skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

Title: Altering DNA-Programmable Colloidal Crystallization Paths by Modulating Particle Repulsion

Abstract

Colloidal crystal engineering with DNA can be used to realize precise control over nanoparticle (NP) arrangement. Here, we investigate a case of DNA-based assembly where the properties of DNA as a polyelectrolyte brush are employed to alter a hybridization-driven NP crystallization pathway. Using the coassembly of DNA-conjugated proteins and spherical gold nanoparticles (AuNPs) as a model system, we explore how steric repulsion between noncomplementary, neighboring NPs due to overlapping DNA shells can influence their ligand-directed behavior. Specifically, our experimental data coupled with coarse-grained molecular dynamics (MD) simulations reveal that, by changing factors related to NP repulsion, two structurally distinct outcomes can be achieved. When steric repulsion between DNA–AuNPs is significantly greater than that between DNA–proteins, a lower packing density crystal lattice is favored over the structure that is predicted by design rules based on DNA hybridization considerations alone. This is enabled by the large difference in DNA density on AuNPs versus proteins and can be tuned by modulating the flexibility, and thus conformational entropy, of the DNA on the constituent particles. At intermediate ligand flexibility, the crystallization pathways are energetically similar, and the structural outcome can be adjusted using the density of DNA duplexes on DNA–AuNPs and by screening themore » Coulomb potential between them. Such lattices are shown to undergo dynamic reorganization upon changing the salt concentration. These data help elucidate the structural considerations necessary for understanding repulsive forces in DNA-mediated assembly and lay the groundwork for using them to increase architectural diversity in engineering colloidal crystals.« less

Authors:
; ; ; ; ; ; ORCiD logo [1]; ORCiD logo
  1. X-Ray Science Division, Argonne National Laboratory, 9700 S. Cass Avenue, Argonne, Illinois 60439, United States
Publication Date:
Research Org.:
Energy Frontier Research Centers (EFRC) (United States). Center for Bio-Inspired Energy Science (CBES); Northwestern Univ., Evanston, IL (United States)
Sponsoring Org.:
USDOE
OSTI Identifier:
1393318
Alternate Identifier(s):
OSTI ID: 1508108
Grant/Contract Number:  
SC0000989
Resource Type:
Published Article
Journal Name:
Nano Letters
Additional Journal Information:
Journal Name: Nano Letters Journal Volume: 17 Journal Issue: 8; Journal ID: ISSN 1530-6984
Publisher:
American Chemical Society
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; colloidal crystals; DNA; nanomaterials; nanoparticle superlattice; protein assembly; self-assembly

Citation Formats

Wang, Mary X., Brodin, Jeffrey D., Millan, Jaime A., Seo, Soyoung E., Girard, Martin, Olvera de la Cruz, Monica, Lee, Byeongdu, and Mirkin, Chad A.. Altering DNA-Programmable Colloidal Crystallization Paths by Modulating Particle Repulsion. United States: N. p., 2017. Web. https://doi.org/10.1021/acs.nanolett.7b02502.
Wang, Mary X., Brodin, Jeffrey D., Millan, Jaime A., Seo, Soyoung E., Girard, Martin, Olvera de la Cruz, Monica, Lee, Byeongdu, & Mirkin, Chad A.. Altering DNA-Programmable Colloidal Crystallization Paths by Modulating Particle Repulsion. United States. https://doi.org/10.1021/acs.nanolett.7b02502
Wang, Mary X., Brodin, Jeffrey D., Millan, Jaime A., Seo, Soyoung E., Girard, Martin, Olvera de la Cruz, Monica, Lee, Byeongdu, and Mirkin, Chad A.. Fri . "Altering DNA-Programmable Colloidal Crystallization Paths by Modulating Particle Repulsion". United States. https://doi.org/10.1021/acs.nanolett.7b02502.
@article{osti_1393318,
title = {Altering DNA-Programmable Colloidal Crystallization Paths by Modulating Particle Repulsion},
author = {Wang, Mary X. and Brodin, Jeffrey D. and Millan, Jaime A. and Seo, Soyoung E. and Girard, Martin and Olvera de la Cruz, Monica and Lee, Byeongdu and Mirkin, Chad A.},
abstractNote = {Colloidal crystal engineering with DNA can be used to realize precise control over nanoparticle (NP) arrangement. Here, we investigate a case of DNA-based assembly where the properties of DNA as a polyelectrolyte brush are employed to alter a hybridization-driven NP crystallization pathway. Using the coassembly of DNA-conjugated proteins and spherical gold nanoparticles (AuNPs) as a model system, we explore how steric repulsion between noncomplementary, neighboring NPs due to overlapping DNA shells can influence their ligand-directed behavior. Specifically, our experimental data coupled with coarse-grained molecular dynamics (MD) simulations reveal that, by changing factors related to NP repulsion, two structurally distinct outcomes can be achieved. When steric repulsion between DNA–AuNPs is significantly greater than that between DNA–proteins, a lower packing density crystal lattice is favored over the structure that is predicted by design rules based on DNA hybridization considerations alone. This is enabled by the large difference in DNA density on AuNPs versus proteins and can be tuned by modulating the flexibility, and thus conformational entropy, of the DNA on the constituent particles. At intermediate ligand flexibility, the crystallization pathways are energetically similar, and the structural outcome can be adjusted using the density of DNA duplexes on DNA–AuNPs and by screening the Coulomb potential between them. Such lattices are shown to undergo dynamic reorganization upon changing the salt concentration. These data help elucidate the structural considerations necessary for understanding repulsive forces in DNA-mediated assembly and lay the groundwork for using them to increase architectural diversity in engineering colloidal crystals.},
doi = {10.1021/acs.nanolett.7b02502},
journal = {Nano Letters},
number = 8,
volume = 17,
place = {United States},
year = {2017},
month = {7}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1021/acs.nanolett.7b02502

