{"id":1618,"date":"2026-02-04T20:03:13","date_gmt":"2026-02-05T01:03:13","guid":{"rendered":"https:\/\/groups.chem.cmu.edu\/ly\/?page_id=1618"},"modified":"2026-02-23T16:39:34","modified_gmt":"2026-02-23T21:39:34","slug":"publications","status":"publish","type":"page","link":"https:\/\/groups.chem.cmu.edu\/ly\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"
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The Ly Group<\/h1>
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Publications<\/h2>\n<\/div><\/div>\n<\/div>\n\n
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Department of Chemistry<\/h3>\n

Carnegie Mellon University<\/p>\n<\/div><\/div>\n<\/div>\n<\/div>\n<\/div>\n\n

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J.D.R. Perera, S.A. Thadke, S.W. Thrikawala, I. Dhami, V.M. Hridya, A. Mukherjee, A. Paul, W.D. Wilson, K.W.R. Tan, N.Z.W. Chan, A.T. Phan, & D.H. Ly. A pothole-filling strategy for selective targeting of rCUG-repeats associated with myotonic dystrophy type 1, Proc. Natl. Acad. Sci.<\/em> U.S.A. 2026<\/strong> 123 (2) e2507065123, https:\/\/doi.org\/10.1073\/pnas.2507065123<\/a><\/span><\/p>\n

Shivaji A. Thadke, <\/span><\/span>J. Dinithi R. Perera, <\/span><\/span>Savani W. Thrikawala and Danith H. Ly. Synthesis of Janus Bases for Targeting C-G and U\u2013U Pairs of CUG-RNA Repeats Associated with Myotonic Dystrophy Type 1. ACS Omega <\/span>2025<\/strong>, 10, 41, 49252\u201349259. <\/span>https:\/\/doi.org\/10.1021\/acsomega.5c09489<\/a><\/p>\n

I. Dhami<\/span>,\u00a0<\/span>S. A. Thadke<\/span>\u00a0and\u00a0<\/span>D. H. Ly. Development of the Right- and Left-Handed Gamma Peptide Nucleic Acid Building Blocks for On-Resin Chemical Functionalization.<\/span>\u00a0<\/span>J. Org. Chem.<\/em>, 2022<\/strong>,\u00a0<\/span>87, 13873 \u201413881. https:\/\/doi.org\/10.1021\/acs.joc.2c01560<\/a><\/span><\/p>\n

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.<\/em>, 2018<\/strong>, 1<\/em>, 89. https:\/\/doi.org\/10.1038\/s42004-018-0089-9<\/a><\/a><\/span><\/p>\n

Shivaji A. Thadke, V. M. Hridya, J. Dinithi R. Perera, Roberto R. Gil, Arnab Mukherjee, and Danith H. Ly. Comms. Chem<\/em>. 2018<\/strong>, 1<\/em>, 79. https:\/\/doi.org\/10.1038\/s42004-018-0080-5<\/span><\/a><\/p>\n

Adele S. Ricciardi, Raman Bahal, James S. Farrelly, Elias Quijano, Anthony H. Bianchi, Valerie L. Luks, Rachael Putman, Francesc L\u00f3pez-Gir\u00e1ldez, S\u00fcleyman Co\u015fkun, Eric Song, Yanfeng Liu, Wei-Che Hsieh, Danith H. Ly, David H. Stitelman, Peter M. Glazer & W. Mark Saltzman. Nat. Commun.<\/em> 2018<\/strong>, 9<\/em>, 2481.<\/p>\n

Zutao Yu, Wei-Che Hsieh, Sefan Asamitsu, Kaori Hashiya, Toshikazu Bando, Danith H. Ly and Hiroshi Sugiyama. Chem. Eur. J.<\/em> 2018<\/strong>, 24<\/em>, 1.<\/p>\n

Mengshen \u201cDavid\u201d Chen, Kaustubh Sinha, Gordon S. Rule, and Danith H. Ly. Interaction of \u03b1\u2011thymidine inhibitors with thymidylate kinase from plasmodium falciparum. Biochemistry<\/em> 2018<\/strong>, 57<\/em>, 2868.<\/p>\n

