BI: Molecular Design and Biomimetics, Biodesign Institute Center for (MDB)

Research Output 2005 2019

2019
1 Citation (Scopus)

A Bayesian Nonparametric Approach to Single Molecule Förster Resonance Energy Transfer

Sgouralis, I., Madaan, S., Djutanta, F., Kha, R., Hariadi, R. & Presse, S., Jan 24 2019, In : Journal of Physical Chemistry B. 123, 3, p. 675-688 14 p.

Research output: Contribution to journalArticle

Bayes Theorem
Energy Transfer
Photons
Energy transfer
energy transfer

An emergent understanding of strand displacement in RNA biology

Hong, F. & Sulc, P., Jan 1 2019, In : Journal of Structural Biology.

Research output: Contribution to journalArticle

RNA
Nucleic Acid Conformation
DNA
Clustered Regularly Interspaced Short Palindromic Repeats
RNA Folding
2 Citations (Scopus)

Autonomous dynamic control of DNA nanostructure self-assembly

Green, L. N., Subramanian, H. K. K., Mardanlou, V., Kim, J., Hariadi, R. & Franco, E., Jan 1 2019, In : Nature Chemistry.

Research output: Contribution to journalArticle

Self assembly
Nanostructures
DNA
Nucleic acids
Nanotechnology
6 Citations (Scopus)

Autonomously designed free-form 2D DNA origami

Jun, H., Zhang, F., Shepherd, T., Ratanalert, S., Qi, X., Yan, H. & Bathe, M., Jan 1 2019, In : Science Advances. 5, 1, eaav0655.

Research output: Contribution to journalArticle

Open Access
DNA
Nanotechnology
3 Citations (Scopus)

Emerging applications of peptide-oligonucleotide conjugates: Bioactive scaffolds, self-assembling systems, and hybrid nanomaterials

Macculloch, T., Buchberger, A. & Stephanopoulos, N., Jan 1 2019, In : Organic and Biomolecular Chemistry. 17, 7, p. 1668-1682 15 p.

Research output: Contribution to journalReview article

Nanostructures
oligonucleotides
activity (biology)
assembling
Nanostructured materials

Enhanced Natural Killer Cell Immunotherapy by Rationally Assembling Fc Fragments of Antibodies onto Tumor Membranes

Ji, T., Lang, J., Ning, B., Qi, F., Wang, H., Zhang, Y., Zhao, R., Yang, X., Zhang, L., Li, W., Shi, X., Qin, Z., Zhao, Y. & Nie, G., Feb 8 2019, In : Advanced Materials. 31, 6, 1804395.

Research output: Contribution to journalArticle

Neoplasm Antibodies
Immunoglobulin Fc Fragments
Antibodies
Tumors
Membranes
1 Citation (Scopus)

Extracellular vesicles as cancer liquid biopsies: From discovery, validation, to clinical application

Zhao, Z., Fan, J., Hsu, Y. M. S., Lyon, C. J., Ning, B. & Hu, Y., Jan 1 2019, In : Lab on a Chip. 19, 7, p. 1114-1140 27 p.

Research output: Contribution to journalReview article

Biopsy
Biomarkers
Tumor Biomarkers
Liquids
Neoplasms

Label-free detection of conformational changes in switchable DNA nanostructures with microwave microfluidics

Stelson, A. C., Liu, M., Little, C. A. E., Long, C. J., Orloff, N. D., Stephanopoulos, N. & Booth, J. C., Dec 1 2019, In : Nature communications. 10, 1, 1174.

Research output: Contribution to journalArticle

Open Access
Microfluidics
Nanostructures
Microwaves
Labels
deoxyribonucleic acid

Nanotrap-enabled quantification of KRAS-induced peptide hydroxylation in blood for cancer early detection

Deng, Z., Zhao, Z., Ning, B., Basilio, J., Mann, K., Fu, J., Gu, Y., Ye, Y., Wu, X., Fan, J., Chiao, P. & Hu, Y., Jan 1 2019, In : Nano Research.

