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All research from our lab which has been published in peer-reviewed scientific journals or books can be found below alongside links to the texts (lab members are underlined)



Immunostimulation of Fibrous Nucleic Acid Nanoparticles Can be Modulated through Aptamer-Based Functional Moieties: Unveiling the Structure–Activity Relationship and Mechanistic Insights (Link)

Rebolledo LP#, Ke W#, Cedrone E, Wang J, Majithia K, Johnson MB, Dokholyan NV, Dobrovolskaia MA, Afonin KA 

ACS Applied Materials and Interfaces, 2024 (doi: 10.1021/acsami.3c17779)

(# – equal contribution)


Design and Characterization of Compact, Programmable, Multistranded Nonimmunostimulatory Nucleic Acid Nanoparticles Suitable for Biomedical Applications (Link)

Brumett R, Danai L, Coffman A, Radwan Y, Teter M, Hayth H, Doe E, Pranger K, Thornburgh S, Dittmer A, Li Z, Kim TJ, Afonin KA, Khisamutdinov E

Biochemistry. 2024 (doi: 10.1021/acs.biochem.3c00615)


cGas Mediates the Inflammatory Responses of Human Microglial Cells to Genotoxic DNA Damage (Link)

Suptela AJ, Radwan Y, Richardson C, Yan S, Afonin KA, Marriot I

Inflammation. 2023 (doi: 10.1007/s10753-023-01946-8)

RNA nanoparticles for targeted therapies of triple-negative breast cancers (Link)

Danai L, Ge E, Afonin KA

Molecular Therapy – Nucleic Acids. 2023 (doi: org/10.1016/j.omtn.2023.08.013)

Demonstrating the Synthesis and Antibacterial Properties of Nanostructured Silver (Link)

Rolband LA#, Godakhindi V#, Vivero-Escoto JL, Afonin KA

Journal of Chemical Education. 2023 (doi: org/10.1021/acs.jchemed.3c00125)

(# – equal contribution)

Anticoagulant Activity of Nucleic Acid Nanoparticles (NANPs) Assessed by Thrombin Generation Dynamics on a Fully Automated System (Link)

Freitas Saito R, Barion BG, Flores da Rocha TR, Rolband A, Afonin KA, Chammas R

Methods Mol Biol. 2023, 2709:319-332. PMID: 35772292

Dynamic Nanostructures for Conditional Activation and Deactivation of Biological Pathways (Link)

Radwan Y, Rebolledo LP, Panigaj M, Afonin KA

Methods Mol Biol. 2023, 2709:309-318. PMID: 37572291

Synthesis of DNA-Templated Silver Nanoclusters and the Characterization of Their Optical Properties and Biological Activity (Link)

Skelly E, Rolband A, Beasock D, Afonin KA

Methods Mol Biol. 2023, 2709:299-307. PMID: 37572290

Aptamer Conjugated RNA/DNA Hybrid Nanostructures Designed for Efficient Regulation of Blood Coagulation (Link)

Rolband A, Ke W, Afonin KA

Methods Mol Biol. 2023, 2709:299-307. PMID: 37572290

Characterization of PAMAM Dendrimers for the Delivery of Nucleic Acid Nanoparticles (Link)

Avila YI, Rebolledo L, Andrade-Muñoz, Afonin KA

Methods Mol Biol. 2023, 2709:253-259. PMID: 37572286

Discriminating Immunorecognition Pathways Activated by RNA Nanostructures (Link)

Danai L, Johnson MB, Afonin KA

Methods Mol Biol. 2023, 2709:229-240. PMID: 37572284

10 Assessment of Intracellular Compartmentalization of RNA Nanostructures (Link)

Radwan Y, Afonin KA, Johnson MB

Methods Mol Biol. 2023, 2709:211-228. PMID: 37572283

11 Characterization of RNA Nanoparticles and Their Dynamic Properties Using Atomic Force Microscopy (Link)

Lushnikov AJ, Avila Y, Afonin KA, Krasnoslobodtsev AV

Methods Mol Biol. 2023, 2709:191-202. PMID: 37572281

12 Small Volume Microrheology to Evaluate Viscoelastic Properties of Nucleic Acid-Based Supra-Assemblies (Link)

Gupta AK, Petersen J, Skelly E, Afonin KA, Krasnoslobodtsev AV

Methods Mol Biol. 2023, 2709:179-189. PMID: 37572280

13 Structural Characterization of DNA-Templated Silver Nanoclusters by Energy Dispersive Spectroscopy (Link)

Beasock D, Afonin KA

Methods Mol Biol. 2023, 2709:163-178. PMID: 37572279

14 Structural Characterization of Nucleic Acid Nanoparticles Using SAXS and SAXS-Driven MD (Link)

Byrnes J*, Chopra K, Rolband A, Danai L, Chodankar S, Yang L, Afonin KA

Methods Mol Biol. 2023, 2709:163-178. PMID: 37572273

15 Editorial: Delivering nucleic acids to immune and non-immune cells (Link)

Afonin KA*, Re F*, Boraschi D*

Frontiers in Immunology, 2023 (doi: 10.3389/fimmu.2023.1237506)

16 Optical, structural and antibacterial properties of silver nanoparticles and DNA-templated silver nanoclusters (Link)

Danai L#, Rolband LA#, Perdomo VA, Skelly E, Kim TJ, Afonin KA

Nanomedicine, 2023 (doi: 10.2217/nnm-2023-0082)

(# – equal contribution)

