|Abstract:||DNA, traditionally known as the carrier of genetic information has proven that it can be utilized as a key player for self-assembly, material synthesis and molecular sensors. Given the ease of synthesis and modification, precise control over sequence and specificity in base pairing, the number of studies with DNA as a functional molecule have increased. Intrigued by the inherent chemical functionality that single stranded DNA (ssDNA) has, i.e., the sugar, the negatively charged phosphate backbone and the nitrogenous bases, we envisaged that the mode of interaction with metal surfaces should vary with the change in DNA sequence. The synthesis of proteins relies on the similar concept where the genetic code, i.e. the gene sequence, determines the final protein structure. However in order to perfect the code for nanoparticle synthesis, one has to take into consideration the effect of factors such as the metal involved, the seed, etc.
The ability to control the arrangement of metal atoms on the nanoscale translates into physical and chemical properties that depend on this specific arrangement. Therefore there is merit in exploring the synthesis of noble metal nanoparticles with different shapes and exposed surfaces. In chapter 2, the facile synthesis and the growth mechanism of high-index faceted tetrahexahedral palladium nanoparticles via an early stage underpotential deposition of silver in the presence of a commonly used capping ligand CTAB is reported. Reports have shown that different DNA sequences can mediate the control of shapes and surface properties of nanoparticles. However, most studies have involved only monometallic particles, most of which were gold nanoparticles. Controlling the shape of bimetallic nanoparticles is more challenging, and there is little research into the use of DNA-based ligands for their morphological control. In chapter 3, we report the DNA-templated synthesis of Pd−Au bimetallic nanoparticles starting from palladium nanocube seeds. The presence of different homo-oligomer DNA sequences containing 10 deoxy-ribonucleotides of thymine, adenine, cytosine, or guanine (referred to as T10, A10, C10, and G10, respectively results in the growth of four distinct morphologies. Through detailed kinetic studies by absorption spectroscopy and scanning electron microscopy (SEM), characterization through scanning transmission electron microscopy (STEM), we have determined the role of DNA in controlling Pd−Au nanoparticle morphologies. One major function of DNA is interacting with the incoming metal atoms and controlling their diffusion and deposition on the Pd nanocubic seed by sequence specifically passivating the seed surface. Interestingly, nanoparticle growth in the presence of A10 follows an aggregative growth mechanism that is unique when compared to the other base oligomers.
Since we utilize the seed-mediated approach for our nanomaterial synthesis, the seed’s surface naturally plays a pivotal role in the growth mechanism. Seeds enclosed by high-energy facets act as facile nucleation sites in nanoparticle growth and could suppress the effect of DNA and dominate the overall growth process. In Chapter 4, we then investigated whether DNA molecules are influential when a seed containing high-energy facets is used. Therefore, a high-indexed concave palladium nanocube seed was adopted as the seed. Based on detailed spectroscopic and microscopic studies on the time-dependent growth of bimetallic nanoparticles, we found that the DNA, A10, T10, G10 and C10 show a unique interaction with the surface of the seed and the precursor. The most important factor is the binding affinity of the nucleobase to the Pd surface; A10 shows the highest binding affinity and can stabilize the high energy surfaces of the seed and the growth consistently proceeds via the aggregative growth mechanism. Initially, the growth of bases with lower binding affinities (T10, G10, and C10) is completely dictated by the seed’s surface energy, but later growth can be influenced by different DNA sequences, providing four Pd@Au bimetallic nanoparticles with unique morphologies. The effect of these DNA molecules with medium or low binding affinities can only be observed when more Au is deposited. We propose a scheme for DNA-controlled growth. The differences in mechanism between the cubic and concave cubic seed are discussed.
Next we explored the application of DNA as a biosensor. In order to expand the scope of DNA based sensors, we combined them with an emerging clinical imaging modality, Photoacoustic Imaging (PAI). PAI, has gained importance as an imaging modality due to its unique ability of scaling spatial resolution and imaging depth across both optical and ultrasonic dimensions. Most PAI contrast agents lack selectivity to their target. While recent literature reports some selective contrast agents, most of them lack generality in the way they have been generated, i.e., methods successful in developing PAI contrast agents for one target can rarely be applied to another target and need a large amount of rational design. On the contrary, functional DNA based recognition units such as aptamers are not only easy to synthesize but also highly selective to their targets that range from small molecule analytes to much larger molecules such as proteins. Functional DNA is selected through a very general approach known as in-vitro selection, which has led to the discovery of many target specific aptamers. We focus our efforts to optimize a structure switching aptamer for the platelet derived growth factor-BB (PDGF-BB) which is overexpressed in cancers. The DNA-based probe is evaluated by gel-shift assays and is optimized to “turn on” only in the presence of the target. Additional fluorescence measurements confirm the specificity of the probe. The acoustic signal arising from the fluorophore quencher tags (IR800/QC1) at the two wavelengths (775 nm/719 nm) can be processed to give a concentration dependent signal which can be monitored using absorption spectroscopy and hence also the acoustic signal. Further, we were able to use this probe in mice models to detect PDGF-BB as a proof of concept. We have also demonstrated that this approach is general enough to be extended to other targets of functional DNA such as thrombin. This approach can help advance the application of a powerful imaging modality, PAI, from the lab to the clinic.
Chapter 6 describes the characterization of DNA aptamer for adenosine using isothermal calorimetry (ITC). Further investigation into the structural components of the aptamer using point mutations, base additions or deletions reveal conserved bases for the successful binding of the aptamer to the target. This study demonstrates that biophysical characterization of functional DNA can potentially better DNA-based sensors.