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

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 salt-dependent 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.