17 Editorial: Nanotechnology to Overcome the World’s Most Critical Health Issues: Liposomes and Beyond—A Themed Issue    Dedicated to Professor Yechezkel Barenholz (Link)

Dobrovolskaia MA*, Afonin KA*

Molecules, 2023 (doi: 10.3390/molecules28124788)

(* – corresponding authors)

18 Optical, structural, and biological properties of silver nanoclusters formed within the loop of C-12 hairpin sequence (Link)

Gupta AK, Marshal N, Yourston L, Rolband L, Beasock D, Danai L, Skelly E, Afonin KA, Krasnoslobodstev A

Nanoscale Advances, 2023 (doi: 10.1039/D3NA00092C)

19 Break to build: isothermal assembly of nucleic acid nanoparticles (NANPs) via enzymatic degradation (Link)

Beasock D#, Ha A#, Halman J, Panigaj M, Wang J, Dokholyan NV, Afonin KA

Bioconjugate Chemistry, 2023 (doi: 10.1021/acs.bioconjchem.3c00167)

(# – equal contribution)

20 Change in lipofectamine carrier as a tool to fine-tune immunostimulation of nucleic acid nanoparticles (Link)

Newton H#, Radwan Y#, Xu J, Clogston JD, Dobrovolskaia MA, Afonin KA

Molecules, 2023 (doi: 10.3390/molecules28114484)

(# – equal contribution)

21 Toehold-Mediated Shape Transition of Nucleic Acid Nanoparticles (Link)

Hartung J, McCann N, Doe E, Hayth H, Benkato K, Johnson MB, Viard M, Afonin KA*, Khisamutdinov EF*

ACS Applied Materials & Interfaces, 2023 (doi: 10.1021/acsami.c01604)

(* – corresponding authors)

22 Cancer Therapy-Induced Inflammation and Its Consequences (Link)

Freitas Saito R, Rangel MC, Chandler MBeasock DAfonin KA, Chammas R 

Biotechnology Applied to Inflammatory Diseases, 2023 (doi: 10.1007/978-981-19-8342-9_4)

23 Nanoscale metal-organic frameworks for the delivery of nucleic acids to cancer cells (Link)

Li X#, Chandler M#Avila YIArroyo-Becker SI, Patriarche G, Vargas-Berenguel A, Casas-Solvas JM, Afonin KA*, Gref R* 

International Journal of Pharmaceutics: X, 2023 (doi: 10.1016/j.ijpx.2023.100161)

(# – equal contribution; * – corresponding authors)

24 Therapeutic Immunomodulation by Rationally Designed Nucleic Acids and Nucleic Acid Nanoparticles (NANPs) (Link)

Panigaj MSkelly E Beasock D, Marriott I, Johnson MB, Salotti J, Afonin KA

Frontiers in Immunology, 2023 (doi: 10.3389/fimmu.2023.1053550)


1 Editorial to "Molecular Engineering of Biomaterials Programmed to Operate in Living Systems" (Link)

Afonin KA* and Dokholyan NV*

Advanced Drug Delivery Reviews, 2022 (doi: 10.1016/j.addr.2022.114669) 

(* – corresponding authors)

2 Biomotors, Viral Assembly, And RNA Nanobiotechnology: Current Achievements And Future Directions (Link)

#Rolband L, #Beasock D, Wang Y, Shu YF, Dinman JD, Schlick T, Zhou Y, Kieft JS, Chen SJ, Bussi G, Oukhaled A, Gao X, Sulc P, Binzel D, Bhullar AS, Liang C, Guo P, Afonin KA

Computational and Structural Biotechnology Journal, 2022 (doi: 10.1016/j.csbj.2022.11.007)

(# – equal contribution)

Design and Self-Assembly of Therapeutic Nucleic Acid Nanoparticles (NANPs) with Controlled Immunological Properties (Link)

Chandler M, Danai L, Afonin KA

Handbook of Chemical Biology of Nucleic Acids, Springer Singapore, 2022 (doi: 10.1007/978-981-16-1313-5_99-1)

Artificial Immune Cell, AI-cell, a New Tool to Predict Interferon Production by Peripheral Blood Monocytes in Response to Nucleic Acid Nanoparticles (Link)

Chandler M, Jain S, Halman J, Hong E, Dobrovolskaia MA, Zakharov AV, Afonin KA

Small, 2022 (doi: 10.1002/smll.202204941)

Adaptation-Proof SARS-CoV-2 Vaccine Design (Link)

Vishweshwaraiah Y, Hnath B, Rackley B, Wang J, Gontu A, Chandler MAfonin KA, Kuchipudi S, Christensen N, Yennawar N, Dokholyan NV

Advanced Functional Materials, 2022 (doi: 10.1002/adfm.202206055)

The Application of Light-Assisted Drying to the Thermal Stabilization of Nucleic Acid Nanoparticles (Link)

Lam PA, Furr DP, Tran A, McKeough RQ, Beasock D, Chandler M, Afonin KA, Trammell SR

Biopreservation and Biobanking, 2022 (doi: 10.1089/bio.2022.0035)

Expanding Structural Space for Immunomodulatory Nucleic Acid Nanoparticles (NANPs) via Spatial Arrangement of Their Therapeutic Moieties (Link)

Chandler M, Rolband L, Johnson MB, Shi D, Avila YI, Cedrone E, Beasock D, Danai L, Stassenko E, Krueger JK, Jiang J, Lee JS, Dobrovolskaia MA, Afonin KA

Advanced Functional Materials, 2022 (doi: 10.1002/adfn.202205581)

