A convenient synthesis of the cytidyl 3′-terminal monomer for solid-phase synthesis of RNG oligonucleotides

Replacing the phosphodiester backbone of RNA with positively charged guanidinium linkages has been shown to enable RNA oligomers to overcome electrostatic repulsion and bind double-stranded DNA in a triplex with high affinity. Ribonucleotide monomers with the ability to form guanidinium linkages have been synthesized for the generation of ribooligonucleotides with guanidinium linkages (RNGs) through solid-phase synthesis. We report herein an efficient method for the synthesis of N⁴-benzoyl-2′-O-(tert-butyldimethylsilyl)-5′-N-(4-monomethoxytritylamino)-3′-O-succinyl-5′-deoxycytidine, a new monomer required for the solid-phase synthesis of cytidyl RNG oligonucleotides.     

Organic Chemistry on Solid Supports

Until recently, repetitive solid-phase synthesis procedures were used predominantly for the preparation of oligomers such as peptides, oligosaccharides, peptoids, oligocarbamates, peptide vinylogues, oligomers of pyrrolin-4-one, peptide phosphates, and peptide nucleic acids. However, the oligomers thus produced have a limited range of possible backbone structures due to the restricted number of building blocks and synthetic techniques available. Biologically active compounds of this type are generally not suitable as therapeutic agents but can serve as lead structures for optimization. “Combinatorial organic synthesis” has been developed with the aim of obtaining low molecular weight compounds by pathways other than those of oligomer synthesis. This concept was first described in 1971 by Ugi.^[56f,g,59c] Combinatorial synthesis offers new strategies for preparing diverse molecules, which can then be screened to provide lead structures. Combinatorial chemistry is compatible with both solution-phase and solid-phase synthesis. Moreover, this approach is conducive to automation, as proven by recent successes in the synthesis of peptide libraries. These developments have led to a renaissance in solid-phase organic synthesis (SPOS), which has been in use since the 1970s. Fully automated combinatorial chemistry relies not only on the testing and optimization of known chemical reactions on solid supports, but also on the development of highly efficient techniques for simultaneous multiple syntheses. Almost all of the standard reactions in organic chemistry can be carried out using suitable supports, anchors, and protecting groups with all the advantages of solid-phase synthesis, which until now have been exploited only sporadically by synthetic organic chemists. Among the reported organic reactions developed on solid supports are Diels–Alder reactions, 1,3-dipolar cycloadditions, Wittig and Wittig–Horner reactions, Michael additions, oxidations, reductions, and Pd-catalyzed C? C bond formation. In this article we present a comprehensive review of the previously published solid-phase syntheses of nonpeptidic organic compounds.     

Synthesis of amine- and thiol-modified nucleoside phosphoramidites for site-specific introduction of biophysical probes into RNA

For studies of RNA structure, folding, and catalysis, site-specific modifications are typically introduced by solid-phase synthesis of RNA oligonucleotides using nucleoside phosphoramidites. Here, we report the preparation of two complete series of RNA nucleoside phosphoramidites; each has an appropriately protected amine or thiol functional group. The first series includes each of the four common RNA nucleotides, U, C, A, and G, with a 2'-(2-aminoethoxy)-2'-deoxy substitution (i.e., a primary amino group tethered to the 2'-oxygen by a two-carbon linker). The second series encompasses the four common RNA nucleotides, each with the analogous 2'-(2-mercaptoethoxy)-2'-deoxy substitution (i.e., a tethered 2'-thiol). The amines are useful for acylation and reductive amination reactions, and the thiols participate in displacement and oxidative cross-linking reactions, among other likely applications. The new phosphoramidites will be particularly valuable for enabling site-specific introduction of biophysical probes and constraints into RNA.     

Combinatorial Solid-Phase Synthesis of Structurally Complex Thiazolylhydantoines

A nine-step (!) solid-phase synthesis and subsequent cleavage with cyclization from the polymeric support were the keys to preparing high-quality molecular libraries of thiazolylhydantoines 1 from modified amino acid building blocks. Each step in the synthesis is different. Because the final cyclization cleaves only molecules that have been successfully constructed, the products obtained are pure. R¹, R²=alkyl; R³=aryl, arylO; R⁴=allyl.     

Oligoribonucleotides containing an aminoalkyl group at the N(4) atom of cytosine as precursors of new reagents for site-specific modifications of biopolymers

A solid-phase H-phosphonate procedure was developed for the synthesis of oligoribonucleotides containing aliphatic amino linkers with different lengths at the N(4) atom of cytosine. The hybridization properties of modified oligoribonucleotides were studied. Thermal stability of the RNA—RNA* and DNA—RNA* duplexes depends on the position of modified cytosine in the chain and the type of the duplex.     

