A series of artificial peptides bearing cationic functional groups with different side chain lengths were designed, and their ability to increase the thermal stability of nucleic acid duplexes was investigated. The peptides with amino groups selectively increased the stability of RNA/RNA duplexes, and a relationship between the side chain length and the melting temperature (Tm) of the peptide–RNA complexes was observed. On the other hand, while peptides with guanidino groups exhibited a similar tendency with respect to the peptide structure and thermal stability of RNA/RNA duplexes, those with longer side chain lengths, such as l-2-amino-4-guanidinobutyric acid (Agb) or l-arginine (Arg) oligomers, stabilized both RNA/RNA and DNA/DNA duplexes, and those with shorter side chain lengths exhibited a higher ability to selectively stabilize RNA/RNA duplexes. In addition, peptides were designed with different levels of flexibility by introducing glycine (Gly) residues into the l-2-amino-3-guanidinopropionic acid (Agp) oligomers. It was found that insertion of Gly did not affect the thermal stability of the peptide–RNA complexes, but an alternate arrangement of Gly and Agp apparently decreased the thermal stability. Therefore, in the Agp oligomer, consecutive Agp sequences are essential for increasing the stability of RNA/RNA duplexes.

A novel glycosylation that uses glycosyl boranophosphate triesters as glycosyl donors and trityl cation (Tr+) as an activator was developed. Two types of reactions were studied: (1) the boranophosphate triester was activated with TrNTf2 to react with an alcohol and (2) O-trityl ethers worked as both glycosyl acceptors and Tr+ sources. The latter gave better results and the desired O-glycosylation products were rapidly generated and isolated in moderate to good yields.

Oligodeoxyribonucleoside boranophosphates (PB-ODNs) were synthesized in a stereocontrolled manner via the corresponding H-phosphonates with fully deprotected nucleobases by using diastereopure 2′-deoxyribonucleoside 3′-O-oxazaphospholidine monomers bearing acid-labile protecting groups on the nucleobases. Using the resultant stereodefined PB-ODNs, we demonstrated that the thermal stability of the duplexes of PB-ODNs with complementary oligonucleotides was dependent on the configuration of their phosphorus atoms.

A method for the synthesis of P-stereodefined phosphorothioate oligoribonucleotides (PS-ORNs) was developed. PS-ORNs of mixed sequence (up to 12mers) were successfully synthesized by this method with sufficient coupling efficiency (94–99%) and diastereoselectivity (≥98:2). The coupling efficiency was greatly improved by the use of 2-cyanoethoxymethyl (CEM) groups in place of the conventional TBS groups for the 2′-O-protection of nucleoside 3′-O-oxazaphospholidine monomers. The resultant diastereopure PS-ORNs allowed us to clearly demonstrate that an ORN containing an all-(Rp)-PS-backbone stabilizes its duplex with the complementary ORN, whereas its all-(Sp)-counterpart has a destabilizing effect.

Oligonucleotides, in which one of the two nonbridging oxygen atoms of internucleotidic phosphates is replaced by a different type of atom or a substituent, are useful as therapeutic agents and probes to elucidate mechanisms of enzymatic reactions. The internucleotidic phosphorus atoms of these oligonucleotides are chiral, and the properties of these oligonucleotides are affected by the absolute configuration of the chiral phosphorus atoms. In order to address the issue of chirality, various methods have been developed to synthesize these P-chiral oligonucleotide analogs in a stereocontrolled manner. This critical review focuses on the recent progress in this field (123 references).

Novel 2′-O-modified oligoribonucleotides with alkoxymethyl skeletons were synthesized, and their ability to hybridize complementary nucleic acids and their nuclease resistance were analyzed. The hybridization ability was improved by introducing electron-withdrawing groups and the increases in melting temperature (Tm value) was particularly high for chlorine-substituted compounds. Nuclease resistance of these 2′-O-alkoxymethylated oligomers was lower than expected, but cyano substitution resulted in a higher nuclease resistance than 2′-O-methylation.

An efficient method for the synthesis of short oligo(α-d-glycosyl boranophosphate) derivatives by using an α-d-glycosyl phosphoramidite as a monomer unit was developed. The synthesis of oligomers was carried out by repeating a cycle consisting of the condensation of the monomer unit with a terminal hydroxy group of carbohydrates, boronation of the resultant phosphite intermediates, and terminal deprotection. The phosphoramidite monomer unit was synthesized from the corresponding glycosyl iodide and methyl N,N-diisopropylphosphonamidate in a highly α-selective manner. Di- and tri(α-d-glycosyl boranophosphate) derivatives obtained by the synthetic cycle were converted into the corresponding H-phosphonate diester derivatives, which were then used to synthesize di- and tri(α-d-glycosyl phosphate) derivatives including a fragment of Leishmania glycocalyx lipophosphoglycans.

Syntheses of the novel oligodiaminosaccharides, α-(1→4)-linked-2,6-diamino-2,6-dideoxy-d-glucopyranose oligomers, and their interactions with nucleic acid duplexes DNA–DNA, RNA–RNA, and DNA–RNA are described. Monomers to tetramers of oligodiaminoglucose derivatives having α-glycosyl bonds were successfully synthesized using a chain elongation cycle including glycosylation reactions of a 6-phthalimide glycosyl donor. UV melting experiments for a variety of nucleic acid duplexes in the absence and presence of the oligodiaminosaccharides were performed. The synthesized oligodiaminosaccharides exhibited notable thermodynamic stabilization effects on A-type RNA–RNA and DNA–RNA duplexes, whereas B-type DNA–DNA duplexes were not stabilized by the synthesized oligodiaminosaccharides. Among the oligodiaminosaccharides, the tetramer exhibited the highest ability to stabilize A-type duplexes, and the increase in Tm values induced by the tetramer were higher than those induced by neomycin B and tobramycin, which are known aminoglycosides having ability to bind and stabilize a variety of RNA molecules. CD spectrometry experiments revealed that the oligodiaminosaccharides caused small structural changes in RNA–RNA duplexes, whereas no appreciable changes were observed in the structure of DNA–DNA duplexes. ITC (isothermal titration calorimetry) experiments demonstrated that the amount of heat generated by the interaction between RNA–RNA duplexes and the tetradiaminosaccharides was approximately double that generated by that between DNA–DNA duplexes and the tetradiaminosaccharides. These results strongly suggested the existence of an A-type nucleic acid specific-binding mode of the oligodiaminosaccharides, which bind to these duplexes and cause small structural changes.

Trifluoromethanesulfonic acid salts of tertiary amines were employed as extremely mild acidic activators for rapid glycosylations. Glycosyl phosphite triesters bearing an acid-labile 4,4′-dimethoxytrityl (DMTr) group for transient protection worked as glycosyl donors effectively in the presence of the activators to afford the corresponding disaccharides in good yields without loss of the DMTr group.

A study on the synthesis of nucleosideH-boranophosphonates, a new class of nucleotide analogues having a P→BH3 and a P–H group, via condensation of the corresponding nucleosides with H-boranophosphonate derivatives is described.

Oligonucleotides, in which one of the two nonbridging oxygen atoms of internucleotidic phosphates is replaced by a different type of atom or a substituent, are useful as therapeutic agents and probes to elucidate mechanisms of enzymatic reactions. The internucleotidic phosphorus atoms of these oligonucleotides are chiral, and the properties of these oligonucleotides are affected by the absolute configuration of the chiral phosphorus atoms. In order to address the issue of chirality, various methods have been developed to synthesize these P-chiral oligonucleotide analogs in a stereocontrolled manner. This critical review focuses on the recent progress in this field (123 references).