The use of aptamers in large arrays for molecular diagnostics

Backgound: Aptamers are single-stranded oligonucleotides derived from an in vitro evolution protocol called systematic evolution of ligands by exponen tial enrichment (SELEX). They bind tightly and specifically to target molec ules; most aptamers to proteins bind with K(d)s (equilibrium dissociation c onstant) in the range of 1 pM to 1 nM. Methods and Results: The SELEX protocol has been automated; therefore, hund reds to thousands of aptamers can be made in an economically feasible fashi on. Blood and urine can be analyzed on chips that capture and quantitate pr oteins. SELEX has been adapted to the use of 5-bromo (5-Br) and 5-iodo (5-I ) deoxyuridine residues. These halogenated bases can be specifically cross- linked to proteins. Selection pressure during in vitro evolution can be app lied for both binding specificity and specific photo-cross-linkability. The se are sufficiently independent parameters to allow one reagent, a photo-cr oss-linkable aptamer, to substitute for two reagents, the capture antibody and the detection antibody, in a typical sandwich array. After a cycle of b inding, washing, cross-linking, and detergent washing, proteins will be spe cifically and covalently linked to their cognate aptamers. Conclusions: Because no other proteins are present on the chips, protein-sp ecific stain will now show a meaningful array of pixels on the chip. Learni ng algorithms and retrospective studies should lead to a robust, simple, di agnostic chip.