The binding affinity and specificity of nucleic acid aptamers have made them valuable candidates for use as sensors in diagnostic applications. In particular, chromophore-functionalized aptamers offer a relatively simple format for detection and quantification of target molecules. We describe the use of nucleic-acid-staining reagents as an effective tool for detecting and signaling aptamer-target interactions. Aptamers varying in size and structure and targeting a range of molecules have been used in conjunction with commercially available chromophores to indicate and quantify the presence of cognate targets with high sensitivity and selectivity. Our assay precludes the covalent modification of nucleic acids and relies on the differential fluorescence signal of chromophores when complexed with aptamers with or without their cognate target. We also evaluate factors that are critical for the stability of the complex between the aptamer and chromophore in presence or absence of target molecules. Our results indicate the possibility of controlling those factors to enhance the sensitivity of target detection by the aptamers used in such assays. 1. Introduction Over the past two decades, the principles underlying nucleic acid structure and the polymeric characteristics of oligonucleotides have been exploited for creation of special ligand sequences that bind specific target molecules with high affinity and specificity [1, 2]. These special sequences or aptamers are discovered from combinatorial oligonucleotide libraries by iterative selection and amplification processes. The rationale for an iterative selection process is explained by the principles of systematic evolution of ligands by exponential enrichment (SELEX) [2]. SELEX has allowed the discovery of aptamers for a plethora of molecular targets including small molecules and proteins [3]. By virtue of their high affinity and specificity aptamers have emerged as a class of molecules that rival antibodies especially in diagnostic and biosensing applications [4]. In particular, aptamers address several shortcomings of antibodies such as the ability to function in nonphysiological buffers and temperatures and the ability to identify reporter molecules such as fluorescein at precise locations. In this regard, aptamer-based optical sensors are extremely attractive and have been the object of extensive research [5–8]. Molecular beacon-inspired optical assays require functionalization of the 5′- and/or 3′-termini of an aptamer with a fluorophore and a quencher. In the presence of or upon binding to the target,
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