Carnegie Mellon University

Danith Ly

Danith Ly

Professor, Chemistry

  • Mellon Institute 841
  • 412-268-4010


1994–1998     Ph.D. in Chemistry, Georgia Institute of Technology


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

Research Problems

Our research program for the past seven years has been focused on the design and development of molecular tools and reagents to regulate gene expression and probe 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 fundamental questions pertaining to the cellular origins of cancer. More recently, we have expanded our research program into other areas including protein design, tissue engineering and molecular self-assembly—taking advantage of the strength of the department, which is interdisciplinary research, combined with our ability to synthesize molecules that integrate all three features of the natural biopolymers: nucleic acids, proteins, and carbohydrates.


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,

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.


2015–present Professor of Chemistry, Carnegie Mellon University
2007–2015 Associate Professor of Chemistry, Carnegie Mellon University
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

2012 Julius Ashkin Teaching Award, Mellon College of Science
2002 Innovative Research Award
2002 The Berkman Faculty Development Award
2000 Honorarium, Cosmetic Society for Chemists
2000 National Institute of Aging Emerging Researcher
1999-2001 American Chemical Society Irving Sigal Postdoctoral Fellowship
1996 House-Flashka-Ashby Award
1994 Albert Einstein Award in Astrophysics/Philosophy