Research output: Contribution to journalArticle

Hydroxylation
Bradykinin
Peptides
Blood
Prolyl Hydroxylases
4 Citations (Scopus)

Paranemic Crossover DNA: There and Back Again

Wang, X., Chandrasekaran, A. R., Shen, Z., Ohayon, Y. P., Wang, T., Kizer, M. E., Sha, R., Mao, C., Yan, H., Zhang, X., Liao, S., Ding, B., Chakraborty, B., Jonoska, N., Niu, D., Gu, H., Chao, J., Gao, X., Li, Y., Ciengshin, T. & 1 others, Seeman, N. C., May 22 2019, In : Chemical reviews. 119, 10, p. 6273-6289 17 p.

Research output: Contribution to journalArticle

DNA
Molecular biology
Nanotechnology
Molecular structure
Transducers

Peptide-Oligonucleotide Hybrid Molecules for Bioactive Nanomaterials

Stephanopoulos, N., Jan 1 2019, In : Bioconjugate Chemistry.

Research output: Contribution to journalReview article

Nanostructures
Oligonucleotides
Nanostructured materials
Peptides
DNA
1 Citation (Scopus)

Redox Engineering of Cytochrome c using DNA Nanostructure-Based Charged Encapsulation and Spatial Control

Ge, Z., Su, Z., Simmons, C. R., Li, J., Jiang, S., Li, W., Yang, Y., Liu, Y., Chiu, W., Fan, C. & Yan, H., Apr 17 2019, In : ACS Applied Materials and Interfaces. 11, 15, p. 13874-13880 7 p.

Research output: Contribution to journalArticle

Cytochromes c
Encapsulation
Nanostructures
DNA
Proteins

Strategies for Stabilizing DNA Nanostructures to Biological Conditions

Stephanopoulos, N., Jan 1 2019, In : ChemBioChem.

Research output: Contribution to journalArticle

Nanostructures
DNA
Nanotechnology
Lipid bilayers
Lipid Bilayers
1 Citation (Scopus)

Tunable Nanoscale Cages from Self-Assembling DNA and Protein Building Blocks

Xu, Y., Jiang, S., Simmons, C. R., Narayanan, R. P., Zhang, F., Aziz, A. M., Yan, H. & Stephanopoulos, N., Mar 26 2019, In : ACS Nano. 13, 3, p. 3545-3554 10 p.

Research output: Contribution to journalArticle

assembling
DNA
deoxyribonucleic acid
proteins
Proteins

Watching a Single Fluorophore Molecule Walk into a Plasmonic Hotspot

Xin, L., Lu, M., Both, S., Pfeiffer, M., Urban, M. J., Zhou, C., Yan, H., Weiss, T., Liu, N. & Lindfors, K., Apr 17 2019, In : ACS Photonics. 6, 4, p. 985-993 9 p.

Research output: Contribution to journalArticle

Open Access
Fluorophores
emitters
Nanosystems
Light
fluorescence
2018
2 Citations (Scopus)

2D Enzyme Cascade Network with Efficient Substrate Channeling by Swinging Arms

Yang, Y. R., Fu, J., Wootten, S., Qi, X., Liu, M., Yan, H. & Liu, Y., Feb 2 2018, In : ChemBioChem. 19, 3, p. 212-216 5 p.

Research output: Contribution to journalArticle

Substrates
Enzymes
NAD
Atomic Force Microscopy
DNA
127 Citations (Scopus)

A DNA nanorobot functions as a cancer therapeutic in response to a molecular trigger in vivo

Li, S., Jiang, Q., Liu, S., Zhang, Y., Tian, Y., Song, C., Wang, J., Zou, Y., Anderson, G. J., Han, J. Y., Chang, Y., Liu, Y., Zhang, C., Chen, L., Zhou, G., Nie, G., Yan, H., Ding, B. & Zhao, Y., Mar 1 2018, In : Nature Biotechnology. 36, 3, p. 258-264 7 p.

