A general transition metal binding aptamer following the Irving-Williams series.

Using both Co and Ni as target metal ions, aptamer selections were carried out by immobilization of a DNA library hybridization. A set of aptamers were obtained although they all showed binding to both metal ions. The Co-1 aptamer was highly enriched in both selections and it is a general metal binding aptamer with binding affinity following the Irving-Williams series: Mn < Fe < Co < Ni < Cu > Zn. Using NMR spectroscopy, Co-1 forms new base pairs with a relatively large structural change upon binding to Zn, whereas a previously reported Zn-1 aptamer shows less conformational change and rigidifies upon Zn binding. The induced-fitting of the Co-1 aptamer and the lock-and-key binding of the Zn-1 aptamer may explain the general metal binding of the former. Using isothermal titration calorimetry, Co-1 binding Co was an enthalpy-driven event and the was determined to be 2.7 μM, whereas the from the strand-displacement assay was 76 nM. The Co-1 aptamer is the first reported aptamer to follow the Irving-Williams series, although this series is very prevalent in proteins. This aptamer can thus serve as a model system for understanding metal binding by DNA and can also be a general first-row transition metal sensing element.