Danith Ly

Professor, Chemistry
Director, Institute for Biomolecular Design and Discovery (IBD)

Bio

Courtesy appointment:

• Professor, University of Pittsburgh, Molecular Biophysics and Structural Biology

Education

Ph.D., Georgia Institute of Technology, 1999
Irving S. Sigal Postdoctoral Fellow, University of California at Berkeley, 1999–2000
Irving S. Sigal Postdoctoral Fellow, The Scripps Research Institute, 2000–2001

Research

Keywords: Bioorganic chemistry, chemical biology, gene regulation, cellular delivery, protein engineering, molecular self-assembly

Projects

Our research program over the past five years has been focused on the design and development of molecular tools and reagents for regulating gene expression and probing protein localization and dynamics in human somatic and embryonic stem (ES) cells. We are particularly interested in dissecting the genetic blueprint of human ESC and addressing the fundamental questions pertaining to the cellular origins of cancer. More recently, we have expanded our research into other areas including protein design, tissue engineering and molecular self-assembly, taking advantage of the strength of the department and our expertise in the design and synthesis of natural and synthetic biopolymers (DNA, RNA, proteins, and biomimetics).

Publications

Design of a “Mini” Nucleic Acid Probe for Cooperative Binding of an RNA-Repeated Transcript Associated with Myotonic Dystrophy Type 1
Wei-Che Hsieh, Raman Bahal, Shivaji A. Thadke, Kirti Bhatt, Krzysztof Sobczak, Charles Thornton, and Danith H. Ly, Biochemistry Article ASAP Publication Date (Web): January 15, 2018 DOI: 10.1021/acs.biochem.7b01239

Anti-tumor Activity of miniPEG-γ-Modified PNAs to Inhibit MicroRNA-210 for Cancer Therapy
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, Peter M. Glazer, Molecular Therapy - Nucleic Acids, 2017, 9,111-119, doi.org/10.1016/j.omtn.2017.09.001

RNA-Templated Concatenation of Triplet Nucleic Acid Probe
Ly, D. H., Bahal, R., Manna, A., Hsieh, W.-C., Thadke, S. A. and Sureshkumar, G.. ChemBioChem doi:10.1002/cbic.201700574

In vivo correction of anaemia in β-thalassemic mice by γPNA-mediated gene editing with nanoparticle delivery
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, and Peter M. Glazer, Nat Commun. 2016; 7: 13304. Published online 2016 Oct 26. doi: 10.1038/ncomms13304

Synthesis of optically pure ɣPNA monomers: A comparative study
Arunava Manna, Rapireddy Srinivas, Gopalsamy Sureshkumar, Danith H. Ly. Tetrahedron 2015, 71, 3507

Gamma peptide nucleic acids: As orthogonal nucleic acid recognition codes for organizing molecular self-assembly
Iulia Sacui, Wei-Che Hsieh, Arunava Manna, Bichismita Sahu, Danith H. Ly, J. Am. Chem. Soc. 2015, 137, 8610

Cooperative hybridization of ɣPNA miniprobes to a repeating sequence motif and application to telomere analysis
Ha H. Pham, Connor T. Murphy, Gopalsamy Sureshkumar, Danith H. Ly, Patricia L. Opresko, Bruce A. Armitage, Org. Biomol. Chem. 2014, 12, 7345

Single-stranded ɣPNAs for in-vivo site-specific gene editing via Watson-Crick recognition
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, Curr. Gene Therap. 2014, 14, 331

Nanoparticle for delivery of antisense ɣPNA oligomers targeting CCR5
Raman Bahal, Nicole Ali McNeer, Danith H. Ly, W. Mark Saltzman, Peter M. Glazer, Artificial DNA: PNA & XNA 2013, 4, 49

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

Strand invasion of DNA quadruplexes by PNA: Comparison of homologous and complementary hybridization
Anisha Gupta, Ling-Ling Lee, Subhadeep Roy, Farial A. Tanious, W. David Wilson, Danith H. Ly, Bruce A. Armitage, ChemBioChem 2013, 14, 1476

Appointments

Years	Position
2018	Co-founded NeuBase Therapeutics
2018	Founding Director of Institute for Biomolecular Design and Discovery (IBD)
2017	Founded ChiraGen (subsequently merged with NeuBase Therapeutics)
2015–present	Professor of Chemistry, Carnegie Mellon University
2013–2015	HelixBind Scientific Advisory Board
2012–2014	Karuna Commune Enterprise Editorial Board
2009	Co-founded PNA Innovations (which subsequently became Vera Therapeutics)
2009	Founded Xpeutics
2009–2015	Associate Professor of Chemistry with tenure, Carnegie Mellon University
2008–present	Principle Investigator, Center for Nucleic Acids Science and Technology (CNAST)
2008–present	Principle Investigator, Molecular Biophysics and Structural Biology (MBSB), by courtesy
2008–2016	Principle Investigator, Head & Neck Cancer SPORE, by courtesy
2007–2009	Associate Professor of Chemistry, Carnegie Mellon University
2006–2020	Principle Investigator, Molecular Biosensor and Imaging Center (MBIC)
2001–2006	Assistant Professor of Chemistry, Carnegie Mellon University
1999–2001	Postdoctoral Fellow, The Scripps Research Institute
1998–1999	Postdoctoral Fellow, UC Berkeley

Awards and Distinctions

Years	Award
2012	Julius Ashkin Teaching Award, Mellon College of Science
2002	Innovative Research Award
2002	The Berkman Faculty Development Award
2000	Cosmetic Society for Chemists Aging Research Breakthrough of the Year
2000	National Institute of Aging Emerging Researcher