# Kirill A. Afonin
**Kirill A. Afonin** is a scientist working in RNA nanotechnology and nucleic acid-based drug delivery, and a professor of chemistry at the [University of North Carolina at Charlotte](https://www.edgepedia.org/university-of-north-carolina-at-charlotte) (UNC Charlotte).[1](https://chemistry.charlotte.edu/directory/kirill-afonin-phd/) His laboratory programs nucleic acid nanoparticles (NANPs), self-assembling structures built from RNA, DNA, or RNA–DNA hybrids, for biomedical uses ranging from programmable gene silencing to immune modulation.[1](https://chemistry.charlotte.edu/directory/kirill-afonin-phd/)
| Fact | Detail |
|---|---|
| Field | RNA nanotechnology and nucleic acid nanoparticles for drug delivery[1](https://chemistry.charlotte.edu/directory/kirill-afonin-phd/) |
| Position | Professor of Chemistry, UNC Charlotte (full professor since 2021)[1](https://chemistry.charlotte.edu/directory/kirill-afonin-phd/) |
| Training | M.S., Saint Petersburg State University; Ph.D. in Photochemistry, Bowling Green State University, 2008, under Prof. Neocles Leontis[1](https://chemistry.charlotte.edu/directory/kirill-afonin-phd/) • [4](http://pubs.acs.org/achre4/article/47/6/1731/1248005/In-Silico-Design-and-Enzymatic-Synthesis-of) |
| Signature work | "In vitro assembly of cubic RNA-based scaffolds designed in silico", Nature Nanotechnology, 2010[2](https://doi.org/10.1038/nnano.2010.160) |
| Major funding | NIH MIRA R35GM139587 (NIGMS), 02/01/2021 to 01/31/2027[5](https://taggs.hhs.gov/Detail/AwardDetail?arg_AwardNum=R35GM139587&arg_ProgOfficeCode=127) |
| Patents | 10 patents since joining UNC Charlotte in 2015[6](https://science.charlotte.edu/2025/05/05/kirill-afonin-receives-de-silva-graduate-mentor-award/) |
| Lab output | Over 100 publications and more than $4.7 million in external funding in just over eight years at UNC Charlotte[6](https://science.charlotte.edu/2025/05/05/kirill-afonin-receives-de-silva-graduate-mentor-award/) |
## Education and career
Afonin graduated from [Saint Petersburg State University](https://www.edgepedia.org/saint-petersburg-state-university) with an M.S. in Chemistry and earned a Ph.D. in [Photochemistry](https://www.edgepedia.org/photochemistry) from [Bowling Green State University](https://www.edgepedia.org/bowling-green-state-university) in Ohio in 2008, under the guidance of Prof. Leontis.[1](https://chemistry.charlotte.edu/directory/kirill-afonin-phd/) • [4](http://pubs.acs.org/achre4/article/47/6/1731/1248005/In-Silico-Design-and-Enzymatic-Synthesis-of) His doctoral training also included a graduate certificate in bioinformatics, proteomics, and genomics completed in a joint program with the Medical University of Ohio and the University of Toledo.[6](https://science.charlotte.edu/2025/05/05/kirill-afonin-receives-de-silva-graduate-mentor-award/)
In 2011 he was invited as a Research Fellow to the [National Cancer Institute](https://www.edgepedia.org/national-cancer-institute) at the NIH, where he established and managed an experimental branch within the Computational RNA Structure Group.[1](https://chemistry.charlotte.edu/directory/kirill-afonin-phd/) His papers from that period carry affiliations at the Center for Cancer Research in [Frederick, Maryland](https://www.edgepedia.org/frederick-maryland).[7](https://pmc.ncbi.nlm.nih.gov/articles/PMC4189619/) He started his tenure-track appointment at UNC Charlotte in 2015, was promoted with permanent tenure to Associate Professor in 2019, and to full Professor in 2021.[1](https://chemistry.charlotte.edu/directory/kirill-afonin-phd/) He is a founding council member and vice-president of the International Society of RNA Nanotechnology and [Nanomedicine](https://www.edgepedia.org/nanomedicine).[1](https://chemistry.charlotte.edu/directory/kirill-afonin-phd/)
