PUBLICATIONS

Publications as an ASU faculty member

(*= corresponding author)

Self-assembly of hybrid peptide-DNA nanostructures using homotrimeric coiled-coil/nucleic acid building blocks. A. Buchberger, Md Al-Amin, C.R. Simmons, N. Stephanopoulos*. (in preparation)

Temporal control of cell adhesion ligands to improve osteogenesis using a reversible in vitro DNA-based hydrogel platform. F.M. Fumasi, T. MacCulloch, N. Stephanopoulos*, J.L. Holloway*. (in preparation)

Coarse-grained simulations for the characterization and optimization of hybrid protein-DNA nanostructures. R.P. Narayananǂ, J. Procykǂ, P. Nandi, A. Prasad, Y. Xu, E. Poppleton, D. Williams, F. Zhang, H. Yan, P.-L. Chiu*, N. Stephanopoulos*, P. Sulc*. (submitted; ǂ co-first authors)

Interactions of DNA Nanostructures with Cells: A Roadmap for Successful Applications in Biomedicine. O. Lunov*, A. Frtús, B. Smolková, M. Uzhytchak, M. Lunova, M. Jirsa, S.J.W. Henry, N. Stephanopoulos, A. Dejneka. (submitted)

Uncovering temporospatial sensitive TBI targeting strategies via in vivo phage display. B.I. Martinez, G. Mousa, K. Fleck, T. MacCulloch, C.W. Diehnelt, N. Stephanopoulos, S.E. Stabenfeldt*. Sci. Adv. (2022; accepted)

Bioactive Fibronectin-III10-DNA Origami Nanofibers Promote Cell Adhesion and Spreading. A. Buchbergerǂ, K. Rikerǂ, J. Bernal-Chanchavac, R.P. Narayanan, C.R. Simmons, N.E. Fahmi, R. Freeman*, N. Stephanopoulos*, “Bioactive Fibronectin-III10-DNA Origami Nanofibers Promote Cell Adhesion and Spreading” (submitted; ǂ co-first authors; pre-print on ChemRxiv)

Supramolecular polymerization of DNA nanostructures using high-affinity host-guest interactions. R.P. Narayanan, A. Buchberger, L. Zhou, N.E. Fahmi, H. Yan, F. Zhang M.J. Webber*, N. Stephanopoulos*. (submitted)

The influence of Holliday junction sequence and dynamics on DNA crystal self-assembly. C.R. Simmonsǂ, T. MacCullochǂ, M. Krepl, M. Matthies, A. Buchberger, I. Crawford, J. Sponer, P. Sulc, Y. Liu, N. Stephanopoulos*, H. Yan*. Nat. Commun. (2022) 13:3112 (ǂ co-first authors)

Nanoscale structures and materials from the self-assembly of polypeptides and DNA. J. Bernal-Chanchavacǂ, M. Al-Aminǂ, N. Stephanopoulos*. Curr. Top. Med. Chem. (2022; accepted; ǂ co-first authors; ASAP online)

The living interface between synthetic biology and biomaterial design. A.P. Liu*, E. Appel, P. Ashby, B. Baker, E. Franco, L. Guo, K. Haynes, N. Joshi, A. Kloxin, P. Kouwer, J. Mittal, L. Morsut, V. Noireaux, S. Parekh, R. Schulman, S. Tang, M. Valentine, S. Vega, W. Weber, N. Stephanopoulos*, O. Chaudhuri*. Nat. Mater. (2022) 21:390-397. (see accompanying editorial)

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Proximity-enhanced synthesis of DNA-peptide-DNA triblock molecules. T. MacCulloch, N. Stephanopoulos*. Chem. Commun. (2022) 58:4044-4047.

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Programmable, self-assembled DNA nanodevices for cellular programming and tissue engineering. A. Gangrade*, N. Stephanopoulos, D. Bhatia*. Nanoscale (2021) 13:16834-16846.

