Rationally Designed Nucleobase and Nucleotide Coordinated Nanoparticles for Selective DNA Adsorption and Detection

This document is the Accepted Manuscript version of a Published Work that appeared in final form in Analytical Chemistry copyright © American Chemical Society after peer review and technical editing by publisher. To access the final edited and published work see Wang, F., Liu, B., Huang, P.-J. J., & Liu, J. (2013). Rationally Designed Nucleobase and Nucleotide Coordinated Nanoparticles for Selective DNA Adsorption and Detection. Analytical Chemistry, 85(24), 12144–12151. https://doi.org/10.1021/ac4033627Nanomaterials for DNA adsorption are useful for sequence-specific DNA detection. Current materials for DNA adsorption employ electrostatic attraction, hydrophobic interaction, or π–π stacking, none of which can achieve sequence specificity. Specificity might be improved by involving hydrogen bonding and metal coordination. In this work, a diverse range of nucleobase/nucleotide (adenine, adenosine, adenosine 5′-triphosphate (ATP), adenosine 5′-monophosphate (AMP), and guanosine 5′-triphosphate (GTP)) coordinated materials containing various metal ions (Au(III), Ag(I), Ce(III), Gd(III), and Tb(III)) are prepared. In most cases, nanoparticles are formed. These materials have different surface charges, and positively charged particles only show nonspecific DNA adsorption. Negatively charged materials give different adsorption kinetics for different DNA sequences, where complementary DNA homopolymers are adsorbed faster than other sequences. Therefore, the bases in the coordinated materials can still form base pairs with the DNA. The adsorption strength is mainly controlled by the metal ions, where Au shows the strongest adsorption while lanthanides are weaker. These materials can be used as sensors for DNA detection and can also deliver DNA into cells with no detectable toxicity. By tuning the nanoparticle formulation, enhanced detection can be achieved. This study is an important step toward rational design of materials to achieve specific interactions between biomolecules and synthetic nanoparticle surfaces.University of Waterloo || Canadian Foundation for Innovation || Ontario Ministry of Research & Innovation || Natural Sciences and Engineering Research Council |

Citrate inhibition of cisplatin reaction with DNA studied using fluorescently labeled oligonucleotides: implication for selectivity towards guanine

The reaction between cisplatin and DNA is conveniently studied using fluorescently labeled oligonucleotides and gel electrophoresis; as an example of application, the inhibition of this reaction by citrate is demonstrated, which might increase selectivity of cisplatin towards guanine over adenine.University of Waterloo || Canadian Foundation for Innovation || Natural Sciences and Engineering Research Council || Ontario Ministry of Research, Innovation and Science |

A Cleavable Molecular Beacon for Hg2+ Detection based on Phosphorothioate RNA Modifications

This document is the Accepted Manuscript version of a Published Work that appeared in final form in Analytical Chemistry copyright © American Chemical Society after peer review and technical editing by publisher. To access the final edited and published work see http://dx.doi.org/ 10.1021/acs.analchem.5b01362Mercury is a highly toxic heavy metal, and detection of Hg2+ by biosensors has attracted extensive research interest in the past decade. In particular, a number of DNA-based sensing strategies have been developed. Well-known examples include thymine-Hg2+ interactions and Hg2+-activated DNAzymes. However, these mechanisms are highly dependent on buffer conditions or require hybridization with another DNA strand. Herein, we report a new mechanism based on Hg2+-induced cleavage of phosphorothioate (PS) modified RNA. Among the various metal ions tested, Hg2+ induced the most significant cleavage (∼16%), while other metals cleaved less than 2% of the same substrate. The uncleaved substrate undergoes desulfurization in the presence of Hg2+. This cleavage reaction yields a similar amount of product from pH 3.5 to 7 and in the temperature range between 20 and 90 °C. Various PS RNA junctions can be cleaved with a similar efficiency, but PS DNA junctions cannot be cleaved. A molecular beacon containing three PS RNA modifications is designed, detecting Hg2+ down to 1.7 nM with excellent selectivity. This sensor can also detect Hg2+ in the Lake Ontario water sample, although its response is significantly masked by fish tissues.Ontario Ministry of Research & Innovation || Natural Sciences and Engineering Research Council |

Defect-engineered graphene for bulk supercapacitors with high energy and power densities

The development of high-energy and high-power density supercapacitors (SCs) is critical for enabling next-generation energy storage applications. Nanocarbons are excellent SC electrode materials due to their economic viability, high-surface area, and high stability. Although nanocarbons have high theoretical surface area and hence high double layer capacitance, the net amount of energy stored in nanocarbon-SCs is much below theoretical limits due to two inherent bottlenecks: i) their low quantum capacitance and ii) limited ion-accessible surface area. Here, we demonstrate that defects in graphene could be effectively used to mitigate these bottlenecks by drastically increasing the quantum capacitance and opening new channels to facilitate ion diffusion in otherwise closed interlayer spaces. Our results support the emergence of a new energy paradigm in SCs with 250% enhancement in double layer capacitance beyond the theoretical limit. Furthermore, we demonstrate prototype defect engineered bulk SC devices with energy densities 500% higher than state-of-the-art commercial SCs without compromising the power density.Comment: 15 pages, 5 figures, and 8 supplemental figure

Parts-per-Million of Polyethylene Glycol as a Non-Interfering Blocking Agent for Homogeneous Biosensor Development