Citation Metrics:
Cited by: 14 works
Citation information provided by
Web of Science

Figures / Tables:

Scheme 1 Scheme 1: Modulating Particle Repulsion in DNA-Assembled Binary Protein−AuNP PAE Superlattices$^a$

Save / Share:

Works referenced in this record:

Structural diversity in binary nanoparticle superlattices
journal, January 2006

  • Shevchenko, Elena V.; Talapin, Dmitri V.; Kotov, Nicholas A.
  • Nature, Vol. 439, Issue 7072, p. 55-59
  • DOI: 10.1038/nature04414

In vitro self-assembly of tailorable nanotubes from a simple protein building block
journal, February 2008

  • Ballister, E. R.; Lai, A. H.; Zuckermann, R. N.
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue 10
  • DOI: 10.1073/pnas.0712247105

The role of interparticle and external forces in nanoparticle assembly
journal, July 2008

  • Min, Younjin; Akbulut, Mustafa; Kristiansen, Kai
  • Nature Materials, Vol. 7, Issue 7
  • DOI: 10.1038/nmat2206

Templated Techniques for the Synthesis and Assembly of Plasmonic Nanostructures
journal, June 2011

  • Jones, Matthew R.; Osberg, Kyle D.; Macfarlane, Robert J.
  • Chemical Reviews, Vol. 111, Issue 6
  • DOI: 10.1021/cr1004452

Generation of protein lattices by fusing proteins with matching rotational symmetry
journal, July 2011

  • Sinclair, John C.; Davies, Karen M.; Vénien-Bryan, Catherine
  • Nature Nanotechnology, Vol. 6, Issue 9
  • DOI: 10.1038/nnano.2011.122

Nanohedra: Using symmetry to design self assembling protein cages, layers, crystals, and filaments
journal, February 2001

  • Padilla, J. E.; Colovos, C.; Yeates, T. O.
  • Proceedings of the National Academy of Sciences, Vol. 98, Issue 5
  • DOI: 10.1073/pnas.041614998

Visualizing Metabolically Labeled Glycoconjugates of Living Cells by Copper-Free and Fast Huisgen Cycloadditions
journal, March 2008

  • Ning, Xinghai; Guo, Jun; Wolfert, Margreet A.
  • Angewandte Chemie International Edition, Vol. 47, Issue 12
  • DOI: 10.1002/anie.200705456

Electrostatic Self-Assembly of Binary Nanoparticle Crystals with a Diamond-Like Lattice
journal, February 2006

  • Kalsin, A. M.; Fialkowski, M.; Paszewski, M.
  • Science, Vol. 312, Issue 5772, p. 420-424
  • DOI: 10.1126/science.1125124

Life as a Nanoscale Phenomenon
journal, July 2008


Nanoscale Forces and Their Uses in Self-Assembly
journal, July 2009

  • Bishop, Kyle J. M.; Wilmer, Christopher E.; Soh, Siowling
  • Small, Vol. 5, Issue 14
  • DOI: 10.1002/smll.200900358

