DNA Adsorption by ZnO Nanoparticles near Its Solubility Limit: Implications for DNA Fluorescence Quenching and DNAzyme Activity Assays

Abstract

Zinc oxide (ZnO) is a highly important material, and Zn 2+ is a key metal ion in biology. ZnO and Zn 2+ interconvert via dissolution and hydrolysis/condensation. In this work, we explore their interactions with DNA, which is important for biointerface, analytical, and bioinorganic chemistry.Fluorescently labeled DNA oligonucleotides were adsorbed by a low concentration (around 5 µg/mL) of ZnO nanoparticles, near the solubility limit. Right after mixing, fluorescence quenching occurred indicating DNA adsorption. Then fluorescence recovered, attributable to ZnO dissolution. The dissolution rate followed A5>T5>C5. Dissolution was slower with longer DNA.The adsorption affinity was also measured by a displacement assay to be G5>C5>T5>A5, suggesting tightly adsorbed DNA can retard ZnO dissolution. Electrostatic interactions are important for DNA adsorption since ZnO is positively charged at neutral pH, and a high salt concentration inhibits DNA adsorption. Next, in-situ formation of ZnO from Zn 2+ was studied.First, titrating Zn 2+ into a fluorescently labeled oligonucleotide at pH 7.5 resulted in an abrupt fluorescence quenching beyond 0.2 mM Zn 2+ . At pH 6, quenching occurred linearly with Zn 2+ concentration, suggesting the effect of Zn 2+ precipitation at pH 7.5. Second, a Zn 2+ -dependent DNA-cleaving DNAzyme was studied. This DNAzyme was inhibited at higher than 2 mM Zn 2+ , attributable to Zn 2+ precipitation and adsorption of the DNAzyme. This paper has established the interplay between DNA, Zn 2+ , and ZnO. This understanding can avoid misinterpretation of DNA assay results, and adds knowledge to DNA immobilization.3

One-dimensional vs. two-dimensional proton transport processes at solid–liquid zinc-oxide–water interfaces

“…As a result, there is no net charge on the surface, and the present results for proton hole diffusion effectively concern ZnO surfaces at the point of zero charge (pzc), in the absence of specifically adsorbed counterions. The pzc of ZnO particles depends on the method of preparation, but is normally found at slightly basic pH, around pH 9 46. A higher pH would result in more deprotonation of O s H – and O*H 2 groups, and a lower pH in the protonation of O s 2– and O*H – groups.…”

Sequence-specific control of inorganic nanomaterials morphologies by biomolecules

“…Moreover, even in the reported case, the relative binding affinity of different DNA sequences towards inorganic materials surface is debatable. For example, oligo-C DNA has later been demonstrated to have stronger binding affinity towards ZnO than oligo-T DNA [32],[33]. No facet specific DNA selection has been reported.…”

Selection and Screening of DNA Aptamers for Inorganic Nanomaterials

“…A single round of aptamer selection was performed by Morse and co‐workers on ZnO, and a simple T 30 DNA sequence was concluded to be its aptamer . By a screening method, however, poly‐C DNA was found to adsorb more strongly than poly‐T DNA . Breaker and co‐workers selected both DNA and RNA aptamers for cellulose …”

“…[25] By as creening method, however,p oly-C DNA was found to adsorb more strongly than poly-T DNA. [17,61] Breaker and co-workers selected both DNA and RNA aptamers for cellulose. [23,24] However,t hese aptamers have not caught much attention for practical applications.…”