Dylan W. Domaille

Biophysically Defined and Cytocompatible Covalently Adaptable Networks as Viscoelastic 3D Cell Culture Systems

Presented here is a cytocompatible covalently adaptable hydrogel uniquely capable of mimicking the complex biophysical properties of native tissue and enabling natural cell functions without matrix degradation. Demonstrated is both the ability to control elastic modulus and stress relaxation time constants by more than an order of magnitude while predicting these values based on fundamental theoretical understanding and the simulation of muscle tissue and the encapsulation of myoblasts.

Enhanced Hydrogen Production from DNA‐Assembled Z‐Scheme TiO2–CdS Photocatalyst Systems

A wide range of inorganic nanostructures have been used as photocatalysts for generating H2. To increase activity, Z-scheme photocatalytic systems have been implemented that use multiple types of photoactive materials and electron mediators. Optimal catalysis has previously been obtained by interfacing different materials through aggregation or epitaxial nucleation, all of which lowers the accessible active surface area. DNA has now been used as a structure-directing agent to organize TiO2 and CdS nanocrystals. A significant increase in H2 production compared to CdS or TiO2 alone was thus observed directly in solution with no sacrificial donors or applied bias. The inclusion of benzoquinone (BQ) equidistant between the TiO2 and CdS through DNA assembly further increased H2 production. While the use of a second quinone in conjunction with BQ showed no more improvement, its location within the Z-scheme was found to strongly influence catalysis.

High density DNA loading on the M13 bacteriophage provides access to colorimetric and fluorescent protein microarray biosensors.

We report the synthesis, characterization, and protein sensing capabilities of M13 bacteriophage-DNA bioconjugates. DNA oligonucleotides were conjugated to M13 through acyl hydrazone linkages. In one case, DNAzymes retained their catalytic ability when anchored to the virus coat, and in a separate study, the dynamic nature of the hydrazone allowed for liberation of DNA from the phage under mild conditions.

Synthesis and Assembly of Click-Nucleic-Acid-Containing PEG–PLGA Nanoparticles for DNA Delivery

Co-delivery of both chemotherapy drugs and siRNA from a single delivery vehicle can have a significant impact on cancer therapy due to the potential for overcoming issues such as drug resistance. However, the inherent chemical differences between charged nucleic acids and hydrophobic drugs have hindered entrapment of both components within a single carrier. While poly(ethylene glycol)-block-poly(lactic-co-glycolic acid) (PEG-PLGA) copolymers have been used successfully for targeted delivery of chemotherapy drugs, loading of DNA or RNA has been poor. It is demonstrated that significant amounts of DNA can be encapsulated within PLGA-containing nanoparticles through the use of a new synthetic DNA analog, click nucleic acids (CNAs). First, triblock copolymers of PEG-CNA-PLGA are synthesized and then formulated into polymer nanoparticles from oil-in-water emulsions. The CNA-containing particles show high encapsulation of DNA complementary to the CNA sequence, whereas PEG-PLGA alone shows minimal DNA loading, and non-complementary DNA strands do not get encapsulated within the PEG-CNA-PLGA nanoparticles. Furthermore, the dye pyrene can be successfully co-loaded with DNA and lastly, a complex, larger DNA sequence that contains an overhang complementary to the CNA can also be encapsulated, demonstrating the potential utility of the CNA-containing particles as carriers for chemotherapy agents and gene silencers.

Catalytic Upgrading in Bacteria-Compatible Conditions via a Biocompatible Aldol Condensation

Integrating non-enzymatic chemistry with living systems has the potential to greatly expand the types and yields of chemicals that can be sourced from renewable feedstocks. The in situ conversion of microbial metabolites to higher order products will ensure their continuous generation starting from a given cellular reaction mixture. We present here a systematic study of different organocatalysts that enable aldol condensation in biological media under physiological conditions of neutral pH, moderate temperature, and ambient pressure. The relative toxicities of each catalyst were tested against bacteria, and the catalysts were found to provide good yields of homoaldol products in bacterial cultures containing aldehydes. Lastly, we demonstrate that a biocompatible oil can be used to selectively extract the upgraded products, which enabes facile isolation and decreases the product toxicity to microbes.