Modeling the Crystallization of Spherical Nucleic Acid Nanoparticle Conjugates with Molecular Dynamics Simulations
journal, April 2012

  • Li, Ting I. N. G.; Sknepnek, Rastko; Macfarlane, Robert J.
  • Nano Letters, Vol. 12, Issue 5
  • DOI: 10.1021/nl300679e

A general strategy for the DNA-mediated self-assembly of functional nanoparticles into heterogeneous systems
journal, October 2013

  • Zhang, Yugang; Lu, Fang; Yager, Kevin G.
  • Nature Nanotechnology, Vol. 8, Issue 11
  • DOI: 10.1038/nnano.2013.209

DNA-guided crystallization of colloidal nanoparticles
journal, January 2008

  • Nykypanchuk, Dmytro; Maye, Mathew M.; van der Lelie, Daniel
  • Nature, Vol. 451, Issue 7178, p. 549-552
  • DOI: 10.1038/nature06560

Morphological Diversity of DNA-Colloidal Self-Assembly
journal, September 2002


Exploring the zone of anisotropy and broken symmetries in DNA-mediated nanoparticle crystallization
journal, September 2016

  • O’Brien, Matthew N.; Girard, Martin; Lin, Hai-Xin
  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 38
  • DOI: 10.1073/pnas.1611808113

A general approach to DNA-programmable atom equivalents
journal, May 2013

  • Zhang, Chuan; Macfarlane, Robert J.; Young, Kaylie L.
  • Nature Materials, Vol. 12, Issue 8
  • DOI: 10.1038/nmat3647

DNA-controlled assembly of a NaTl lattice structure from gold nanoparticles and protein nanoparticles
journal, October 2010

  • Cigler, Petr; Lytton-Jean, Abigail K. R.; Anderson, Daniel G.
  • Nature Materials, Vol. 9, Issue 11, p. 918-922
  • DOI: 10.1038/nmat2877

Metal-directed, chemically tunable assembly of one-, two- and three-dimensional crystalline protein arrays
journal, March 2012

  • Brodin, Jeffrey D.; Ambroggio, X. I.; Tang, Chunyan
  • Nature Chemistry, Vol. 4, Issue 5
  • DOI: 10.1038/nchem.1290

A DNA-based method for rationally assembling nanoparticles into macroscopic materials
journal, August 1996

  • Mirkin, Chad A.; Letsinger, Robert L.; Mucic, Robert C.
  • Nature, Vol. 382, Issue 6592, p. 607-609
  • DOI: 10.1038/382607a0

DNA-mediated engineering of multicomponent enzyme crystals
journal, March 2015

  • Brodin, Jeffrey D.; Auyeung, Evelyn; Mirkin, Chad A.
  • Proceedings of the National Academy of Sciences, Vol. 112, Issue 15
  • DOI: 10.1073/pnas.1503533112

Computational design of a protein crystal
journal, April 2012

  • Lanci, C. J.; MacDermaid, C. M.; Kang, S. -g.
  • Proceedings of the National Academy of Sciences, Vol. 109, Issue 19
  • DOI: 10.1073/pnas.1112595109

Modulating the Bond Strength of DNA–Nanoparticle Superlattices
journal, December 2015


Establishing the Design Rules for DNA-Mediated Programmable Colloidal Crystallization
journal, May 2010

  • Macfarlane, Robert J.; Jones, Matthew R.; Senesi, Andrew J.
  • Angewandte Chemie, Vol. 122, Issue 27, p. 4693-4696
  • DOI: 10.1002/ange.201000633

DNA-mediated nanoparticle crystallization into Wulff polyhedra
journal, November 2013

  • Auyeung, Evelyn; Li, Ting I. N. G.; Senesi, Andrew J.
  • Nature, Vol. 505, Issue 7481
  • DOI: 10.1038/nature12739

Self-Assembly of a Tetrahedral Lectin into Predesigned Diamondlike Protein Crystals
journal, August 1999


Self-Assembly of Proteins into Designed Networks
journal, October 2003


From Artificial Atoms to Nanocrystal Molecules: Preparation and Properties of More Complex Nanostructures
journal, March 2010


