Overview and Motivation
Graphene possesses exceptional mechanical and electronic properties for applications ranging from catalysis and electronics to sensors and solar cells. While much of the research interest on this material has centered on the synthesis strategies, effects of doping and defects on structure, and the intrinsic properties of graphene and graphene-related materials (e.g. graphene oxide, graphene nanoribbons, etc.) far fewer studies are directed towards incorporating surface functional groups without the use of harsh processing conditions in order to tailor synthesis-structure-property interrelationships. The proposed work explores (i) identifying sequences of single-stranded oligonucleotides called aptamers that strongly bind to graphene to enhance its functionality and processing in various materials-related applications (Milam) and (ii) using quantum mechanical methods to model molecular interactions between the graphene surface and the base, sugar, and phosphate groups in oligonucleotides (Jang).
If successful, the proposed work has significant potential as an enabling route to achieve the following:
Noncovalent-based Approach to Surface Functionalization of Graphene and Its Derivatives: Covalent conjugation strategies are likely to introduce unintentional defects or even disrupt the overall structural framework of graphene and carbon allotropes such as carbon nanotubes. Aptamers can serve as noncovalent-based linkers between graphene and other surface functionalities that cannot or should not be directly conjugated to a graphene surface.
Enhance the Stability of Graphene-based Materials in Aqueous Dispersions for Materials Processing: The hydrophilic nature of the sugar-phosphate backbone of oligonucleotides enables the preparation of aqueous suspensions of dispersed nanoparticles of many chemical compositions (e.g. polystyrene, gold, etc.) and thus is likely to promote aqueous stability of aptamer-coated, graphene-based nanomaterials.
Elucidate Fundamental Interaction of Aptamers with Graphene: The molecular interaction of graphene with the structural units of aptamers such as base, sugar, and phosphate will be rigorously quantified using quantum mechanical density functional theory (DFT), which will serve to establish a sequence design guide in developing aptamers with specific sequences for finely tuned binding energy with graphene and graphene-related materials.
Relevance to Expertise in Milam and Jang Research Groups
As highlighted in a recent review article , the Milam group has employed oligonucleotides such as DNA as a programmable and reversible materials assembly tool. Unlike her prior work involving only oligonucleotide-based targets, a newer recent research thrust in the Milam group the last three years has begun exploring single-stranded oligonucleotides called aptamers that bind to nonnucleotide targets. In brief, this research thrust involves “panning” for single-stranded oligonucleotide sequences from a random sequence library that bind to various targets ranging from single crystal planar gold to nanoparticles of gold nanospheres and nanorods. We aim to identify specific sequences (related or unrelated) and/or secondary structures (shared or unique among various sequence winners) from random sequence libraries that bind with a high degree of specificity and affinity to colloidal gold targets. The experimental work of the IGERT trainee would entail identifying specific DNA sequences that bind with a high degree of specificity and affinity to pristine graphene (e.g. planar graphene with minimal defects) or its derivatives (e.g. graphene flakes, planar graphene with various surface functionalites achieved through different processing pathways).
The Jang group has investigated various systems in nanometer-scale using the first principles atomistic computational methods such as DFT and molecular dynamics (MD) simulation, which includes polymer membranes, hydrogels, organic molecular self-assemblies on solid surfaces and on liquid phase, nanostructured semiconductors, protein-drug interaction, and mechanical properties of DNA. Recently, the Jang group has been modeling the interaction of polymers with carbon allotropes such as carbon nanotube and graphene. From this, accurate molecular interaction between polymer chain and carbon nanotube was evaluated using DFT modeling, and accordingly new potential energy functions have been developed. The IGERT trainee will use these theoretical methods to develop DFT-based potential energy functions and thereby to perform molecular dynamics simulations of adsorptive binding of aptamers on graphene or its derivatives.
- B. A. Baker, G. Mahmoudabadi, V. T. Milam, Strand displacement strategies in DNA-based materials systems, Soft Matter, 2013 (DOI:10.1039/c3sm52157e)