Research output: Contribution to journalArticle

Nanorobots
Tumors
DNA
Neoplasms
Thrombin
11 Citations (Scopus)

A Synthetic Light-Driven Substrate Channeling System for Precise Regulation of Enzyme Cascade Activity Based on DNA Origami

Chen, Y., Ke, G., Ma, Y., Zhu, Z., Liu, M., Liu, Y., Yan, H. & Yang, C. J., Jul 18 2018, In : Journal of the American Chemical Society. 140, 28, p. 8990-8996 7 p.

Research output: Contribution to journalArticle

DNA
Enzymes
Light
Synthetic Biology
Substrates
4 Citations (Scopus)

Chemoresistance transmission via exosome-Mediated EphA2 transfer in pancreatic cancer

Fan, J., Wei, Q., Koay, E. J., Liu, Y., Ning, B., Bernard, P. W., Zhang, N., Han, H., Katz, M. H., Zhao, Z. & Hu, Y., Jan 1 2018, In : Theranostics. 8, 21, p. 5986-5994 9 p.

Research output: Contribution to journalArticle

Exosomes
Pancreatic Neoplasms
gemcitabine
Cell Line
Eph Family Receptors
47 Citations (Scopus)

Complex silica composite nanomaterials templated with DNA origami

Liu, X., Zhang, F., Jing, X., Pan, M., Liu, P., Li, W., Zhu, B., Li, J., Chen, H., Wang, L., Lin, J., Liu, Y., Zhao, D., Yan, H. & Fan, C., Jul 26 2018, In : Nature. 559, 7715, p. 593-598 6 p.

Research output: Contribution to journalLetter

Nanostructures
Silicon Dioxide
DNA
Biomimetics
Nanotechnology
1 Citation (Scopus)

Constructing Submonolayer DNA Origami Scaffold on Gold Electrode for Wiring of Redox Enzymatic Cascade Pathways

Ge, Z., Fu, J., Liu, M., Jiang, S., Andreoni, A., Zuo, X., Liu, Y., Yan, H. & Fan, C., Jan 1 2018, (Accepted/In press) In : ACS Applied Materials and Interfaces.

Research output: Contribution to journalArticle

Electric wiring
Scaffolds
Microelectronics
Gold
DNA
4 Citations (Scopus)

Direct Covalent Chemical Functionalization of Unmodified Two-Dimensional Molybdenum Disulfide

Chu, X. S., Yousaf, A., Li, D. O., Tang, A. A., Debnath, A., Ma, D., Green, A., Santos, E. J. G. & Wang, Q., Mar 27 2018, In : Chemistry of Materials. 30, 6, p. 2112-2128 17 p.

Research output: Contribution to journalArticle

Molybdenum
Transition metals
Salts
Scanning probe microscopy
Electronic properties
15 Citations (Scopus)

DNA-Guided Plasmonic Helix with Switchable Chirality

Lan, X., Liu, T., Wang, Z., Govorov, A. O., Yan, H. & Liu, Y., Sep 19 2018, In : Journal of the American Chemical Society. 140, 37, p. 11763-11770 8 p.

Research output: Contribution to journalArticle

Chirality
Nanotubes
DNA
Nanorods
Gold
10 Citations (Scopus)

DNA origami nanostructures can exhibit preferential renal uptake and alleviate acute kidney injury

Jiang, D., Ge, Z., Im, H. J., England, C. G., Ni, D., Hou, J., Zhang, L., Kutyreff, C. J., Yan, Y., Liu, Y., Cho, S. Y., Engle, J. W., Shi, J., Huang, P., Fan, C., Yan, H. & Cai, W., Nov 1 2018, In : Nature Biomedical Engineering. 2, 11, p. 865-877 13 p.

Research output: Contribution to journalArticle

Nanostructures
Acute Kidney Injury
DNA
Kidney
Positron emission tomography
1 Citation (Scopus)

Electrophysiological assessment of a peptide amphiphile nanofiber nerve graft for facial nerve repair

Greene, J. J., Mcclendon, M. T., Stephanopoulos, N., Álvarez, Z., Stupp, S. I. & Richter, C. P., Jan 1 2018, (Accepted/In press) In : Journal of Tissue Engineering and Regenerative Medicine.

