Carnegie Mellon University Department of Chemistry
photo of Subha R. Das

Subha R. Das

Associate Professor

Carnegie Mellon University

email:

Phone: (412) 268-6871

Fax: (412) 268-1061

Office: Mellon Institute 740A

Faculty & Research

Subha R. Das

Associate Professor

Research Areas

Organic Synthesis, Nucleic Acids Chemistry, RNA Biochemistry, RNA-Protein Recognition, Nanotechnology

Nucleic Acids Chemistry – Labelling and Ligations

We have recently introduced "click-chemistry" for labeling or ligating RNA. Any RNA – not just synthetic RNA – can be labeled with another molecule or ligated to another RNA for the detection, handling or delivery or RNA. This powerful chemical tools enables a number of projects. One current project in this area seeks to label cellular RNA with different markers through which altered states or transport of the RNAs due to different environmental or epigenetic factors can be investigated.

Backbone Branched RNAs

The process of splicing generates the correct messenger RNA for the cellular synthesis of proteins by removing non-coding intron sequences as 'lariats'. These lariat RNAs have a branched structure and have been long desired in order to investigate splicing and related processes. We have accomplished the synthesis of backbone branched RNAs and these provide a unique opportunity to investigate splicing and related processes such as debranching through biochemical assays and biophysical methods such as single-molecule spectroscopy.

Nucleic Acids Nano-bio-technology

Backbone branched DNA provides a simple and powerful avenue to engineer precisely the angles between DNA helices in self-assembled DNA nanostructures. We are exploring the design and construction of nanoscale DNA objects that have been inaccessible by traditional DNA nanotechnologies. Our ability to synthesize and functionalize DNA provides additional opportunities to enhance the function of these objects by incorporating metal or polymer nanoparticles or biomolecules. Polymer DNA hybrids synergistically capitalize on the power of polymeric materials with the tunable hybridization and reversible assembly properties of DNA.

Science Education and Communication

The Kitchen Chemistry Sessions course uses food and molecular cuisine to teach the concepts of chemistry and science. The use of food ingredients and their preparation in laboratory settings are based on the molecular properties. Modules based on water, fats/oils and lipids, carbohydrates, proteins and aroma volatiles and flavor compounds provide a context to highlight how chemical and scientific principles permeate students’ everyday life chemical concepts to a wide audience – from K-12 to non-science majors. Science majors are engaged with the cooking focus that serves to reinforce, re-organize, and extend students’ knowledge of chemistry and biochemistry. The food context also provides a significant opportunity to communicate and promote science concepts to the public. See Chemistry in the Kitchen (Pittsburgh Post-Gazette, Nov 4, 2010) and Carnegie Mellon's Kitchen Chemistry Course Makes Science Palatable (University Press Release, March 25, 2010) for more information.

Education and Appointments
2012–present Associate Professor of Chemistry, Carnegie Mellon University
2006–2012 Assistant Professor of Chemistry, Carnegie Mellon University
2000–2006 Postdoctoral Research Associate, Howard Hughes Medical Institute, The University of Chicago
2000 Ph.D., Auburn University
Selected Publications

Averick, S. E.; Dey, S. K.; Grahacharya, D.; Matyjaszewski, K.; Das, S. R. Solid Phase Incorporation of an ATRP Initiator for Polymer-DNA Biohybrids Angewandte Chemie Intl Ed.  2014, 53, 2739 – 2744
doi: 10.1002/anie.201308686

Averick, S. E.; Paredes, E.; Dey, S. K.; Snyder, K. M.; Tapinos, N.; Matyjaszewski, K.; Das, S. R. Auto-transfecting siRNA through Facile Covalent Polymer Escorts. J Am Chem Soc 2013, 135, 12508–12511
doi: 10.1021/ja404520j

Das, S. R. The Kitchen Chemistry Sessions : Palatable Chemistry through Molecular Gastronomy and Cuisine. In Using Food to Stimulate Interest in the Chemistry Classroom; Symox, K., Ed.; American Chemical Society: Washington, DC, 2013.
doi: 10.1021/bk-2013-1130.ch007

Paredes, E.; Das, S. R. RNA Conjugations and Ligations for RNA Nanotechnology. In RNA Nanotechnology and Therapeutics; Guo, P.; Haque, F., Eds.; CRC Press, 2013; pp. 197–211.

Cho, H. Y.; Averick, S. E.; Paredes, E.; Wegner, K.; Averick, A.; Jurga, S.; Das, S. R.; Matyjaszewski, K. Star Polymers with a Cationic Core Prepared by ATRP for Cellular Nucleic Acids Delivery. Biomacromolecules 2013, 14, 1262–1267.
doi: 10.1021/bm4003199

Paredes, E.; Zhang, X.; Ghodke, H.; Yadavalli, V. K.; Das, S. R. Backbone-Branched DNA Building Blocks for Facile Angular Control in Nanostructures. ACS Nano 2013, 7, 3953–3961.
doi: 10.1021/nn305787m

Dey, S. K.; Paredes, E.; Evans, M.; Das, S. R. The Diverse Active Sites in Splicing, Debranching, and MicroRNA Processing Around RNA Phosphodiester Bonds. In From Nucleic Acids Sequences to Molecular Medicine; Erdmann, V. A.; Barciszewski, J., Eds.; Springer Berlin Heidelberg: Berlin, Heidelberg, 2012; pp. 475–501.
doi: 10.1007/978-3-642-27426-8

Averick, S. E.; Paredes, E.; Grahacharya, D.; Woodman, B. F.; Miyake-Stoner, S. J.; Mehl, R. A.; Matyjaszewski, K.; Das, S. R. A Protein-Polymer Hybrid Mediated By DNA. Langmuir  2012, 28, 1954-1958
doi: 10.1021/la204077v

Averick, S. E.; Paredes, E.; Irastorza, A.; Shrivats, A. R.; Srinivasan, A.; Siegwart, D. J.; Magenau, A. J.; Cho, H. Y.; Hsu, E.; Averick, A. A.; Kim, J.; Liu, S. G.; Hollinger, J. O.; Das, S. R.; Matyjaszewski, K. Preparation of Cationic Nanogels for Nucleic Acid Delivery. Biomacromolecules 2012, 13, 3445–3449.
doi: 10.1021/bm301166s

Paredes, E.; Das, S. R. Optimization of acetonitrile co-solvent and copper stoichiometry for pseudo-ligandless click chemistry with nucleic acids. Bioorganic & Medicinal Chemistry Letters 2012, 22, 5313–5316.
doi: 10.1016/j.bmcl.2012.06.027

Paredes, E.; Das, S. R. Click Chemistry for Rapid Labeling and Ligation of RNA. ChemBioChem 2011, 12, 125–131.
doi: 10.1002/cbic.201000466

Averick, S.; Paredes, E.; Li, W.; Matyjaszewski, K.; Das, S. R. Direct DNA conjugation to star polymers for controlled reversible assemblies. Bioconjugate chemistry 2011, 22, 2030–2037.
doi: 10.1021/bc200240q

Paredes, E.; Evans, M.; Das, S. R. RNA labeling, conjugation and ligation. Methods 2011, 54, 251–259.
doi: 10.1016/j.ymeth.2011.02.008