Research from our lab has been published in peer-reviewed scientific journals and books

(lab personnel are underlined)





34. Jordan Hartung, Nathan McCann, Erwin Doe, Hannah Hayth,

Kheiria Benkato, M. Brittany Johnson, Mathias Viard, Kirill Afonin*, and Emil F. Khisamutdinov*. Toehold-Mediated Shape Transition of Nucleic Acid Nanoparticles, ACS applied Materials and Interfaces 2023, doi:


33. Erwin Doe, Hannah Hayth, Ross Brummett

and Emil F. Khisamutdinov*. Effective, Rapid, and Small-scale Bioconjugation and Purification of “Clicked” Small Molecule-DNA oligonucleotides for Nucleic Acid Nanoparticles Functionalization, IJMS, 2023, 24(5), 4797




ACS nano

32. Morgan Chandler, Brittany Johnson, Emil Khisamutdinov, Marina A. Dobrovolskaia, Joanna Sztuba-Solinska, Aliasger K. Salem, Koen Breyne, Roger Chammas, Nils G. Walter, Lydia M. Contreras, Peixuan Guo*, Kirill A. Afonin*. The International Society of RNA Nanotechnology and Nanomedicine (ISRNN): The Present and Future of the Burgeoning Field, ACS Nano, 2021, 15 (11) 16957-16973.


31. Emil F. Khisamutdinov*, Blake A. Sweeney, and Neocles B. Leontis. Context-sensitivity of Isosteric Substitutions of non-Watson-Crick Basepairs in Recurrent RNA 3D Motifs., Nucleic Acids Res, 2021 49, 9574-9593.


2130. M Brittany Johnson,Justin R Halman, Daniel K Miller, Joseph S. Cooper, Emil F. Khisamutdinov, Ian Marriott. and Kirill A. Afonin*. The immunorecognition, subcellular compartmentalization, and physicochemical properties of nucleic acid nanoparticles can be controlled by composition modification. Nucleic Acids Res, 2020 48, 11785-11798.


29. M Brittany Johnson, Justin R Halman, Amanda R Burmeister, Saralynn Currin, Emil F Khisamutdinov, Kirill A Afonin, Ian Marriott*. Retinoic acid inducible gene-I mediated detection of bacterial nucleic acids in human microglial cells. J Neuroinflammation, 2020, 17, 139.



28. Jake K. Durbin, Daniel K. Miller, Julia Niekamp, and Emil F. Khisamutdinov*.Modulating Immune Response with Nucleic Acid Nanoparticles”. Molecules, 2019, 24(20), p E3740 (doi: 10.3390/molecules24203740).



27. Weina Ke, Enping Hong, Renata Saito, Maria Cristina Rangel, Jian Wang, Mathias Viard, Melina Richardson, Emil Khisamutdinov, Martin Panigaj, Nikolay Dokholyan, Roger Chammas, Marina Dobrovolskaia*, Kirill A. Afonin*. “RNA–DNA fibers and polygons with controlled immunorecognition activate RNAi, FRET, and transcriptional regulation of NF-κB in human cells”. Nucleic Acids Res. 2019, Feb 20;47(3):1350-1361. (doi: 10.1093/nar/gky1215.)


26. Tori Goldsworthy, Geneva La’Force, Seth Abels, and Emil F. Khisamutdinov*. “Fluorogenic RNA Aptamers: a Nano-platform for Fabrication of Simple and Combinatorial Logic Gates”. Nanomaterials. 2018, 8(12). pii: E984. (doi: 10.3390/nano812098)




25. Rabah N. Alsulami, Darya S. Budkina, Larry Sallans, Emil F. Khisamutdinov, U. Pandey, Ksenija Glusac, Alexander N. Tarnovsky and R. Marshall Wilson*. Oxidation of Nucleic Acids: Chemistry of Pyrene Quinone (PQ1) and Development of Dihydrodioxins (DHD 2) as DNA Photooxidizing.  Journal of Photochemistry and Photobiology A: Chemistry. 2018 (





24. Enping Hong, Justin R. Halman, A. B. Shah, Emil F. Khisamutdinov, Marina A. Dobrovolskaia* and Kirill A. Afonin*, Structure and Composition Define Immunorecognition of Nucleic Acid Nanoparticles. Nano letters. 2018, 18, pp.4309-432






