{"id":164,"date":"2017-03-08T15:29:54","date_gmt":"2017-03-08T20:29:54","guid":{"rendered":"https:\/\/research.cbc.osu.edu\/bong.6\/?page_id=164"},"modified":"2023-05-31T13:53:41","modified_gmt":"2023-05-31T17:53:41","slug":"publications","status":"publish","type":"page","link":"https:\/\/research.cbc.osu.edu\/bong.6\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"

2023<\/strong><\/p>\n

Liang, Y.; Willey, S.; Chung, Y.-C.; Lo, Y.-M.; Miao, S.; Rundell, S.; Tu, L.-C.; Bong, D. Intracellular RNA and DNA Tracking by Uridine-Rich Internal Loop Tagging with Fluorogenic bPNA. Nat. Commun.<\/i> 2023<\/b>, 14<\/i> (1), 1\u201312. https:\/\/doi.org\/10.1038\/s41467-023-38579-2.<\/p>\n

2022<\/strong><\/p>\n

Rundell, S.; Munyaradzi, O.; Bong, D. Enhanced Triplex Hybridization of DNA and RNA via Syndiotactic Side Chain Presentation in Minimal bPNAs. Biochemistry<\/i> 2022<\/b>, 61<\/i> (2), 85\u201391. https:\/\/doi.org\/10.1021\/acs.biochem.1c00693.<\/p>\n

Liang, Y.; Miao, S.; Mao, J.; Devari, S.; Gonzalez, M.; Bong, D. Screening of Minimalist Noncanonical Sites in Duplex DNA and RNA Reveals Context and Motif-Selective Binding by Fluorogenic Base Probes. Chemistry<\/i> 2022<\/b>, 28<\/i> (2), e202103616. https:\/\/doi.org\/10.1002\/chem.202103616.<\/p>\n

Devari, S.; Bhunia, D.; Bong, D. Synthesis of Bifacial Peptide Nucleic Acids with Diketopiperazine Backbones. Synlett<\/i> 2022<\/b>, 33<\/i> (10), 965\u2013968. https:\/\/doi.org\/10.1055\/a-1802-6873.<\/p>\n

Bong, D.; Holliger, P.; Yang, C. Introduction to the Themed Collection on XNA Xeno-Nucleic Acids. RSC Chem Biol<\/i> 2022<\/b>, 3<\/i> (11), 1299\u20131300. https:\/\/doi.org\/10.1039\/d2cb90036j.<\/p>\n

Munyaradzi, O.; Rundell, S.; Bong, D. Impact of bPNA Backbone Structural Constraints and Composition on Triplex Hybridization with DNA. Chembiochem<\/i> 2022<\/b>. https:\/\/doi.org\/10.1002\/cbic.202100707.<\/p>\n

2021<\/strong><\/p>\n

Rundell, S.; Munyaradzi, O.; Bong, D. Enhanced Triplex Hybridization of DNA and RNA via Syndiotactic Side Chain Presentation in Minimal bPNAs. Biochemistry<\/i> 2021<\/b>. https:\/\/doi.org\/10.1021\/acs.biochem.1c00693.<\/p>\n

Liang, Y.; Miao, S.; Mao, J.; Devari, S.; Gonzalez, M.; Bong, D. Screening of Minimalist Noncanonical Sites in Duplex DNA and RNA Reveals Context and Motif-Selective Binding by Fluorogenic Base Probes. Chemistry<\/i> 2021<\/b>. https:\/\/doi.org\/10.1002\/chem.202103616.<\/p>\n

Miao, S.; Bhunia, D.; Devari, S.; Liang, Y.; Munyaradzi, O.; Rundell, S.; Bong, D. Bifacial PNAs Destabilize MALAT1 by 3\u2019 A-Tail Displacement from the U-Rich Internal Loop. ACS Chem. Biol.<\/i> 2021<\/b>. https:\/\/doi.org\/10.1021\/acschembio.1c00575.<\/p>\n

