Applications of aptamers for cell biology; intracellular DRAGINs and IMAGEmates

Project

The presence of mobile aptamers ​in the cell presents the possibility that they would bind their small molecule targets and move them away from the membrane, thereby increasing the intracellular concentration of the aptamer target by preventing its export. This would provide a means of increasing the effectiveness of drugs. To evaluate this possibility, Nilsen-Hamilton collaborated with Boushaba and Levine to develop a mathematical model of partial differential equations (PDEs) using known thermodynamic and flux parameters and the basic format of a cell with a plasma membrane and efflux pumps. The model predicted that: 1) mobile intracellular receptors will increase the intracellular concentration of their ligand, 2) the increased intracellular ligand concentration would be associated with different distributions between receptor-bound and unbound ligand depending on the affinity of the receptor for the ligand. The higher the affinity of the receptor, the more of the increased intracellular ligand would be associated with the receptors, and 3) mobility is necessary for the receptor effect on intracellular ligand concentrations.

To test the ability of aptamers to increase the intracellular concentrations of their ligands, we used E. coli and yeast as model systems. E. coli is sensitive to a range of aminoglycosides for which there are existing aptamers that function inside bacterial cells. We found that expression of neomycin-B aptamers by E. coli increases the total intracellular concentration of Cy3-paromomycin by 4-6-fold and the free intracellular concentration of paromomycin by 2-3-fold.  The ability of aptamers to increase the intracellular concentration of their chemical targets opens the way to increasing drug efficacy, such as for anticancer drugs where the export pumps are particularly a problem. Aptamers with the ability of increasing the intracellular concentrations of drugs are referred to as DRAGINS (Drug Binding Aptamers for Growing Intracellular Numbers).

We are currently collaborating with the Kraus and VanBrocklin groups to develop aptamers for signaling cell distress. Placed after the Lcn2 promoter, the IMAGEtags will provide a monitor of inflammation. This will provide a means of detecting local sites of inflammation in transplanted tissues using radiolabeled aptamer ligands. Aptamers that function to increase their intracellular ligand concentration and can be used for imaging are referred to as IMAGEmates (IMAGe Enhancement by Mobile ApTamErs). Subclinical inflamed sites lead to cell death and the formation of scar tissue which does not perform desired the tissue function. Thus, the ability to monitor local sites of inflammation in transplanted tissue will enable better management of transplanted tissues and thus lengthen their life spans. 

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