This document is the Accepted Manuscript version of a Published Work that appeared in final form in Analytical Chemistry copyright © American Chemical Society after peer review and technical editing by publisher. To access the final edited and published work see Liu, B., Huang, P.-J. J., Zhang, X., Wang, F., Pautler, R., Ip, A. C., & Liu, J. (2013). Parts-per-Million of Polyethylene Glycol as a Non-Interfering Blocking Agent for Homogeneous Biosensor Development. Analytical Chemistry, 85(21), 10045–10050. https://doi.org/10.1021/ac4024654Many homogeneous assays are complicated by the adsorption of probe molecules by the surface of reaction vessels, which are often made of polypropylene or polystyrene-based plastics. To solve this problem, many protein and surfactant-based blocking agents are used. However, these blockers may interfere with intended assays by sequestering transition-metal ions, inducing protein denaturing, generating air bubbles or making pores in membranes. Coating surfaces with polyethylene glycol (PEG) through covalent linkages has been proven to be an effective method to minimize protein adsorption. However, this method is more difficult to apply on plastic surfaces and is quite expensive. While unmodified PEG is often considered as a nonadsorbing polymer, in this Technical Note, we report that PEG at very low concentration (ppm level) can still effectively block plastic surfaces. This method works for DNA, protein, and liposome-based assays as long as the molecular weight of PEG is greater than 2000. PEG works because of multivalent hydrophobic interaction from its repeating methylene units. This Technical Note will not only facilitate biosensor development, but also enhance our understanding of the interaction between various molecules and plastic surfaces.University of Waterloo || Canadian Foundation for Innovation || Ontario Ministry of Research & Innovation || Canadian Institutes of Health Research || Natural Sciences and Engineering Research Council |

Liposome/Graphene Oxide Interaction Studied by Isothermal Titration Calorimetry

This document is the Accepted Manuscript version of a Published Work that appeared in final form in Langmuir, © DATE American Chemical Society after peer review and technical editing by publisher. To access the final edited and published work see Huang, P.-J. J., Wang, F., & Liu, J. (2016). Liposome/Graphene Oxide Interaction Studied by Isothermal Titration Calorimetry. Langmuir, 32(10), 2458–2463. https://doi.org/10.1021/acs.langmuir.6b00006The interaction between graphene oxide (GO) and lipid bilayers is important for fundamental surface science and many applications. In this work, isothermal titration calorimetry (ITC), cryo-TEM, and fluorescence spectroscopy were used to study the adsorption of three types of liposomes. Heat release was observed when GO was mixed with zwitterionic DOPC liposomes, while heat absorption occurred with cationic DOTAP liposomes. For comparison,. anionic DOPG liposomes released heat when mixed with DOTAP. DOPC was adsorbed as intact liposomes, but DOTAP ruptured and induced stacking and folding of GO sheets. This study suggests the release of more water molecules from the GO surface when mixed with DOTAP liposomes. This can be rationalized by the full rupture of the DOTAP liposomes interacting with the whole GO surface, including hydrophobic regions, while DOPC liposomes only interact with a small area on GO near the edge, which is likely to be more hydrophilic. This interesting biointerfacial observation has enhanced our fundamental understanding of lipid/GO interactions.Natural Sciences and Engineering Research Council of Canada (NSERC

AnyFlow: Arbitrary Scale Optical Flow with Implicit Neural Representation

To apply optical flow in practice, it is often necessary to resize the input to smaller dimensions in order to reduce computational costs. However, downsizing inputs makes the estimation more challenging because objects and motion ranges become smaller. Even though recent approaches have demonstrated high-quality flow estimation, they tend to fail to accurately model small objects and precise boundaries when the input resolution is lowered, restricting their applicability to high-resolution inputs. In this paper, we introduce AnyFlow, a robust network that estimates accurate flow from images of various resolutions. By representing optical flow as a continuous coordinate-based representation, AnyFlow generates outputs at arbitrary scales from low-resolution inputs, demonstrating superior performance over prior works in capturing tiny objects with detail preservation on a wide range of scenes. We establish a new state-of-the-art performance of cross-dataset generalization on the KITTI dataset, while achieving comparable accuracy on the online benchmarks to other SOTA methods.Comment: CVPR 2023 (Highlight

Raw Garlic Consumption and Risk of Liver Cancer: A Population-Based Case-Control Study in Eastern China.

Although the major risk factors for liver cancer have been established, preventive factors for liver cancer have not been fully explored. We evaluated the association between raw garlic consumption and liver cancer in a large population-based case-control study in Eastern China. The study was conducted in Jiangsu, China, from 2003 to 2010. A total of 2011 incident liver cancer cases and 7933 randomly selected population-controls were interviewed. Epidemiological data including raw garlic intake and other exposures were collected, and serum markers of hepatitis B virus (HBV) and hepatitis C virus (HCV) infection were assayed. Overall, eating raw garlic twice or more per week was inversely associated with liver cancer, with an adjusted odds ratio (aOR) of 0.77 (95% confidence interval (CI): 0.62-0.96) compared to those ingesting no raw garlic or less than twice per week. In stratified analyses, high intake of raw garlic was inversely associated with liver cancer among Hepatitis B surface antigen (HBsAg) negative individuals, frequent alcohol drinkers, those having history of eating mold-contaminated food or drinking raw water, and those without family history of liver cancer. Marginal interactions on an additive scale were observed between low raw garlic intake and HBsAg positivity (attributable proportion due to interaction (AP) = 0.31, 95% CI: -0.01-0.62) and heavy alcohol drinking (AP = 0.28, 95% CI: 0.00-0.57). Raw garlic consumption is inversely associated with liver cancer. Such an association shed some light on the potential etiologic role of garlic intake on liver cancer, which in turn might provide a possible dietary intervention to reduce liver cancer in Chinese population