PUBLICATIONS

Publications as an ASU faculty member

(*= corresponding author)

T. MacCulloch, N. Stephanopoulos*, “Proximity-enhanced synthesis of DNA-peptide-DNA triblock molecules” (submitted)

J. Bernal-Chanchavacǂ, M. Al-Aminǂ, N. Stephanopoulos*, “Nanoscale structures and materials from the self-assembly of polypeptides and DNA” (submitted; ǂ co-first authors)

C.R. Simmonsǂ, T. MacCullochǂ, M. Krepl, M. Matthies, A. Buchberger, I. Crawford, J. Sponer, P. Sulc, Y. Liu, N. Stephanopoulos*, H. Yan*, “A Comprehensive Structural and Computational Toolbox of Immobile Holliday Junctions for DNA-directed Self-assembly” (submitted; ǂ co-first authors)

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*, “The ‘living interface’: a bridge between synthetic biology and biomaterial” (in revision; invited perspective/review for Nature Materials)

T. Yuan, Y. Shao, X. Zhou, Q. Liu, Z. Zhu, B. Zhou, Y. Dong, N. Stephanopoulos, S. Gui*, H. Yan*, D. Liu*, “Highly permeable DNA hydrogel promotes neurogenesis and functional recovery after completely transected spinal cord injury” (submitted)

B.I. Martinez, G. Mousa, K. Fleck, T. MacCulloch, C.W. Diehnelt, N. Stephanopoulos, S.E. Stabenfeldt*, “Uncovering temporally sensitive targeting domains for traumatic brain injury via phage display(submitted) pre-print on bioRxiv

A. Buchberger, R.P. Narayanan, J. Bernal-Chanchavac, C.R. Simmons, K. Riker, N.E. Fahmi, R. Freeman, N. Stephanopoulos*, “Integrating proteins and DNA nanostructures using orthogonal coiled-coil peptides” (submitted)

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

A. Gangrade*, N. Stephanopoulos, D. Bhatia*, “Programmable, self-assembled DNA nanodevices for cellular programming and tissue engineering” (accepted)

“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*, “Effect of the protein corona on endosomal escape of functionalized DNA nanostructuresACS Appl. Mater. Interfaces (accepted; ASAP online)

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

2021 WIREs TOC figure.tif

A. Buchbergerǂ, H. Sainiǂ, K.R. Eliatoǂ, R. Merkley, Y. Xu, A. Zare, J. Bernal, R. Ros*, M. Nikkhah*, N. Stephanopoulos*, “Reversible control of gelatin hydrogel stiffness using DNA crosslinkersChemBioChem (2021) 22:1755–1760. (ǂco-first authors) 

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

N. Stephanopoulos*, “Hybrid nanostructures from the self-assembly of proteins and DNA” Chem (2020) 6:364–405.

Download PDF

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

A. Buchberger, C.R. Simmons, N.E. Fahmi, R. Freeman, N. Stephanopoulos* "Hierarchical Assembly of Nucleic Acid/Coiled-Coil Peptide Nanostructures" J. Am. Chem. Soc. (2020) 3:1406-1416.

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

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

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

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

Label-Free Detection of Conformational.j

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

download.png

M. Liu, S. Jiang, O. Loza, P. Sulc, N.E. Fahmi, N. Stephanopoulos* “Rapid Photoactuation of a DNA Nanostructure using an Internal Photocaged Trigger StrandAngew. 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)

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

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

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

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*, “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)Acta Biomater. (2017) 48:120-130.

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)

Publications prior to ASU 

(* = co-first authors)

 

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, “Reversible self-assembly of superstructured networksScience (2018) 362:808-813.

2018 Science PA-DNA.jpg

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

Instructing cells with programmable DNA-peptide hybrids

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 “Creating a stem cell niche in the inner ear using self-assembling peptide amphiphiles PLoS ONE (2017) 12:e0190150.

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

Instructing cells with programmable DNA-peptide hybrids

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

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

Bioactive DNA-Peptide Nanotubes Enhance the Differentiation of Neural Stem Cells Into Neurons

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

A bioengineered peripheral nerve construct using aligned peptide amphiphile nanofibers

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

 

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

Antibody-guided photoablation of voltage-gated potassium channels

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

 

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

Dramatic Thermal Stability of Virus-Polymer Conjugates in Hydrophobic Solvents

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

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

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

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

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

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

N. Stephanopoulos, Z.M. Carrico, M.B. Francis, “Nanoscale Integration of Sensitizing Chromophores and Porphyrins Using Bacteriophage MS2Angew. Chem. Int. Ed. (2009) 121:9662-9666.

Nanoscale Integration of Sensitizing Chromophores and Porphyrins Using Bacteriophage MS2

N. Stephanopoulos, E.O.P. Solis, G. Stephanopoulos, “Nanoscale process systems engineering: Toward molecular factories, synthetic cells, and adaptive devices” (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)