Effect of Macromolecular Crowding on DNA:Au Nanoparticle Bioconjugate Assembly

Abstract

DNA:Au nanosphere bioconjugates have applications in biosensing and in the bottom-up assembly of materials. These bioconjugates can be selectively assembled into three-dimensional aggregates upon addition of complementary DNA oligonucleotides and can be dissociated by heating above a melting transition temperature at which the DNA duplexes are denatured. Herein we describe the impact of polymeric solutes on the thermal denaturation behavior of DNA:Au nanoparticle bioconjugate assemblies. Polymeric solutes can dramatically impact biochemical reactions via macromolecular crowding. Poly(ethylene glycol)s (PEGs) and dextrans of varying molecular weights were used as crowding reagents. While both PEG and dextran increased the stability of DNA:Au aggregates, melting transition temperatures in the presence of PEG were impacted more significantly. Polymer molecular weight was less important than polymer chemistry and weight percent in solution. For a high (15%) weight percent of PEG, aggregation was observed even in the absence of complementary oligonucleotides. These results underscore the importance of polymer chemistry in addition to physical volume exclusion in macromolecular crowding and point to the importance of understanding these effects when designing biorecognition-based nanoparticle assembly schemes in complex matrixes (i.e., any involving polymeric solutes).

Using theory and computation to model nanoscale properties

“…In the last 10 years, there has been growing interest in the use of DNA to make nanoscale structures. One version of this has involved using DNA to link together nanoparticles, viruses, and polymeric materials (9)(10)(11)(12)(13)(14). These materials have found use in sensing applications, in part because they exhibit much narrower melting transitions (thermal dehybridization) than occur for the same duplexes in solution (15).…”

Exploring the thermal stability of DNA-linked gold nanoparticles in ionic liquids and molecular solvents

“…For example, to mimic the macromolecularly crowded environment in cells, polymers such as polyethylene glycol (PEG) and dextran have been added. [31][32][33][34][35][36] DNA is also soluble in the presence of molecular solvents such as ethanol, dimethyl sulfoxide (DMSO), dimethylformamide (DMF) and acetonitrile (ACN), which can significantly accelerate DNA hybridization. [37][38][39][40] At the same time, these molecular solvents contain hydrophobic groups that can solvate the DNA bases and reduce DNA duplex stability.…”

Single-Nucleotide Polymorphism Genotyping by Nanoparticle-Enhanced Surface Plasmon Resonance Imaging Measurements of Surface Ligation Reactions

“…Gold nanoparticles prepared using this method are known to have average diameters of 12-13 nm with a standard deviation of less than 10%. 37 DNA:Au conjugate preparation: DNA:Au nanoparticle conjugates were prepared using procedures described by Keating et al 38 Briefly, 50 μL of freshly purified 100 μM thiol-modified oligonucleotide was added to 800 μL of Au nanoparticle solution in an eppendorf tube. The tube was then placed in a heat block at 37 °C for a minimum of 4 h before the addition of 230 μL of H 2 O and 120 μL of 1 M NaCl/100 mM phosphate (pH 7.4).…”