Miao, S.; Liang, Y.; Rundell, S.; Bhunia, D.; Devari, S.; Munyaradzi, O.; Bong, D. Unnatural Bases for Recognition of Noncoding Nucleic Acid Interfaces. Biopolymers<\/i> 2021<\/b>, 112<\/i> (1), e23399. https:\/\/doi.org\/10.1002\/bip.23399.<\/p>\n

2020<\/strong><\/p>\n

Liang, Y.; Miao, S.; Mao, J.; DeSantis, C.; Bong, D. Context-Sensitive Cleavage of Folded DNAs by Loop-Targeting bPNAs. Biochemistry<\/i> 2020<\/b>, 59<\/i> (26), 2410\u20132418. https:\/\/doi.org\/10.1021\/acs.biochem.0c00362.<\/p>\n

2019<\/strong><\/p>\n

Liang, Y., Mao, J., and Bong, D. (2019). Synthetic bPNAs as allosteric triggers of hammerhead ribozyme catalysis. In Methods in Enzymology, (Academic Press), DOI:10.1016\/bs.mie.2019.04.028.<\/p>\n

Xia, X., Zhou, Z., DeSantis, C., Rossi, J.J., and Bong, D. (2019). Triplex Hybridization of siRNA with Bifacial Glycopolymer Nucleic Acid Enables Hepatocyte-Targeted Silencing. ACS Chem. Biol., DOI: 10.1021\/acschembio.9b00273<\/p>\n

Miao, S., Liang, Y., Marathe, I., Mao, J., DeSantis, C., and Bong, D. (2019). Duplex stem replacement with bPNA+ triplex hybrid stems enables reporting on tertiary interactions of internal RNA domains. J. Am. Chem. Soc. DOI: 10.1021\/jacs.9b03435<\/p>\n

2017<\/strong><\/p>\n

Mao, J., DeSantis, C., and Bong, D. (2017). Small Molecule Recognition Triggers Secondary and Tertiary Interactions in DNA Folding and Hammerhead Ribozyme Catalysis. J. Am. Chem. Soc. 139<\/i>, 9815\u20139818.<\/p>\n

2016<\/strong><\/p>\n

Zhang, Y., Beckstead, A.A., Hu, Y., Piao, X., Bong, D., and Kohler, B. (2016). Excited-State Dynamics of Melamine and Its Lysine Derivative Investigated by Femtosecond Transient Absorption Spectroscopy. Molecules 21<\/i>.<\/p>\n

Zhou, Z., Munyaradzi, O., Xia, X., Green, D., and Bong, D. (2016). High-Capacity Drug Carriers from Common Polymer Amphiphiles. Biomacromolecules 17<\/i>, 3060\u20133066.<\/p>\n

Pratumyot, Y., Torres, O.B., and Bong, D. (2016). Assessment of RNA carrier function in peptide amphiphiles derived from the HIV fusion peptide. Peptides 79<\/i>, 27\u201330.<\/p>\n

2015<\/strong><\/p>\n

Zhou, Z., Xia, X., and Bong, D. (2015). Synthetic Polymer Hybridization with DNA and RNA Directs Nanoparticle Loading, Silencing Delivery, and Aptamer Function. J. Am. Chem. Soc. 137<\/i>, 8920\u20138923.<\/p>\n

Mao, J., and Bong, D. (2015). Synthesis of DNA-Binding Peptoids. Synlett 26<\/i>, 1581\u20131585.<\/p>\n

Piao, X., Xia, X., Mao, J., and Bong, D. (2015). Peptide ligation and RNA cleavage via an abiotic template interface. J. Am. Chem. Soc. 137<\/i>, 3751\u20133754.<\/p>\n

2014<\/strong><\/p>\n

Xia, X., Piao, X., and Bong, D. (2014). Bifacial peptide nucleic acid as an allosteric switch for aptamer and ribozyme function. J. Am. Chem. Soc. 136<\/i>, 7265\u20137268.<\/p>\n