Locking and Unlocking Thrombin Function Using Immunoquiescent Nucleic Acid Nanoparticles with Regulated Retention In Vivo (Link)

Ke W, Chandler M, Cedrone E, Saito RF, Rangel MC, Junqueira MS, Wang J, Shi D, Truong N, Richardson M, Rolband LA, Dréau D, Bedocs P, Chammas R, Dokholyan NV, Dobrovolskaia MA, Afonin KA

Nano Letters, 2022 (doi: 10.1021/acs.nanolett.2c02019)

The natural versatility of RNA (Link)

Rolband LA, Shevchenko O, West CW, Conway CE, Striplin CD, Afonin KA

RNA Nanotechnology and Therapeutics. CRC Press, 2nd edition, 2022, ISBN: 113831286X

10 Nucleic acids as building material in nanotechnology (Link)

Halman J, Afonin KA

RNA Nanotechnology and Therapeutics. CRC Press, 2nd edition, 2022, ISBN: 113831286X

11 Driving dynamic functions with programmable RNA nanostructures (Link)

Chandler M, Elasmar D, Eisen S, Schmedake L, Afonin KA

RNA Nanotechnology and Therapeutics. CRC Press, 2nd edition, 2022, ISBN: 113831286X

12 Delivery of RNA nanoparticles (Link)

Ke W, Kozlov SS, Afonin KA

RNA Nanotechnology and Therapeutics. CRC Press, 2nd edition, 2022, ISBN: 113831286X

13 Electron microscopy of Nucleic acid nanoparticles (Link)

Beasock D, Afonin KA

RNA Nanotechnology and Therapeutics. CRC Press, 2nd edition, 2022, ISBN: 113831286X

14 Viral noncodong RNA in modulating cellular defense and their potential for RNA nanotechnology (Link)

Panigaj M, Dobrovolskaia MA, Afonin KA 

RNA Nanotechnology and Therapeutics. CRC Press, 2nd edition, 2022, ISBN: 113831286X

15 RNA-based devices for diagnostic and biosensing (Link)

Chandler M, Afonin KA

RNA Nanotechnology and Therapeutics. CRC Press, 2nd edition, 2022, ISBN: 113831286X

16 Discrimination of RNA Fiber Structures Using Solid-State Nanopores (Link)

Tripathi P, Chandler M, Maffeo C, Fallahi A, Makhamreh A, Halman J, Aksimentiev A*, Afonin KA*, Wanunu M*.

Nanoscale, 2022 (doi: 10.1039/D1NR08002D)

(* – corresponding authors)

17 Anhydrous Nucleic Acid Nanoparticles for Storage and Handling at Broad Range of Temperatures (Link)

Tran ANChandler M, Halman J, Beasock D, Fessler A, McKeough RQ, Lam PA, Furr DP, Wang J, Cedrone E, Dobrovolskaia MA, Dokholyan NV, Trammell SR, Afonin KA 

Small, 2021 (doi: 10.1002/smll.202104814


1 Editorial to “Journey into the immunological properties of engineered nanomaterials: There and back again” (Link)

Dobrovolskaia MA, Afonin KA, Gonzalez-Fernandez A

Advanced Drug Delivery Reviews, 2021 (doi: 10.1016/j.addr.2021.114100) 

2 Critical review of nucleic acid nanotechnology to identify gaps and inform a strategy for accelerated clinical translation (Link)

Afonin KA#*, Dobrovolskaia MA#, Ke W#, Grodzinski P#, Bathe M#*

Advanced Drug Delivery Reviews, 2021 (doi: 10.1016/j.addr.2021.114081

(# – equal contribution; * – corresponding authors)

To PEGylate or not to PEGylate: immunological properties of nanomedicine's most popular component, poly(ethylene) glycol and its alternatives (Link)

Shi D#, Beasock D#, Fessler A, Szebeni J, Ljubimova JY, Afonin KA, Dobrovolskaia MA

Advanced Drug Delivery Reviews, 2021 (doi: 10.1016/j.addr.2021.114079) 

(# – equal contribution)

The International Society of RNA Nanomedicine and Nanotechnology (ISRNN): The Present and Future of the Burgeoning Field (Link)

Chandler M, Johnson B, Khisamutdinov E, Dobrovolskaia MA, Sztuba-Solinska J, Salem AK, Breyne K, Chammas R, Walter NG, Contreras LM, Guo P, Afonin KA

ACS Nano, 15(11): 16957-16973, 2021 (doi: 10.1021/acsnano.0c10240)

5 Controlled Organization of Inorganic Materials Using Biological Molecules for Activating Therapeutic Functionalities (Link)

Chandler M, Minevich B, Roark B, Viard M, Johnson MB, Rizvi MH, Deaton TA, Kozlov S, Panigaj M, Tracy JB, Yingling YG, Gang O, Afonin KA

ACS Applied Materials & Interfaces, 2021 (doi: 10.1021/acsami.1c09230)

6   Programmable DNA-Augmented Hydrogels for Controlled Activation of Human Lymphocytes (Link)

Zhovmer AS, Chandler M, Manning A, Afonin KA*, Tabdanov E* 

Nanomedicine: Nanotechnology, Biology and Medicine, 2021 (doi: 10.1016/j.nano.2021.102442)

(* – corresponding authors)

The Recognition of and Reactions to Nucleic Acid Nanoparticles by Human Immune Cells (Link) 

Bila D, Radwan Y, Dobrovolskaia MA, Panigaj MAfonin KA

Molecules, 2021 (doi: 10.3390/molecules26144231)

