All Publications

  • ARHGAP6 inhibits bladder cancer cell viability, migration, and invasion via beta-catenin signaling and enhances mitomycin C sensitivity. Human cell Chen, W., Tan, M., Yu, C., Liao, G., Kong, D., Bai, J., Yang, B., Gong, H. 2023

    Abstract

    The Rho/ROCK pathway regulates diverse cellular processes and contributes to the development and advancement of several types of human cancers. This study investigated the role of specific Rho GTPase-activating proteins (RhoGAP), ARHGAP6, in bladder cancer (BC). In this study, ARHGAP6 expression in BC and its clinical significance were investigated. In vitro and in vivo assays were used to explore the tumor-related function and the underlying molecular mechanism ARHGAP6 of in BC. The mRNA and protein levels of ARHGAP6 significantly reduced in human BC tissues and cell lines compared with corresponding adjacent non-cancerous tissues and normal urothelial cells. In vitro, ARHGAP6 overexpression markedly decreased the viability, migration, and invasion of BC cells. Interestingly, low ARHGAP6 expression in BC strongly correlated with poor patient survival and was highly associated with metastasis and beta-catenin signaling. Furthermore, ARHGAP6 expression strongly influenced the sensitivity of BC cells to mitomycin C treatment. Together, our results demonstrate that ARHGAP6 plays critical roles in regulating the proliferation, migration, invasion, and metastasis of BC cells possibly via the modulation of beta-catenin and strongly influences the chemosensitivity of BC cells.

    View details for DOI 10.1007/s13577-023-00860-3

    View details for PubMedID 36715867

  • Flow-Cell-Based Technology for Massively Parallel Characterization of Base-Modified DNA Aptamers. Analytical chemistry Wu, D., Feagin, T., Mage, P., Rangel, A., Wan, L., Kong, D., Li, A., Coller, J., Eisenstein, M., Soh, H. 2023

    Abstract

    Aptamers incorporating chemically modified bases can achieve superior affinity and specificity compared to natural aptamers, but their characterization remains a labor-intensive, low-throughput task. Here, we describe the "non-natural aptamer array" (N2A2) system, in which a minimally modified Illumina MiSeq instrument is used for the high-throughput generation and characterization of large libraries of base-modified DNA aptamer candidates based on both target binding and specificity. We first demonstrate the capability to screen multiple different base modifications to identify the optimal chemistry for high-affinity target binding. We next use N2A2 to generate aptamers that can maintain excellent specificity even in complex samples, with equally strong target affinity in both buffer and diluted human serum. For both aptamers, affinity was formally calculated with gold-standard binding assays. Given that N2A2 requires only minor mechanical modifications to the MiSeq, we believe that N2A2 offers a broadly accessible tool for generating high-quality affinity reagents for diverse applications.

    View details for DOI 10.1021/acs.analchem.1c04777

    View details for PubMedID 36693249

  • Evolutionary Outcomes of Diversely Functionalized Aptamers Isolated from in Vitro Evolution ACS SYNTHETIC BIOLOGY Kong, D., Movahedi, M., Mandavi-Arniri, Y., Yeung, W., Tiburcio, T., Chen, D., Hili, R. 2020; 9 (1): 43-52

    Abstract

    Expanding the chemical diversity of aptamers remains an important thrust in the field in order to increase their functional potential. Previously, our group developed LOOPER, which enables the incorporation of up to 16 unique modifications throughout a ssDNA sequence, and applied it to the in vitro evolution of thrombin binders. As LOOPER-derived highly modified nucleic acids polymers are governed by two interrelated evolutionary variables, namely, functional modifications and sequence, the evolution of this polymer contrasts with that of canonical DNA. Herein we provide in-depth analysis of the evolution, including structure-activity relationships, mapping of evolutionary pressures on the library, and analysis of plausible evolutionary pathways that resulted in the first LOOPER-derived aptamer, TBL1. A detailed picture of how TBL1 interacts with thrombin and how it may mimic known peptide binders of thrombin is also proposed. Structural modeling and folding studies afford insights into how the aptamer displays critical modifications and also how modifications enhance the structural stability of the aptamer. A discussion of benefits and potential limitations of LOOPER during in vitro evolution is provided, which will serve to guide future evolutions of this highly modified class of aptamers.

