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Open Access Publications from the University of California

Scholarly Works (6 results)

  • Thesis
  • Peer Reviewed
UC San Diego Electronic Theses and Dissertations (2023)

Noncovalent assemblies constitute some of the most robust and keystone interactions in biology. Hydrogen bonding, for example, drives hybridization between single DNA strands into double helices for genetic informational storage, while the combination of electrostatic, Van der Waals, and hydrophobic amino acid sequences underpin binding specificity between antibodies and antigens as well as stability in proteins. Similarly, intermolecular forces can yield novel physical, chemical, and optical properties for new materials, such as tunable self-quenching between fluorophores and functionalized surfaces on nanoparticles. Engineered biomolecular self-assembly can thus be a tool to design nanomaterials with specificity to biological events or targets for (1) drug delivery to diseased tissue, (2) signaling for biosensing, or (3) contrast for bioimaging. This dissertation presents strategies for engineered molecular contrast agents and drug delivery platforms using bottom-up bio- and inter-molecular self-assembly pathways. In chapter one, electrostatic interactions establish DNA origami’s ability to cover and disguise the surfaces of herpes simplex virus 1 particles for infection against cancer cells, even when the mammalian strain of the virus is different from the mammalian strain of the host cell. Chapter two outlines the value of enzyme free and isothermal self-assembly between oligonucleotides via strand amplification for resultant signal amplification to detect nucleic acid biomarkers. Chapter three demonstrates this value by presenting strand amplification for triggered contact quenching between NIR fluorophores, leading to enhanced and ratiometric photoacoustic contrast when miR-21 is detected in live cells and within sub-centimeter penetration depths in tissue mimicking phantoms. Chapter four leverages aggregative photoacoustic enhancement when an NIR dye-tagged chemotherapeutic is densely intercalated into a DNA-clad hydrogel for real-time pharmacokinetic tracking. Chapter five examines the resultant geometries from two self-assembly pathways between an engineered tumor-homing peptide and an NIR molecular dye for targeted tumor photoacoustic imaging and targeted photodynamic therapy, underscoring the significance in nanoparticle architecture on resultant interactions with biology at the live cell and live tissue scales.

