Oligonucleotide strategies

The other therapeutic approach to treat cancers is to block the expression of certain oncogenes such as C-raf and C-ras and kinases. The antisense oligonucleotide strategy is focused on blocking the activity of these genes. However, oligonucleotides are unstable in the body and are not taken up very efficiently by the cells. Nanospheres could facilitate the uptake of... 

By similar logic, protein affinity Hbraries have been constmcted to identify protein—protein combining sites, as in antibody—antigen interaction (19) and recombinant Hbraries have been made which produce a repertoire of antibodies in E. coli (20). In another case, a potential DNA-based therapeutic strategy has been studied (21). DNAs from a partially randomized Hbrary were selected to bind thrombin in vitro. Oligonucleotides, termed aptamers that bound thrombin shared a conserved sequence 14—17 nucleotides long. 

In this section, the chemistry and structure of nucleic acids and oligonucleotides is discussed with a view to creating functional conjugates with detectable molecules. The corresponding strategies and protocols associated with DNA or RNA modification and conjugation can be found in Chapter 27. 

Many of the chemical derivatization methods employed in these strategies involve the use of an activation step that produces a reactive intermediary. The activated species then can be used to couple a molecule containing a nucleophile, such as a primary amine or a thiol group. The following sections describe the chemical modification methods suitable for derivatizing individual nucleic acids as well as oligonucleotide polymers. 

This same strategy can be attempted at the mRNA level to inhibit the translation of individual mRNAs. These experiments are almost never 100% efficient hence, the problem becomes how much neutralization is necessary to elicit the desired effect. If the antisense oligonucleotide is targeted toward the mRNA for a particular transcription factor or splice form of a transcription factor, then it may be possible to knock down or reduce the expression of that particular protein. The result of such a knockdown will be a new balance of transcription factor subunits in the cell, probably resulting in alteration of the relative amounts of particular homo- and heterodimers. 

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