    View details for DOI 10.1021/acssynbio.9b00222

    View details for Web of Science ID 000508474400006

    View details for PubMedID 31774997

  • Expanding the Chemical Diversity of DNA SYNLETT Guo, C., Kong, D., Lei, Y., Hili, R. 2018; 29 (11): 1405-1414

    View details for DOI 10.1055/s-0036-1591959

    View details for Web of Science ID 000435602300001

  • Numerical study on impact of non-heating surface temperature on the heat output of radiant floor heating system ENERGY AND BUILDINGS Zheng, X., Han, Y., Zhang, H., Zheng, W., Kong, D. 2017; 155: 198-206

    View details for DOI 10.1016/j.enbuild.2017.09.022

    View details for Web of Science ID 000414107200018

  • In Vitro Selection of Diversely Functionalized Aptamers JOURNAL OF THE AMERICAN CHEMICAL SOCIETY Kong, D., Yeung, W., Hili, R. 2017; 139 (40): 13977-13980

    Abstract

    We describe the application of T4 DNA ligase-catalyzed DNA templated oligonucleotide polymerization toward the evolution of a diversely functionalized nucleic acid aptamer for human α-thrombin. Using a 256-membered ANNNN comonomer library comprising 16 sublibraries modified with different functional groups, a highly functionalized aptamer for thrombin was raised with a dissociation constant of 1.6 nM. The aptamer was found to be selective for thrombin and required the modifications for binding affinity. This study demonstrates the most differentially functionalized nucleic acid aptamer discovered by in vitro selection and should enable the future exploration of functional group dependence during the evolution of nucleic acid polymer activity.

    View details for DOI 10.1021/jacs.7b07241

    View details for Web of Science ID 000413057100004

    View details for PubMedID 28938065

  • Enzymatic Synthesis of Sequence-Defined Synthetic Nucleic Acid Polymers with Diverse Functional Groups ANGEWANDTE CHEMIE-INTERNATIONAL EDITION Kong, D., Lei, Y., Yeung, W., Hili, R. 2016; 55 (42): 13164-13168

    Abstract

    The development and in-depth analysis of T4 DNA ligase-catalyzed DNA templated oligonucleotide polymerization toward the generation of diversely functionalized nucleic acid polymers is described. The NNNNT codon set enables low codon bias, high fidelity, and high efficiency for the polymerization of ANNNN libraries comprising various functional groups. The robustness of the method was highlighted in the copolymerization of a 256-membered ANNNN library comprising 16 sub-libraries modified with different functional groups. This enabled the generation of diversely functionalized synthetic nucleic acid polymer libraries with 93.8 % fidelity. This process should find ready application in DNA nanotechnology, DNA computing, and in vitro evolution of functional nucleic acid polymers.

    View details for DOI 10.1002/anie.201607538

    View details for Web of Science ID 000385799200041

    View details for PubMedID 27633832

    View details for PubMedCentralID PMC5330676

  • Generation of Synthetic Copolymer Libraries by Combinatorial Assembly on Nucleic Acid Templates ACS COMBINATORIAL SCIENCE Kong, D., Yeung, W., Hili, R. 2016; 18 (7): 355-370

    Abstract

    Recent advances in nucleic acid-templated copolymerization have expanded the scope of sequence-controlled synthetic copolymers beyond the molecular architectures witnessed in nature. This has enabled the power of molecular evolution to be applied to synthetic copolymer libraries to evolve molecular function ranging from molecular recognition to catalysis. This Review seeks to summarize different approaches available to generate sequence-defined monodispersed synthetic copolymer libraries using nucleic acid-templated polymerization. Key concepts and principles governing nucleic acid-templated polymerization, as well as the fidelity of various copolymerization technologies, will be described. The Review will focus on methods that enable the combinatorial generation of copolymer libraries and their molecular evolution for desired function.

    View details for DOI 10.1021/acscombsci.6b00059

    View details for Web of Science ID 000379637100001

    View details for PubMedID 27275512

  • A High-Fidelity Codon Set for the T4 DNA Ligase-Catalyzed Polymerization of Modified Oligonucleotides ACS COMBINATORIAL SCIENCE Lei, Y., Kong, D., Hili, R. 2015; 17 (12): 716-721

    Abstract

    In vitro selection of nucleic acid polymers can readily deliver highly specific receptors and catalysts for a variety of applications; however, it is suspected that the functional group deficit of nucleic acids has limited their potential with respect to proteinogenic polymers. This has stimulated research toward expanding their chemical diversity to bridge the functional gap between nucleic acids and proteins to develop a superior biopolymer. In this study, we investigate the effect of codon library size and composition on the sequence specificity of T4 DNA ligase in the DNA-templated polymerization of both unmodified and modified oligonucleotides. Using high-throughput DNA sequencing of duplex pairs, we have uncovered a 256-membered codon set that yields sequence-defined modified ssDNA polymers in high yield and with high fidelity.

    View details for DOI 10.1021/acscombsci.5b00119

    View details for Web of Science ID 000366616300004

    View details for PubMedID 26513677