Wei-Che Hsieh, Gustavo R. Martinez, Ashley Wang, Sharon F. Wu, Raunaq Chamdia & Danith H. Ly. Stereochemical conversion of nucleic acid circuits via strand displacement, Commn.Chem., 2018, 1, 89.
Shivaji A. Thadke, V. M. Hridya, J. Dinithi R. Perera, Roberto R. Gil, Arnab Mukherjee, and Danith H. Ly. Comms. Chem. 2018, 1, 79.
Adele S. Ricciardi, Raman Bahal, James S. Farrelly, Elias Quijano, Anthony H. Bianchi, Valerie L. Luks, Rachael Putman, Francesc López-Giráldez, Süleyman Coşkun, Eric Song, Yanfeng Liu, Wei-Che Hsieh, Danith H. Ly, David H. Stitelman, Peter M. Glazer & W. Mark Saltzman. Nat. Commun. 2018, 9, 2481.
Zutao Yu, Wei-Che Hsieh, Sefan Asamitsu, Kaori Hashiya, Toshikazu Bando, Danith H. Ly and Hiroshi Sugiyama. Chem. Eur. J. 2018, 24, 1.
Mengshen “David” Chen, Kaustubh Sinha, Gordon S. Rule, and Danith H. Ly. Interaction of α‑thymidine inhibitors with thymidylate kinase from plasmodium falciparum. Biochemistry 2018, 57, 2868.
Shivaji A. Thadke, J. Dinithi R. Perera, V. M. Hridya, Kirti Bhatt, Ashif Y. Shaikh, Wei-Che Hsieh, Mengshen Chen, Chaki cherla Gayathri, Roberto R. Gil, Gordon S. Rule, Arnab Mukherjee, Charles A. Thornton, and Danith H. Ly. Design of bivalent nucleic acid ligands for recognition of RNA-repeated expansion associated with Huntington’s disease. Biochemistry 2018, 57, 2094.
Raman Bahal, Arunava Manna, Wei-Che Hsieh, Shivaji A. Thadke, Gopalsamy Sureshkumar, and Danith H. Ly. RNA-templated concatenation of triplet nucleic-acid probe. ChemBioChem 2018, 19, 674.
Wei-Che Hsieh, Raman Bahal, Shivaji A. Thadke, Kirti Bhatt, Krzysztof Sobczak, Charles Thornton, and Danith H. Ly. Design of a “mini” nucleic acid probe for cooperative binding of an RNA-repeated transcript associated with Myotonic Dystrophy type 1. Biochemistry 2018, 57, 907.
Anisha Gupta, Elias Quijano, Yanfeng Liu, Raman Bahal, Susan E. Scanlon, Eric Song, Wei-Che Hsieh, Demetrios E. Braddock, Danith H. Ly, W. Mark Saltzman, and Peter M. Glazer. Anti-tumor activity of miniPEG-g-modified PNAs to inhibit microRNA-210 for cancer therapy. Mol. Ther. Nucleic Acids 2017, 9, 111.
Raman Bahal, Nicole Ali McNeer, Elias Quijano, Yanfeng Liu, Parker Sulkowski, Audrey Turchick, Yi-Chien Lu, Dinesh C. Bhunia, Arunava Manna, Dale L. Greiner, Michael A. Brehm, Christopher J. Cheng, Francesc López-Giráldez, Adele Ricciardi, Jagadish Beloor, Diane S. Krause, Priti Kumar, Patrick G. Gallagher, Demetrios T. Braddock, W. Mark Saltzman, Danith H. Ly & Peter M. Glazer. In vivo correction of anaemia in β-thalassemic mice by gPNA-mediated gene editing with nanoparticle delivery. Nat. Commun. 2016, 7, 13304.
Iulia Sacui, Wei-Che Hsieh, Arunava Manna, Bichismita Sahu, Danith H. Ly. Gamma peptide nucleic acid: As orthogonal nucleic acid recognition codes for organizing molecular self-assembly. J. Am. Chem. Soc. 2015, 137, 8603-8610.
Ha H. Pham, Connor T. Murphy, Gopalsamy Sureshkumar, Danith H. Ly, Patricia L. Opresko, Bruce A. Armitage. Cooperative hybridization of γPNA miniprobes to a repeating sequence motif and application to telomere analysis. Org. Biomol. Chem. 2014, 12, 7345.
Raman Bahal, Elias Quijano, Nicole A. McNeer, Yanfeng Liu, Dinesh C. Bhunia, Francesco Lopez-Giraldez, Rachel J. Fields, Williams M. Saltzman, Danith H. Ly, Peter M. Glazer. Single-stranded γPNAs for in-vivo site-specific gene editing via Watson-Crick recognition. Curr. Gene Therap. 2014, 14, 331.
