Oligonucleotide aptamers

Capture array Non-protein molecules that interact with proteins are immobilized on the surface. These may be broad capture agents based on surface chemistries such as the Ciphergen Protein Chip, or may be highly specific such as molecular imprinted polymers or oligonucleotide aptamers... 

Probes can be antibodies, other binding proteins constructed from protein fusions, or even oligonucleotide aptamers. While completion of the Human Genome Project has enabled access to content for nuclide acid arrays, the content for protein arrays is largely based upon available antibody libraries. Thus, the commercialization of protein microarrays remains largely dependent upon both commercial and institutional providers of protein content. These providers must also permit access to the data-based protein annotations. These are necessary in order for the protein array to be useful as a bioinformatics tool. 

Mongelard F, Bouvet P (2010) AS-1411, a guanosine-rich oligonucleotide aptamer targeting nucleolin for the potential treatment of cancer, including acute myeloid leukemia. Curr Opin Mol Ther 1 107-114... 

C.W. Lange, H.F. VanBrocklin, S.E. Taylor, Photoconjugation of 3-azido-5-nitroben-zyl [ F]fluoride to an oligonucleotide aptamer, J. Label. Compds Radiopharm. 45 (2002) 257-268. 

King, D.J., Ventura, D.A., Brasier, A.R. and Gorenstein, D.G. (1998) Novel combinatorial selection of phosphorothioate oligonucleotide aptamers. Biochemistry, 37,16489-16493. 

Tucker, C.E., Chen, L.S., Judkins, M.B., Farmer, J.A., Gill, S.C. and Drolet, D.W. (1999) Detection and plasma pharmacokinetics of an anti-vascular endothelial growth factor oligonucleotide-aptamer (NX 1838) in rhesus monkeys. J. Chromatogr. B., 732, 203-212. 

FIGURE 21.1 Flow chart for selection and subsequent optimization of oligonucleotide aptamers. 

Finally, it is important to recognize that folded oligonucleotides can also be functional. For example, Sen s group has described a series of DNA oligonucleotide aptamers that are catalysts. Aptamers, selected with a transition state analog A-methylmesoporphyrin, catalyzed the Cu and Zn metallation of porphyrins. This catalytic DNA, which requires for its... 

Famulok, M. (1999). Oligonucleotide aptamers that recognize small molecules. Curr Opin Struct Biol 9, 324-329. 

Fattal, E., Bochot, A. (2006). Ocular delivery of nucleic acids antisense oligonucleotides, aptamers and srRNA. Adv Drug Deliv Rev 58, 1203-1223. 

KCE methods represent a new generation of affinity methods for selection, characterization, and analytical utilization of oligonucleotide aptamers. This development can be considered still in its infancy, with only the surface of capabilities being scratched. Much more needs to be done to understand how methods other than NECEEM and ECEEM can be used for the selection of aptamers and what their properties are in other applications. KCE itself requires a great deal of work to establish a complete space of KCE methods and classify them. A new nomenclature is required for KCE methods to become attractive to a wide community... 

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