Research output: Contribution to journalArticle

Nanofibers
Amphiphiles
Facial Nerve
Grafts
Peptides
15 Citations (Scopus)

Exploring the speed limit of toehold exchange with a cartwheeling DNA acrobat

Li, J., Johnson-Buck, A., Yang, Y. R., Shih, W. M., Yan, H. & Walter, N. G., May 7 2018, (Accepted/In press) In : Nature Nanotechnology. p. 1-7 7 p.

Research output: Contribution to journalArticle

DNA
deoxyribonucleic acid
Kinetics
locomotion
oligonucleotides
2 Citations (Scopus)

Layered-Crossover Tiles with Precisely Tunable Angles for 2D and 3D DNA Crystal Engineering

Hong, F., Jiang, S., Lan, X., Narayanan, R. P., Sulc, P., Zhang, F., Liu, Y. & Yan, H., Nov 7 2018, In : Journal of the American Chemical Society. 140, 44, p. 14670-14676 7 p.

Research output: Contribution to journalArticle

Crystal engineering
Tile
DNA
Nanotechnology
Nanoparticles
5 Citations (Scopus)

Metal-chelating non-canonical amino acids in metalloprotein engineering and design

Almhjell, P. J. & Mills, J., Aug 1 2018, In : Current Opinion in Structural Biology. 51, p. 170-176 7 p.

Research output: Contribution to journalReview article

Metalloproteins
Metals
Amino Acids
Ions
Proteins
4 Citations (Scopus)

PHF20 collaborates with PARP1 to promote stemness and aggressiveness of neuroblastoma cells through activation of SOX2 and OCT4

Long, W., Zhao, W., Ning, B., Huang, J., Chu, J., Li, L., Ma, Q., Xing, C., Wang, H. Y., Liu, Q. & Wang, R. F., Apr 1 2018, In : Journal of Molecular Cell Biology. 10, 2, p. 147-160 14 p.

Research output: Contribution to journalArticle

Octamer Transcription Factors
Neuroblastoma
Proteins
Stem Cells
Histone Code
29 Citations (Scopus)

Programmed coherent coupling in a synthetic DNA-based excitonic circuit

Boulais, E., Sawaya, N. P. D., Veneziano, R., Andreoni, A., Banal, J. L., Kondo, T., Mandal, S., Lin, S., Schlau-Cohen, G. S., Woodbury, N., Yan, H., Aspuru-Guzik, A. & Bathe, M., Feb 1 2018, In : Nature Materials. 17, 2, p. 159-166 8 p.

Research output: Contribution to journalArticle

DNA
deoxyribonucleic acid
Coloring Agents
Dyes
dyes
2 Citations (Scopus)

Programming molecular topologies from single-stranded nucleic acids

Qi, X., Zhang, F., Su, Z., Jiang, S., Han, D., Ding, B., Liu, Y., Chiu, W., Yin, P. & Yan, H., Dec 1 2018, In : Nature Communications. 9, 1, 4579.

Research output: Contribution to journalArticle

Nanostructures
nucleic acids
programming
Nucleic Acids
topology
7 Citations (Scopus)

Rapid Photoactuation of a DNA Nanostructure using an Internal Photocaged Trigger Strand

Liu, M., Jiang, S., Loza, O., Fahmi, N. E., Sulc, P. & Stephanopoulos, N., Jul 20 2018, In : Angewandte Chemie - International Edition. 57, 30, p. 9341-9345 5 p.

Research output: Contribution to journalArticle

Nanostructures
DNA
Bearings (structural)
Poly T
Poly A
11 Citations (Scopus)

Reversible self-assembly of superstructured networks

Freeman, R., Han, M., Álvarez, Z., Lewis, J. A., Wester, J. R., Stephanopoulos, N., McClendon, M. T., Lynsky, C., Godbe, J. M., Sangji, H., Luijten, E. & Stupp, S. I., Jan 1 2018, (Accepted/In press) In : Science.