Raman Bahal, Nicole Ali McNeer, Danith H. Ly, W. Mark Saltzman, Peter M. Glazer. Nanoparticle for delivery of antisense γPNA oligomers targeting CCR5. Artificial DNA: PNA & XNA 2013, 4, 49.
Johnathan M. Goldman, Li Ang Zhang, Arunava Manna, Bruce A. Armitage, Danith H. Ly, James W. Schneider. High affinity γPNA sandwich hybridization assay for rapid detection of short nucleic acid targets with single mismatch discrimination. Biomacromolecules 2013, 14, 2253.
Anisha Gupta, Ling-Ling Lee, Subhadeep Roy, Farial A. Tanious, W. David Wilson, Danith H. Ly, Bruce A. Armitage. Strand invasion of DNA quadruplexes by PNA: Comparison of homologous and complementary hybridization. ChemBioChem 2013, 14, 1476.
Malabika Sen, Sufi M. Thomas, Seungwon Kim, Joanne I. Yeh, Robert L. Ferris, Jonas T. Johnson, Umamaheswar Duvvuri, Jessica Lee, Nivedita Sahu, Sonali Joyce, Maria L. Freilino, Haibin Shin, Changyou Li, Danith Ly, Srinivas Rapireddy, Jonathan P. Etter, Pui-Kai Li, Lin Wang, Simion Chiosea, Raja R. Seethala, William E. Gooding, Xiaomin Chen, Naftali Kaminski, Kusum Pandit, Daniel E. Johnson, Jennifer R. Grandis. First-in-human trial of a STAT3 decoy oligonucleotide in head and neck tumors: Implications for cancer therapy. Cancer Discov. 2012, 2, 694.
Srinivas Rapireddy, Linda Nhon, Robert E. Meehan, Jonathan Franks, Donna Beer Stolz, Dat Tran, Michael E. Selsted, Danith H. Ly RTD-1 mimic containing γPNA scaffold exhibits broad-spectrum antibacterial activities. J. Am. Chem. Soc. 2012, 134, 4041, DOI: 10.1021/ja211867j
Alon Singer, Srinivas Rapireddy, Danith H. Ly, Amit Meller Electronic barcoding of a viral genet at the single-molecule level. Nano Lett. 2012, 12, 1722, DOI: 10.1021/nl300372a
Emil Wierzbinski, Arnie de Leon, Xing Lin, Alexander Balaeff, Kathryn L. Davis, Srinivas Rapireddy, Ravindra Venkatramani, Shahar Keinan, Danith H. Ly, Marcela Madrid, David N. Beratan, Catalina Achim, David H. Waldeck Effect of backbone flexibility on charge transfer rates in peptide nucleic acid duplexes, DOI: 10.1021/ja301677z
Raman Bahal, Bichismita Sahu, Srinivas Rapireddy, Chong-Min Lee, and Danith H. Ly Sequence-Unrestricted, Watson-Crick Recognition of Double Helical B-DNA by (R)-MiniPEG-gammaPNAs. Chembiochem, 2012, 13, 56 - 60, DOI: 10.1002/cbic.201100646
Bichismita Sahu, Iulia Sacui, Srinivas Rapireddy, Kimberly J. Zanotti, Raman Bahal, Bruce A. Armitage, and Danith H. Ly "Synthesis and Characterization of Conformationally Preorganized, (R)-Diethylene Glycol-Containing γ-Peptide Nucleic Acids with Superior Hybridization Properties and Water Solubility" J. Org. Chem. (ASAP articles), DOI: 10.1021/jo200482d
Srinivas Rapireddy, Raman Bahal, and Danith H. Ly, "Strand Invasion of Mixed-Sequence, Double-Helical B-DNA by γ-Peptide Nucleic Acids Containing G-Clamp Nucleobases under Physiological Conditions" Biochemistry 2011, 50, 3913–3918, DOI: 10.1021/bi2002554
Joanne I. Yeh, Boris Shivachev, Srinivas Rapireddy, Matthew J. Crawford, Roberto R. Gil, Shoucheng Du, Marcela Madrid, and Danith H. Ly "Crystal Structure of Chiral γPNA with Complementary DNA Strand: Insights into the Stability and Specificity of Recognition and Conformational Preorganization" J. Am. Chem. Soc., 2010, 132, 10717–10727, DOI: 10.1021/ja907225d