2013<\/strong><\/p>\n

Piao, X., Xia, X., and Bong, D. (2013). Bifacial Peptide Nucleic Acid Directs Cooperative Folding and Assembly of Binary, Ternary, and Quaternary DNA Complexes. Biochemistry 52<\/i>, 6313\u20136323.<\/p>\n

Zhou, Z., and Bong, D. (2013). Small-Molecule\/Polymer Recognition Triggers Aqueous-Phase Assembly and Encapsulation. Langmuir 29<\/i>, 144\u2013150.<\/p>\n

Ma, M., and Bong, D. (2013). Controlled Fusion of Synthetic Lipid Membrane Vesicles. Acc. Chem. Res. 46<\/i>, 2988\u20132997.<\/p>\n

Xia, X., Piao, X., Fredrick, K., and Bong, D. (2013). Bifacial PNA complexation inhibits enzymatic access to DNA and RNA. Chembiochem 15<\/i>, 31\u201336.<\/p>\n

2012<\/strong><\/p>\n

Bandyopadhyay, S., Xia, X., Maiseiyeu, A., Mihai, G., Rajagopalan, S., and Bong, D. (2012). Z-Group ketone chain transfer agents for RAFT polymer nanoparticle modification via hydrazone conjugation. Macromolecules 45<\/i>, 6766\u20136773.<\/p>\n

Zeng, Y., Pratumyot, Y., Piao, X., and Bong, D. (2012). Discrete assembly of synthetic peptide-DNA triplex structures from polyvalent melamine-thymine bifacial recognition. J. Am. Chem. Soc. 134<\/i>, 832\u2013835.<\/p>\n

2011<\/strong><\/p>\n

Bandyopadhyay, S., and Bong, D. (2011). Synthesis of Trifunctional Phosphatidylserine Probes for Identification of Lipid-Binding Proteins. Eur. J. Org. Chem. 2011<\/i>, 751\u2013758.<\/p>\n

Ma, M., and Bong, D. (2011). Determinants of cyanuric acid and melamine assembly in water. Langmuir 27<\/i>, 8841\u20138853.<\/p>\n

Ma, M., Chatterjee, S., Zhang, M., and Bong, D. (2011). Stabilization of vesicular and supported membranes by glycolipid oxime polymers. Chem. Commun. 47<\/i>, 2853\u20132855.<\/p>\n

Torres, O., and Bong, D. (2011). Determinants of Membrane Activity from Mutational Analysis of the HIV Fusion Peptide. Biochemistry 50<\/i>, 5195\u20135207.<\/p>\n

Ma, M., and Bong, D. (2011). Directed peptide assembly at the lipid-water interface cooperatively enhances membrane binding and activity. Langmuir 27<\/i>, 1480\u20131486.<\/p>\n

Bandyopadhyay, S., and Bong, D. (2011). Synthesis of Trifunctional Phosphatidylserine Probes for Identification of Lipid-Binding Proteins. Eur. J. Org. Chem. 2011<\/i>, 751\u2013758.<\/p>\n

2010<\/strong><\/p>\n

Ma, M., and Bong, D. (2010). Directed Peptide Assembly at the Lipid- Water Interface Cooperatively Enhances Membrane Binding and Activity\u2020. Langmuir 27<\/i>, 1480\u20131486.<\/p>\n

2009<\/strong><\/p>\n

Ma, M., Gong, Y., and Bong, D. (2009). Lipid Membrane Adhesion and Fusion Driven by Designed, Minimally Multivalent Hydrogen-Bonding Lipids. J. Am. Chem. Soc. 131<\/i>, 16919\u201316926.<\/p>\n

2008<\/strong><\/p>\n

Ma, M., Paredes, A., and Bong, D. (2008). Intra- and intermembrane pairwise molecular recognition between synthetic hydrogen-bonding phospholipids. J. Am. Chem. Soc. 130<\/i>, 14456\u201314458.<\/p>\n

