Stabilization of DNA by sodium and magnesium ions during the synthesis of DNA-bridged gold nanoparticles

Abstract

Nanostructures synthesized using DNA-conjugated gold nanoparticles have a wide range of applications in the field of biosensorics. The stability of the DNA duplex plays a critical role as it determines the final geometry of these nanostructures. The main way to control DNA stability is to maintain a high ionic strength of the buffer solution; at the same time, high salt concentrations lead to an aggregation of nanoparticles. In this study, by means of the instrumentality of DNA-bridged seeds using tris(hydroxymethyl)aminomethane as a soft reducing agent the dumbbell-like gold nanoparticles up to 35 nm were synthesized with a high concentration of sodium ions of up to 100 mM and magnesium ions up to 1 mM. We also examined at the atomic level the details of the effect of the gold nanoparticle surface, as well as Na+ and Mg2+ ions, on the stability of nucleotide pairs located in close proximity to the grafting site.

Hybridization-Driven Adsorption of Polyadenine DNA onto Gold Nanoparticles

“…5 nm AuNPs were synthesized according to the protocol given earlier. 18 The optical density at 520 nm (OD 520 ) of the AuNP colloid was 1.67. Then, the AuNPs were washed on a 30 kDa spin filter, transferred to Milli-Q, and concentrated to OD 520 = 8.35.…”

“…5 nm AuNPs were synthesized according to the protocol given earlier . The optical density at 520 nm (OD 520 ) of the AuNP colloid was 1.67.…”

Structure and Dynamics of dsDNA in Cell-like Environments

“…A high salt concentration or a higher number of cations may disturb the balance between positive and negative charge forces, which results in dsDNA destabilization [ 111 ]. Such behaviour of DNA stability can also be observed when DNA-conjugated gold nanoparticles are used to synthesize nanostructures [ 112 ]. The DNA duplex, bridging two nanoparticles, is significantly destabilized with an increase in the diameter of the nanoparticles, even in the presence of sodium or magnesium ions.…”

“…The DNA duplex, bridging two nanoparticles, is significantly destabilized with an increase in the diameter of the nanoparticles, even in the presence of sodium or magnesium ions. This may occur due to partial winding of the DNA duplex onto the nanoparticle, accompanied by disturbance of the secondary DNA structure [ 112 ].…”

Self‐Assembly of DNA Nanostructures in Different Cations

“…Magnesium is widely considered as an essential component of DNA self‐assembly for its role in screening the inter‐helical repulsion [ 19 ] and stabilizing the stacked form of branched DNA junctions. [ 20 ] Despite this critical role in DNA self‐assembly, magnesium ions can sometimes have adverse effects by causing aggregation of DNA‐nanoparticle complexes at high ionic concentrations, [ 21 ] enhancing nuclease activity, [ 22 ] affecting mineralization of DNA origami structures, [ 23 ] interfering with drug loading due to metal complexation of small molecule drugs [ 24 ] or by modulating intercalative properties, [ 25 ] and by affecting reconfiguration of pH responsive DNA nanostructures. [ 26 ] Further, some applications may require a different ion for DNA nanostructure assembly such as to stabilize proteins arranged on DNA nanostructures, [ 27 ] for cation‐responsive reconfiguration [ 28 ] and for metal‐mediated base pairing.…”