DNA-Templated Fluorescent Silver Nanoclusters Inhibit Bacterial Growth While Being Non-Toxic to Mammalian Cells (Link)

Rolband L, Yourston L, Chandler M, Beasock D, Danai L, Kozlov S, Marshall N, Shevchenko O, Krasnoslobodtsev AV, Afonin KA

Molecules, 2021 (doi: 10.3390/molecules26134045) 

Simultaneous silencing of Lysophosphatidylcholine Acyltransferases 1-4 by nucleic acid nanoparticles (NANPs) improves radiation response of melanoma cells (Link)

Saito RF, Rangel MC, Halman JR, Chandler M, Andrade LNS, Odete-Bustos S, Furuya TK, Carrasco AGM, Chaves-Filho Ab, Yoshinaga MY, Miyamoto S, Afonin KA*, Chammas R*

Nanomedicine: Nanotechnology, Biology and Medicine, 2021 (doi: 10.1016/j.nano.2021.102418) 

(* – corresponding authors)

10 2021: an immunotherapy odyssey and the rise of nucleic acid nanotechnology (Link)

Panigaj M, Dobrovolskaia MA, and Afonin KA

Nanomedicine, 2021 (doi: 10.2217/nnm-2021-0097)

11 Exosomes as Natural Delivery Carriers for Programmable Therapeutic Nucleic Acid Nanoparticles (NANPs) (Link)

Ke W, and Afonin KA

Advanced Drug Delivery Reviews, 2021 (doi: 10.1016/j.addr.2021.113835)

12  Nucleic Acid Nanoparticles (NANPs) as Molecular Tools to Direct Desirable and Avoid Undesirable Immunological           Effects (Link)  

Johnson MB, Chandler M, and Afonin KA

Advanced Drug Delivery Reviews, 173: 427-438, 2021 (doi: 10.1016/j.addr.2021.04.011)

13 Induction of cytokines by Nucleic Acid Nanoparticles (NANPs) depends on the type of delivery carrier (Link)

Avila YI, Chandler M, Cedrone E, Newton HS, Richardson M, Xu J, Clogston J, Liptrott N, Afonin KA*, and Dobrovolskaia MA*

Molecules, 26(3): 652, 2020 (doi: 10.3390/molecules26030652)

(* – corresponding authors)


1  Use of human peripheral blood mononuclear cells to define immunological properties of nucleic acid nanoparticles (Link)

Dobrovolskaia MA and Afonin KA

Nature Protocols, 15(11): 3678-3698, 2020 (doi: 10.1038/s41596-020-0393-6)

2  The immunorecognition, subcellular compartmentalization, and physicochemical properties of nucleic acid nanoparticles can be controlled by composition modification (Link)

Johnson MB, Halman JR, Miller DK, Cooper JS, Khisamutdinov EF, Marriott I, and Afonin KA 

Nucleic Acids Research, 48(20): 11785-11798, 2020 (doi: 10.1093/nar/gkaa908)

3  Exosome mediated delivery of functional nucleic acid nanoparticles (NANPs) (Link)

Nordmeier S#, Ke W#, Afonin KA*, and Portnoy V*

Nanomedicine: Nanotechnology, Biology and Medicine, 30: 102285, 2020 (doi: 10.1016/j.nano.2020.102285)

(# – equal contribution; * – corresponding authors)


4  Combination of Nucleic Acid and Mesoporous Silica Nanoparticles: Optimization and Therapeutic Performance In Vitro (Link)

Juneja R#, Vadarevu H#, Halman J#, Tarannum M, Rackley L, Dobbs J, Marquez J, Chandler M, Afonin KA*, and Vivero-Escoto JL*

ACS Applied Materials & Interfaces, 2020 (doi: 10.1021/acsami.0c07106)

(# – equal contribution; * – corresponding authors)

5  Opportunities, Barriers, and a Strategy for Overcoming Translational Challenges to Therapeutic Nucleic Acid Nanotechnology (Link)

Afonin KA*, Dobrovolskaia MA, Church G, and Bathe M*

ACS Nano, 14(8): 9221-9227, 2020 (doi: 10.1021/acsnano.0c04753)

(* – corresponding authors)

6  Tuning properties of silver nanoclusters with RNA nanoring assemblies (Link)

Yourston L, Rolband L, West C, Lushnikov A, Afonin KA, and Krasnoslobodtsev AV

Nanoscale, 12(30): 16189, 2020 (doi: 10.1039/D0NR03589K)

7  DNA-Templated Synthesis of Fluorescent Silver Nanoclusters (Link)

Chandler M, Shevchenko O, Vivero-Escoto JL, Striplin CD, and Afonin KA

Journal of Chemical Education, 97(7), 1992-1996, 2020 (doi: 10.1021/acs.jchemed.0c00158)

8  Challenges to optimizing RNA nanostructures for large scale production and controlled therapeutic properties (Link)

Chandler M, Panigaj M, Rolband LA, and Afonin KA

Nanomedicine, 15(19): 1915, 2020 (doi: 10.2217/nnm-2020-0034)

9  Retinoic acid inducible gene-I mediated detection of bacterial nucleic acids in human microglial cells (Link)

Johnson MB, Halman JR, Burmeister AR, Currin S, Khisamutdinov EF, Afonin KA, and Marriott I

Journal of Neuroinflammation, 17(1): 139, 2020 (doi: 10.1186/s12974-020-01817-1)