Torres, O., Y\u00fcksel, D., Bernardina, M., Kumar, K., and Bong, D. (2008). Peptide tertiary structure nucleation by side-chain crosslinking with metal complexation and double \u201cclick\u201d cycloaddition. Chembiochem 9<\/i>, 1701\u20131705.<\/p>\n

Gong, Y., Ma, M., Luo, Y., and Bong, D. (2008). Functional determinants of a synthetic vesicle fusion system. J. Am. Chem. Soc. 130<\/i>, 6196\u20136205.<\/p>\n

2006<\/strong><\/p>\n

Gong, Y., Luo, Y., and Bong, D. (2006). Membrane activation: selective vesicle fusion via small molecule recognition. J. Am. Chem. Soc. 128<\/i>, 14430\u201314431.<\/p>\n

Prior to OSU<\/strong><\/p>\n

Bong, D., Tam, I., and Breslow, R. (2004). Oligothiophene isocyanides for platinum-based molecular electronic applications. J. Am. Chem. Soc. 126<\/i>, 11796\u201311797.<\/p>\n

Bong, D.T.-Y., Chan, E.W.L., Diercks, R., Dosa, P.I., Haley, M.M., Matzger, A.J., Miljanic, O.\u0160., Vollhardt, K.P.C., Bond, A.D., Teat, S.J., et al. (2004b). Syntheses of syn and anti doublebent [5] phenylene. Org. Lett. 6<\/i>, 2249\u20132252.<\/p>\n

Bong, D.T., Gentric, L., Holmes, D., Matzger, A.J., Scherhag, F., and Vollhardt, K.P. (2002). Synthesis of bent [4]phenylene (cyclobuta[1,2-\u03b1:3,4-\u03b2\u2019]bisbiphenylene) and structure of a bis(trimethylsilyl) derivative: the last [4]phenylene isomer. Chem. Commun. 278\u2013279.<\/p>\n

Bong, D.T., and Ghadiri, M.R. (2001a). Chemoselective Pd(0)-catalyzed peptide coupling in water. Org. Lett. 3<\/i>, 2509\u20132511.<\/p>\n

Bong, D.T., Clark, T.D., Granja, J.R., and Ghadiri, M.R. (2001). Self-Assembling Organic Nanotubes. Angew. Chem. Int. Ed. 40<\/i>, 988\u20131011.<\/p>\n

Bong, D.T., and Ghadiri, M.R. (2001b). Self-assembling cyclic peptide cylinders as nuclei for crystal engineering. Angew. Chem. Int. Ed. 40<\/i>, 2163\u20132166.<\/p>\n

Bong, D.T., Janshoff, A., Steinem, C., and Ghadiri, M.R. (2000). Membrane partitioning of the cleavage peptide in flock house virus. Biophys. J. 78<\/i>, 839\u2013845.<\/p>\n

Bong, D.T., Steinem, C., Janshoff, A., Johnson, J.E., and Reza Ghadiri, M. (1999). A highly membrane-active peptide in Flock House virus: implications for the mechanism of nodavirus infection. Chem. Biol. 6<\/i>, 473\u2013481.<\/p>\n

Janshoff, A., Bong, D.T., Steinem, C., Johnson, J.E., and Ghadiri, M.R. (1999). An animal virus-derived peptide switches membrane morphology: possible relevance to nodaviral transfection processes. Biochemistry 38<\/i>, 5328\u20135336.<\/p>\n","protected":false},"excerpt":{"rendered":"

2023 Liang, Y.; Willey, S.; Chung, Y.-C.; Lo, Y.-M.; Miao, S.; Rundell, S.; Tu, L.-C.; Bong, D. Intracellular RNA and DNA Tracking by Uridine-Rich Internal Loop Tagging with Fluorogenic bPNA. Nat. Commun. 2023, 14 (1), 1\u201312. https:\/\/doi.org\/10.1038\/s41467-023-38579-2. 2022 Rundell, S.; Munyaradzi, O.; Bong, D. Enhanced Triplex Hybridization of DNA and RNA via Syndiotactic Side Chain … <\/p>\n

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