Chemical synthesis of an artificially branched hairpin ribozyme variant with RNA cleavage activity

Due to the development in the field of RNA synthesis over the past decade of years, preparation of RNA oligonucleotides longer than 50 nucleotides is possible today. In this report, we describe the chemical preparation of a branched RNA molecule with RNA cleavage activity consisting of 81 nucleotides. It is derived from the hairpin ribozyme, a small catalytic RNA occurring in nature. The hairpin ribozyme consists of two separately folded domains (loop A and loop B domain), which can be joined in a number of different ways without loss of activity. In the construct presented here, 2′-deoxy-N4-(6-hydroxyhexyl)-5-methylcytidine was introduced to connect the loop B domain with the loop A domain via an artificial branch. The synthesized branched RNA is able to catalyze the cleavage of a number of suitable substrates. Compared with the corresponding non-branched reverse-joined ribozyme it cleaves its substrates only 5-fold slower. Surprisingly, no ligation activity could be detected.     

On-resin cyclization and antimicrobial activity of Laterocidin and its analogues

Total synthesis of cyclodecapeptide antibiotics from Bacillus laterosporus, laterocidin and its analogues, was accomplished for the first time by solid-phase peptide synthesis followed by traceless on-resin cyclization of the linear precursors with protection of α-carboxyl group on the Asp residue by Dmab as a temporary blocking group for on-resin head-to-tail cyclization, in which the carboxyl group of side chain of Asp was linked to Rink resin. Single alanine substitution or Asn substitution (Asp¹⁰→Asn¹⁰) demonstrated improvements in antibacterial activity. Of note, d-Phe² and Pro⁴ play an important role in on-resin head-to-tail cyclization and exerting antibacterial activity of Laterocidin.     

A convenient automated solid-phase synthesis of PNA-(5′)-DNA-(3′)-PNA chimera

An automated online solid-phase synthesis of Ac-cac ct T¹GG TC t¹ac ct-Gly-OH¹ using standard DNA and appropriately protected PNA building blocks (2–5) is described. This chimera forms stable duplexes with complementary DNA and RNA.     

Solid-Phase Synthesis of Nitrogen-Containing Five-Membered Heterocycles

In recent decades, a large number of reports related to solid-phase synthesis of heterocycles have appeared, owing to the wide variety of their biological activity. This review introduces the key concepts of solid-phase methodology and combinatorial synthesis with particular focus on the important role of solid-phase synthesis in the synthesis of nitrogen-containing five-membered ring heterocycles.     

Quantitative Monitoring of Solid-Phase Synthesis Using Gated Decoupling 13C NMR Spectroscopy with a 13C-Enriched Protecting Group and an Internal Standard in the Synthesis of Sialyl LewisX Tetrasaccharide

Just tagging along. For the nondestructive quantitative monitoring of solid-phase oligosaccharide synthesis a ¹³C-enriched tag (*) was incorporated in the linker and a ¹³C-enriched protecting group (⧫) was included in the growing molecule. By integration of the signals in a gated decoupling ¹³C NMR experiment the reaction progress can be monitored. This method was demonstrated with the synthesis of sialyl Lewis^x tetrasaccharide on a Tentagel support ((P)). Bn=benzyl, PEG=poly(ethylene glycol).     

Synthesis of thiol-modified peptide nucleic acids designed for post-assembly conjugation reactions

Two orthogonally protected PNA monomers were prepared having the mercaptomethyl moiety attached to the PNA backbone. These building blocks were employed in solid-phase PNA synthesis and it was shown that Boc/S-p-methoxybenzyl protection scheme was only satisfactory for the introduction of N-terminal thiol modification while the Fmoc/S-butylthio protected monomer proved to be amenable to elongation. The mercaptomethyl modification did not influence the thermal stability of a PNA/RNA duplex. The feasibility of PNA-PNA native ligation was demonstrated.     

Solid-phase synthesis of N-labeled acylpentamines as reference compounds for the MS/MS investigation of spider toxins

A solid-phase route for synthesis of ¹⁵N-labeled acylpolyamines is described. Utilizing alkylation at benzylic N-atom as a key step, ¹⁵N-atoms are incorporated by stepwise construction of the polyamine framework on the solid support. The derivatives were used as reference compounds for the investigation of the MS/MS behavior of spider toxins.     