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Effect of the protein corona on endosomal escape of functionalized DNA nanostructures. B. Smolková, T. MacCulloch, T. Rockwood, M. Liu, S.J.W. Henry, A. Frtús, M. Uzhytchak, M. Lunova, M. Hof, P. Jurkiewicz, A. Dejneka, N. Stephanopoulos*, O. Lunov*. ACS Appl. Mater. Interfaces (2021) 13:46375–46390.

Highly permeable DNA supramolecular hydrogel promotes neurogenesis and functional recovery after completely transected spinal cord injury. T. Yuan, Y. Shao, X. Zhou, Q. Liu, Z. Zhu, B. Zhou, Y. Dong, N. Stephanopoulos, S. Gui*, H. Yan*, D. Liu*. Adv. Mater. (2021) 33:2102428.

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Functionalizing DNA nanostructures for therapeutic applications. S.J.W. Henry, N Stephanopoulos*. Wiley Interdiscip. Rev. Nanomed. Nanobiotechnol. (2021) 13:e1729.

Reversible control of gelatin hydrogel stiffness using DNA crosslinkers. A. Buchbergerǂ, H. Sainiǂ, K.R. Eliatoǂ, R. Merkley, Y. Xu, A. Zare, J. Bernal, R. Ros*, M. Nikkhah*, N. Stephanopoulos*. ChemBioChem (2021) 22:1755–1760. (ǂco-first authors; selected as a “Very Important Paper” by the journal)

DNA nanodevices as mechanical probes of protein structure and functionN. Stephanopoulos*, P. Sulc. Appl. Sci. (2021) 11:2802.

A Self‐Assembled Rhombohedral DNA Crystal Scaffold with Tunable Cavity Sizes and High‐Resolution Structural Detail. C.R. Simmonsǂ, T. MacCullochǂ, F. Zhang, Y. Liu, N. Stephanopoulos*, H. Yan*. Angew. Chem. Int. Ed. (2020) 59:18619-18626. (ǂco-first authors)

Hybrid nanostructures from the self-assembly of proteins and DNAN. Stephanopoulos*.  Chem (2020) 6:364–405.

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Reversible Control of Biomaterial Properties for Dynamically Tuning Cell Behavior. F.M. Fumasi, N. Stephanopoulos, J.L. Holloway*. J. Appl. Polym. Sci. (2020) 137:e49058.

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Hierarchical Assembly of Nucleic Acid/Coiled-Coil Peptide Nanostructures. A. Buchberger, C.R. Simmons, N.E. Fahmi, R. Freeman, N. Stephanopoulos*. J. Am. Chem. Soc. (2020) 3:1406-1416. (selected as “ACS Editor’s Choice” article)

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Peptide–Oligonucleotide Hybrid Molecules for Bioactive NanomaterialsN. Stephanopoulos*. Bioconj. Chem. (2019) 30:1915-1922.

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Strategies for stabilizing DNA nanostructures to biological conditions.   N. Stephanopoulos* . ChemBioChem (2019) 20:2191-2197.

Tunable nanoscale cages from self-assembling DNA and protein building blocks. Y. Xu, S. Jiang, C. Simmons, R.P. Narayanan, F. Zhang, A.-M. Aziz, H. Yan, N. Stephanopoulos*.  ACS Nano (2019) 13:3545–3554.

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Label-Free Detection of Conformational Changes in Switchable DNA Nanostructures with Microwave Microfluidics. A. Stelson, M. Liu, C.A.E. Little, C.J. Long, N.D. Orloff, N. Stephanopoulos*, J.C. Booth*. Nat. Commun. (2019) 10:1174.

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Emerging applications of peptide–oligonucleotide conjugates: bioactive scaffolds, self-assembling systems, and hybrid nanomaterials. T. MacCulloch, A. Buchberger, N. Stephanopoulos*. Org. Biomol. Chem. (2019) 17:1668-1682.