10  Characterization of Cationic Bolaamphiphile Vesicles for siRNA Delivery into Tumors and Brain (Link)

Kim T, Viard M, Afonin KA, Gupta K, Popov M, Salotti J, Johnson PF, Linder C, Heldman E, and Shapiro BA

Molecular Therapy Nucleic Acids, 20: 359-372, 2020 (doi: 10.1016/j.omtn.2020.02.011)

11  A cationic amphiphilic co-polymer as a carrier of nucleic acid nanoparticles (NANPs) for controlled gene silencing, immunostimulation, and biodistribution (Link)

Halman JR, Kim KT, Gawk SJ, Pace R, Johnson MB, Chandler MR, Rackley L, Viard M, Marriott I, Lee JS, and Afonin KA

Nanomedicine: Nanotechnology, Biology and Medicine, 23: 102094, 2020 (doi: 10.1016/j.nano.2019.102094)

12  Innate immune responses triggered by nucleic acids inspire the design of immunomodulatory nucleic acid nanoparticles (NANPs) (Link)

Chandler M, Panigaj M, Johnson MB, and Afonin KA

Current Opinion in Biotechnology, 63: 8-15, 2020 (doi: 10.1016/j.copbio.2019.10.011)



1  Aptamers as Modular Components of Therapeutic Nucleic Acid Nanotechnology (Link)

Panigaj M, Johnson MB, Ke W, McMillan J, Goncharova EA, Chandler M, and Afonin KA

ACS Nano, 13(11): 12301-12321, 2019 (doi: 10.1021/acsnano.9b06522)

2  Editorial for the Special Issue on "Nucleic Acid Architectures for Therapeutics, Diagnostics, Devices and Materials" (Link)

Halman JR and Afonin KA

Nanomaterials, 9(7): 951, 2019 (doi: 10.3390/nano9070951)

3  Small-Angle Scattering as a Structural Probe for Nucleic Acid Nanoparticles (NANPs) in a Dynamic Solution Environment (Link)

Oliver RC, Rolband LA, Hutchinson-Lundy AM, Afonin KA, and Krueger JK

Nanomaterials, 9(5): 681, 2019 (doi: 10.3390/nano9050681)

4  Smart-Responsive Nucleic Acid Nanoparticles (NANPs) with the Potential to Modulate Immune Behavior (Link)

Chandler M and Afonin KA

Nanomaterials, 9(4): 611, 2019 (doi: 10.3390/nano9040611)

5  First Step Towards Larger DNA-Based Assemblies of Fluorescent Silver Nanoclusters: Template Design and Detailed Characterization of Optical Properties (Link)

Yourston LE, Lushnikov AY, Shevchenko OA, Afonin KA, and Krasnoslobodtsev AV

Nanomaterials, 9(4): 613, 2019 (doi: 10.3390/nano9040613)

6  Toll-Like Receptor-Mediated Recognition of Nucleic Acid Nanoparticles (NANPs) in Human Primary Blood Cells (Link)

Hong E, Halman JR, Shah A, Cedrone E, Truong N, Afonin KA*, Dobrovolskaia MA* 

Molecules, 24(6), 2019 (doi: 10.3390/molecules24061094)

(* – corresponding authors)

7  Multimodal Polysilsesquioxane Nanoparticles for Combinatorial Therapy and Gene Delivery in Triple-Negative Breast Cancer (Link)

Juneja R, Lyles Z, Vadarevu H, Afonin KA, Vivero-Escoto JL 

ACS Applied Materials & Interfaces, 11(13): 12308-12320, 2019 (doi: 10.1021/acsami.9b00704)

RNA-DNA fibers and polygons with controlled immunorecognition activate RNAi, FRET, and transcriptional regulation of NF-κB in human cells (Link)

Ke W, Hong E, Saito RF, Rangel MC, Wang J, Viard M, Richardson M, Khisamutdinov EF, Panigaj M, Dokholyan NV, Chammas R, Dobrovolskaia MA, Afonin KA  

Nucleic Acids Research, 47(3): 1350-1361, 2019 (doi: 10.1093/nar/gky1215)




1  Broccoli Fluorets: Split Aptamers as a User-Friendly Fluorescent Toolkit for Dynamic RNA Nanotechnology (Link)

Chandler M, Lyalina T, Halman J, Rackley L, Lee L, Dang D, Ke W, Sajja S, Woods S, Acharya S, Baumgarten E, Christopher J, Elshalia E, Hrebien G, Kublank K, Saleh S, Stallings B, Tafere M, Striplin C, Afonin KA  

Molecules, 23(12), 2018 (doi: 10.3390/molecules23123178)


2  RNA fibers as optimized nanoscaffolds for siRNA coordination and reduced immunological recognition (Link)

Rackley L, Stewart JM, Salotti J, Krokhotin A, Shah A, Halman JR, Juneja R, Smollett J, Lee L, Roark K, Viard M, Tarannum M, Vivero-Escoto J, Johnson PF, Dobrovolskaia MA, Dokholyan NV, Franco E, Afonin KA  

Advanced Functional Materials, 28: 1805959, 2018 (doi: 10.1002/adfm.201805959)


3  Magnetic nanoparticles loaded with functional RNA nanoparticles (Link)

Cruz-Acuña M, Halman JR, Afonin KA, Dobson J, Rinaldi C

Nanoscale, 10(37): 1761-1770, 2018.


4  Activation of Split RNA Aptamers: Experiments Demonstrating the Enzymatic Synthesis of Short RNAs and Their Assembly As Observed by Fluorescent Response (Link)

Sajja S, Chandler M, Striplin CD, Afonin KA

Journal of Chemical Education, 95(10): 1861-1866, 2018.