23. M. Brittany Johnson, Justin R. Halman, Emily Satterwhite, Alexey V. Zakharov, My N. Bui, Kheiria Benkato, Victoria Goldsworthy, Taejin Kim, Enping Hong, Marina A. Dobrovolskaia, Emil F. Khisamutdinov*, Ian Marriott*, Kirill A. Afonin*. Programmable Nucleic Acid-based Polygons with Controlled Neuroimmunomodulatory Properties for Predictive QSAR Modeling. Small. 2017, 13(42); (doi: 10.1002/smll.201701255)


22. My N. Bui, Brittany M Johnson, Mathew Viard, Emily Satterwhite, Angelica N. Martins, Zhihai Li, Ian Marriott, Kirill Afonin, Emil F. Khisamutdinov*. Versatile RNA tetra-U helix linking motif as a toolkit for nucleic acid nanotechnology, Nanomedicine. 2017, 13 (3), pp. 1549-9634 (doi: 10.1016/j.nano.2016.12.018)



21. Justin R. Halman, Emily Satterwhite, Brandon Roark, Morganl Chandler, Mathias Viard, Anna Ivanina, Eckart Bindewald, Wojciech Kasprzak, Martin Panigaj, My N. Bui, Jacob S. Lu, Johann Miller, Emil F. Khisamutdinov, Bruce A. Shapiro, Marina A. Dobrovolskaia,  Kirill A. Afonin*. Functionally-interdependent shape-switching nanoparticles with controllable properties. Nucleic Acids Res. 2017 45(4), pp. 2210-2220. (doi: 10.1093/nar/gkx008).





20. Morgan Chandler, Justin R. Halman, and Emil F. Khisamutdinov*.  Activation of Multiple Functionalities through Interacting Nanoparticles. Vision Paper in DNA and RNA Nanotechnology 2017; 4: 24–26.



19. Emil F. Khisamutdinov, Daniel L. Jasinski, Hui Li, Kaiming Zhang, Wah Chiu, and Peixuan Guo*. Fabrication of RNA 3D Nanoprism for Loading and Protection of Small RNAs and Model Drugs. Adv Mater. 2016, 28(45) pp. 10079-10087. (doi: 10.1002/adma.201603180)




18. Daniel W. Binzel, Emil F. Khisamutdinov, Mario Vieweger, Janice Ortega, Jingyuan Li, and Peixuan Guo*. Mechanism of Three-Component Collision to Produce Ultra Stable pRNA-3WJ of Phi29 DNA Packaging Motor by Kinetic assessment. RNA, 2016, 22(11) pp.1710-1718


17. Seth G. Abels and Emil F. Khisamutdinov*. Nucleic Acid Computing and its Potential to Transform Silicon-Based Technology. DNA and RNA nanotechnology journal 2015, 2(1) pp. 13-22 (DOI: 10.1515/rnan-2015-0003)





Book Chapters:

16. Megan Teter, Ross Brumett, Abigail Coffman, and Emil F. Khisamutdinov*. Thermodynamic Characterization of Nucleic Acid Nanoparticles Hybridization by UV Melting, In Methods in Molecular Biology. Edited by K. Afonin, Springer 2022, In print

15. Erwin Doe, Hannah Hayth, and Emil F. Khisamutdinov* Bioconjugation of Functionalized Oligodeoxynucleotides with Fluorescence Reporters for Nanoparticle Assembly, In Methods in Molecular Biology. Edited by K. Afonin, Springer 2022, In print

14. Daniel K Miller and Emil Khisamutdinov*. “Physicochemical Characterization of Nucleic Acid Nanoparticles.” In RNA Nanotechnology and Therapeutics,  2ndEdition, Edited by P. Guo and K. Afonin, CRC press 2021, 21 (ISBN: 978-1-78326-926-6)

13. Trinity Jackson, Rachel Fitzgerald, Daniel K. Miller, and Emil F. Khisamutdinov* “Development of Logic Gate Nanodevices from Fluorogenic RNA Aptamers.” In DNA and RNA-Based Computing Systems. Edited by Evgeniy Katz, Wiley-VCH 2021, Chapt. 5. pp57-76. (doi: 10.1002/9783527825424)

12. Kheiria Benkato, Ben O’Brien, My N. Bui, Daniel Jasinski, Peixuan Guo,  and Emil F. Khisamutdinov*. Evaluation of Thermal Stability of RNA Nanoparticles by Temperature Gradient Gel Electrophoresis (TGGE) in Native Condition. In Methods in Molecular Biology. Edited by Eckart Bindewald and Bruce Shapiro, Springer, 2017, Vol: 1632; pp 123-133. (doi: 10.1007/978-1-4939-7138-1_8)

11. Emil F. Khisamutdinov*, My N. Bui, Daniel Jasinski, Zhengyi Zhao, Zheng Cui, Peixuan Guo. Simple Method for Constructing RNA Triangle, Square, Pentagon by Tuning Interior RNA 3WJ Angle from 60° to 90° or 108°. In RNA Scaffolds: Methods and Protocols, Methods in Molecular Biology edited by L. Ponchon. Springer, 2015, Vol: 1316; pp181-193. (doi: 10.1007/978-1-4939-2730-2_15).