Research output: Contribution to journalArticle

Hydrogels
Self assembly
Peptides
Molecules
Charge density
3 Citations (Scopus)

Ribocomputing: Cellular Logic Computation Using RNA Devices

Kim, J., Yin, P. & Green, A., Feb 13 2018, In : Biochemistry. 57, 6, p. 883-885 3 p.

Research output: Contribution to journalReview article

Animals
RNA
Messenger RNA
Synthetic Biology
3 Citations (Scopus)

Self-Assembly of a 3D DNA Crystal Structure with Rationally Designed Six-Fold Symmetry

Zhang, F., Simmons, C. R., Gates, J., Liu, Y. & Yan, H., Sep 17 2018, In : Angewandte Chemie - International Edition. 57, 38, p. 12504-12507 4 p.

Research output: Contribution to journalArticle

Crystal symmetry
Crystal lattices
Self assembly
DNA
Crystal structure

Use of a conformational switching aptamer for rapid and specific ex vivo identification of central nervous system lymphoma in a xenograft model

Georges, J. F., Liu, X., Eschbacher, J., Nichols, J., Mooney, M. A., Joy, A., Spetzler, R. F., Feuerstein, B. G., Anderson, T., Preul, M. C., Yan, H. & Nakaji, P., Jan 1 2018, Clinical and Translational Neurophotonics 2018. SPIE, Vol. 10480. 104800G

Research output: Chapter in Book/Report/Conference proceedingConference contribution

central nervous system
Neurology
B-Cell Lymphoma
Heterografts
Lymphoma
2017
3 Citations (Scopus)

A coarse-grained model captures the temporal evolution of DNA nanotube length distributions

Mardanlou, V., Yaghoubi, K. C., Green, L. N., Subramanian, H. K. K., Hariadi, R., Kim, J. & Franco, E., Dec 7 2017, (Accepted/In press) In : Natural Computing. p. 1-17 17 p.

Research output: Contribution to journalArticle

Nanotubes
DNA
Bins
Tile
Ordinary differential equations
6 Citations (Scopus)

A highly stable and scalable photosynthetic reaction center-graphene hybrid electrode system for biomimetic solar energy transduction

Zhang, H., Carey, A. M., Jeon, K. W., Liu, M., Murrell, T. D., Locsin, J., Lin, S., Yan, H., Woodbury, N. & Seo, D., 2017, In : Journal of Materials Chemistry A. 5, 13, p. 6038-6041 4 p.

Research output: Contribution to journalArticle

Photosynthetic Reaction Center Complex Proteins
Graphite
Biomimetics
Solar energy
Graphene
4 Citations (Scopus)

A robust vitronectin-derived peptide for the scalable long-term expansion and neuronal differentiation of human pluripotent stem cell (hPSC)-derived neural progenitor cells (hNPCs)

Varun, D., Srinivasan, G. R., Tsai, Y. H., Kim, H. J., Cutts, J., Petty, F., Merkley, R., Stephanopoulos, N., Dolezalova, D., Marsala, M. & Brafman, D., Jan 15 2017, In : Acta Biomaterialia. 48, p. 120-130 11 p.

Research output: Contribution to journalArticle

Vitronectin
Pluripotent Stem Cells
Neurology
Stem cells
Neurodegenerative diseases
2 Citations (Scopus)

Circulating Peptidome and Tumor-Resident Proteolysis

Fan, J., Ning, B., Lyon, C. J. & Hu, Y., Jan 1 2017, Enzymes. Academic Press, p. 1-25 25 p. (Enzymes; vol. 42).

Research output: Chapter in Book/Report/Conference proceedingChapter

Proteolysis
Tumors
Peptide Hydrolases
Neoplasms
Tumor Biomarkers
62 Citations (Scopus)

Complex cellular logic computation using ribocomputing devices

Green, A., Kim, J., Ma, D., Silver, P. A., Collins, J. J. & Yin, P., Aug 3 2017, In : Nature. 548, 7665, p. 117-121 5 p.