    Cover page: Engineered scaffolds for targeted molecular imaging and drug delivery via biomolecular self-assembly
    • Article
    • Peer Reviewed
    UC San Diego Previously Published Works (2021)
    Nucleic acids have become viable prognostic and diagnostic biomarkers for a diverse class of diseases, particularly cancer. However, the low femtomolar to attomolar concentration of nucleic acids in human samples require sensors with excellent detection capabilities; many past and current platforms fall short or are economically difficult. Strand-mediated signal amplifiers such as hybridization chain reaction (HCR) and catalytic hairpin assembly (CHA) are superior methods for detecting trace amounts of biomolecules because one target molecule triggers the continuous production of synthetic double-helical DNA. This cascade event is highly discriminatory to the target via sequence specificity, and it can be coupled with fluorescence, electrochemistry, magnetic moment, and electrochemiluminescence for signal reporting. Here, we review recent advances in enhancing the sensing abilities in HCR and CHA for improved live-cell imaging efficiency, lowered limit of detection, and optimized multiplexity. We further outline the potential for clinical translatability of HCR and CHA by summarizing progress in employing these two tools for in vivo imaging, human sample testing, and sensing-treating dualities. We finally discuss their future prospects and suggest clinically-relevant experiments to supplement further related research.
      Cover page: Hybridizing clinical translatability with enzyme-free DNA signal amplifiers: recent advances in nucleic acid detection and imaging
      • Article
      • Peer Reviewed
      UC San Diego Previously Published Works (2022)
      DNA nanostructures are well-established vectors for packaging diversified payloads for targeted cellular delivery. Here, DNA origami rectangular sheets were combined with Herpes Simplex Virus 1 (HSV1) capsids to demonstrate surface coverage of the particle via electrostatic interactions. The optimized origami:HSV1 molar ratios led to characteristic packaging geometries ranging from dispersed HSV1 pockets to agglomerated HSV1 sleeves. Pockets were disguised from cells in HeLa and B16F10 cells and were 44.2% less infective than naked HSV1 particles. However, the pockets were 117% more infective than naked HSV1 particles when the origami sheets were coated with folic acid. We observed infectivity from naked origami, but they are 99.1% less infective with respect to HSV1 and 99.6% less infective with respect to the pocket complexes. This work suggests that DNA origami can selectively modulate virus infectivity.
        Cover page: DNA Origami Disguises Herpes Simplex Virus 1 Particles and Controls Their Virulence.Creative Commons 'BY' version 4.0 license
        • Article
        • Peer Reviewed
        UC San Diego Previously Published Works (2023)
        Transmembrane protease serine 2 (TMPRSS2) is a plasma membrane protease that activates both spike protein of coronaviruses for cell entry and oncogenic signaling pathways for tumor progression. TMPRSS2 inhibition can reduce cancer invasion and metastasis and partially prevent the entry of SARS-CoV-2 into host cells. Thus, there is an urgent need for both TMPRSS2-selective imaging and precise screening of TMPRSS2 inhibitors. Here, we report a TMPRSS2-responsive surface-potential-tunable peptide-conjugated probe (EGTP) with aggregation-induced emission (AIE) features for TMPRSS2 selective imaging and accurate inhibitor screening. The amphiphilic EGTP was constructed with tunable surface potential and responsive efficiency with TMPRSS2 and its inhibitor. The rational construction of AIE luminogens (AIEgens) with modular peptides indicated that the cleavage of EGTP led to a gradual aggregation with bright fluorescence in high TMPRSS2-expressing cells. This strategy may have value for selective detection of cancer cells, SARS-CoV-2-target cells, and screening of protease inhibitors.
          Cover page: Protease-Responsive Potential-Tunable AIEgens for Cell Selective Imaging of TMPRSS2 and Accurate Inhibitor Screening.
          • Article
          • Peer Reviewed
          UC San Diego Previously Published Works (2023)
          While vaccines have been highly successful in protecting against various infections, there are still many high-priority pathogens for which there are no clinically approved formulations. To overcome this challenge, researchers have explored the use of nanoparticulate strategies for more effective antigen delivery to the immune system. Along these lines, nanotoxoids are a promising biomimetic platform that leverages cell membrane coating technology to safely deliver otherwise toxic bacterial antigens in their native form for antivirulence vaccination. Here, in order to further boost their immunogenicity, nanotoxoids formulated against staphylococcal α-hemolysin are embedded into a DNA-based hydrogel with immunostimulatory CpG motifs. The resulting nanoparticle-hydrogel composite is injectable and improves the in vivo delivery of vaccine antigens while simultaneously stimulating nearby immune cells. This leads to elevated antibody production and stronger antigen-specific cellular immune responses. In murine models of pneumonia and skin infection caused by methicillin-resistant Staphylococcus aureus, mice vaccinated with the hybrid vaccine formulation are well-protected. This work highlights the benefits of combining nanoparticulate antigen delivery systems with immunostimulatory hydrogels into a single platform, and the approach can be readily generalized to a wide range of infectious diseases.
            Cover page: Immunostimulatory DNA Hydrogel Enhances Protective Efficacy of Nanotoxoids against Bacterial Infection.
            • Article
            • Peer Reviewed
            UC San Diego Previously Published Works (2022)
            Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a serious threat to human health and lacks an effective treatment. There is an urgent need for both real-time tracking and precise treatment of the SARS-CoV-2-infected cells to mitigate and ultimately prevent viral transmission. However, selective triggering and tracking of the therapeutic process in the infected cells remains challenging. Here, we report a main protease (Mpro)-responsive, mitochondrial-targeting, and modular-peptide-conjugated probe (PSGMR) for selective imaging and inhibition of SARS-CoV-2-infected cells via enzyme-instructed self-assembly and aggregation-induced emission (AIE) effect. The amphiphilic PSGMR was constructed with tunable structure and responsive efficiency and validated with recombinant proteins, cells transfected with Mpro plasmid or infected by SARS-CoV-2, and a Mpro inhibitor. By rational construction of AIE luminogen (AIEgen) with modular peptides and Mpro, we verified that the cleavage of PSGMR yielded gradual aggregation with bright fluorescence and enhanced cytotoxicity to induce mitochondrial interference of the infected cells. This strategy may have value for selective detection and treatment of SARS-CoV-2-infected cells.
              Cover page: Protease-Responsive Peptide-Conjugated Mitochondrial-Targeting AIEgens for Selective Imaging and Inhibition of SARS-CoV-2-Infected Cells.
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