RESEARCH

Our group is interested in tackling biological, biomedical, agricultural and environmental challenges through three routes: (1) studying two and three dimensional nanoparticles, (2) DNA/RNA biotechnology and (3) CRISPR nuclease mediated signaling.

I. Optical machine-learning nanodiagnostics using two dimensional nanoparticle and DNA nanosensors: The goal of this research direction is to engineer water-soluble two-dimensional (2D) nanosensors and develop methodologies to apply state-of-the art diagnostics towards biomedicine, agriculture and food-safety challenges. The development of cost-efficient, rapid and small-scale diagnostic tools offer an alternative to conventional diagnostics, requiring minimal sample and instrumentation for analysis. Our translational approach combines two emerging fields, the role of two dimensional nanosheets and DNA/RNA biotechnology. The proposed detection approach is simple, rapid, inexpensive, enables simultaneous detection, eliminates labor-intensive multi-step procedures, and can be performed in a high-throughput fashion using simple equipment and has minimum background signal. Furthermore, we have combined our methodology with machine learning to enhance the performance of our approach and guide our diagnostic design for a first-generation sensing system. Currently, we are exploring in applying our technology towards food health and safety; looking at factors of adulteration and contamination in animal and plant based products. With the rise in supply and demand shortages of many food products, it can be expected that manufacturers and producers may fraud or provide lower quality products. It is our goal to be at the forefront of this issue by developing a simple and easy-to-use tool that can be readily utilized for the most challenging food safety challenges.

Publications on Topic I:

1. Machine Learning Enabled Nanosensor Array for "Monitoring" Citrus Juice Adulteration. ACS Food Science and Technology, 2022, 2, 8, pp 1217-1223.

2. Algorithmically Guided Optical Nanosensor Selector (AGONS): Guiding Data Acquisition, Processing, and Discrimination for Biological Sampling. Analytical Chemistry, 2022, 94, 2, 1195-1202.

3. Machine-Learning Single-Stranded DNA Nanoparticles for Bacterial Analysis. ACS Appl. Nano Mater. 2020, 3, (12), 11709–11714.

4. Homologous miRNA analyses using a combinatorial nanosensor array with two-dimensional nanoparticles. Analytical Chemistry, 2018, 90 (10), pp 6300–6306.

5. Systematic investigation of two-dimensional DNA nanoassemblies for construction of a nonspecific sensor array. Langmuir, 2018, 34, 14983-14992.

6. Universal sensor array for highly selective system identification using two-dimensional nanoparticles, Chemical Science, 2017, 8, 5735 - 5745.

7. Complex Thermodynamic Behavior of Single-Stranded Nucleic Acid Adsorption to Graphene Surfaces, Langmuir, 2016, 32 (24), pp 6028–6034.

8. Unlocked Nucleic Acids for miRNA Detection Using Two Dimensional Nano-Graphene Oxide”, Biosensors and Bioelectronics, 2017, 551-557.

9. Discriminating a single nucleotide difference for enhanced miRNA detection using tunable graphene and oligonucleotide nanodevices, Langmuir, 2015, 31 (36), pp 9943–9952.

10. Monitoring the multitask mechanism of DNase I activity using graphene nano assemblies”, Bioconjugate Chemistry, 2015, 26 (4), pp 735–745.

11. Smart polymer functionalized graphene nano-devices for thermo-switch controlled biodetection”, ACS Biomaterials Science & Engineering, 2015, 1 (1), pp 27–36.

12. Simultaneous detection of circulating oncomiRs from body fluids for prostate cancer staging using nano-graphene oxide, ACS Applied Materials & Interfaces, 2014, 6 (17), pp 14772–14778.

13. DNA-Length-Dependent Quenching of Fluorescently Labeled Iron Oxide Nanoparticles with Gold, Graphene Oxide and MoS2 Nanostructures”, ACS Applied Materials & Interfaces, 6 (15), 2014, 12100–12110.

14. Nano-graphene oxide as a novel platform for monitoring the effect of LNA modification in nucleic acid interactions”, Analyst, 2014, 139 (4), 714 - 720

15. Doxorubicin loading on graphene oxide, iron oxide and gold nanoparticle hybrid”, Journal of Materials Chemistry B, 2013, 1 (45), 6187 - 6193

II. Three dimensional nanoparticle and oligonucleotide assemblies for ultrasensitive detection in agriculture: The goal of this research direction is to create a transformative approach for the ultrasensitive, cost-efficient and programmable detection of three classes of analytes: (a) oligonucleotides (DNA/RNA), (b) proteins and (c) heavy metal ions using DNA nanotechnology coupled with metallic particles. Our studies illustrate that our instrument-free colorimetric detection approach is simple, but much more sensitive than any other colorimetric methods reported to date. The proposed methodology offers detection of the target analytes from their native environment without any isolation steps. This is particularly important for point-of-care diagnosis or real-time environmental monitoring for translational research. The detection is multiplexed where a single sensor template can be programmed for the detection of multiple analytes in various combinations and formats. The approach relies on the important discovery in the DNA nanotechnology field known as hybridization chain reaction (HCR), where a single short stranded DNA can trigger the formation of a large double stranded DNA polymer by activating two metastable short DNA hairpins. We have previously demonstrated that our colorimetric, enzyme-free methodology is both highly sensitive and specific, discriminating not only highly fatal disease biomarkers but even environmental contaminants when coupled with nanotechnology. The rise in DNA enabled nanotechnology is necessary to develop field-deployable tools to combat the spread of diseases such as Huanglongbing (HLB) which is devasting the citrus crop economy. Currently, we are seeking to develop a low-cost, and colorimetric tool that can enable rapid detection of various agricultural microbial related diseases.