Rapid photo-actuation of a DNA nanostructure using an internal photocaged trigger strand

Rapid Photoactuation of a DNA Nanostructure using an Internal Photocaged Trigger Strand. M. Liu, S. Jiang, O. Loza, P. Sulc, N.E. Fahmi, N. Stephanopoulos*. Angew. Chem. Int. Ed. (2018) 57:9341 –9345. (selected as paper for Wiley’s Joint Special Collection on Biopolymers, for the Murray Goodman Award Symposium at the 2019 ACS Spring Meeting: bit.ly/wileybiopolymers19)

Tuning the Cavity Size and Chirality of Self-Assembling 3D DNA Crystals

Tuning the Cavity Size and Chirality of Self-Assembling 3D DNA Crystals. C. Simmons, F. Zhang, T. MacCulloch, N.E. Fahmi, N. Stephanopoulos, Y. Liu, N. Seeman, H. Yan*, J. Am. Chem. Soc. (2017) 139:11254-11260.

A Robust Vintronectin-Derived Peptide for the Scalable Long-term Expansion and Neuronal Differentiation of Human Pluripotent Stem Cell (hPSC)-derived Neural Progenitor Cells (hNPCs)

A Robust Vintronectin-Derived Peptide for the Scalable Long-term Expansion and Neuronal Differentiation of Human Pluripotent Stem Cell (hPSC)-derived Neural Progenitor Cells (hNPCs). D. Varun, G.R. Srinivaan, Y.-H. Tsai, H.-J. Kim, J. Cutts, F. Petty, R. Merkley, N. Stephanopoulos, D. Dolezalova, M. Marsala, D.A. Brafman*. Acta Biomater. (2017) 48:120-130.

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Publications prior to ASU 

(* = co-first authors)

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Reversible self-assembly of superstructured networks. R. Freeman, M. Han, Z. Álvarez, J.A. Lewis, J.R. Wester, N. Stephanopoulos, M.T. McClendon, C. Lynsky, J.M. Godbe, H. Sangji, E. Luijten, S.I. Stupp. Science (2018) 362:808-813.

Instructing cells with programmable DNA-peptide hybrids

Electrophysiological assessment of a peptide amphiphile nanofiber nerve graft for facial nerve repair. J.J. Greene, M.T. McClendon, N. Stephanopoulos, S.I. Stupp, C.-P. Richter. J. Tissue Eng. Regen. Med. (2018) 12:1389–1401.

Creating a stem cell niche in the inner ear using self-assembling peptide amphiphiles. A.J. Matsuoka , Z.A. Sayed, N. Stephanopoulos, E.J. Berns, A.R. Wadhwani, Z.D. Morrissey, D.M. Chadly, S. Kobayashi, A.N. Edelbrock, T. Mashimo, C.A. Miller, T.L. McGuire, S.I. Stupp, J.A. Kessler. PLoS ONE (2017) 12:e0190150.

Instructing cells with programmable DNA-peptide hybrids

Instructing cells with programmable DNA-peptide hybrids. R. Freeman*, N. Stephanopoulos*, Z. Álvarez, J.A. Lewis, S. Sur, C.M. Serrano, J. Boekhoven, S.S. Lee, S.I. Stupp. Nat. Commun. (2017) 8:15982

The Powerful Functions of Peptide-Based Bioactive Matrices for Regenerative Medicine. C. Rubert-Perez, N. Stephanopoulos, S.S. Lee, S. C. Newcomb, Sur, S.I. Stupp. (invited review) Ann. Biomed. Eng. (2015) 43:501-514.

Bioactive DNA-Peptide Nanotubes Enhance the Differentiation of Neural Stem Cells Into Neurons
A bioengineered peripheral nerve construct using aligned peptide amphiphile nanofibers

Bioactive DNA-Peptide Nanotubes Enhance the Differentiation of Neural Stem Cells Into NeuronsN. Stephanopoulos, R. Freeman, H.N. Scheler, S. Sur, S. Jeong, F. Tantakitti, J.A. Kessler, S.I. Stupp. Nano Lett. (2015) 15:603-609.