Lusvarghi, S., Murphy, C,T., Roy, S., Tanious, F,A., Sacui, I., Wilson, W,D., Ly, D. H. Armitage . B,A. “Loop and Backbone Modifications of Peptide Nucleic Acid Improve G-Quadruplex Binding Selectivity” J. Am. Chem. Soc., 2009, 131 (51), pp 18415–18424, DOI: 10.1021/ja907250j
He, G., Rapireddy, S., Bahal, R., Sahu, B., and Ly, D. H. “Strand Invasion of Extended, Mixed-Sequence B-DNA by γPNAs” J. Am. Chem. Soc. 2009, 131, 12088–12090, DOI: 10.1021/ja900228j
Sahu, B., Chenna, V., Lathrop, K.L., Thomas, S.M., Zon, G., Livak, K, J., Ly, D. H. “Synthesis of Conformationally Preorganized and Cell-Permeable Guanidine-Based γ-Peptide Nucleic Acids (γGPNAs)” J. Org. Chem., 2009, 74, 1509–1516, DOI: 10.1021/jo802211n
Wu, Z., Lanni, E., Chen, W., Bier, M,E., Ly, D. H. Jin, R. “High Yield, Large Scale Synthesis of Thiolate-Protected Ag7 Clusters” J. Am. Chem. Soc., 2009, 131, 16672–16674, DOI: 10.1021/ja907627f
Chenna, V., Rapireddy, S., Sahu, B., Ausin, C., Pedroso, E., Ly, D. H. “A Simple Cytosine to G-Clamp Nucleobase Substitution Enables Chiral -PNAs to Invade Mixed-Sequence Double-Helical B-form DNA” ChemBioChem., 2008, 9, 2388–2391, DOI: 10.1002/cbic.200800441
Rapireddy, S., He, G., Roy, S., Armitage . B,A. Ly, D. H. “Strand Invasion of Mixed-Sequence B- DNA by Acridine-Linked, γ-Peptide Nucleic Acid (γ-PNA)” J. Am. Chem. Soc., 2007,129, 15596–15600, DOI: 10.1021/ja074886j
Zhou, P., Dragulescu-Andrasi, A., Bhattacharya, B., Hyldig-Nielsen, J. J., Ly, D. H. “Synthesis of cell-permeable peptide nucleic acid monomers and oligomers, and characterization of their hybridization and uptake properties”. Bioorg. Med. Chem. Lett. 2006, 16, 4931–4935, DOI: 10.1016/j.bmcl.2006.06.052
Dragulescu-Andrasi, A., Rapireddy, S., Frezza, B. M., Gayathri, C., Gil, R. R., Ly, D. H. “A simple γ-backbone modification preorganizes peptide nucleic acid into a helical structure.” J. Am. Chem. Soc.2006, 128, 10258–10267, DOI: 10.1021/ja0625576
Dragulescu-Andrasi, A., Rapireddy, S., He, G., Bhattacharya, B., Hyldig-Nielsen, J. J., Zon, G., Ly, D. H. “Cell-permeable peptide nucleic acid designed to bind to the 5’-untranslated region of E-cadherin transcript induces potent and sequence-specific antisense effects”. J. Am. Chem. Soc. 2006, 128, 16104–16112, DOI: 10.1021/ja063383v
Dragulescu-Andrasi, A., Zhou, P., He, G., Ly, D. H. “Cell-Permeable GPNA Containing Appropriate Backbone Stereochemistry and Spacing Binds Sequence-Specifically to RNA” Chem. Comm. 2005, 244–246, DOI: 10.1039/B412522C
Lagerholm, C. B., Wang, M., Ernst, L. A., Ly, D. H. Bruchez, M. P., Waggoner, A. S. “Multicolor Coding of Cells with Cationic Peptide Coated Quantum Dots” Nano Lett. 2004, 4, 2019–2022, DOI: 10.1021/nl049295v
Zhou, P., Wang, M., Du, L., Fisher, G., Waggoner, A., Ly, D. H. “Novel Binding and Efficient Cellular Uptake of Guanidine-Based Peptide Nucleic Acid (GPNA)” J. Am. Chem. Soc. 2003, 125, 6878–6879, DOI: 10.1021/ja029665m
Simbulan-Rosenthal, C.M., Ly, D.H., Rosenthal, D.S., Konopka, G., Luo, R-B., Wang, Z-Q., Schultz, P.G., Smulson, M.E. “Misregulation of Gene Expression in Primary Fibroblasts Lacking Poly(ADP-ribose) Polymerase” Proc. Nat. Acad. Sci. 2000, 97, 11274–11279, DOI: 10.1073/pnas.200285797
Ly, D.H., Lockhart, D.J., Schultz, P. G., Lerner, R. A. “Mitotic Misregulation and Human Aging” Science. 2000, 287, 2486–2492, DOI: 10.1126/science.287.5462.2486