Current Medicinal Chemistry - Volume 8, Issue 10, 2001

In boranophosphate-oligodeoxynucleosides (BH 3- -ODN) a borane group replaces one of the two non-bridging oxygen atoms in the phosphodiester backbone of the naturally occurring congener. The chemical and biophysical properties of BH 3 - -ODN are reviewed, as are their interactions with enzymes such as DNA polymerases, exo- and endonucleases, and ribonuclease H. Three approaches to synthesis of BH 3- -ODN are described in solution, on solid supports, and by template directed enzymatic polymerization of appropriately modified nucleoside triphosphates. Comparisons are made to other members of the family of phosphorus modified nucleic acids, the phosphorothioates and methylphosphonates. The potential applications of boranophosphate modified compounds to antisense therapeutics and DNA sequencing are discussed.

Nucleic acids have been extensively modified by replacing the phosphodiester group or the whole sugar-phosphodiester backbone with alternative anionic, neutral and cationic structures. Several of these modified oligonucleotides exhibit improved properties including enhanced recognition and binding to RNA, duplex DNA and proteins. This has resulted in the development of new and more potent antisense and antigene agents, as well as aptamers. Furthermore, backbone modified oligonucleotides have also been used in the development of several alternative strategies, which rely on altogether different mechanisms of action and show significant promise for therapeutic intervention. In this review the latest advances in the synthesis and evaluation of the most promising backbone modified oligos will be discussed, with a view to their future as novel pharmaceuticals.

Ribozymes are catalytic RNAs that can cleave substrate RNAs in a sequence specific manner. Here we survey, in brief, the structure of hammerhead and hairpin ribozymes and discuss their applications as molecular antiviral molecules for HIV-1.

This review describes the application of a natural defense mechanism to develop effective agents for The post-transcriptional control of gene expression. 2-5A is a unique 2',5'-phosphodiester bond linked oligoadenylate, (pp)p5'A2'(p5'A)n , that is elaborated in virus-infected interferon-treated cells. The 2-5A System is an RNA degradation pathway that is an important mechanistic component of interferon's action against certain viruses. It may also play a role in the anticellular effects of interferon and in general RNA decay. A major player in the 2-5A-system is the latent and constitutive 2-5A-dependent ribonuclease (RNase L) which upon activation by 2-5A, degrades RNA. This RNase L enzyme can be recruited for antisense therapeutics by linking it to an appropriate oligonucleotide targeted to a chosen RNA. Syntheses of 2-5A, its analogues, 2-5A-antisense, and its modifications are detailed herein. Applications of 2-5A-antisense to particular targets such as HIV, PKR, chronic myelogenous leukemia, telomerase, and respiratory syncytical Virus is described.

This report emphasizes the interfacial chemistry that is required to ensure proper attachment of oligonucleotides onto the surface of microarrays. For example, strategies for the covalent attachment of pre-synthesized oligonucleotides to glass slides, gold films, polyacrylamide gel pads, polypyrrole films, and optical fibers are surveyed in an attempt to better define the parameters for optimal formation and detection of DNA hybrids. These parameters include among others, the nature and length of the linkers attaching oligonucleotides to the arrays, and the surface density of oligonucleotides required for unhindered hybridization with DNA targets. Sensitive detection methods such as the use of light-scattering techniques, molecular beacons, surface plasmon resonance, attenuated total internal reflection-FTIR, and the evanescent field excitation of fluorescence from surface-bound fluorophores have been developed to study the kinetics and specificity of hybridization events. Finally, the synthesis of oligonucleotides directly on glass surfaces and polypropylene sheets has been investigated to enable DNA sequencing by hybridization and achieve oligonucleotide densities of ca.