Soumitra Basu
Biography
Dr. Basu received his PhD from Sidney Kimmel Cancer Center in Philadelphia in Prof Eric Wickstrom’s lab. He did his post-doctoral research in Prof Scott Strobel’s lab at Yale University’s Molecular Biophysics and Biochemistry department. Following which Dr. Basu joined as an assistant professor at University of Pittsburgh’s Center for Pharmacogenetics. In 2005 Dr. Basu moved to Kent State University’s department of Chemistry and Biochemistry. In 2013 Dr. Basu obtained an MBA just for fun!
Research
One of the major goals of the Basu lab is to understand structure-function relationship of nucleic acids, that adopt non-canonical structures. Of particular interest is studying a secondary non-canonical structure known as a G-quadruplex (GQ) that both DNA and RNA sequences rich in guanosine residues can adopt. The lab is interested in learning the role of such structures in regulation of fundamental cellular processes and strives to utilize such knowledge for development of therapeutics. Recently, we have expanded our interests to how CRSPR/Cas9 function is affected when placed in the vicinity of GQ structures and understanding of the role of RNA oxidation in various neurological disorders, especially multiple sclerosis and Parkinson’s disease as it relates to mitochondrial energy production. Finally, we study the “Ping-Pong” cycle, a secondary biogenesis pathway for piRNAs. Overall, we want to contribute to the understanding and appreciation of the amazing versatility of RNA as a class of molecule.
Overall goal of my laboratory is to understand structure-function relationship of nucleic acids, which primarily adopt non-canonical structures. We are interested in learning the role of such structures in regulation of fundamental cellular processes, and utilize such molecules for therapeutic purposes.
We are particularly interested in studying a structural form known as G-quadruplex that both DNA and RNA sequences rich in guanosine residues can adopt. We intend to learn how the DNA G-quadruplexes regulate transcription and how the RNA G-quardruplexes can control translation. We will utilize biochemical and biophysical along with molecular biology and cell biology techniques to achieve these objectives.
Education
Post-doctoral Fellow, Yale University
Expertise
Biochemistry
Publications
- “Decay of piwi interacting RNAs in human cells is primarily mediated by 5' to 3' exoribonucleases”, Balaratnam, S, Hoque, E.H., West, N. and S. Basu,*, ACS Chemical Biology, 2022, cb-2022-00007f.
- “Rationally designed DNA therapeutics can modulate human TH expression by controlling specific GQ formation in its promoter”, Beals, N., Farhath, M.M., Kharel, P., Mahendran, T., Johnson, J. and Basu, S., 2021, Molecular Therapy, DOI:https://doi.org/10.10
- “Encounters between Cas9/dCas9 and G-Quadruplexes: Implications for Transcription Regulation and Cas9-Mediated DNA Cleavage”, Enamul, M.H., Mustafa, G., Basu, S.*, and Balci, H.*, ACS Synth. Biol. 2021, 10, 5, 972–97, https://doi.org/10.1021/acssynbio.1c0
- “A Physico-chemical Investigation into Major League Baseballs in the Era of Unprecedented Rise in Home Runs”, Beals, N., Zhang, L., Law, M., Hwang, D., Acharya, J. and Basu, S.*, 2019, ACS Omega, 2019, 4, 23, 20109. Featured in C&EN: https://cen.acs.org/
- “A piRNA utilizes HILI and HIWI2 mediated pathway to down regulate ferritin heavy chain 1 mRNA in human somatic cells” Balaratnam, S, West, N. and Basu, S.* Nucleic Acids Res., 2018, 10.1093/nar/gky728.
- “Intermolecular G-Quadruplex Induces Hyaluronic Acid–DNA Superpolymers Causing Cancer Cell Swelling, Blebbing, and Death”, Beals, N., Model, M.A., Worden, M., Hegmann, T., and Basu, S.*, ACS Appl. Mater. Interfaces, 2018, 10, 6869–6878
- “Metal Cations in G-Quadruplex Folding and Stability”, Bhattacharyya, D., Arachchilage, G. and Basu, S*, Front Chem. (2016), 4: 38, doi: 10.3389/fchem.2016.00038 (Peer-reviewed Review)
- “Human post-mortem multiple sclerosis brain shows extensive RNA damage”, Kharel, P., McDonough, J. and Basu, S.*, (2015), Neurochem Int., DOI 10.1016/j.neuint.2015.12.002.
- “An independently folding RNA G-quadruplex domain directly recruits 40S ribosomal subunit”, (2014), Bhattacharyya, D., Diamond, P., and Basu, S.* (2015), Biochemistry (accelerated publication), 10.1021/acs.biochem.5b00091.
- “A potassium ion dependent RNA structural switch regulates human pre-miRNA 92b maturation”, Mirihana Arachchilage, G., Dassanayake, A, and Basu, S.* (2015), Chemistry & Biology (Currently known as Cell Chemical Biology, Cell Press) , 22, 2, 262–272.
- "A library screening approach identifies naturally occurring RNA sequences for a G-quadruplex binding ligand", Arachchilage, G. M., Morris, M.J. and Basu, S.* (2013), Chem. Commun., DOI: 10.1039/C3CC47381C.
- "The porphyrin TmPyP4 unfolds the extremely stable G-quadruplex in MT3-MMP mRNA and alleviates its repressive effect to enhance translation in eukaryotic cells", Morris, M. J., Wingate, K. L., Silwal, J., Leeper, T C., and Basu, S.* (2012), Nucleic Acids
- "An RNA G-Quadruplex Is essential for cap-independent translation initiation in human VEGF IRES" Morris, M.J., Negishi, Y., Pazsint, C., Schonhoft, J.D. and Basu, S.* (2010), J. Am. Chem. Soc., 132, 17831–17839.
- "An unusually stable G-quadruplex within 5'-UTR of the MT3 matrix metalloproteinase mRNA represses translation in eukaryotic cells", Morris, M.J. and Basu, S.* (2009), Biochemistry, 48, 5313-5319.
- "Direct Experimental Evidence for Quadruplex-Quadruplex Interaction within the Human ILPR", Schonhoft, J.D., Bajracharya, R., Dhakal, S., Zhongbo, Y., Mao, H.* and Basu, S.* (2009), Nucleic Acids Res. 37, 3310-3320.
- "ILPR G-Quadruplexes Formed in Seconds Demonstrate High Mechanical Stabilities" Zhongbo, Y., Schonhoft, J.D., Dhakal, S., Bajracharya, R., Hegde, R., Basu, S.* and Mao, H.* (2009), J. Am. Chem. Soc., 131, 1876-1882.
- "Direct detection of specific monovalent metal ion binding to a DNA G-quartet by Tl-205 NMR". Basu, S., Szewczak, A, Cocco, M, and Strobel, S.A., (2000), J. Am. Chem. Soc.,122, 3240-3241.
- "A specific monovalent metal ion integral to the A-A platform of the RNA tetraloop receptor". Basu, S., Rambo, R. P., Cate, J. H., Ferré-D´Amarre, A R., Strobel, S. A. and Doudna, J. A. (1998), Nature Structural Biology, 5, 986-992.