## Representative work
The 2010 Nature Nanotechnology paper "In vitro assembly of cubic RNA-based scaffolds designed in silico" reported the assembly, in vitro, of cubic RNA-based scaffolds whose sequences were produced by computational design, with Afonin as lead author; it has been cited about 357 times.[8](https://www.afoninlab.com/publications) • [2](https://doi.org/10.1038/nnano.2010.160) The work demonstrated that three-dimensional RNA assemblies could be specified first as geometries and then realized as sequences, the reverse of the usual RNA structure-prediction problem.[4](http://pubs.acs.org/achre4/article/47/6/1731/1248005/In-Silico-Design-and-Enzymatic-Synthesis-of)
## Research program: computable RNA nanoparticles
Afonin's design pipeline produces three-dimensional assemblies first and then uses algorithms to generate sequences that assemble into the designated construct.[4](http://pubs.acs.org/achre4/article/47/6/1731/1248005/In-Silico-Design-and-Enzymatic-Synthesis-of) A 2013 Nature Nanotechnology paper showed that different split functionalities can be activated on re-association of RNA–DNA hybrids.[3](https://doi.org/10.1038/nnano.2013.44) In the companion system, multiple split functionalities are embedded in cognate pairs of RNA–DNA hybrids programmed to recognize each other; on re-association they form a DNA duplex while releasing split RNA fragments that regain their original functions.[9](https://doi.org/10.1093/nar/gkt1001) Simultaneous activation of three functionalities, [RNA interference](https://www.edgepedia.org/rna-interference) (RNAi), Förster resonance energy transfer (FRET), and an RNA aptamer, was confirmed in vitro and in cell culture.[9](https://doi.org/10.1093/nar/gkt1001) Once inside target cells, built-in complementary single-stranded DNA toeholds (short single-stranded DNA overhang that starts strand invasion) trigger re-association of the hybrids and release of specific siRNAs, and the approach has been expanded to deliver aptamers, FRET pairs, and up to seven siRNAs at once.[4](http://pubs.acs.org/achre4/article/47/6/1731/1248005/In-Silico-Design-and-Enzymatic-Synthesis-of) Hybrids carrying longer RNAs can be produced by [RNA polymerase II](https://www.edgepedia.org/rna-polymerase-ii)-dependent transcription of single-stranded DNA templates.[9](https://doi.org/10.1093/nar/gkt1001) RNA–DNA hybrids also show significantly reduced intravascular degradation compared with naked RNAs, which nucleases can degrade within minutes.[4](http://pubs.acs.org/achre4/article/47/6/1731/1248005/In-Silico-Design-and-Enzymatic-Synthesis-of)
At the NCI, his group built multifunctional RNA nanoparticles on RNA nanorings functionalized with multiple siRNAs against HIV-1 genes, RNA aptamers, fluorescent dyes, proteins, and RNA–DNA hybrids.[7](https://pmc.ncbi.nlm.nih.gov/articles/PMC4189619/) Cube/anti-cube pairs of RNA and DNA re-associate under isothermal conditions to activate split functionalities including Dicer substrate RNAs against BCL2, PLK1, and GFP, split Broccoli aptamers, FRET pairs, and T7 promoters.[10](https://www.mdpi.com/2079-4991/9/4/611)
**Immune recognition** is a central theme. A systematic study using peripheral blood mononuclear cells (PBMCs) from more than 100 healthy human donors found that all NANPs used without a delivery carrier were immunoquiescent, and that type I and III interferons are the key cytokines triggered by NANPs after internalization by phagocytic cells.[10](https://www.mdpi.com/2079-4991/9/4/611) The 2020 Nucleic Acids Research study of NANP immunorecognition, subcellular compartmentalization, and physicochemical properties appeared in volume 48, pages 11785–11798.