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The Influence of Specific Ions and System Architecture on the Recognition and Reactivity of Two Charged Materials: DNA-Modified Gold Nanoparticle Aggregates and Planar Silica Open Access


Other title
Specific Ions
System Architecture
Charged Materials
Type of item
Degree grantor
University of Alberta
Author or creator
Sikder, Md Delwar Hossain
Supervisor and department
Gibbs-Davis, Julianne (Department of Chemistry)
Examining committee member and department
Veinot, Jonathan (Department of Chemistry)
Hanna, Gabriel (Department of Chemistry)
Brown, Alex (Department of Chemistry)
Yu, Hua-Zhong ((Department of Chemistry, SFU)
Department of Chemistry

Date accepted
Graduation date
Doctor of Philosophy
Degree level
DNA functionalized gold nanoparticles (GNP–DNA) offer simple colorimetric nucleic acid sensing with high selectivity and sensitivity. Consequently, they are promising in genetic profiling, disease diagnostics, and forensic applications. In the presence of a target nucleic acid, GNP–DNA forms reversible aggregates, which undergo sharp thermal melting transitions. The abrupt transition is associated with cooperativity, which provides selectivity in GNP-DNA based assays, important for the detection of single base-pair mismatches. Therefore, we have studied the effect of DNA structure and ion polarizability on cooperativity, and the thermodynamics and kinetics of aggregation. We first explore a three-strand system where a linker or target DNA strand hybridized to two different GNP–DNA resulting in duplex-linked aggregates. We find that the presence of single stranded DNA gaps in the linker strand has a strong influence on all of these parameters. For example, upon inserting one unhybridized base on the target sequence such that the hybridizing strands on the GNP–DNA formed a gap rather than a nick, the extent of cooperative interactions was significantly reduced. We also observe a stark decrease in the rate of aggregation with the one-base gap compared with the nicked system. The aggregation rate and the size of the aggregates are also found to be inversely proportional to the length of the gap present in the target-linked aggregate. Next, we evaluate the effect of loop and stem size on the properties of GNP–DNA assemblies using a linker strand that possessed a hairpin at the nicked site rather than a gap sequence as in the previous experiments. We observe that increasing the stem length increases cooperativity but decreases the thermodynamic stability, aggregation kinetics and aggregate size. However, increasing the loop size decreases the thermodynamic stability, cooperativity, rate of aggregation and the aggregate size. These results strongly indicate that bulky secondary structures can significantly modulate the behavior of the aggregates. We then explore the influence of specific ions on aggregate behavior in a two-strand system with a complementary mixture of GNP–DNA. We find that the ion identity has a dramatic effect on the aggregate properties. Specifically, we observe that the largest unhydrated cation cesium greatly increases the number of cooperative DNA duplexes in the aggregates. On the other hand, the smallest cation explored, lithium, is found to enhance the thermal stability and aggregation rate as well as increase the size of the aggregates. Regarding anions, our results also show that iodide causes irreversible aggregation, consistent with previous reports. However, bromide completely prevents aggregation. The very interesting effect of Br– is not seen with unmodified duplexes and requires further investigation to understand on the molecular level. Finally, we extend the specific ion effect study from nanoparticle surfaces to planar silica surfaces due to their importance in DNA microarray based detection. We observe a dramatic increase in the binding affinity of Ca2+ and Mg2+ at higher pH, which is strongly suggestive of silica surface charge neutralization and charge reversal unlike the simple screening effects observed for monovalent cations under similar conditions. These results impact not just biodiagnostics but are also relevant in the oil–sands processing.
This thesis is made available by the University of Alberta Libraries with permission of the copyright owner solely for the purpose of private, scholarly or scientific research. This thesis, or any portion thereof, may not otherwise be copied or reproduced without the written consent of the copyright owner, except to the extent permitted by Canadian copyright law.
Citation for previous publication
Sikder, M. D. H. and Gibbs-Davis, J. M. “The Influence of Gap Length on Cooperativity and Rate of Association in DNA-Modified Gold Nanoparticle Aggregates,” J. Phys. Chem. C, 2012, 116 (21), 11694-11701.

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