The chemical synthesis of phosphoramidite derivatives of all four 5′-deoxy-5′-thioribonucleosides is described. These phosphoramidites contained trityl (A, G, C, and U), dimethoxytrityl (A and G), or tert-butyldisulfanyl (G) as the 5′-S-protecting group. The application of several of these phosphoramidites for solid-phase synthesis of oligoribonucleotides containing a 2′-O-photocaged 5′-S-phosphorothiolate linkage or 5′-thiol-labeled RNAs is also further investigated.

A pair of synthetic approaches to linear dasatinib–DNA conjugates via click chemistry are described. The first approach involves the reaction of excess azido dasatinib derivative with 5′-(5-hexynyl)-tagged DNAs, and the second involves the reaction of excess alkynyl-linked dasatinib with 5′-azido-tagged DNA. The second approach using alkynyl-derived dasatinib and 5′-azido-tagged DNA yielded the corresponding dasatinib-DNA conjugates in higher yield (47% versus 10–33% for the first approach). Studies have shown these linear dasatinib–DNA conjugates-derived gold nanoparticles exhibit efficacy against leukemia cancer cells with reduced toxicity toward normal cells compared to that of free dasatinib.

β-d-Mannosyl phosphomycoketide (C32-MPM), a naturally occurring glycolipid found in the cell walls of Mycobacterium tuberculosis, acts as a potent antigen to activate T-cells upon presentation by CD1c protein. The lipid portion of C32-MPM contains a C32-mycoketide, consisting of a saturated oligoisoprenoid chain with five chiral methyl branches. Here we develop several stereocontrolled approaches to assemble the oligoisoprenoid chain with high stereopurity (>96%) using Julia–Kocienski olefinations followed by diimide reduction. By careful choice of olefination sites, we could derive all chirality from a single commercial compound, methyl (2S)-3-hydroxy-2-methylpropionate (>99% ee). Our approach is the first highly stereocontrolled method to prepare C32-MPM molecule with >96% stereopurity from a single >99% ee starting material. We anticipate that our methods will facilitate the highly stereocontrolled synthesis of a variety of other natural products containing chiral oligoisoprenoid-like chains, including vitamins, phytol, insect pheromones, and archaeal lipids.

Starting from methyl 3,5-di-O-benzyl-2-keto-α-D-ribofuranoside, a convergent, six-step synthesis is developed to give efficiently all four 2′-C-α-aminomethyl-2′-deoxynucleosides (U, C, A, G) in 38%, 42%, 12%, 12% yield, respectively. Convergence is achieved by the glycosylation of persilylated nucleobases with methyl 2-α-phthalimidomethyl ribofuranoside.

This work describes a general method for the synthesis of oligoribonucleotides containing a site-specific nonbridging phosphorodithioate linkage via automated solid-phase synthesis using 5′-O-DMTr-2′-O-TBS-ribonucleoside 3′-N,N-dimethyl-S-(2,4-dichlorobenzyl) phosphorothioamidites (2a–2d). The 3′-phosphorothioamidites (2a–2d) can be conveniently prepared in good yields (86–99%) via a one-pot reaction from the corresponding 5′-O-DMTr-2′-O-TBS-ribonucleosides (1a–1d).

RNA represents a prominent class of biomolecules. Present in all living systems, RNA plays many essential roles in gene expression, regulation, and development. Accordingly, many biological processes depend on the accurate enzymatic processing, modification, and cleavage of RNA. Understanding the catalytic mechanisms of these enzymes therefore represents an important goal in defining living systems at the molecular level.In this context, RNA molecules bearing 3′- or 5′-S-phosphorothiolate linkages comprise what are arguably among the most incisive mechanistic probes available. They have been instrumental in showing that RNA splicing systems are metalloenzymes and in mapping the ligands that reside within RNA active sites. The resulting models have in turn verified the functional relevance of crystal structures. In other cases, phosphorothiolates have offered an experimental strategy to circumvent the classic problem of kinetic ambiguity; mechanistic enzymologists have used this tool to assign precise roles to catalytic groups as general acids or bases. These insights into macromolecular function are enabled by the synthesis of nucleic acids bearing phosphorothiolate linkages and the unique chemical properties they impart. In this Account, we review the synthesis, properties, and applications of oligonucleotides and oligodeoxynucleotides containing an RNA dinucleotide phosphorothiolate linkage.Phosphorothioate linkages are structurally very similar to phosphorothiolate linkages, as reflected in the single letter of difference in nomenclature. Phosphorothioate substitutions, in which sulfur replaces one or both nonbridging oxygens within a phosphodiester linkage, are now widely available and are used routinely in numerous biochemical and medicinal applications. Indeed, synthetic phosphorothioate linkages can be introduced readily via a sulfurization step programmed into automated solid-phase oligonucleotide synthesizers.In contrast, phosphorothiolate oligonucleotides, in which sulfur replaces a specific 3′- or 5′-bridging oxygen, have presented a more difficult synthetic challenge, requiring chemical alterations to the attached sugar moiety. Here we begin by outlining the synthetic strategies used to access these phosphorothiolate RNA analogues. The Arbuzov reaction and phosphoramidite chemistry are often brought to bear in creating either 3′- or 5′-S-phosphorothiolate dinucleotides. We then summarize the responses of the phosphorothiolate derivatives to chemical and enzymatic cleavage agents, as well as mechanistic insights their use has engendered. They demonstrate particular utility as probes of metal-ion-dependent phosphotransesterification, general acid-base-catalyzed phosphotransesterification, and rate-limiting chemistry. The 3′- and 5′-S-phosphorothiolates have proven invaluable in elucidating the mechanisms of enzymatic and nonenzymatic phosphoryl transfer reactions. Considering that RNA cleavage represents a fundamental step in the maturation, degradation, and regulation of this important macromolecule, the significant synthetic challenges that remain offer rich research opportunities.

Starting from methyl 3,5-di-O-benzyl-2-keto-α-D-ribofuranoside, a convergent, six-step synthesis is developed to give efficiently all four 2′-C-α-aminomethyl-2′-deoxynucleosides (U, C, A, G) in 38%, 42%, 12%, 12% yield, respectively. Convergence is achieved by the glycosylation of persilylated nucleobases with methyl 2-α-phthalimidomethyl ribofuranoside.