[8](https://www.afoninlab.com/publications) [Quantitative structure–activity relationship](https://www.edgepedia.org/quantitative-structure-activity-relationship) (QSAR) machine-learning models have been developed to predict and engineer NANPs that stimulate an intended immune response, or lack thereof.[10](https://www.mdpi.com/2079-4991/9/4/611) By optimizing the size, shape, and composition of NANPs delivered into human immune cells, one can regulate the extent of their immunorecognition and tune the profile of induced cytokines.[11](https://pmc.ncbi.nlm.nih.gov/articles/PMC8886801/)
## How NANPs compare with other platforms
NANPs made from RNA, DNA, RNA–DNA hybrids, and chemical analogs can be programmed to self-assemble reproducibly into discrete, monodisperse structures with well-defined secondary and tertiary structure, at nearly any geometry and size on the 10–100 nm scale.[11](https://pmc.ncbi.nlm.nih.gov/articles/PMC8886801/) On assembly conditions, [DNA origami](https://www.edgepedia.org/dna-origami) is typically annealed by heating to 70–90 °C followed by cooling over hours, while single-stranded [RNA origami](https://www.edgepedia.org/rna-origami) structures can co-transcriptionally assemble in high yield at 37 °C within minutes.[12](https://pmc.ncbi.nlm.nih.gov/articles/PMC10376919/) On size, the largest achieved RNA origami, a diamond structure of 6,320 nucleotides, is slightly smaller than half the size of a DNA origami using the full m13mp18 scaffold (14,498 nucleotides), and computational design tools for RNA origami still lag behind those for DNA origami.[12](https://pmc.ncbi.nlm.nih.gov/articles/PMC10376919/) Lipid, polymer, peptide, and exosome nanomaterials have been investigated for RNA delivery, and their cytotoxicity and immune responses have motivated nucleic acid nanoassemblies as an alternative.[13](https://pmc.ncbi.nlm.nih.gov/articles/PMC10031267/)
## Funding, honors, and patents
Afonin is principal investigator of the NIH MIRA award R35GM139587, "SMART NANPs: new molecular platform for communication with human immune system and modulation of therapeutic responses", funded by NIGMS, with a period of performance from 02/01/2021 to 01/31/2027.[5](https://taggs.hhs.gov/Detail/AwardDetail?arg_AwardNum=R35GM139587&arg_ProgOfficeCode=127) SMART NANPs stands for specific, modular, adjustable, reproducible, and targeted nucleic acid nanoparticles, a data-driven platform encoded by self-assembling nucleic acids.[5](https://taggs.hhs.gov/Detail/AwardDetail?arg_AwardNum=R35GM139587&arg_ProgOfficeCode=127) His awards also include two NIH Fellows Awards for Research Excellence (FARE) and two NIH R01s.[1](https://chemistry.charlotte.edu/directory/kirill-afonin-phd/)
His patents include "RNA complexes featuring paranemic binding" (US8129516B1), "RNA Nanoparticles and Nanotubes" (US9732337B2), therapeutic RNA–DNA chimeric nanoparticles (US9631192), RNA switches (WO2013075132A1), co-transcriptional assembly of modified RNA nanoparticles (US9719084B2), nucleic acid nanoparticles for analyte detection (US 10,900,067), and a 2018 filing on NANPs for controlled immunomodulation.[14](https://www.afoninlab.com/patents) The NCI Technology Transfer Center executed start-up-exclusive evaluation licenses with Sixfold Bioscience, Inc. for two of his RNA nanoparticle technologies, "Multifunctional RNA Nanoparticles" (E-765-2013) and "Triggering of multiple functionalities using minimal RNA toeholds" (E-078-2016).[14](https://www.afoninlab.com/patents)
