Publications & Scholarly Work

Tokmina-Roszyk, D., Singh, C., Chen, F., Anderson, M., Heinz, N., Warner, B., Winters, M. K., Shelley, B. T., Raagel, H., Smith, A. L., Clement, B. G., Jorgensen, M., Yildirim, I., Lauer, D. L., and Fields, G. B., "Heat Inactivation of Proteins: Implications for the Mars Sample Return Program", Int J. Astrobiology 24, 1-24, 2025.

Yildirim, I.*, Andralojc, W., Taghavi, A., Baranowski, D., Gdaniec, Z., Kierzek, R., and Kierzek, E., "Experimental and computational investigations of RNA duplexes containing N7-regioisomers of adenosine and LNA-adenosine", Nucleic Acids Res. gkae1222, 1-12, 2024.

Riveros, I. I. and Yildirim, I.*, "Prediction of 3D RNA Structures from Sequence Using Energy Landscapes of RNA Dimers: Application to RNA Tetraloops", J. Chem. Theory Comput. 20, 4363-4376, 2024.

Taghavi, A., Baisden, J., Yildirim, I.,* and Disney, M. D., "Conformational Dynamics of RNA G4C2 and C2G4 Repeat Expansions causing ALS/FTD using NMR and Molecular Dynamics Studies", Nucleic Acids Res. 51, 5325-5340, 2023.

Wang, K. W., Riveros, I., DeLoye, J., and Yildirim, I.,* "Dynamic Docking of Small Molecules Targeting RNA CUG Repeats Causing Myotonic Dystrophy Type 1 (DM1)", Biophys. J. 122, 180-196, 2023.

Taghavi, A., Riveros, I., Wales, D. J., and Yildirim, I.,* "Evaluation of geometrical definition of stacked/unstacked conformers in RNA dinucleotides using molecular mechanics calculations", J. Chem. Theory and Comput. 18, 3637-3653, 2022.

Taghavi, A. and Yildirim, I.,* "Computational investigation of bending properties of RNA AUUCU, CCUG, CAG and CUG repeat expansions associated with Neuromuscular disorders", Front. Mol. Biosci. 9, doi.org/10.3389/fmolb.2022.830161, 2022.

Bush, J. A., Aikawa, H., Fuerst, R., Li, Y., Ursu, A., Chen, J. L., Khan, T., Wagner-Griffin, S., Van Meter, M. J., Olafson, H., McKee, K. K., Childs-Disney, J. L., Gendron, T. F., Zhang, Y., Coyne, A. N., Wang, E. T., Yildirim, I., Wang, K. W., Petrucelli, L., Rothstein, J. D., Disney, M. D., "Ribonuclease recruitment using a small molecule reduced c9ALS/FTD r(G4C2) repeat expansion in vitro and in vivo ALS model", Sci. Transl. Med. 13, eabd5991, 2021.

Ursu, A., Baisden, J., Bush, J., Taghavi, A., Choudhary, S., Zhang, Y. J., Gendron, T., Petrucelli, L., Yildirim, I.*, and Disney, M. D., "A Small Molecule Exploits Hidden Structural Features within the RNA Repeat Expansion that Causes c9ALS/FTD and Rescues Pathological Hallmarks", ACS Chem. Neurosci., 2021.

Vezina-Dawod, S., Angelbello, A. J., Choudhary, S., Wang, K. W., Yildirim, I., and Disney, M. D., "Massively Parallel Optimization of the Linker Domain in Small Molecule Dimers Targeting a Toxic r(CUG) Repeat Expansion", ACS Med. Chem. Lett., 2021.

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. 117, 33197-33203, 2020.

Ursu, A., Wang, K. W., Bush, J. A., Choudhary, S., Chen, J. L., Baisden, J. T., Zhang, J. Z., Gendron, T. F., Petrucelli, L., Yildirim, I., and Disney, M. D., "Structural Features of Small Molecules Targeting the RNA Repeat Expansion That Causes Genetically Defined ALS/FTD", ACS Chem. Bio. 15, 3112-3123, 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.

Angelbello, 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 Chem. Biol. 25, 34-45.e6, 2020.

Benhamou, R. I., Vezina-Dawod, S., Choudhary, S., Wang, K. W., Meyer, S. M., Yildirim, I., and Disney, M. D., "Macrocyclization of a ligand targeting a toxic RNA dramatically improves potency", ChemBioChem 21, 3229-3233, 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., and 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.

Yildirim, I.* "Improvement of RNA Simulations with Torsional Revisions of the AMBER Force Field", invited chapter in Biomolecular Simulations. Methods in Molecular Biology 2022, 55-74, ed. by M. Bonomi and C. Camilloni, Humana, New York, NY, 2019.

Wales, D. J., Disney, M. D., and 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.

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. (doi.org/10.1016/j.chembiol.2018.10.018), 2018.

Fujii, T., Thazhathveetil, A. K., Yildirim, I.,* Young, R. M., Wasielewski, M. R., Schatz, G. C., and Lewis, F. D. "Structure and Dynamics of Electron Injection and Charge Recombination in i-Motif DNA Conjugates" J. Phys. Chem. B 121, 8058-8068, 2017.

Chen, J. L., VanEtten, D. M., Fountian, M. A., Yildirim, I.,* and Disney, M. D., "Structure and Dynamics of RNA Repeat Expansions That Cause Huntington's Disease and Myotonic Dystrophy Type 1" Biochemistry 56, 3463-3474, 2017.

