Triplex-forming oligonucleotides for modulating interactions of aptamers with their ligands

Jiyeong Hong, Harun Kapidzic, Yulia Gerasimova

Chemistry Department, University of Central Florida

Aptamers are oligonucleotide-based functional analogs of protein receptors or antibodies. They fold into three-dimensional structures with a binding site for their specific ligands, thus ensuring binding affinity and specificity of ligand-aptamer recognition. Due to a limited number of functional groups available for aptamers and their limited size, the ligands can be insufficiently occluded from solvent, which may affect the rate of dissociation and, ultimately, binding affinity of the aptamer.

In this work, we hypothesized that bringing extra nucleotides toward the ligand-binding site of an aptamer with the help of triplex-forming oligonucleotide (TFO) locks interacting with duplex portions of the aptamer can help modulating its interactions with the corresponding ligand. As a model ligand-aptamer system, we utilized a DNA-based fluorescent light-up aptamer (FLAP) DAP-10, which was originally isolated to bind to and thereby enhance fluorescence of dapoxyl sulfonyl dyes¹ and later shown to bind other fluorogenic dyes including a well-known molecular rotor auramine O.² DAP-10 core was split into two parts extended to form two duplex regions – sites for interactions with TFOs. Both parallel and antiparallel TFOs were designed according to the previously reported rules.³ The designed TFOs were tested in their abilities to form triplex DNA structures with the split DAP-10 constructs, using native gel electrophoresis. Effect of TFOs on fluorescence of auramine O in complex with DAP-10 was studied using fluorescence spectroscopy.

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