Oligonucleotide Imprinting in Aqueous Environment

Abstract

AbstractThe development of synthetic receptors that recognize nucleotide bases and their derivatives is an important area of research [1-3]. Applications are envisioned in separation science, biosensors, drug therapy and genetic engineering. Previously in this laboratory, we have developed a molecularly imprinted synthetic receptor for 9-ethyladenine (9-EA). The network polymer has an affinity for adenine and its derivatives with an average association constant (Ka) of 75,000 M–1 in CHCl3 [4]. When a 9-EA imprinted polymer was used as the chromatographic support, adenine eluted at 27 minutes using 92.5/5/0/2.5 CH3CN/H2O/CH3CO2H as the mobile phase, while cytosine, guanine and thymine derivatives all eluted close to the void volume (2.0 min). In addition, imprinted polymers have been made with complementary binding sites for cytosine and guanine [5], as well as other nucleotide base analogues [6].The extension of these results to construct robust receptors for oligonucleotides requires fundamental changes in imprinting strategies. Most importantly, since oligonucleotides are water soluble, strategies that employ EGDMA/MAA formulations in organic solvents will need to be replaced with those that do not compromise the interactions between template (the oligo) and functional monomer.Initially, the imprinting of a 2'-deoxyadenosine dimer (1) was attempted. Due to the hydrophilicity of a DNA oligomer, it was difficult to find a suitable organic solvent that would solubilize the oligomers without disrupting the template's interaction with the polymer matrix [7]. To combat the solubility problems and to insure the homogeniety of the polymerization solution, we examined various polymer formulations with organic and/or aqueous-based solvents that would dissolve the template without disrupting these key interactions.