5  Self-Assembling Programmable RNA Nanoparticles: From Design and Characterization to Use as an siRNA Delivery Platform (Link)

Roark B, Chandler M, Walker F, Milanova L, Viglasky V, Panigaj M, Afonin KA

Molecular Medicines for Cancer: Concepts and Applications of Nanotechnology, 2018.

Published by CRC Press/Taylor & Francis, Chapter 17: 491-526 (ISBN: 978-1138035157)


6  Structure and composition define immunorecognition of nucleic acid nanoparticles (Link)

Hong E, Halman J, Shah A, Khisamutdinov EF, Dobrovolskaia MA, Afonin KA

Nano Letters, 18(7): 4309-4321, 2018 (doi: 10.1021/acs.nanolett.8b01283)


7  Reconfigurable Nucleic Acid Materials for Cancer Therapy (Link)

Chandler M, Ke W, Halman JR, Panigaj M, Afonin KA

Nanooncology, 2018 (doi: 10.1007/978-3-319-89878-0_11)


8  Dynamic behavior of RNA nanoparticles analyzed by AFM on a mica/air interface (Link)

Sajja S#, Chandler M#, Federov D, Kasprzak WK, Lushnikov AY, Viard M, Shah A, Dang D, Dahl J, Worku B, Dobrovolskaia MA, Krasnoslobodtsev A, Shapiro BA, Afonin KA

Langmuir, 34(49): 15099-15108, 2018 (doi: 10.1021/acs.langmuir.8b00105)

(# – equal contribution)



1  Label-free single-molecule thermoscopy using a laser-heated nanopore (Link)

Yamazaki H, Hu R, Henley RY, Halman J, Afonin KA, Yu D, Zhao Q, Wanunu M

Nano Letters, 17(11): 7067-7074, 2017 (doi: 10.1021/acs.nanolett.7b03752)


2  Programmable nucleic acid-based polygons with controlled neuroimmunomodulatory properties for predictive QSAR modeling (Link)

Johnson MB#, Halman JR#, Satterwhite E, Zakharov AV, Bui MN, Benkato K, Goldsworthy V, Kim TJ, Hong E, Dobrovolskaia MA, Khisamutdinov E, Marriott I, Afonin KA

Small, 13(42), 2017 (doi: 10.1002/smll.201701255)

(# – equal contribution)


3  Picomolar fingerprinting of nucleic acid nanoparticles using solid-state nanopores (Link)

Alibakhshi MA#, Halman JR#, Wilson J#, Aksimentiev A*, Afonin KA*, Wanunu M*

ACS Nano, 11(10): 9701-9710, 2017  (doi: 10.1021/acsnano.7b04923)

(# – equal contribution; * – corresponding authors) 


4  Preparation of a conditional RNA switch (Link)

Zakrevsky P, Parlea L, Viard M, Bindewald E, Afonin KA, Shapiro BA

Methods Mol Biol, 1632: 303-324, 2017 (doi: 10.1007/978-1-4939-7138-1_20)


5   Intracellular reassociation of RNA-DNA hybrids that activates RNAi in HIV-infected cells (Link)

Martins AN, Ke W, Jawahar V, Striplin M, Striplin C, Freed EO, Afonin KA

Methods Mol Biol, 1632: 269-283, 2017 (doi: 10.1007/978-1-4939-7138-1_18)


6   Cotranscriptional production of chemically modified RNA nanoparticles (Link)

Kireeva ML, Afonin KA, Shapiro BA, Kashlev M

Methods Mol Biol, 1632: 91-105, 2017 (doi: 10.1007/978-1-4939-7138-1_6)


7   Functionally-interdependent shape-switching nanoparticles with controllable properties (Link)

Halman JR, Satterwhite E, Roark B, Chandler M, Viard M, Ivanina A, Bindewald E, Kasprzak WK, Panigaj M, Bui MN, Lu JS, Miller J, Khisamutdinov EF, Shapiro BA, Dobrovolskaia MA, Afonin KA

Nucleic Acids Research, 45(4): 2210-2220, 2017 (doi: 10.1093/nar/gkx008)


8   Versatile RNA tetra-U helix linking motif as a toolkit for nucleic acid nanotechnology (Link)

Bui MN, Johnson MB, Viard M, Satterwhite E, Martins AN, Li Z, Marriott I, Afonin KA, Khisamutdinov EF

Nanomedicine: Nanotechnology, Biology, and Medicine, 13(3): 1137-1146, 2017 (doi: 10.1016/j.nano.2016.12.018)



1  Meeting Report: 2016 RNA Nanotechnology Conference – Fusion Conferences Limited (Link)

Haque F and Afonin KA

DNA and RNA Nanotechnology, 3: 23-27, 2016 (doi: 10.1515/rnan-2016-0004)


2  Fluorescence blinking as an output signal for biosensing (Link)

Roark B, Tan JA, Ivanina A, Chandler M, Castaneda J, Kim HS, Jawahar S, Viard M, Talic S, Wustholz KL, Yingling YG, Jones M, Afonin KA

ACS Sensors, 1(11): 1295-1300, 2016 (doi: 10.1021/acssensors.6b00352)


3  Programmable RNA microstructures for coordinated delivery of siRNAs (Link)

Stewart JM, Viard M, Subramanian HKK, Roark BKAfonin KA*, Franco E*

Nanoscale. 8(40): 17542-17550, 2016 (* – corresponding authors) (doi: 10.1039/C6NR05085A)