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\u2019s disease. Biochemistry<\/em> 2018<\/strong>, 57<\/em>, 2094.<\/p>\n

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<\/em> 2018<\/strong>, 19<\/em>, 674.<\/p>\n

Wei-Che Hsieh, Raman Bahal, Shivaji A. Thadke, Kirti Bhatt, Krzysztof Sobczak, Charles Thornton, and Danith H. Ly. Design of a \u201cmini\u201d nucleic acid probe for cooperative binding of an RNA-repeated transcript associated with Myotonic Dystrophy type 1. Biochemistry<\/em> 2018<\/strong>, 57<\/em>, 907.<\/p>\n

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<\/em> 2017<\/strong>, 9<\/em>, 111.<\/p>\n

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 L\u00f3pez-Gir\u00e1ldez, Adele Ricciardi, Jagadish Beloor, Diane S. Krause, Priti Kumar, Patrick G. Gallagher, Demetrios T. Braddock, W. Mark Saltzman, Danith H. Ly & Peter M. Glazer.\u00a0In vivo correction of anaemia in \u03b2-thalassemic mice by gPNA-mediated gene editing with nanoparticle delivery. Nat. Commun.<\/em> 2016<\/strong>, 7<\/em>, 13304.<\/p>\n

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.<\/em> 2015<\/strong>, 137<\/em>, 8603-8610.<\/p>\n

Ha H. Pham, Connor T. Murphy, Gopalsamy Sureshkumar, Danith H. Ly, Patricia L. Opresko, Bruce A. Armitage. Cooperative hybridization of \u03b3PNA miniprobes to a repeating sequence motif and application to telomere analysis. Org. Biomol. Chem.<\/em> 2014<\/strong>, 12<\/em>, 7345.<\/p>\n

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 \u03b3PNAs for in-vivo site-specific gene editing via Watson-Crick recognition. Curr. Gene Therap.<\/em> 2014<\/strong>, 14<\/em>, 331.<\/p>\n

Raman Bahal, Nicole Ali McNeer, Danith H. Ly, W. Mark Saltzman, Peter M. Glazer. Nanoparticle for delivery of antisense \u03b3PNA oligomers targeting CCR5. Artificial DNA: PNA & XNA<\/em> 2013<\/strong>, 4<\/em>, 49.<\/p>\n

Johnathan M. Goldman, Li Ang Zhang, Arunava Manna, Bruce A. Armitage, Danith H. Ly, James W. Schneider. High affinity \u03b3PNA sandwich hybridization assay for rapid detection of short nucleic acid targets with single mismatch discrimination. Biomacromolecules<\/em> 2013<\/strong>, 14<\/em>, 2253.<\/p>\n

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<\/em> 2013<\/strong>, 14<\/em>, 1476.<\/p>\n

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.<\/em> 2012<\/strong>, 2<\/em>, 694.<\/p>\n

Srinivas Rapireddy, Linda Nhon, Robert E. Meehan, Jonathan Franks, Donna Beer Stolz, Dat Tran, Michael E. Selsted, Danith H. Ly RTD-1 mimic containing \u03b3PNA scaffold exhibits broad-spectrum antibacterial activities. J. Am. Chem. Soc.<\/em> 2012<\/strong>, 134<\/em>, 4041, DOI: 10.1021\/ja211867j<\/a><\/p>\n

Alon Singer, Srinivas Rapireddy, Danith H. Ly, Amit Meller Electronic barcoding of a viral genet at the single-molecule level. Nano Lett.<\/em> 2012<\/strong>, 12, 1722, DOI:\u00a0 10.1021\/nl300372a<\/a><\/p>\n

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<\/a><\/p>\n

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<\/a><\/p>\n

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 \u03b3-Peptide Nucleic Acids with Superior Hybridization Properties and Water Solubility\" J. Org. Chem. (ASAP articles)<\/em>, DOI: 10.1021\/jo200482d<\/a><\/p>\n

