DNA and RNA aptamers are becoming increasingly popular as biotechnological tools and possible therapeutic molecules, as they often match or surpass the binding affinity and specificity of antibodies for their target in a much smaller molecule that is often better suited to experimental conditions. Aminoglycoside antibiotics were among the first targets for aptamers due to their high natural affinity for RNA, binding to many different sequence and structural motifs, resulting in a "selective" affinity for RNA which is less than specific, yet not quite broad enough to qualify as nonspecific binding. This selective binding allows aminoglycosides to bind to aptamers selected against other ligands, potentially altering the behavior of aptamer constructs containing aptamers not specifically targeted towards aminoglycosides. A selective aptamer binding enhancement by neomycin and a smaller increase by tobramycin is reported here when two aptamers are joined together into Cis-Linked Aptamers for Microanalyitical Procedures (CLAMPs), even when the aptamers were not designed to bind aminoglycosides. This results in allosteric binding behavior in these CLAMPs, where selective binding by aminoglycosides increases the binding ability of one of the aptamers. This allostery may be the result of these aminoglycosides binding to a portion of the aptamer constructs that is distinct from the regulated aptamer, stabilizing the structure of that portion of the construct so it does not interfere with the folding and binding of the regulated aptamer. This restores higher binding in an aptamer construct in which additional sequence adds to folding options and interferes with aptamer binding. In this way; aminoglycosides may act as generic allosteric activators for many different aptamer constructs. CLAMPs can also be used to link different species of fluorescent mesoporous silica nanospheres. In this way the fluorescent nanospheres can form optical logic gates, where two species of nanosphere are bound close enough by the CLAMP to produce fluorescence resonance energy transfer (FRET), an unique output from the input of the two nanospheres.