Carnegie Mellon University
Phone: (412) 268-6871
Fax: (412) 268-1061
Office: Mellon Institute 740A
Organic Synthesis, Nucleic Acids Chemistry, RNA Biochemistry, RNA-Protein Recognition, Nanotechnology
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.
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.
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.
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.
|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|
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
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
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.
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.
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.
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.
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
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.
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.
Paredes, E.; Das, S. R. Click Chemistry for Rapid Labeling and Ligation of RNA. ChemBioChem 2011, 12, 125–131.
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.
Paredes, E.; Evans, M.; Das, S. R. RNA labeling, conjugation and ligation. Methods 2011, 54, 251–259.