Improvement of DNA recognition through molecular imprinting: hybrid oligomer imprinted polymeric nanoparticles (oligoMIP NPs)

Abstract

High affinity and specific binding are cardinal properties of nucleic acids in relation to their biological function and their role in biotechnology. To this end, structural preorganization of oligonucleotides can significantly improve their binding performance, and numerous examples of this can be found in Nature as well as in artificial systems. Here we describe the production and characterization of hybrid DNA-polymer nanoparticles (oligoMIP NPs) as a system in which we have preorganized the oligonucleotide binding by molecular imprinting technology. Molecularly imprinted polymers (MIPs) are cost-effective "smart" polymeric materials capable of antibody-like detection, but characterized by superior robustness and the ability to work in extreme environmental conditions. Especially in the nanoparticle format, MIPs are dubbed as one of the most suitable alternatives to biological antibodies due to their selective molecular recognition properties, improved binding kinetics as well as size and dispersibility. Nonetheless, there have been very few attempts at DNA imprinting in the past due to structural complexity associated with these templates. By introducing modified thymine bases into the oligonucleotide sequences, which allow establishing covalent bonds between the DNA and the polymer, we demonstrate that such hybrid oligoMIP NPs specifically recognize their target DNA, and that the unique strategy of incorporating the complementary DNA strands as "preorganized selective monomers" improves the recognition properties without affecting the NPs physical properties such as size, shape or dispersibility.

Molecularly Imprinted Polymers for Cell Recognition

“…aeruginosa cells, thus generating polymers directly in situ at the surface of the microorganisms [25]. The cells also doubled as a solid-phase to isolate high-affinity from low-affinity polymer products, similar to the technique pioneered by Piletsky and colleagues [8,[26][27]. A "click" chemistry reaction was used to attach fluorescent reporters on the polymers, to simultaneously bind and visualise the pathogens (Figure 3).…”

Molecular Imprinting with Functional DNA

“…In addition to DNA aptamers, imprinting using double‐strand DNA was also reported . By anchoring one of the strands as a monomer and removing the other strand as the target, the generated DNA‐MIPs specifically recognized the target DNA strand through complementary binding.…”

Acrylamide-dT: a polymerisable nucleoside for DNA incorporation

“…Therefore these conditions were chosen for automated oligonucleotide synthesis. Given the ongoing interest in functionalising aptameric DNA sequences with polymerisable groups, 9,10,17,18 and our recent work on such systems, 21 it was decided to incorporate Acrylamide-dT into the thrombin binding aptamer (TBA). Different positions in the TBA sequence were chosen, including internal T sites and endfunctionalisation, as shown in Table 1.…”

“…16 For example, Jie and coworkers used this acrylamide reagent to integrate uorescent DNA into hydrogels, whereas others have incorporated it into aptameric systems for molecular imprinting applications. 9,10,17,18 However, the placement of Acrydite™ is limited to the 5 0 end of the oligonucleotide. We reasoned that a synthon such as Acrylamide-dT would allow placement of acrylamide moieties not only internally, but also at multiple positions within a strand.…”