Srinivas Rapireddy, Raman Bahal, and Danith H. Ly, \"Strand Invasion of Mixed-Sequence, Double-Helical B-DNA by \u03b3-Peptide Nucleic Acids Containing G-Clamp Nucleobases under Physiological Conditions\" Biochemistry<\/em> 2011<\/strong>, 50, 3913\u20133918, DOI: 10.1021\/bi2002554<\/a><\/p>\n

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 \u03b3PNA with Complementary DNA Strand: Insights into the Stability and Specificity of Recognition and Conformational Preorganization\" J. Am. Chem. Soc.<\/em>, 2010<\/strong>, 132, 10717\u201310727, DOI: 10.1021\/ja907225d<\/a><\/p>\n

Lusvarghi, S., Murphy, C,T., Roy, S., Tanious, F,A., Sacui, I., Wilson, W,D., Ly, D. H. Armitage . B,A. \u201cLoop and Backbone Modifications of Peptide Nucleic Acid Improve G-Quadruplex Binding Selectivity\u201d J. Am. Chem. Soc.<\/em>, 2009<\/strong>, 131 (51), pp 18415\u201318424, DOI: 10.1021\/ja907250j<\/a><\/p>\n

He, G., Rapireddy, S., Bahal, R., Sahu, B., and Ly, D. H. \u201cStrand Invasion of Extended, Mixed-Sequence B-DNA by \u03b3PNAs\u201d J. Am. Chem. Soc.<\/em> 2009<\/strong>, 131<\/em>, 12088\u201312090, DOI: 10.1021\/ja900228j<\/a><\/p>\n

Sahu, B., Chenna, V., Lathrop, K.L., Thomas, S.M., Zon, G., Livak, K, J., Ly, D. H. \u201cSynthesis of Conformationally Preorganized and Cell-Permeable Guanidine-Based \u03b3-Peptide Nucleic Acids (\u03b3GPNAs)\u201d J. Org. Chem.<\/em>, 2009<\/strong>, 74<\/em>, 1509\u20131516, DOI: 10.1021\/jo802211n<\/a><\/p>\n

Wu, Z., Lanni, E., Chen, W., Bier, M,E., Ly, D. H. Jin, R. \u201cHigh Yield, Large Scale Synthesis of Thiolate-Protected Ag7 Clusters\u201d J. Am. Chem. Soc.<\/em>, 2009<\/strong>, 131<\/em>, 16672\u201316674, DOI: 10.1021\/ja907627f<\/a><\/p>\n

Chenna, V., Rapireddy, S., Sahu, B., Ausin, C., Pedroso, E., Ly, D. H. \u201cA Simple Cytosine to G-Clamp Nucleobase Substitution Enables Chiral -PNAs to Invade Mixed-Sequence Double-Helical B-form DNA\u201d ChemBioChem.<\/em>, 2008<\/strong>, 9, 2388\u20132391, DOI: 10.1002\/cbic.200800441<\/a><\/p>\n

Rapireddy, S., He, G., Roy, S., Armitage . B,A. Ly, D. H. \u201cStrand Invasion of Mixed-Sequence B- DNA by Acridine-Linked, \u03b3-Peptide Nucleic Acid (\u03b3-PNA)\u201d J. Am. Chem. Soc.<\/em>, 2007<\/strong>,129<\/em>, 15596\u201315600, DOI: 10.1021\/ja074886j<\/a><\/p>\n

Zhou, P., Dragulescu-Andrasi, A., Bhattacharya, B., Hyldig-Nielsen, J. J., Ly, D. H. \u201cSynthesis of cell-permeable peptide nucleic acid monomers and oligomers, and characterization of their hybridization and uptake properties\u201d. Bioorg. Med. Chem. Lett.<\/em> 2006<\/strong>, 16<\/em>, 4931\u20134935, DOI: 10.1016\/j.bmcl.2006.06.052<\/a><\/p>\n

