The Influence of Gap Length on Cooperativity and Rate of Association in DNA-Modified Gold Nanoparticle Aggregates

Abstract

Polyvalent gold nanoparticle−DNA conjugates hybridize with complementary linker DNA strands to form aggregates that exhibit sharp dissociation curves indicative of cooperative behavior. Introducing single-stranded gaps consisting of thymidines (T 1 −T 20 ) into the linker strand resulted in a decrease in the number of duplexes that dissociate cooperatively. Upon adding one base insertion (T 1 ) the cooperative number drops from 6.3(2) to 2.8(2) duplexes. The cooperative number then increases slightly for the T 3 gap and thereafter decreases for T 8 and T 10 , with a slight increase again for the T 20 gap. As the presence of a shared condensed cation cloud has been implicated in neighboring duplex cooperativity, we measured the saltdependent behavior of T n gap-linked unmodified duplexes and the number of ions released per duplex dissociation. Interestingly, the number of cations released for the duplexes with a longer gap sequence is significantly larger than the number released for a T 1 gap-linked duplex or a nicked duplex (T 0 ). Overall there is a correlation between the change in condensed cation density and the dissociation entropy for the unmodified T n gap-linked duplexes, and the cooperative unit for the T n gap-linked GNP−DNA aggregates. Using dynamic light scattering and changes in optical absorbance, we also found that aggregation of GNP−DNA is more rapid when hybridization occurs at a nicked versus gap site, which was previously observed but attributed to slower hybridization as a result of the longer linker strand. By comparing the aggregation rate of a prehybridized GNP−DNA:T 10 -linker complex with a completely complementary GNP−DNA and a GNP−DNA that led to a T 10 gap, we were able to establish that the presence of the gap, not DNA length or accessibility, caused the decrease in aggregation rate. Our results support that flexibility in aggregates decreases the rate of aggregation as well as the extent of cooperativity, which has important implications in genomic DNA detection.

Cooperativity in Noncovalent Interactions

“…Gibbs-Davis and co-workers have studied the influence of gap length on cooperativity and rate of association in DNA-modified gold nanoparticle aggregates. 764 The flexibility in aggregates decreases the rate of aggregation as well as the extent of cooperativity, suggesting implications in genomic DNA detection. Thus, a substantial number of studies including the above-mentioned specific examples clearly illustrate the relevance and importance of cooperativity among noncovalent interactions in wide-ranging novel materials.…”

Monitoring DNA Hybridization and Thermal Dissociation at the Silica/Water Interface Using Resonantly Enhanced Second Harmonic Generation Spectroscopy

“…In contrast, the hybridization of free DNA in solution requires 10−100 s depending on the sequence length and concentration, 17,52 while hybridization of DNA-modified materials that form three-dimensional assemblies requires hours. 53,54 This comparison indicates that the restricted degrees of freedom of the immobilized strand significantly impact the rate of hybridization, but that the "two-dimensional" environment of the interface is not as constrained as that of materials forming three-dimentional aggregates through DNA hybridization.…”

Polarity Control for Nonthiolated DNA Adsorption onto Gold Nanoparticles

“…[3][4][5][6] At the same time, many fundamental insights have been obtained using this hybrid material. [7][8][9][10][11][12][13][14][15][16][17][18] To enable these applications, the first step is DNA attachment and there are two main approaches to achieve this. This field started with thiolated DNA, where a very high DNA density can be immobilized.…”