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Publication List

At Florida Atlantic University (since 2017) (* = Corresponding Author)

43. 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",  ChemRxiv  https://doi.org/10.26434/chemrxiv-2023-c14qf,  2023. [ChemRxiv link]
42. 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. [JCTC link]
41. Taghavi, A., Baisden, J. R., Childs-Disney, J. L.,  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. [NAR link]
40. Wang, K. W., Riveros, I. 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. [Biophys J link]
39. Taghavi, A., Riveros, I. I., Wales, D. J., and  Yildirim, I.*, "Evaluating Geometric Definitions of Stacking for RNA Dinucleoside Monophosphates Using Molecular Mechanics Calculations",  J. Chem. Theory Comput.  18, 3637-3653,  2022. [JCTC link  |  Free PMC link]
38. 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. [Front Mol Biosci link]
37. 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. [Sci Transl Med link]
36. 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.  DOI: https://doi.org/10.1021/acschemneuro.1c00470,  2021. [ACS Chem Neurosci link]
35. 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.  DOI: https://doi.org/10.1021/acsmedchemlett.1c00027,  2021. [ACS Med Chem Lett link]
34. 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. [PNAS link]
33. 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. [ACS Chem Bio link]
32. 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. [Nat. Chem. link]
31. 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 Chemical Biology  DOI: https://doi.org/10.1016/j.chembiol.2020.10.007,  2020. [Cell Chem Bio link]
30. 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  DOI: https://doi.org/10.1002/cbic.202000445  2020. [ChemBioChem link]
29. 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. [PNAS link]
28. 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. [Springer link]
27. 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. [JPC B link]
26. 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. [Cell Chem Bio link]
25. Fujii, T., Thazhathveetil, A. K.,  Yildirim, I.*, Young, R. M., Wasielewski, M. R., Schatz, G. C., 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. [JPCB link]
24. Chen, J. L., VanEtten, D. M., Fountian, M. A.,  Yildirim, I.*, 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. [Biochemistry link]
23. 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. [JPCB link]

Postdoctoral Training at Northwestern University and University of Cambridge (2010-2016) (* = Corresponding Author)

22. 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. [Free JCTC link]
21. 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. [Science link]
20. Park, H., González, A. L.,  Yildirim, I., Tran, T., Lohman, J. R., Fang, P., Guo, M., and Disney, M. D., "Crystallographic and computational analyses of AUUCU  repeating RNA that causes spinocerebellar ataxia type 10 (SCA10)",  Biochemistry  54, 3851-3859,  2015. [Biochemistry link]
19. 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. [ Free JCTC link ]
18. 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. [ JPCB link ]
17. 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. [ Free JPCB link ]
16. 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. [ Free JPCB link  |  Free PMC link ]
15. Childs-Disney, J. L.,  Yildirim, I., 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. [ACS Chem. Biol. link  |  Free PMC link]
(News item for this paper at  http://biobeat.nigms.nih.gov/2014/01/targeting-toxic-rna-molecules-in-muscular-dystrophy )
14. 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. [  Org. Biomol. Chem. link  |  Free PMC link]
13. 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 . [ Nat. Commun. link  |  Free PMC link ]
12. 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 . [ JACS link  |  Free PMC link ]
11. Eryazici, I.,  Yildirim, I. , 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 . [  JACS link ]

Graduate Studies and Postdoctoral Training at University of Rochester (2003-2010)

10. 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 . [ Free Biochemistry link  |  Free PMC link ]
9.  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 . [ JCTC link  |  Free PMC link ]
8. 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 . [ JPCB link  |  Free PMC link ]
7. 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 . [ JCTC link  |  Free PMC link ]
6. 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 . [ JCTC link  |  Free PMC link ]
5. 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 . [ JCTC link  |  Free PMC link ]
4. 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 . [. [ Biochemistry link  |  Free PMC link ]
3. 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 . [ PNAS link  |  Free PMC link ]
2. 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 . [ JCB link  |  Free PMC link ]
1. Yildirim, I.  and Turner, D. H., “RNA challenges for computational chemists”,  Biochemistry  44, 13225-13234,  2005 .  [ Biochemistry link  |  Free PMC link ]

Conference proceeding and abstract papers

1. Yildirim, I., Park, H., Childs-Disney, J. L., Disney, M. D., Schatz, G. C., “Computational analyses of RNA repeat expansions causing genetic disease”,  Abstr. Papers Am. Chem. Soc.  247,  2014 . [ LINK ]
2. Condon, D. E., Tubbs, J. D., Yildirim, I., Mort, B. C., Kierzek, R., Kennedy, S. D., Turner, D. H., “Experimental benchmarks for RNA force fields”,  Abstr. Papers Am. Chem. Soc.  246,  2013 . [ LINK ]
3. Turner, D. H., Yildirim, I., Stern, H. A., Condon, D. E., Tubbs, J. D., Liu, B., Hart, J. M., Chen, J. L., Dela-Moss, I., Priore, S. F., Moss, W. N., Mathews, D. H., Kierzek, R., Kennedy, S. D., “Predicting RNA structure and stability”,  Abstr. Papers Am. Chem. Soc.  243,  2012 . [ LINK ]
4. Moss, W. N., Kennedy, S. D., Yildirim, I., Priore, S. F., Chen, J. L., Lerman, Y., Tubbs, J. D., Hart, J. M., Stern, H. A., Mathews, D. H., Kierzek, R., Kierzek, E., Turner, D. H., "RNA structure: Finding and folding",  Abstr. Papers Am. Chem. Soc.  242,  2011 . [ LINK ]

 

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