Nanoparticle Superlattice Engineering with DNA
journal, October 2011


Design of ordered two-dimensional arrays mediated by noncovalent protein-protein interfaces
journal, June 2015


DNA-Driven Assembly: From Polyhedral Nanoparticles to Proteins
journal, July 2017


Probability of DNA knotting and the effective diameter of the DNA double helix.
journal, June 1993

  • Rybenkov, V. V.; Cozzarelli, N. R.; Vologodskii, A. V.
  • Proceedings of the National Academy of Sciences, Vol. 90, Issue 11
  • DOI: 10.1073/pnas.90.11.5307

Nucleic Acid-Modified Nanostructures as Programmable Atom Equivalents: Forging a New “Table of Elements”
journal, May 2013

  • Macfarlane, Robert J.; O'Brien, Matthew N.; Petrosko, Sarah Hurst
  • Angewandte Chemie International Edition, Vol. 52, Issue 22
  • DOI: 10.1002/anie.201209336

Protein crystalline frameworks with controllable interpenetration directed by dual supramolecular interactions
journal, August 2014

  • Sakai, Fuji; Yang, Guang; Weiss, Manfred S.
  • Nature Communications, Vol. 5, Issue 1
  • DOI: 10.1038/ncomms5634

Programmable materials and the nature of the DNA bond
journal, February 2015


A Strain-Promoted [3 + 2] Azide−Alkyne Cycloaddition for Covalent Modification of Biomolecules in Living Systems
journal, November 2004

  • Agard, Nicholas J.; Prescher, Jennifer A.; Bertozzi, Carolyn R.
  • Journal of the American Chemical Society, Vol. 126, Issue 46
  • DOI: 10.1021/ja044996f

Dynamics and Statics of DNA-Programmable Nanoparticle Self-Assembly and Crystallization
journal, May 2011


Entropy-Driven Crystallization Behavior in DNA-Mediated Nanoparticle Assembly
journal, June 2015


Small Angle X-ray Scattering for Nanoparticle Research
journal, April 2016


The Significance of Multivalent Bonding Motifs and “Bond Order” in DNA-Directed Nanoparticle Crystallization
journal, May 2016

  • Thaner, Ryan V.; Eryazici, Ibrahim; Macfarlane, Robert J.
  • Journal of the American Chemical Society, Vol. 138, Issue 19
  • DOI: 10.1021/jacs.6b02479

Strong scaling of general-purpose molecular dynamics simulations on GPUs
journal, July 2015

  • Glaser, Jens; Nguyen, Trung Dac; Anderson, Joshua A.
  • Computer Physics Communications, Vol. 192
  • DOI: 10.1016/j.cpc.2015.02.028

DNA-programmable nanoparticle crystallization
journal, January 2008

  • Park, Sung Yong; Lytton-Jean, Abigail K. R.; Lee, Byeongdu
  • Nature, Vol. 451, Issue 7178, p. 553-556
  • DOI: 10.1038/nature06508

Self-assembly of coherently dynamic, auxetic, two-dimensional protein crystals
journal, May 2016

  • Suzuki, Yuta; Cardone, Giovanni; Restrepo, David
  • Nature, Vol. 533, Issue 7603
  • DOI: 10.1038/nature17633

Small-angle scattering of particle assemblies
journal, July 2015


Modulating Nanoparticle Superlattice Structure Using Proteins with Tunable Bond Distributions
journal, January 2017

  • McMillan, Janet R.; Brodin, Jeffrey D.; Millan, Jaime A.
  • Journal of the American Chemical Society, Vol. 139, Issue 5
  • DOI: 10.1021/jacs.6b11893

Self-Assembly of Colloidal Nanocrystals: From Intricate Structures to Functional Materials
journal, August 2016


Epitaxy: Programmable Atom Equivalents Versus Atoms
journal, December 2016


Designed, Helical Protein Nanotubes with Variable Diameters from a Single Building Block
journal, August 2015

  • Brodin, Jeffrey D.; Smith, Sarah J.; Carr, Jessica R.
  • Journal of the American Chemical Society, Vol. 137, Issue 33
  • DOI: 10.1021/jacs.5b05755

Electrostatic assembly of binary nanoparticle superlattices using protein cages
journal, December 2012

  • Kostiainen, Mauri A.; Hiekkataipale, Panu; Laiho, Ari
  • Nature Nanotechnology, Vol. 8, Issue 1
  • DOI: 10.1038/nnano.2012.220

    Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.