4  Cellular delivery of RNA Nanoparticles (Link)

Parlea L, Puri A, Kasprzak WK, Bindewald W, Zakrevsky P, Satterwhite E, Joseph K, Afonin KA, Shapiro BA

ACS Combinatorial Science. 18(9): 527-547, 2016 (doi: 10.1021/acscombsci.6b00073)


5  Ring catalog: a resource for designing self-assembling RNA nano-structures (Link)

Parlea L, Bindewald E, Sharan R, Bartlett N, Moriarty D, Oliver J, Afonin KA, Shapiro BA

Methods. 103(2): 128-137, 2016 (doi: 10.1016/j.ymeth.2016.04.016)


6  Multistrand structure prediction of nucleic acid assemblies and design of RNA switches (Link)

Bindewald E#, Afonin KA#, Viard M, Zakrevsky P, Kim T, Shapiro BA

Nano Letters. 16(3): 1726-1735, 2016 (# – equal contribution) (doi: 10.1021/acs.nanolett.5b04651)


7  The use of minimal RNA toeholds to trigger the activation of multiple functionalities (Link)

Afonin KA*, Viard M, Tedbury P, Bindewald E, Parlea L, Howington M, Valdman M, Johns-Boehme A, Brainerd C, Freed EO, Shapiro BA*

Nano Letters. 16(3): 1746-1753, 2016 (* – corresponding authors) (doi: 10.1021/acs.nanolett.5b04676)


8  Triggerable RNA nanodevices (Link)

Halman J, Satterwhite E, Smollett J, Bindewald E, Parlea L, Viard M, Zakrevsky P, Kasprzak WK, Afonin KA*, Shapiro BA*

RNA and Disease. 3: e1349, 2016 (* – corresponding authors) (doi: 10.14800/rd.1349)



1  Bolaamphiphiles as carriers for siRNA delivery: from chemical syntheses to practical applications (Link)

Gupta K#, Afonin KA#, Viard M#, Herrero V, Kasprzak W, Kagiampakis I, Kim TJ Koyfman AY, Puri A, Stepler A, Sappe A, KewalRamani VN, Grinberg S, Linder C, Heldman E, Blumenthal R, Shapiro BA

Journal of Controlled Release. 213: 142-151, 2015 (# – equal contribution) (doi: 10.1016/j.jconrel.2015.06.041)


2  Oxime ether lipids containing hydroxylated head groups are more superior siRNA delivery agents than their nonhydroxylated counterparts (Link)

Gupta K, Mattingly SJ, Knipp RJ, Afonin KA, Viard M, Bergman JT, Stepler M, Nantz MH, Puri A, Shapiro BA

Nanomedicine. 10(18): 2805-2818, 2015 (doi: 10.2217/nnm.15.105)


3  Triggering of RNA interference with RNA-RNA, RNA-DNA and DNA-DNA nanoparticles (Link)

Afonin KA, Viard M, Kagiampakis I, Case C, Dobrovolskaia M, Hofmann J, Vrzak A, Kireeva M, Kasprzak WK, KewalRamani VN, Shapiro BA.

ACS Nano. 9(1): 251-259, 2015 (doi: 10.1021/nn504508s)


4  Triggering RNAi with multifunctional RNA nanoparticles and their delivery (Link)

Dao BN, Viard M, Martins AN, Kasprzak WK, Shapiro BA, Afonin KA

DNA and RNA Nanotechnology. 2(1): 1-12, 2015 (doi: 10.1515/rnan-2015-0001)


5  Silver nanoclusters for RNA nanotechnology: steps towards visualization and tracking of RNA nanoparticle assemblies (Link)

Afonin KA, Schultz D, Jaeger L, Gwinn E, Shapiro BA

Methods in Molecular Biology. 1297: 59-66, 2015 (doi: 10.1007/978-1-4939-2562-9_4)


6  Computational and experimental studies of re-associating RNA/DNA hybrids containing split functionalities (Link)

Afonin KA, Bindewald E, Kireeva M, Shapiro BA  

Methods in Enzymology. 553: 313-334, 2015 (doi: 10.1016/bs.mie.2014.10.058)


7  RNA and DNA nanoparticles for triggering RNA interference (Link)

El Tannir Z, Afonin KA*, and Shapiro BA*

RNA and Disease. 2(3): e724, 2015 (* – corresponding authors) (doi: 10.14800/rd.724)



1  Multifunctional RNA nanoparticles (Link)

Afonin KA, Viard M, Koyfman AY, Martins AN, Kasprzak WK, Panigaj M, Desai R, Santhanam A, Grabow WW, Jaeger L, Heldman E, Reiser J, Chiu W, Freed EO, Shapiro BA

Nano Letters. 14(10): 5662-5671, 2014 (doi: 10.1021/nl502385k)


2  Co-transcriptional production of RNA-DNA hybrids for simultaneous release of multiple split functionalities (Link)

Afonin KA, Desai R, Viard M, Kireeva M, Bindewald E, Case CL, Maciag AE,  Kasprzak WK, Kim T, Sappe A, Stepler M, KewalRamani VN, Kashlev M, Blumenthal R, Shapiro BA

Nucleic Acids Research. 42(3): 2085-2097, 2014 (doi: 10.1093/nar/gkt1001)


3  In silico design and enzymatic synthesis of functional RNA nanoparticles (Link)

Afonin KA, Kasprzak WK, Bindewald E, Kireeva M, Viard M, Kashlev M, Shapiro B.