A bioengineered peripheral nerve construct using aligned peptide amphiphile nanofibers. A. Li, A. Hokugo, A. Yalom, E.J. Berns, N. Stephanopoulos, M.T. McClendon, L.A. Segovia, I. Spigelman, S.I. Stupp, R. Jarrahy. Biomaterials (2014) 35:8780-8790.

Self-Assembly for the Synthesis of Functional BiomaterialsN. Stephanopoulos, J.H. Ortony, S.I. Stupp. (invited review) Acta Materialia (2013) 61:912-930.

Antibody-guided photoablation of voltage-gated potassium channels

Antibody-guided photoablation of voltage-gated potassium channels. J. Sack, N. Stephanopoulos, D.C. Austin, M.B. Francis, J.S. Trimmer. J. Gen. Physiol. (2013) 142:315-324.

Choosing an Effective Protein Bioconjugation StrategyN. Stephanopoulos, M.B. Francis. (invited review) Nat. Chem. Biol. (2011) 7:876-884.

Dramatic Thermal Stability of Virus-Polymer Conjugates in Hydrophobic Solvents

Dramatic Thermal Stability of Virus-Polymer Conjugates in Hydrophobic Solvents. P.G. Holder, D.T. Finley, N. Stephanopoulos, R. Walton, D.S. Clark, M.B. Francis. Langmuir (2010) 26:17383–17388.

Dual-Surface Modified Virus Capsids for Targeted Delivery of Photodynamic Agents to Cancer Cells

Dual-Surface Modified Virus Capsids for Targeted Delivery of Photodynamic Agents to Cancer CellsN. Stephanopoulos, G.J. Tong, S.C. Hsiao, M.B. Francis. ACS Nano (2010) 4:6014-6020.

Immobilization and One-Dimensional Arrangement of Virus Capsids with Nanoscale Precision Using DNA Origami

Immobilization and One-Dimensional Arrangement of Virus Capsids with Nanoscale Precision Using DNA OrigamiN. Stephanopoulos*, M. Liu*, G.J. Tong, Z. Li, Y. Liu, H. Yan, M.B. Francis. Nano Lett. (2010) 10:2714-2720.

The Impact of Assembly State on the Defect Tolerance of TMV-based Light Harvesting Arrays

The Impact of Assembly State on the Defect Tolerance of TMV-based Light Harvesting Arrays. R.A. Miller, N. Stephanopoulos, J.M. McFarland, A.S. Rosko, P.L. Geissler, M.B. Francis. J. Am. Chem. Soc. (2010) 132:6068-6074.

Nanoscale Integration of Sensitizing Chromophores and Porphyrins Using Bacteriophage MS2

Nanoscale Integration of Sensitizing Chromophores and Porphyrins Using Bacteriophage MS2N. Stephanopoulos, Z.M. Carrico, M.B. Francis. Angew. Chem. Int. Ed. (2009) 121:9662-9666.

Nanoscale process systems engineering: Toward molecular factories, synthetic cells, and adaptive devicesN. Stephanopoulos, E.O.P. Solis, G. Stephanopoulos. (invited perspective) AIChE J. (2005) 51:1858-1869.

Invited book chapters

(*= corresponding author)

N. Stephanopoulos*, R. Freeman*, “DNA-based materials as self-assembling scaffolds for interfacing with cells”, “Self-Assembling Biomaterials: Molecular Design, Characterization and Application in Biology and Medicine, 1st Edition” 2018, pp. 157-175. (Elsevier)

L. Avolio, D. Sipes, N. Stephanopoulos, S. Sur*, “Recreating stem-cell niches using self-assembling biomaterials”, “Self-Assembling Biomaterials: Molecular Design, Characterization and Application in Biology and Medicine, 1st Edition” 2018, pp. 421-454. (Elsevier)

N. Stephanopoulos, M.B. Francis*, “Making New Materials from Viral Capsids”, “Polymer Science: A Comprehensive Reference, 1st Edition” 2012, Vol. 9, pp. 247-266. (Elsevier)