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.

Park, H., González, A. L., Yildirim, I., Tran, T., Lohman, J. R., and Disney, M. D., "Crystallographic and computational analyses of AUUCU repeat RNA causing spinocerebellar ataxia type 10 (SCA10)", Biochemistry 54, 3851-3859, 2015.

Condon, D. E., Kennedy, S. D., Mort, B. C., Kierzek, R., Yildirim, I., and Turner, D. H., "Stacking in RNA: NMR of Four Tetramers Benchmark Molecular Dynamics", J. Chem. Theory Comput. 11, 2729-2742, 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.

Condon, D. E., Yildirim, I., Kennedy, S. D., Mort, B. C., Kierzek, R., Turner, D. H., "Optimization of an AMBER Force Field for the Artificial Nucleic Acid, LNA, and Benchmarking with NMR of L(CAAU)", J. Phys. Chem. B 118, 1216-1228, 2014.

Childs-Disney, J. L., Yildirim, I., 1 Park, H., Lohman, J., Guan, L., Tran, T., Sarkar, P., Schatz, G. C., Disney, M. D., "Structure of the Myotonic Dystrophy Type 2 RNA and Designed Small Molecules That Reduce Toxicity", ACS Chem. Biol. 9, 538-550, 2014.

Disney, M. D., Yildirim, I., and Child-Disney, J. L., "Methods to enable the design of bioactive small molecules targeting RNA", Org. Biomol. Chem. 12, 1029-1039, 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.

Yildirim, I.,* Park, H., Disney, M. D., Schatz, G. C., "A dynamic structural model of expanded r(CAG) repeats: A refined X-ray structure and computational investigations using molecular dynamics and umbrella sampling simulations", J. Am. Chem. Soc. 135, 3528−3538, 2013.

Eryazici, I., Yildirim, I., 1 Schatz, G. C., Nguyen, S. T., "Enhancing the melting properties of small molecule-DNA hybrids through designed hydrophobic interactions-an experimental-computational study", J. Am. Chem. Soc. 134, 7450-7458, 2012.

Chen, J. L., Dishler, A. L., Kennedy, S. D., Yildirim, I., Liu, B., Turner, D. H., and Serra, M. J., "Testing the nearest neighbor model for canonical RNA base pairs: Revision of GU parameters", Biochemistry 51, 3508-3522, 2012.

Yildirim, I., Kennedy, S. D., Stern, H. A., Hart, J. M., Kierzek, R., and Turner, D. H., "Revision of AMBER torsional parameters for RNA improves free energy predictions for tetramer duplexes with GC and iGiC base pairs", J. Chem. Theory Comput. 8, 172-181, 2012.

Yildirim, I., Stern, H. A., Kennedy, S. D., Tubbs, J. D., and Turner, D. H., "Benchmarking AMBER force fields for RNA: Comparisons to NMR spectra for single-stranded r(GACC) are improved by revised χ torsions", J. Phys. Chem. B 115, 9261-9270, 2011.

Yildirim, I., Stern, H. A., Kennedy, S. D., Tubbs, J. D., and Turner, D. H., "Re-parameterization of RNA χ torsion parameters for the AMBER force field and comparison to NMR spectra for cytidine and uridine", J. Chem. Theory and Comput. 6, 1520-1531, 2010.

Reblova, K., Strelcova, Z., Kulhanek, P., Besseova, I., Mathews, D. H., Van Nostrand, K., Yildirim, I., Turner, D. H., and Sponer, J., "An RNA molecular switch: Intrinsic flexibility of 23S rRNA helices 40 and 68 5'-UAA/5'-GAN internal loops studied by Molecular Dynamics methods", J. Chem. Theory and Comput. 6, 910-929, 2010.

Yildirim, I., Stern, H. A., Sponer, J., Spackova, N., and Turner, D. H., "Effects of restrained sampling space and non-planar amino groups on free energy predictions for RNA with imino and sheared tandem GA base pairs flanked by GC, CG, iGiC or iCiG base pairs", J. Chem. Theory Comput. 5, 2088-2100, 2009.

Kierzek, E., Pasternak, A., Pasternak, K., Gdaniec, Z., Yildirim, I., Turner, D. H., and Kierzek, R., "The contribution of stacking and hydrogen bonding to the thermodynamic stability of duplexes between RNA and 2'-O-methyl RNA with Locked Nucleic Acids (LNA)" Biochemistry 48, 4377-4387, 2009.

Ensign, A. A., Jo, I., Yildirim, I., Krauss, T. D., and Bren, K. L., "Zinc porphyrin: A fluorescent acceptor in studies of Zn-cytochrome c unfolding by fluorescence resonance energy transfer", Proc. Natl. Acad. Sci. U.S.A. 105, 10779-10784, 2008.

Chen, G., Kierzek, R., Yildirim, I., Krugh, T. R., Turner, D. H., and Kennedy, S. D., "Stacking effects on local structure in RNA: The structure of tandem GA pairs changes when flanking GC pairs are replaced by isoG-isoC pairs", J. Phys. Chem. B 111, 6718-6727, 2007.

Yildirim, I. and Turner, D. H., "RNA challenges for computational chemists", Biochemistry 44, 13225-13234, 2005.