Publications on topic II:

1. Rapid Visual Screening and Programmable Subtype Classification of Ebola Virus Biomarkers, Advanced Healthcare Materials, 2016, 6(2), 1600739.

2. Low picomolar, instrument-free visual detection of mercury and silver ions using low-cost programmable nanoprobes, Chemical Science, 2017, 8, 1200-1208 .

3. Reprogrammable Multiplexed Detection of Circulating OncomiRs Using Hybridization Chain Reaction, Chemical Communications, 2016, 52, 3524-3527.

4. Multiplexed activity of perAuxidase: DNA-capped AuNPs act as adjustable peroxidase, Analytical Chemistry, 2016, 88 (1), pp 600–605.

5. Locked nucleic acid-modified antisense miR-10b oligonucleotides form stable duplexes on gold nanoparticles, BioNanoScience, 4(2), 2014, 195-200.

III. Machine learning data driven methods for new image-guided nanodrugs. The goal of this “technology-development” research is to engineer nanoparticles that are responsive to non-toxic, but highly selective chemical triggers for image-guided delivery and controlled-activation of different types of therapeutic cargoes: small chemodrug molecules and functional RNA macromolecules .Nanoparticles are well-established delivery vehicles capable of shuttling molecular cargoes across different types of biological membranes. A major flaw of the standard nanoparticle assembly is lack of selective control over cargo release. Functional cargoes are typically released by environmental factors, such as pH, redox potential and ATP gradient, that cause cleavage of chemical linkers. Lack of control over this process can result in premature payload release, before the nanoparticles reached their intended target. In turn, this can lead to highly undesirable cytotoxicity and off-target affects. Our research direction for this topic aims to address this flaw using a transformative approach involving bio-orthogonal chemistry. This process can be precisely controlled and chemical design of the bio-orthogonal groups provides for flexibility of the release kinetics. We are looking into improving our therapeutic design by incorporating machine learning to overcome excessive experimentation. The approach has potential to revolutionize the currently used nanoparticle-based delivery methods.

Publications on topic III:

1. Switchable fluorescence of doxorubicin for label-free imaging of bioorthogonal drug release. ChemMedChem, 2020, 15, 11, 988-994.

2. Single-trigger dual-responsive nanoparticles for controllable and sequential prodrug activation, Nanoscale, 2017, 9, 10020-10030.

3. Controlled in-cell activation of RNA therapeutics using bond-cleaving bio-orthogonal chemistry, Chemical Science, 2017, 8, 5705 - 5712.

4. In situ activation of a doxorubicin prodrug using imaging-capable nanoparticles, Chemical Communications, 2016,52, 6174-6177.

5. Controlling RNA expression in cancer using iron oxide nanoparticles detectable by MRI and in vivo optical imaging, Methods Mol. Biol., 2016;1372:163-79.

6. Context-dependent differences in miR-10b breast oncogenesis can be targeted for the prevention and arrest of lymph node metastasis, Oncogene, 2013, 32(12), 1530-1538.

IV. CRISPR Nucleic Acid Sensing Mediated Platforms. The discovery of Clustered Regularly Interspaced Palindromic Repeat (CRISPR) and CRISPR associated proteins (Cas) has revolutionized not only genomic editing technology but also rapid diagnostic tools with Cas12a. The conventional mechanism of Cas12a utilizes the CRISPR RNA (crRNA) programmability to recognize a specific DNA sequence. Upon recognition of a DNA sequence, Cas12a activates its DNA nuclease activity and indiscriminately shreds all single-stranded (ss) DNA in its presence. To utilize this activity for diagnostics, the ssDNA can be repurposed as a probe, labeled on opposing ends with fluorescent and quencher molecules; where an activated Cas12a will shred this ssDNA signaling recognition of target DNA sequence. However, a flaw with the conventional diagnostic method is that ssDNA sequences are susceptible to false-positives, expensive probe design, and lack tunability to control reaction rate. Recently, we began investigating methods to integrate Cas12a with our current tools. Our research objective with Cas12a tools has been to seek new methods of (i) cheaper and more stable DNA probe designs as well as (ii) coupling the nuclease activity with existing DNA biotechnology diagnostic reporting methods such as hybridization chain reaction for highly-sensitive and specific detection of agriculturally and medically relevant pathogens. These approaches have potential to open up the utility pool of CRISPR-Cas12a reporting methods as well as lead to advanced purposing of existing DNA biotechnology methods.

Publications on topic IV:

1. Recombinase Amplified CRISPR Enhanced Chain Reaction (RACECAR) for Viral Genome Detection. Nanoscale, 2022, 14, 37, 13500-13504.

2. Recognition of DNA target formulations by CRISPR-Cas12a using a dsDNA reporter. ACS Synth. Biol. 2021, 10, 7, 1785–1791.

3. Reprogrammable Gel Electrophoresis Detection Assay Using CRISPR-Cas12a and Hybridization Chain Reaction. Analytical Chemistry, 2021, 93, 4, 1934–1938.

4. Probing CRISPR-Cas12a nuclease activity using dsDNA-templated fluorescent substrates. Biochemistry. 2020, 59, 15, 1474–1481.

V. Paper based diagnostics using synthetic biology. We are developing paper-based sensors that incorporates elements of synthetic biology for molecular diagnostics. This approach utilizes toehold switch DNA and a cell-free protein reaction to induce a ‘yellow to red’ color transition upon target recognition. The inclusion of CRISPR-Cas enhances the assay’s sensitivity and diversify our target pool from short RNA sequences to any ss- or ds-DNA sequence of interest. The continued progression of paper analytical devices, like this visual diagnostic, is required to bolster the efforts for more mobile on-site diagnostic tests.”