Combinatorial methods: aptamers and aptazymes

Combinatorial methods have been used to generate nucleic acid molecules with specific characteristics. Aptamers are nucleic acid binding species, and can be modified to directly transduce molecular recognition to optical signals. Aptazymes are allosteric or effector-activated ribozymes. We have designed or selected aptazymes that are responsive to a variety of ligands. En particular, we have selected a ribozyme ligase that is activated 10,000-fold in the presence of an oligonucleotide effector, and have designed ligases that are up to 1,600-fold dependent on small molecule effecters. Even in those instances where designed constructs were initially unresponsive, we have been able to use selection to optimize their response characteristics. Aptamers and aptazymes can be readily adapted for use in biosensor applications. For example, aptamers can potentially be selected against molecules that may be difficult to raise antibodies against, such as toxins, and subsequently modified to signed interactions in heterogenous mixtures. Aptazymes can be engineered to ligate fluorescent tags to themselves in the presence of effecters, and aptazyme chips that sense individual metabolites can be envisioned. With a simple switch of substrate, aptazymes can ligate enzymes to themselves, such as horse radish peroxidase, and be used for amperometric sensing.