Duplex‐forming Oligonucleotide of Triazole‐linked RNA

An oligonucleotide of triazole‐linked RNA (^TLRNA) was synthesized by performing consecutive copper‐catalyzed azide‐alkyne cycloaddition reactions for elongation. The reaction conditions that had been optimized for the synthesis of 3‐mer ^TLRNA were found to be inappropriate for longer oligonucleotides, and the conditions were reoptimized for the solid‐phase synthesis of an 11‐mer ^TLRNA oligonucleotide. Duplex formation of the 11‐mer ^TLRNA oligonucleotide was examined with the complementary oligonucleotide of natural RNA to reveal the effects of the 2′‐OH groups on the duplex stability.     

Chemo‐Enzymatic Synthesis of Position‐Specifically Modified RNA for Biophysical Studies including Light Control and NMR Spectroscopy

The investigation of non‐coding RNAs requires RNAs containing modifications at every possible position within the oligonucleotide. Here, we present the chemo‐enzymatic RNA synthesis containing photoactivatable or ¹³C,¹⁵N‐labelled nucleosides. All four ribonucleotides containing ortho‐nitrophenylethyl (NPE) photocages, photoswitchable azobenzene C‐nucleotides and ¹³C,¹⁵N‐labelled nucleotides were incorporated position‐specifically in high yields. We applied this approach for the synthesis of light‐inducible 2′dG‐sensing riboswitch variants and detected ligand‐induced structural reorganization upon irradiation by NMR spectroscopy. This chemo‐enzymatic method opens the possibility to incorporate a wide range of modifications at any desired position of RNAs of any lengths beyond the limits of solid‐phase synthesis.     

Amidoglycosylation of Polymer-Bound Glycals: A Complete Solid-Phase Synthesis of the Oligosaccharide Domain of the Lewisb Blood Group Determinant

A new general method for the preparation of N-acetylglucosamine glycosidic linkages has been developed for solid-phase synthesis. The complete pentasaccharide domain of the Lewis^b blood group antigen, which is a mediator in the formation of ulcers and gastric cancer, has now been synthesized on solid support (see 1 ; the shaded circle is the polystyrene support; TIPS=triisopropylsilyl).     

Enzymatic Synthesis of a DNA Triblock Copolymer that is Composed of Natural and Unnatural Nucleotides

DNA molecules have come under the spotlight as potential templates for the fabrication of nanoscale products, such as molecular‐scale electronic or photonic devices. Herein, we report an enhanced approach for the synthesis of oligoblock copolymer‐type DNA by using the Klenow fragment exonuclease minus of E. coli DNA polymerase I (KF^?) in a multi‐step reaction with natural and unnatural nucleotides. First, we confirmed the applicability of unnatural nucleotides with 7‐deaza‐nucleosides—which was expected because they were non‐metalized nucleotides—on the unique polymerization process known as the “strand‐slippage model”. Because the length of the DNA sequence could be controlled by tuning the reaction time, analogous to a living polymerization reaction on this process, stepwise polymerization provided DNA block copolymers with natural and unnatural bases. AFM images showed that this DNA block copolymer could be metalized sequence‐selectively. This approach could expand the utility of DNA as a template.     

Nitrogen-Containing Six-Membered Heterocycles: Solid-Phase Synthesis

Solid-phase organic synthesis is a rapidly expanding area of synthetic chemistry that is being widely exploited in the search for new medicinally important compounds using combinatorial techniques. In recent decades, a large number of reports related to solid-phase synthesis of heterocycles have appeared because of the wide variety of their biological activity. In this review, we report the important role of solid-phase synthesis in the synthesis of nitrogen containing six-membered ring heterocycles.     

Solid-phase synthesis of new ribo and deoxyribo BrdU probes for labeling and detection of nucleic acids

A facile and efficient solid-phase synthesis of BrdU-14-UTP and BrdU-14-dUTP is reported. The method involves a nucleophilic addition of CPG-supported Br-dU with a 5′-carboxy modifier amidite, followed by the coupling with AA-UTP or AA-dUTP and finally the solid-support is cleaved under basic conditions. The newly prepared non-radioactive probes may have important applications in immunocytochemistry spatially in labeling and detection assays. BrdU moiety is coupled with nucleotides like dUTP and UTP and incorporated into nucleic acids using generally available polymerase like Taq polymerase or RNA polymerase. The probes thus generated can be used in standard blotting and hybridization procedures including in situ hybridization and detection with anti-BrdU conjugates.     

Solid-Phase Synthetic Approach Toward the Synthesis of Oxygen-Containing Heterocycles

Solid-phase organic synthesis is a rapidly expanding area of synthetic chemistry which is being widely exploited in the search for new medicinally important compounds using combinatorial techniques. In recent decades, a large number of reports related to solid-phase synthesis of heterocycles have appeared because of the wide variety in their biological activity. In this review, we report the important role of solid-phase synthesis in the synthesis of oxygen-bearing heterocycles.