its conjugation to RNA for in vitro selection of a cytidine deaminase ribozyme

• Nico Rublack and
• Sabine Müller

Beilstein J. Org. Chem. 2014, 10, 1906–1913, doi:10.3762/bjoc.10.198

• Information File 658: Experimental part. Acknowledgements The authors wish to thank Dr. Bettina Appel and Julia Drenckhan for RNA synthesis service.

A reductive coupling strategy towards ripostatin A

• Kristin D. Schleicher and
• Timothy F. Jamison

Beilstein J. Org. Chem. 2013, 9, 1533–1550, doi:10.3762/bjoc.9.175

• ribonucleic acid polymerase. These compounds inhibit chain initiation of RNA synthesis in Staphylococcus aureus, a particularly infectious bacterial strain with reported drug resistance to the antibiotics vancomycin and methicillin [3]. Ripostatin A exists as an equilibrium mixture of ketone and hemiketal