Research output: Contribution to journalArticle

RNA
Equipment and Supplies
Synthetic Biology
Synthetic Genes
Equipment Design

Construction and in vivo testing of prokaryotic riboregulators

Green, A., 2017, Methods in Molecular Biology. Humana Press Inc., Vol. 1632. p. 285-302 18 p. (Methods in Molecular Biology; vol. 1632).

Research output: Chapter in Book/Report/Conference proceedingChapter

RNA
Cues
Plasmids
Escherichia coli
Equipment and Supplies
2 Citations (Scopus)

Creating a stem cell niche in the inner ear using self-assembling peptide amphiphiles

Matsuoka, A. J., Sayed, Z. A., Stephanopoulos, N., Berns, E. J., Wadhwani, A. R., Morrissey, Z. D., Chadly, D. M., Kobayashi, S., Edelbrock, A. N., Mashimo, T., Miller, C. A., McGuire, T. L., Stupp, S. I. & Kessler, J. A., Dec 1 2017, In : PLoS One. 12, 12, e0190150.

Research output: Contribution to journalArticle

isoleucyl-lysyl-valyl-alanyl-valine
Stem Cell Niche
Amphiphiles
Inner Ear
Stem cells
26 Citations (Scopus)

Cuboid Vesicles Formed by Frame-Guided Assembly on DNA Origami Scaffolds

Dong, Y., Yang, Y. R., Zhang, Y., Wang, D., Wei, X., Banerjee, S., Liu, Y., Yang, Z., Yan, H. & Liu, D., Feb 1 2017, In : Angewandte Chemie - International Edition. 56, 6, p. 1586-1589 4 p.

Research output: Contribution to journalArticle

Scaffolds
DNA
Amphiphiles
Surface-Active Agents
Nanostructures
178 Citations (Scopus)

DNA Origami: Scaffolds for Creating Higher Order Structures

Hong, F., Zhang, F., Liu, Y. & Yan, H., Oct 25 2017, In : Chemical Reviews. 117, 20, p. 12584-12640 57 p.

Research output: Contribution to journalArticle

Scaffolds
DNA
Single-Stranded DNA
Materials science
Oligonucleotides
5 Citations (Scopus)

DNA origami tiles: Nanoscale mazes

Zhang, F., Hong, F. & Yan, H., Mar 7 2017, In : Nature Nanotechnology. 12, 3, p. 189-190 2 p.

Research output: Contribution to journalComment/debate

Tile
DNA
7 Citations (Scopus)

DNA self-assembly scaled up

Zhang, F. & Yan, H., Jan 1 2017, In : Nature. 552, 7683, p. 34-35 2 p.

Research output: Contribution to journalShort survey

DNA
57 Citations (Scopus)

Engineering nucleic acid structures for programmable molecular circuitry and intracellular biocomputation

Li, J., Green, A., Yan, H. & Fan, C., Sep 25 2017, In : Nature Chemistry. 9, 11, p. 1056-1067 12 p.

Research output: Contribution to journalReview article

Nucleic acids
RNA
Nanotechnology
Nucleic Acids
Nanostructures
2 Citations (Scopus)

Enhancing Photocurrent Generation in Photosynthetic Reaction Center-Based Photoelectrochemical Cells with Biomimetic DNA Antenna

Carey, A. M., Zhang, H., Liu, M., Sharaf, D., Akram, N., Yan, H., Lin, S., Woodbury, N. & Seo, D., 2017, (Accepted/In press) In : ChemSusChem.

Research output: Contribution to journalArticle

Photosynthetic Reaction Center Complex Proteins
Photoelectrochemical cells
Biomimetics
Photocurrents
Energy transfer
8 Citations (Scopus)

Formation of MoO3 and WO3 nanoscrolls from MoS2 and WS2 with atmospheric air plasma

Chu, X. S., Li, D. O., Green, A. & Wang, Q., 2017, In : Journal of Materials Chemistry C. 5, 43, p. 11301-11309 9 p.

Research output: Contribution to journalArticle

Oxides
Plasmas
Air
Electrochemical properties
Transition metals