Oligonucleotide affinity

Azema L, Bathany K, Rayner B (2010) 2 -0-Appended polyamines that increase triple-helixforming oligonucleotide affinity are selected by dynamic combinatorial chemistry. Chembiochem 11 2513-2516... 

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. 

An effective therapeutic agent must also have the abiUty to reach its target sequence m vivo. BioavailabiUty requires that the antisense oligonucleotide be able to pass through the cell membrane, and that it have a low affinity for nontarget cellular compartments and, in animal systems, nontarget organs. 

Recombinant DNA technology can also be used to create modified proteins that are readily purified by affinity chromatography. The gene of interest is Unked to an oligonucleotide sequence that encodes a carboxyl or amino terminal extension to the encoded protein. The... 

SIAB and sulfo-SIAB have been used to make a high-capacity RNA affinity column for the purification of human IRP1 and IRP2 (Allerson et al., 2003), to couple antibodies or Fab fragments to amine-modified microparticles (Harma et al., 2000), and in the attachment of oligonucleotides to surfaces for detection arrays (Adessi et al., 2000). 

Capture array involves the immobilization of non-protein molecules onto the surface which can interact with proteins in the solute phase. Generally, capture molecules may be broad capture agents based on chromatography type surface chemistries such as ion exchange, hydrophobic and metal affinity functionality, or they may be highly specific such as molecular imprinted polymers or oligonucleotide aptamers. 

At the EM level, detection usually involves using a probe (oligonucleotide) in which a hapten has been incorporated. Incorporation of the hapten does not interfere with the hybridization of the complementary sequences. The next step is the binding of a reporter (may be an antibody) to the hapten. The reporter is then subjected to a binding molecule (may be a secondary antibody) that is coupled with an electron-dense material such as colloidal gold for visualization. Nonetheless, the many affinity-detection and immunodetection systems developed for immuno-cytochemistry may now with ingenuity be applied to molecular biology at the EM level. 

With the development of appropriate cartridges and proper chemistry that would allow the synthesis of the molecule on the disk and than the use of the same disk directly for affinity chromatography by placing it in a chromatographic cartridge, it is reasonable to expect that SMC will become a very efficient tool in the solid phase synthesis of peptides, oligonucleotides, and similar molecules. 

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