����Vlog

Research Interests

Theoretical and computational biophysical chemistry; developing new computational methods and models to study nucleic acids; drug design targeting RNA molecules causing genetic disease (such as Huntington Disease, Myotonic Dystrophy, and Fragile X-Syndrome); investigating properties of microRNA/AGO complex; force field development for modified RNA residues; interactions of transcription factors with DNA; DNA based nanomaterials.

Recent Publications

• Suresh, B. M., Li, W., Zhang, P., Wang, K. W., Yildirim, I., Parker C., and Disney, M. D., "A general fragment-based approach to identify and optimize bioactive ligands targeting RNA", Proc. Natl. Acad. Sci. U.S.A. DOI: https://doi.org/10.1073/pnas.2012217117, 2020.������

• Haniff, H. S., Knerr, L., Liu, X., Crynen, G., Boström, J., Abegg, D., Adibekian, A., Lekah, E., Wang, K. W., Cameron, M. D., Yildirim, I., Lemurell, M., and Disney, M. D., "Design of a small molecule that stimulates vascular endothelial growth factor A enabled by screening RNA fold–small molecule interactions", Nature Chemistry 12, 952–961, 2020.����

• Costales, M. G., Aikawa, H., Li, Y., Childs-Disney, J. L., Abegg, D., Hoch, D. G., Velagapudi, S. P., Nakai, Y., Khan, T., Wang, K. W., Yildirim, I., Adibekian, A., Wang, E. T., Disney, M. D., "Small-Molecule Targeted Recruitment of a Nuclease to Cleave an Oncogenic RNA in a Mouse Model of Metastatic Cancer", Proc. Natl. Acad. Sci. U.S.A. 117, 2406-2411, 2020.������

• ello, A. J., Benhamou, R. I., Rzuczek, S. G., Choudhary, S., Tang, Z., Chen, J. L., Roy, M., Wang, K. W., Yildirim, I., Jun, A. S., Thornton, C. A., and Disney, M. D., "A small molecule that binds an RNA repeat expansion stimulates its decay via the exosome complex", Cell Chemical Biology DOI: https://doi.org/10.1016/j.chembiol.2020.10.007, 2020.������

• Yildirim, I. "Improvement of RNA Simulations with Torsional Revisions of the AMBER Force Field", In: Bonomi M., Camilloni C. (eds) Biomolecular Simulations. Methods in Molecular Biology 2022, 55-74, (Humana, New York, NY) 2019.��������

• Wales, D. J., Disney, M. D., Yildirim, I. "Computational Investigation of RNA A-Bulges Related to Microtubule-Associated Protein Tau Causing Frontotemporal Dementia and Parkinsonism", J. Phys. Chem. B 123, 57-65, 2019.��������

• Alicia J. Angelbello, Wang, Z-F., Ursu, A., Childs-Disney, J. L., Guertler, R., Yang, W-Y., Bernat, V., Rzuczek, S. G., Fuerst, R., Zhang, Y-J., Gendron, T. F., Yildirim, I., Dwyer, B. G., Rice, J. E., Petrucelli, L., Disney, M. D., "The Hairpin Form of r(G4C2)exp in c9ALS/FTD Is Repeat-Associated Non-ATG Translated and a Target for Bioactive Small Molecules", Cell Chem. Biol. 26, 179-190, 2019.��������

• Wales, D. J., and Yildirim, I., "Improving Computational Predictions of Single-Stranded RNA Tetramers with Revised α/γ Torsional Parameters for the Amber Force Field", J. Phys. Chem. B 121, 2989-2999, 2017.��������

• Yildirim, I., Chakraborty, D., Disney, M. D., Wales, D. J., and Schatz, G. C., “Computational Investigation of RNA CUG repeats responsible for Myotonic Dystrophy 1”, J. Chem. Theory Comput. 11, 4943–4958, 2015.��������

• Philips, S. J., Hernandez, M. C., Yildirim, I., Schatz, G. C., Mondragón, A., O’Halloran, T. V., “Allosteric Transcriptional Regulation via Changes in the Overall Topology of the Core Promoter”, Science 349, 877-881, 2015.��������

• Yildirim, I., Kierzek, E., Kierzek, R., and Schatz, G. C., “Interplay of LNA and 2ʹ-O-methyl RNA in the structure and thermodynamics of RNA hybrid systems: A molecular dynamics study using revised AMBER force field and comparison to experimental results”, J. Phys. Chem. B 118, 14177–14187, 2014.��������

• Yildirim, I., Eryazici, I., Nguyen, S. T., Schatz, G. C., “Hydrophobic Organic Linkers in the Self-assembly of Small Molecule-DNA hybrid Dimers:�� A Computational-Experimental Study of the Role of Linkage Direction in Product Distributions and Stabilities”, J. Phys. Chem. B 118, 2366–2376, 2014.��������

• Childs-Disney, J. L., Stepniak-Konieczna E., Tran, T., Yildirim, I., Park, H., Chen., C. Z., Hoskins, J., Southall, N., Marugan, J. J., Patnaik, S., Zheng, W., Austin, C. P., Schatz, G. C., Sobczak, K., Thornton, C. A., Disney, M. D., “Induction and Reversal of Myotonic Dystrophy Type 1 Pre-mRNA Splicing Defects by Small Molecules”, Nat. Commun. 4, 2044, 2013.����

Other Information

Member, American Chemical Society