10. Taek Lee, Seth Abels, Emil Khisamutdinov, Meikang Qiu, Daniel L. Jasinski, Zhengyi Zhao, Tao Qu, Jeong-Woo Choi, and Peixuan Guo*. Conceptual, Potential and Advance in Computer Design and in vivo Computation Applying RNA Nanotechnology. In Molecular Nanostructure and Nanotechnology edited by Chunli Bai and Chen Wang, World Scientific, 2015, Chapt. 8 (ISBN: 978-1-78326-926-6).

Prior to Ball State
9. Emil F. Khisamutdinov, Alexey E. Shamaev, Philip A. Boda, Kanikey Karabaeva, Andrey Mereshenko, Alexander N. Tarnovsky, Neocles B. Leontis, R. Marshall Wilson*. A Pyrene Dihydrodioxin with Pyridinium “Arms”: A Photochemically Activatable DNA Cleaving Agent with Unusual Duplex Stabilizing Properties. Journal of Photochemistry and Photobiology A: Chemistry, 2015, Vol: 307-308, pp 131-146. (doi:10.1016/j.jphotochem.2015.03.017).

8. Emil F. Khisamutdinov, Hui Li, Daniel L. Jasinski, Jiao Chen, Jian Fu, and Peixuan Guo*. Enhancing Immunomodulation on Innate Immunity by Shape Transition Among RNA Triangle, Square, and Pentagon Nanovehicles. Nucleic Acids Res, 2014, 42(15):9996-10004. (doi: 10.1093/nar/gku516)

7. Emil F. Khisamutdinov, Daniel L. Jasinski, and Peixuan Guo*. RNA as a Boiling-Resistant Anionic Polymer Material To Build Robust Structures with Defined Shape and Stoichiometry. ACS Nano, 2014, 8 (5), pp 4771–4781. (doi: 10.1021/nn5006254) (editor’s choice)

6. Daniel Binzel, Emil F. Khisamutdinov, and Peixuan Guo*. Entropy-driven one-step formation of Phi29 pRNA 3WJ from three RNA fragments. Biochemistry, 2014, 53 (14), pp 2221–2231. (doi: 10.1021/bi4017022)

5. Daniel L. Jasinski, Emil F. Khisamutdinov, and Peixuan Guo*. Physicochemically Tunable Polyfunctionalized RNA Square Architecture with Fluorogenic and Ribozymatic Properties Properties.  ACS Nano, 2014, 8 (8), pp 7620–7629. (DOI: 10.1021/nn502160s)

4. Zhao Zhengyi, Emil F. Khisamutdinov, Chad Schwartz, and Peixuan Guo*. Mechanism of One-Way Traffic of Hexameric Phi29 DNA Packaging Motor with Four Electropositive Relaying Layers Facilitating Antiparallel Revolution. ACS Nano. 2013, 28;7(5), pp 4082-4092. (doi: 10.1021/nn4002775)

3. Dan Shu, Emil F. Khisamutdinov, Le Zhang, and Peixuan Guo*. Programmable folding of fusion RNA in vivo and in vitro driven by pRNA 3WJ motif of phi29 DNA packaging motor. Nucleic Acid Research 2013.  (doi: 10.1093/nar/gkt885)

Book Chapters:

2. Meikang Qiu, Emil F. Khisamutdinov, Zhengyi Zhao, Cheryl Pan, Jeong-Woo Choi, Neocles B. Leontis, Peixuan Guo*. RNA nanotechnology for computer design and in vivo computation.  Phil. Trans. R. Soc. A 2013 , 371: 1471-2962. (doi: 10.1098/rsta.2012.0310).

1. Neocles B. Leontis* and Emil F. Khisamutdinov. RNA Nanotechnology: Learning from Biologically active RNA Nano-machines. In “RNA Nanotechnology and Therapeutics” edited by P. Guo and F. Haque. CRC press, Taylor and Francis Group, 2013, Chapter #4; 73-108.