Search

Innovative approaches to controlled nucleobase-modified RNA synthesis are urgently needed to support RNA biology exploration and to synthesize potential RNA therapeutics. Here we present a strategy for enzymatic construction of nucleobase-modified RNA based on primer-dependent engineered thermophilic DNA polymerases – SFM4-3 and TGK. We demonstrate introduction of one or several different base-modified nucleotides in one strand including hypermodified RNA containing all four modified nucleotides bearing four different substituents, as well as strategy for primer segment removal. We also show facile site-specific or segmented introduction of fluorophores or other functional groups at defined positions in variety of RNA molecules, including structured or long mRNA. Intriguing translation efficacy of single-site modified mRNAs underscores the necessity to study isolated modifications placed at designer positions to disentangle their biological effects and enable development of improved mRNA therapeutics. Our toolbox paves the way for more precise dissecting RNA structures and functions, as well as for construction of diverse types of base-functionalized RNA for therapeutic applications and diagnostics. A general method for enzymatic synthesis of base-modified RNA was developed using engineered thermostable DNA polymerases enabling introduction of site-specific modifications or synthesis of hypermodified RNA not accessible by in vitro transcription. [ABSTRACT FROM AUTHOR]

A series of benzofuro‐fused 7‐deazapurine (6H‐furo[2,3‐e]pyrimido[4,5‐b]indole) 2'‐deoxyribo‐ and ribonucleosides was designed and synthesized. The synthesis of key compound 10‐chloro‐6H‐furo[2,3‐e]pyrimido[4,5‐b]indole was based on the Negishi cross‐coupling of iodobenzofurane with zincated 4,6‐dichloropyrimidine followed by azidation and photochemical cyclization. Glycosylation of the heterocycle with either Hoffer's chlorodeoxyribose or protected ribose followed by cross‐coupling or substitution reactions at position 10 gave the desired two sets of final nucleosides that showed moderate to weak cytostatic activity and interesting fluorescence properties. [ABSTRACT FROM AUTHOR]

This addendum to the article "Expedient production of site specifically nucleobase-labelled or hypermodified RNA with engineered thermophilic DNA polymerases" published in Nature Communications provides information about a related work that was published during the peer review process. The related work, titled "Extending the toolbox for RNA biology with SegModTeX: a polymerase-driven method for site-specific and segmental labeling of RNA," was authored by Haslecker, Pham, Glänzer, et al. and published in Nature Communications in 2023. The addendum acknowledges the existence of this related work and provides the necessary citation information. [Extracted from the article]

2‐Formyl‐2′‐deoxyadenosine triphosphate (dCHOATP) was synthesized and tested as a substrate in enzymatic synthesis of DNA modified in the minor groove with a reactive aldehyde group. The multistep synthesis of dCHOATP was based on the preparation of protected 2‐dihydroxyethyl‐2′‐deoxyadenosine intemediate, which was triphosphorylated and converted to aldehyde through oxidative cleavage. The dCHOATP triphosphate was a moderate substrate for KOD XL DNA polymerase, and was used for enzymatic synthesis of some sequences using primer extension (PEX). On the other hand, longer sequences (31‐mer) with higher number of modifications, or sequences with modifications at adjacent positions did not give full extension. Single‐nucleotide extension followed by PEX was used for site‐specific incorporation of one aldehyde‐linked adenosine into a longer 49‐mer sequence. The reactive formyl group was used for cross‐linking with peptides and proteins using reductive amination and for fluorescent labelling through oxime formation with an AlexaFluor647‐linked hydroxylamine. [ABSTRACT FROM AUTHOR]

Ribonuclosides derived from 6‐hetaryl‐7‐dezapurines are potent cytostatics, but their mechanism of action is unknown. Here we designed and synthesized a series of cyclic and acyclic nucleoside phosphonates, as well as carboxy, cyano, sulfo, and sulfonamide acyclic analogues derived from 6‐thiophen‐2‐yl‐7‐deazapurine and 7‐fluoro‐6‐thiophen‐2‐yl‐7‐deazapurine as ribonucleoside monophosphate mimics. None of these analogues exerted significant cytotoxic and antiviral activity. [ABSTRACT FROM AUTHOR]