Dragulescu-Andrasi, A., Rapireddy, S., Frezza, B. M., Gayathri, C., Gil, R. R., Ly, D. H. \u201cA simple \u03b3-backbone modification preorganizes peptide nucleic acid into a helical structure.\u201d J. Am. Chem. Soc.<\/em>2006<\/strong>, 128<\/em>, 10258\u201310267, DOI: 10.1021\/ja0625576<\/a><\/p>\n

Dragulescu-Andrasi, A., Rapireddy, S., He, G., Bhattacharya, B., Hyldig-Nielsen, J. J., Zon, G., Ly, D. H. \u201cCell-permeable peptide nucleic acid designed to bind to the 5\u2019-untranslated region of E-cadherin transcript induces potent and sequence-specific antisense effects\u201d. J. Am. Chem. Soc.<\/em> 2006<\/strong>, 128<\/em>, 16104\u201316112, DOI: 10.1021\/ja063383v<\/a><\/p>\n

Dragulescu-Andrasi, A., Zhou, P., He, G., Ly, D. H. \u201cCell-Permeable GPNA Containing Appropriate Backbone Stereochemistry and Spacing Binds Sequence-Specifically to RNA\u201d Chem. Comm.<\/em> 2005<\/strong>, 244\u2013246, DOI: 10.1039\/B412522C<\/a><\/p>\n

Lagerholm, C. B., Wang, M., Ernst, L. A., Ly, D. H. Bruchez, M. P., Waggoner, A. S. \u201cMulticolor Coding of Cells with Cationic Peptide Coated Quantum Dots\u201d Nano Lett.<\/em> 2004<\/strong>, 4<\/em>, 2019\u20132022, DOI: 10.1021\/nl049295v<\/a><\/p>\n

Zhou, P., Wang, M., Du, L., Fisher, G., Waggoner, A., Ly, D. H. \u201cNovel Binding and Efficient Cellular Uptake of Guanidine-Based Peptide Nucleic Acid (GPNA)\u201d J. Am. Chem. Soc.<\/em> 2003<\/strong>, 125<\/em>, 6878\u20136879, DOI: 10.1021\/ja029665m<\/a><\/p>\n

Simbulan-Rosenthal, C.M., Ly, D.H., Rosenthal, D.S., Konopka, G., Luo, R-B., Wang, Z-Q., Schultz, P.G., Smulson, M.E. \u201cMisregulation of Gene Expression in Primary Fibroblasts Lacking Poly(ADP-ribose) Polymerase\u201d Proc. Nat. Acad. Sci.<\/em> 2000<\/strong>, 97<\/em>, 11274\u201311279, DOI: 10.1073\/pnas.200285797<\/a><\/p>\n

Ly, D.H., Lockhart, D.J., Schultz, P. G., Lerner, R. A. \u201cMitotic Misregulation and Human Aging\u201d Science.<\/em> 2000<\/strong>, 287<\/em>, 2486\u20132492, DOI: 10.1126\/science.287.5462.2486<\/a><\/p>\n<\/div><\/div>\n<\/div>\n<\/div>\n<\/div>","protected":false},"excerpt":{"rendered":"","protected":false},"author":21,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-1618","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/groups.chem.cmu.edu\/ly\/wp-json\/wp\/v2\/pages\/1618","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/groups.chem.cmu.edu\/ly\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/groups.chem.cmu.edu\/ly\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/groups.chem.cmu.edu\/ly\/wp-json\/wp\/v2\/users\/21"}],"replies":[{"embeddable":true,"href":"https:\/\/groups.chem.cmu.edu\/ly\/wp-json\/wp\/v2\/comments?post=1618"}],"version-history":[{"count":5,"href":"https:\/\/groups.chem.cmu.edu\/ly\/wp-json\/wp\/v2\/pages\/1618\/revisions"}],"predecessor-version":[{"id":1663,"href":"https:\/\/groups.chem.cmu.edu\/ly\/wp-json\/wp\/v2\/pages\/1618\/revisions\/1663"}],"wp:attachment":[{"href":"https:\/\/groups.chem.cmu.edu\/ly\/wp-json\/wp\/v2\/media?parent=1618"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}