Accounts of Chemical Research. 47(6): 1731–1741, 2014 (doi: 10.1021/ar400329z)



1  Activation of different split functionalities on re-association of RNA–DNA hybrids (Link)

Afonin KA, Viard M, Martins AN, Lockett SJ, Maciag AE, Freed EO, Heldman E, Jaeger L, Blumenthal R, Shapiro BA.

Nature Nanotechnology. 8(4): 296-304, 2013 (doi: 10.1038/nnano.2013.44)


2  Computational and experimental characterization of RNA cubic nanoscaffolds (Link)

Afonin KA, Kasprzak WK, Bindewald E, Puppala PS, Diehl ER, Kim TJ, Zimmermann MT, Jernigan RL, Jaeger L, Shapiro BA.

Methods. 67(2): 256-265, 2013 (doi: 10.1016/j.ymeth.2013.10.013)


3  Engineered RNA nanodesigns for applications in RNA nanotechnology (Link)

Afonin KA, Lindsay B, Shapiro BA

DNA and RNA Nanotechnology. 1(1): 1-15, 2013 (doi: 10.2478/rnan-2013-0001)


4  In silicoin vitro and in vivo studies indicate the potential use of bolaamphiphiles for therapeutic siRNAs delivery (Link)

Kim TJ#, Afonin KA#, Viard M, Koyfman AY, Sparks S, Heldman E, Grinberg S, Linder C, Blumenthal RP, Shapiro BA

Molecular Therapy-Nucleic Acids. 2(3): e80, 2013 (# – equal contribution) (doi: 10.1038/mtna.2013.5)



1  Co-transcriptional assembly of chemically modified RNA nanoparticles functionalized with siRNAs (Link)

Afonin KA, Kireeva M, Grabow WW, Kashlev M, Jaeger L, Shapiro BA

Nano Letters. 12(10): 5192-5195, 2012 (doi: 10.1021/nl302302e)


2  Attenuation of loop-receptor interactions with pseudoknot formation (Link)

Afonin KA, Lin YP, Calkins ER, Jaeger L

Nucleic Acids Research. 40(5): 2168-2180, 2012 (doi: 10.1093/nar/gkr926)


3  RNA nanotechnology in nanomedicine (Link)

Grabow WW, Afonin KA, Geary C, Walker FM, Shapiro BA, and Jaeger L

Chapter in Nanomedicine and Drug Delivery, edited by Sebastian M, Ninan N, and Haghi AK

ISBN 978-1-926895-17-8. Toronto, New Jersey: Apple Academic Press, (Vol. 1),  208-221, 2012. 



1  Design and self-assembly of siRNA-functionalized RNA nanoparticles for use in automated nanomedicine (Link)

Afonin KA, Grabow WW, Walker FM, Bindewald E, Dobrovolskaia MA, Shapiro BA. Jaeger L

Nature Protocols. 6(12): 2022-2034, 2011 (doi: 10.1038/nprot.2011.418)


2  Multi-strand RNA structure prediction and nanostructure design including pseudoknots (Link)

Bindewald E, Afonin K, Jaeger L, Shapiro BA

ACS Nano. 5(12): 9542-9551, 2011 (doi: 10.1021/nn202666w)


3  Self-assembling RNA nanorings based on RNAI/II inverse kissing complexes (Link)

Grabow WW, Zakversky P, Afonin KA, Chworos A, Shapiro BA, Jaeger L

Nano Letters. 11(2): 878-887, 2011 (doi: 10.1021/nl104271s)



1  In vitro assembly of cubic RNA-based scaffolds designed in silico (Link)

Afonin KA, Bindewald E, Yaghoubian AJ, Voss N, Jacovetty E, Shapiro BA, and Jaeger L

Nature Nanotechnology. 5(9): 676-682, 2010 (doi: 10.1038/nnano.2010.160)


2  New ideas for in vivo detection of RNA (Link)

Novikova IV, Afonin KA, and Leontis NB

Chapter in Biosensors, edited by Serra PA 

ISBN 978-953-7619-99-2. Vienna, Austria: InTech Publishers, (Vol. 1), 127-150, 2010.



Specific RNA self-assembly with minimal paranemic motifs (Link)

Afonin KA, Cieply DJ, and Leontis NB

Journal of the American Chemical Society. 130(1): 93-102, 2008 (doi: 10.1021/ja071516m)


TokenRNA: A new type of sequence specific, label-free fluorescent biosensor for folded RNA molecules (Link)

Afonin KA, Danilov E, Novikova IV, Leontis NB

ChemBioChem. 9(12): 1902-1905, 2008 (doi: 10.1002/cbic.200800183)


Calculation of splicing potential from the alternative splicing mutation database (Link)

Bechtel J. M Rajesh P, Deng Y, Ilikchya I, Mishra P, Afonin KA, Wang Q, Wu X, Grose W, Wang Y, Khuder S, and Fedorov A

BMC Research Notes. 1:4: 1-6, 2008 (doi: 10.1186/1756-0500-1-4)


The alternative splicing mutation database: A hub for investigations of alternative splicing using mutational evidence (Link)

Bechtel JM, Ilikchyan I, Rajesh P, Deng Y, Mishra P, Afonin KA, Wang Q, Wu X, Grose W, Wang Y, Khuder S, and Fedorov A

BMC Research Notes. 1:3: 1-7, 2008 (doi: 10.1186/1756-0500-1-3)


Generating new specific RNA interaction interfaces using C-loops (Link)

Afonin KA and Leontis NB

Journal of the American Chemical Society. 128(50): 16131-16137, 2006 (doi: 10.1021/ja064289h)

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