Comparison of rigid and flexible backbones in antisense oligonucleotides

Synthesis and Properties of RNA Modified with Cationic Amine Internucleoside Linkage

Chemical modifications of RNA are important tools for the development of RNA therapeutics. The present study reports a novel RNA backbone modification that replaces the negatively charged phosphate with a positively charged amine linkage. Despite being thermally destabilizing in RNA duplexes, the amine linkage caused a relatively modest decrease of activity of a modified short interfering RNA (siRNA). At position 2 of the guide strand, the amine modification strongly enhanced the specificity of siRNA while causing an ∼5-fold drop of on-target activity. These results support the future development of amines as cationic RNA modifications and novel tools to modulate protein-RNA interactions.

Preparation of 3'-C-branched uridine analogues, suitable for conversion into functionalised 3'-C-methylene derivatives

A novel method for preparation of 1-[2-O-(tert-butyldimethylsilyl)-3- deoxy-3-C-hydroxymethyl-5-O-monomethoxytrityl-beta-D-ribo- pentofuranosyl]uracil by hydroboration of corresponding 3'-deoxy-3'-C-methyleneuridine derivative has been developed. Further conversion of the hydroxyl function into different leaving groups was carried out to afford derivatives suitable for conversion into various 3'-C-branched uridine analogues through substitution.

Reading DNA differently

Product inhibition has provided the limiting barrier to efficient template-directed ligation and polymerization reactions. Here we review the attempts to circumvent this limitation and outline a translation strategy that does overcome the barrier and allows the information encoded in DNA to be read and amplified into backbone-modified oligonucleotides.

Backbone modifications in oligonucleotides and peptide nucleic acid systems

In the past year major advances have been made in the design, synthesis and characterization of two classes of modified oligonucleotides. In the first class, the phosphodiester backbone of 2'-deoxyribo-oligonucleotides has been replaced in several different ways. The second group represents a completely different type of oligonucleotide modification in which the backbone and the 2'-deoxyribose moieties are replaced by amino acids. These advances present new possibilities for the pharmaceutical applications of modified oligonucleotides in antisense strategies.

Modified oligonucleotides as therapeutic and diagnostic agents

Modified oligonucleotides and their analogs represent an exciting new class of agents with potential therapeutic and diagnostic applications. Among the most extensively investigated analogs are oligonucleoside phosphorothioates, some of which incorporate 'hairpin' structures at the 3' end and 'chimeras' that bear two modified oligonucleotides, all potential therapeutic candidates. To further enhance their potential, bio-reversible analogs of oligonucleotides have been synthesized. Several isosteric analogs of phosphoric diester oligonucleotides with neutral achiral backbones, and other novel molecules, such as peptide nucleic acids and circular oligonucleotides, are also reported to form stable duplexes with complementary RNA/DNA and are currently under investigation. Additionally, oligonucleotides carrying a variety of fluorescent tags have been used as probes with potential for diagnostic applications.