## Recent developments
On May 1, 2025, Afonin was named one of two recipients of the Harshini V. de Silva Graduate Mentor Award at UNC Charlotte's Spring Faculty Awards ceremony.[6](https://science.charlotte.edu/2025/05/05/kirill-afonin-receives-de-silva-graduate-mentor-award/) A July 2025 Advanced Functional Materials paper introduced reconfigurable nucleic acid nanoparticles (recNANPs) that recognize overexpressed cancer biomarkers and conditionally release RNAi inducers targeting apoptosis inhibitors in pancreatic cancer cells; the recNANPs are non-immunostimulatory, achieve prolonged gene silencing compared with conventional RNAi inducers, and can be combined with chemotherapy.[15](https://doi.org/10.1002/adfm.202508122) A January 2026 paper in the same journal showed that varying the chemical composition of NANPs while keeping architecture constant tunes their immunorecognition and stability, with specific compositions boosting [T cell](https://www.edgepedia.org/t-cell) effector functions, promoting [B cell](https://www.edgepedia.org/b-cell) proliferation, and activating innate immune populations in human PBMCs; in vivo studies showed NANPs functioning as efficiently as traditional clinically used adjuvants without increasing the risk of autoimmunity.[16](https://doi.org/10.1002/adfm.202515585)
## References
1. [Kirill Afonin, Ph.D., Department of Chemistry, UNC Charlotte](https://chemistry.charlotte.edu/directory/kirill-afonin-phd/)
2. [In vitro assembly of cubic RNA-based scaffolds designed in silico (Nature Nanotechnology, 2010)](https://doi.org/10.1038/nnano.2010.160)
3. [Activation of different split functionalities on re-association of RNA–DNA hybrids (Nature Nanotechnology, 2013)](https://doi.org/10.1038/nnano.2013.44)
4. [In Silico Design and Enzymatic Synthesis of Functional RNA Nanoparticles (Accounts of Chemical Research, 2014)](http://pubs.acs.org/achre4/article/47/6/1731/1248005/In-Silico-Design-and-Enzymatic-Synthesis-of)
5. [Award Information, HHS TAGGS, R35GM139587](https://taggs.hhs.gov/Detail/AwardDetail?arg_AwardNum=R35GM139587&arg_ProgOfficeCode=127)
6. [Kirill Afonin recognized with de Silva graduate mentor award, Klein College of Science, UNC Charlotte](https://science.charlotte.edu/2025/05/05/kirill-afonin-receives-de-silva-graduate-mentor-award/)
7. [Multifunctional RNA Nanoparticles (Nano Letters, 2014)](https://pmc.ncbi.nlm.nih.gov/articles/PMC4189619/)
8. [Publications, The Afonin Lab at UNC Charlotte](https://www.afoninlab.com/publications)
9. [Co-transcriptional production of RNA–DNA hybrids for simultaneous release of multiple split functionalities (Nucleic Acids Research, 2013)](https://doi.org/10.1093/nar/gkt1001)
10. [Smart-Responsive Nucleic Acid Nanoparticles (NANPs) with the Potential to Modulate Immune Behavior (Nanomaterials, 2019)](https://www.mdpi.com/2079-4991/9/4/611)
11. [Critical review of nucleic acid nanotechnology to identify gaps and inform a strategy for accelerated clinical translation](https://pmc.ncbi.nlm.nih.gov/articles/PMC8886801/)
12. [RNA origami: design, simulation and application](https://pmc.ncbi.nlm.nih.gov/articles/PMC10376919/)
13. [Nucleic acid nanoassembly-enhanced RNA therapeutics and diagnosis](https://pmc.ncbi.nlm.nih.gov/articles/PMC10031267/)
14. [& Patents, The Afonin Lab at UNC Charlotte](https://www.afoninlab.com/patents)
15. [Reconfigurable Nucleic Acid Nanoparticles with Therapeutic RNAi Responses to Intracellular Disease Markers (Advanced Functional Materials, 2025)](https://doi.org/10.1002/adfm.202508122)
16. [Expanding Chemical Space of Nucleic Acid Nanoparticles for Tunable Antiviral-Like Immunomodulatory Responses and Potent Adjuvant Activity (Advanced Functional Materials, 2026)](https://doi.org/10.1002/adfm.202515585)
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*Topic: Encyclopedia › Life and health › Life and health scientists › Life scientists › Researchers in chemical biology › Nucleic acid chemical biology researchers*
*Initially written Sep 21, 2026 · Reviewed: Sep 25, 2026; Sep 30, 2026 · Edited: Sep 25, 2026; Oct 11, 2026; Oct 15, 2026 · Last review: Sep 30, 2026*
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License: Edgepedia Community License 1.0, https://www.edgepedia.org/edgepedia/license