High-Yielding and Photolabile Approaches to the Covalent Attachment of Biomolecules to Surfaces via Hydrazone Chemistry

The development of strategies to couple biomolecules covalently to surfaces is necessary for constructing sensing arrays for biological and biomedical applications. One attractive conjugation reaction is hydrazone formation--the reaction of a hydrazine with an aldehyde or ketone--as both hydrazines and aldehydes/ketones are largely bioorthogonal, which makes this particular reaction suitable for conjugating biomolecules to a variety of substrates. We show that the mild reaction conditions afforded by hydrazone conjugation enable the conjugation of DNA and proteins to the substrate surface in significantly higher yields than can be achieved with traditional bioconjugation techniques, such as maleimide chemistry. Next, we designed and synthesized a photocaged aryl ketone that can be conjugated to a surface and photochemically activated to provide a suitable partner for subsequent hydrazone formation between the surface-anchored ketone and DNA- or protein-hydrazines. Finally, we exploit the latent functionality of the photocaged ketone and pattern multiple biomolecules on the same substrate, effectively demonstrating a strategy for designing substrates with well-defined domains of different biomolecules. We expect that this approach can be extended to the production of multiplexed assays by using an appropriate mask with sequential photoexposure and biomolecule conjugation steps.

Synthesis and phase transfer of well-defined BiVO4 nanocrystals for photocatalytic water splitting

A method to synthesize BiVO4 nanoparticles and nanorods hydrothermally using sodium oleate as a capping ligand is presented. The BiVO4 nanocrystals possessed the expected blue shift in absorbance relative to bulk that occurs with scaling of particle size. Next, we transferred the BiVO4 nanoparticles from organic solvents to water using two different ligands. These particles were tested as water oxidation and dye reduction catalysts.

Synthesis of Small-Molecule/DNA Hybrids through On-Bead Amide-Coupling Approach

Small molecule/DNA hybrids (SMDHs) have been considered as nanoscale building blocks for engineering 2D and 3D supramolecular DNA assembly. Herein, we report an efficient on-bead amide-coupling approach to prepare SMDHs with multiple oligodeoxynucleotide (ODN) strands. Our method is high yielding under mild and user-friendly conditions with various organic substrates and homo- or mixed-sequenced ODNs. Metal catalysts and moisture- and air-free conditions are not required. The products can be easily analyzed by LC-MS with accurate mass resolution. We also explored nanometer-sized shape-persistent macrocycles as novel multitopic organic linkers to prepare SMDHs. SMDHs bearing up to six ODNs were successfully prepared through the coupling of arylenethynylene macrocycles with ODNs, which were used to mediate the assembly of gold nanoparticles.

Post-synthetic functionalization of a polysulfone scaffold with hydrazone-linked functionality

The synthesis, characterization, and post-synthetic functionalization of a readily functionalized step-growth linear polymer derived from divinyl sulfone (DVS) and tert-butylcarbazate (TBC) is presented. Construction of this atom-economic polymer under thermal conditions proceeds in high yield (>94%) at 75 °C, achieving a number average molecular weight of 17.0 kDa, a weight-average molecular weight of 26.2 kDa, and a polydispersity of 1.54, corresponding to a number-average degree of polymerization >60, despite the step-growth nature of the reaction. Removal of the Boc-groups yields a polymeric scaffold with hydrazine moieties that are readily reacted with aldehydes to yield the corresponding functional polyhydrazone materials. A variety of hydrazone-linked functionalities are readily added under mild conditions, including cationic, anionic, electron-rich/poor, and hetereoatom-containing aromatics. Owing to its rapid functionalization and simple and scalable synthesis, this material is an accommodating and generalized polymer scaffold that is rapidly tailored to a variety of applications with easily introduced functionality.

Dynamic and Responsive DNA-like Polymers

The synthesis of thiolactone monomers that mimic natural nucleosides and engage in robust ring opening polymerizations (ROP) is herein described. As each repeat unit contains a thioester functional group, dynamic rearrangement of the polymer is feasible via thiol-thioester exchange, demonstrated here by depolymerization of the polymers and coalescing of two polymers of different molecular weight or chemical composition. This approach constitutes the first step toward a platform that enables for the routine synthesis of sequence controlled polymers via dynamic template directed synthesis.