Danith Ly-The Center for Nucleic Acids Science and Technology - Carnegie Mellon University

Danith Ly

Professor of Chemistry

Phone: (412) 268-4010


Our research lies at the interface of chemistry and biology, with emphasis on the design and development of molecular tools and reagents and their application to addressing mechanistic questions in biology and treatment of genetic diseases. One aspect of our ongoing research is focused on the design and development of peptide nucleic acid (PNA) as a synthetic reagent for manipulating nucleic acid structures, regulating gene expression, and programming molecular self-assembly.


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 (download pdf)

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 (download pdf)

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 (download pdf)

Raman Bahal, Bichismita Sahu, Srinivas Rapireddy, Chong-Min Lee, and Danith H. Ly Sequence-Unrestricted, WatsonˆCrick Recognition of Double Helical B-DNA by (R)-MiniPEG-gammaPNAs. Chembiochem, 2012, 13, 56 ˆ 60. (download pdf)

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) (download pdf)

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 (download pdf)

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. (download pdf)

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 (download pdf)

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. (download pdf)

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. (download pdf)

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. (download pdf)