Small DNAs that Bind Nickel(II) Specifically and Tightly

Abstract

Metal recognition by nucleic acids provides an intriguing route for biosensing of metal. Toward this goal, a key prerequisite is the acquisition of nucleic acids that can selectively respond to specific metals. Herein, we report for the first time the discovery of two small DNAs that can specifically bind Ni 2+ and discriminate against similar ions, particularly, Co 2+ . Their minimal effective constructs are 60−70 nucleotides (nt) in length with Ni 2+ binding even at harsh denaturing conditions of 8 M urea and 50 mM EDTA. Using isothermal titration calorimetry (ITC), we estimated the dissociation constant (K D ) of a representative DNA to be 24.0 ± 4.5 μM, with a 9:1 stoichiometry of Ni 2+ bound to DNA. As being engineered into nanosized particles, these DNAs can act like nanosponges to specifically adsorb Ni 2+ from artificial wastewater, demonstrating their potential as a novel molecular tool for high-quality nickel enrichment and detection.

Small DNAs That Specifically and Tightly Bind Transition Metal Ions

“…Usually, transition metal ions tend to lose their coordinated water molecules to produce inner-sphere complexes (stronger interactions) with DNA bases. Perhaps the near-CP conditions further promote the formation of inner-sphere M 2+ –DNA complexes by generating polynuclear M 2+ complexes , that are more robust to interact with DNA. In the future, an atomic-resolution structural model should help to decipher the binding mechanism.…”

“…Previously, in the search for metal ion-dependent DNA-cleaving DNAzymes, , we serendipitously discovered a series of Ni 2+ -binding DNAs, which generated tight Ni 2+ –DNA complexes that caused DNA band shifting in denaturing polyacrylamide gel electrophoresis (dPAGE) to sneak through the DNAzyme selection. The high stability of these Ni 2+ -bound DNAs, i.e., nondenatured even under harsh denaturing conditions of 8 M urea and 50 mM EDTA, was impressive and inspiring.…”

“…Starting from a single-stranded (ss)­DNA sequence library (G0), we incubated the library with certain metal ions (M n + ) and then loaded the library into dPAGE (8 M urea) for band separation (Figure ). According to the Ni 2+ -binding DNAs’ performance, we reasoned that the potential tightly bound M n + –DNA complexes could migrate slower or faster to M n+ -unbound DNA. Thus, we separately collected gels up and below the M n + -unbound DNA band (as the band migrated to nearly the middle of a 22 cm-in-length dPAGE gel, excise a section of 6 cm long gel top and bottom of the band), and eluted DNA from the gels for PCR amplification to rebuild the ssDNA library (G1, Pool A and B refer to the upper- and lower-shifted DNAs, respectively).…”

“…In order to showcase the generality of the strategy, we initiated parallel selection on two readily attainable transition metal ions, Zn 2+ and Cd 2+ , with the corresponding G0 ssDNA libraries carrying distinct primer-binding domain to avoid potential cross-contamination (Figure S1). Based on the previous finding of the preference of Ni 2+ -binding DNAs for conditions that approach the critical point (CP) of forming Ni­(OH) 2 /NiO precipitation, herein we set similar CP-approaching conditions (2 mM Zn 2+ , pH 7.0; 2 mM Cd 2+ , pH 8.2) during the incubation of the DNA library with the metal ions to presumably favor the generation and isolation of Zn 2+ (Cd 2+ )-binding DNAs. In each round of the selection, we recorded the fraction of the shifted DNA bands to monitor the progression, and apparent signals were seen starting from G5 Pool B for both selections (Figure S1).…”

“…After overnight elution, DNAs from the shifted bands regained the no-shifting position in dPAGE in the absence of the metal ions (Figure S5), suggesting that the observed band shifting results from the metal ion-binding induced conformational change rather than cleavage of DNA. Although none of the three DNAs generates upper-shifted DNA bands upon M 2+ binding, from the selection perspective we think it is necessary to collect the top area in the gel since the upper-shifting has been seen on Ni 2+ -binding DNAs …”