Synthetic oligonucleotides as RNA mimetics: 2′-modified RNAs and N3′→P5′ phosphoramidates

Abstract

Significant interest in synthetic DNA and RNA oligonucleotides and their analogues has marked the past two decades of research in chemistry and biochemistry. This attention was largely determined by the great potential of these compounds for various therapeutic applications such as antisense, antigene and ribozyme-based agents. Modified oligonucleotides have also become powerful molecular biological and biochemical research tools that allow fast and efficient regulation of gene expression and gene functions in vitro and in vivo. These applications in turn are based on the ability of the oligonucleotides to form highly sequence-specific complexes with nucleic acid targets of interest. This review summarizes recent advances in the design, synthesis, biochemical and structural properties of various RNA analogues. These comprise 3'-modified oligonucleotide N3'-->P5' phosphoramidates, analogues with modifications at the 2'-position of nucleoside sugar rings, or combinations of the two. Among the properties of the RNA minetics reviewed here are the thermal stability of their duplexes and triplexes, hydrolytic resistance to cellular nucleases and biological activity in in vitro and in vivo systems. In addition, key structural aspects of the complexes formed by the RNA analogues, including interaction with water molecules and ions, are analyzed and presented.

In vivo Inhibition of Lung Cancer by GRN163L: A Novel Human Telomerase Inhibitor

“…Chemical structures of the potential therapeutic oligonucleotides, the proper choice of suitable and biologically important molecular targets, and delivery methods may play a crucial role in ensuring the success of oligonucleotide-based therapeutic approaches (32). This is the first report of beneficial effects of the telomerase inhibitor GRN163L as a therapeutic cancer treatment in an experimental animal model of lung tumor metastases, suggesting that lipidated N3 !…”

“…P5V -phosphoramidates, the 3V amino group is substituted for 3V -oxygen in the 2V -deoxyribose ring, and the nucleosides are linked together via phosphoramidate monoester linkages instead of natural phosphodiester counterparts (30). Replacing the 3V -oxygen by an amino group introduces a moiety into the oligonucleotide backbone that can act as both hydrogen bond donor and acceptor (31,32). Oligonucleotide N3V !…”

Asynchronous replication timing of telomeres at opposite arms of mammalian chromosomes

“…After being air-dried, the slides were denatured in 70% formamide͞2ϫ SSC (pH 7.0) at 70°C for 2 min. The C-rich strands (templates for leading strand synthesis) were revealed by hybridizing (20 l) in 70% formamide, 20 ng of Cy3-conjugated (TTAGGG) 3 2Ј-deoxyoligonucleotide N 3Ј -P 5Ј phosphoramidate probe (27,28), 0.25% (wt͞vol) blocking reagent (Roche), and 5% MgCl 2 in 10 mM Tris, pH 7.2, which was added to the slides containing single-stranded chromosomal target DNA. After a 2-h incubation at room temperature, the slides were washed twice with 70% formamide͞0.1% BSA͞10 mM Tris, pH 7.2, and washed twice with 0.15 M NaCl͞0.05% Tween 20͞0.05 M Tris.…”

Synthesis and Conformational Analysis of 1′‐ and 3′‐Substituted 2‐Deoxy‐2‐fluoro‐D‐ribofuranosyl Nucleosides

“…Furthermore, 3'-amino-2',3'-dideoxy-2'-fluoro-b-d-ribofuranosyl purine nucleosides are of significant interest as constituents of the N(3') ! P(5') phosphoramidate oligonucleotides [26]; such oligonucleotides, which are complementary to the RNA template region of human telomerase (hTR), have been shown to be effective inhibitors of the enzyme and, consequently, inhibited cancer cell growth in vitro [37].…”