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.)



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

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

Journal of Chemical Education, 2020. (doi: 10.1021/acs.jchemed.0c00158)

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

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

Nanomedicine, 2020. (doi: 10.2217/nnm-2020-0034)

3  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, 2020. (doi: 10.1186/s12974-020-01817-1)

4  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, 2020. (doi: 10.1016/j.omtn.2020.02.011)

5  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)

6  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. (# – equal contribution). (doi: 10.1021/acs.langmuir.8b00105)



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 (# – equal contribution). (doi: 10.1002/smll.201701255)


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 (# – equal contribution; * – corresponding authors). (doi: 10.1021/acsnano.7b04923) 


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 Mathew Sebastian, Neethu Ninan, and A.K. Haghi.

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 Pier Andrea Serra. 

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)