Cooperative Metal Ion-Mediated Adsorption of Spherical Nucleic Acids with a Large Hysteresis

Abstract

Spherical nucleic acids (SNA) refer to nanoparticles attached with a high density of oligonuleotides. Linear and spherical nucleic acids have many differences such as hybridization affinity, melting transition, and cellular uptake. In this work, these two types of DNA of the same sequence were compared for adsorption on polydopamine (PDA) nanoparticles and graphene oxide (GO). We focused on the effect of metal ions including Na + , Ca 2+ , and Zn 2+ since metal ions are indispensible for DNA adsorption on PDA and GO. Gold nanoparticles (AuNPs) of various sizes were used to prepare the SNAs. For both PDA and GO, a normal binding curve of one metal ion was obtained for adsorbing the linear DNA, while the spherical DNAs larger than 5 nm showed a sigmoidal binding curve requiring multiple metal ions. Urea and EDTA were used to probe DNA adsorption affinity, where the spherical DNA showed stronger adsorption in general. In the presence of 300 mM Na + , 4 M urea or 4 mM EDTA failed to desorb the 13 nm spherical DNA. The spherical DNA showed a very large hysteresis of metal-dependent adsorption. This study demonstrates another unique property of SNA compared to linear DNA, revealing interesting orientation and packing of DNA on AuNPs, which has deepened our understanding of DNA interface chemistry.

Metal-Doped Polydopamine Nanoparticles for Highly Robust and Efficient DNA Adsorption and Sensing

“…On the other hand, Gd 3+ and Zn 2+ showed the highest adsorption efficiency of 84 and 73% DNA, respectively. The higher DNA adsorption on PDA­(Gd 3+ ) was probably due to the stronger binding affinity between lanthanides and DNA, , as well as the higher affinity of PDA for Gd 3+ . , The general trend of the effectiveness of metal ions in the metal-doped NPs was similar to that on metal-adsorbed PDA NPs, − where a higher DNA adsorption efficiency of lanthanides and transition metal ions was observed compared to Ca 2+ .…”

“…To quantify the concentration of leached Zn 2+ ions, 8-hydroxy-5-quinolinesulfonic acid (HQS) was used as a fluorescent probe, since Zn 2+ can induce its fluorescent emission at 521 nm (Figure A). , Using this standard curve, the Zn 2+ concentration in the supernatant of the 50 μg/mL PDA­(Zn 2+ ) was measured to be ∼0.7 μM (Figure A). Such a low concentration of free Zn 2+ ions was not expected to promote DNA adsorption. , …”

“…Such a low concentration of free Zn 2+ ions was not expected to promote DNA adsorption. 33,34 We then estimated the concentration of the free Gd 3+ ions in the supernatant of the PDA(Gd 3+ ) NPs by taking advantage of the strong fluorescence quenching property of Gd 3+ . As shown in Figure 3B, even 1 μM Gd 3+ led to ∼30% quenching of 100 nM FAM-DNA.…”

“…From the standpoint of charge interactions, since PDA is negatively charged at physiological pH, it repels negatively charged DNA . Polyvalent metal ions such as Ca 2+ and Ni 2+ and Zn 2+ are quite efficient to bridge DNA adsorption on PDA NPs. , Since catecholamines are strong metal ligands, − an interesting question is whether metal ions can be doped in PDA NPs (as compared to add externally) to achieve DNA adsorption. In this case, metal ions need to be stably embedded in PDA without leaching.…”

Spherical Nucleic Acid Mediated Functionalization of Polydopamine-Coated Nanoparticles for Selective DNA Extraction and Detection

“…33 We previously showed that SNA can readily adsorb on PDA with a high affinity comparable to covalent linkages. 35,36 By closely packing SNA on PDA, a very high DNA density might be achieved. In this work, we designed a three-component hybrid material consisting of a Fe 3 O 4 core, a PDA shell, and a SNA decoration.…”