Suitably protected (R)‐ and (S)‐HPEP {9‐[3‐hydroxy‐2‐(phosphonoethoxy)propyl]} derivatives containing adenine and thymine nucleobases were prepared as monomers for the introduction of acyclic nucleotide units into oligonucleotides. The solid phase synthesis of a series of ribo and 2′‐deoxyribo nonamers containing (R)‐HPEP and (S)‐HPEP units was successfully performed in both 5′ → 3′ and 3′ → 5′ directions. The measurement of thermal characteristics of the complexes of modified nonamers with complementary DNA and RNA strands revealed a general destabilizing effect of the introduced acyclic units on the thermal stability, but in several cases [modif.RNA*RNA and modif.DNA*RNA with (S)‐HPEPA units], the duplexes were characterized in terms of Tm values. A solid‐phase synthesis afforded a series of ribo and 2′‐deoxyribo nonamers containing acyclic nucleotide units. A general destabilizing effect of the introduced acyclic units on the thermal stability of complexes of modified nonamers with the complementary DNA and RNA strands was observed, but in cases with (S)‐HPEPA units, the duplexes were characterized in terms of Tm values. [ABSTRACT FROM AUTHOR]

A general access to 4-substituted 6-arylpyrrolo[2,3- d]pyrimidine (6-substituted 8-aryl-7-deazapurine derivatives) was developed based on iridium-catalyzed C-H borylations of pyrrolo[2,3- d]pyrimidines at the 6-position followed by the Suzuki cross-coupling reactions or other functional group transformations of the boronates. Biologically relevant 6-arylpyrrolo[2,3- d]pyrimidin-4-amines (8-aryl-7-deazaadenines) and pyrrolo[2,3- d]pyrimidin-4-ones (-7-deazahypoxanthines) were synthesized starting from SEM-protected 4-methylsulfanyl- or 4-methoxypyrrolo[2,3- d]pyrimidine. The one-pot borylation/Suzuki coupling reactions were followed either by demethylation and deprotection to yield deazahypoxanthine bases, or by oxidation of sulfide to sulfone, amination and deprotection to give deazaadenines. In addition, the boronate intermediates were converted into 6-halo- or 6-(trifluoromethyl)pyrrolo[2,3- d]pyrimidine (8-halo- or 8-trifluoromethyl-7-deazapurine) derivatives. [ABSTRACT FROM AUTHOR]

A general and modular synthesis of substituted benzene and pyridine 2′- C-methyl- C-ribonucleosides was developed. Benzyl-protected haloaryl- C-nucleoside intermediates were prepared by the addition of bromo(het)aryllithium reagents to a protected lactone, followed by acetylation and reduction. These halogenated intermediates were further transformed by Pd-catalysed cross-couplings, aminations, or hydroxylations. The final deprotection was rather troublesome, and different procedures involving catalytic hydrogenation on Pd/C, or treatment with BCl3, were optimized for each derivative. The final C-nucleosides were also all converted into the corresponding NTPs. None of the C-nucleosides showed any activity in the HCV replicon assay, and none of the NTPs showed any significant inhibition of the HCV polymerase. [ABSTRACT FROM AUTHOR]

An efficient route to acylated acyclic nucleosides containing a branched hemiaminal ether moiety is reported via three-component alkylation of N-heterocycle (purine nucleobase) with acetal (cyclic or acyclic, variously branched) and anhydride (preferentially acetic anhydride). The procedure employs cheap and easily available acetals, acetic anhydride, and trimethylsilyl trifluoromethanesulfonate (TMSOTf). The multi-component reaction is carried out in acetonitrile at room temperature for 15 min and provides moderate to high yields (up to 88%) of diverse acyclonucleosides branched at the aliphatic side chain. The procedure exhibits a broad substrate scope of N-heterocycles and acetals, and, in the case of purine derivatives, also excellent regioselectivity, giving almost exclusively N-9 isomers. [ABSTRACT FROM AUTHOR]