Direct visualization of floppy two-dimensional DNA origami using cryogenic electron microscopy

Ni, Heng; Fan, Xiao; Zhou, Feng; Guo, Galio; Lee, Jae Young; Seeman, Nadrian C.; Kim, Do-Nyun; Yao, Nan; Chaikin, Paul M.; Han, Yimo

doi:10.1016/j.isci.2022.104373

Title: Direct visualization of floppy two-dimensional DNA origami using cryogenic electron microscopy

Abstract

Two-dimensional (2D) DNA origami that is capable of self-assembling into complex 2D and 3D geometries pave the way for a bottom-up synthesis for various applications in nano/biotechnology. Here, we directly visualized the aqueous structure of 2D DNA origami cross-tiles and their assemblies using cryogenic electron microscopy. We uncovered flexible arms in cross-tile monomers and designated inter-tile folding. In addition, we observed the formation of clusters and stacks of DNA cross-tiles in solution, which could potentially affect the interaction and assembly of DNA origami. Finally, we quantitatively evaluated the flexibility of DNA origami in solution using finite element analysis. Our discovery has laid the foundation for investigating the dynamic structures of 2D DNA origami assemblies in solution, providing insights regarding the self-assembly and self-replication mechanisms of 2D DNA origami.

Authors:

Ni, Heng; Fan, Xiao;

;

; Seeman, Nadrian C.;

; Yao, Nan; Chaikin, Paul M.;

Publication Date:: Wed Jun 01 00:00:00 EDT 2022

Research Org.:: Northwestern Univ., Evanston, IL (United States); New York Univ. (NYU), NY (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Basic Energy Sciences (BES); Welch Foundation; National Research Foundation of Korea (NRF); National Science Foundation (NSF)

OSTI Identifier:: 1867311

Alternate Identifier(s):: OSTI ID: 1977224

Grant/Contract Number:: SC0000989; SC0007991; C-2065-20210327; 2020M3F7A1094299; 2019R1A2C4069541; DMR-2011750

Resource Type:: Published Article

Journal Name:: iScience

Additional Journal Information:: Journal Name: iScience Journal Volume: 25 Journal Issue: 6; Journal ID: ISSN 2589-0042

Publisher:: Elsevier

Country of Publication:: Netherlands

Language:: English

Subject:: 36 MATERIALS SCIENCE; biomaterials; materials characterization

Citation Formats


                    Ni, Heng, Fan, Xiao, Zhou, Feng, Guo, Galio, Lee, Jae Young, Seeman, Nadrian C., Kim, Do-Nyun, Yao, Nan, Chaikin, Paul M., and Han, Yimo. Direct visualization of floppy two-dimensional DNA origami using cryogenic electron microscopy.  Netherlands: N. p., 2022. 
Web.  doi:10.1016/j.isci.2022.104373.

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                    Ni, Heng, Fan, Xiao, Zhou, Feng, Guo, Galio, Lee, Jae Young, Seeman, Nadrian C., Kim, Do-Nyun, Yao, Nan, Chaikin, Paul M., & Han, Yimo. Direct visualization of floppy two-dimensional DNA origami using cryogenic electron microscopy.  Netherlands.  https://doi.org/10.1016/j.isci.2022.104373

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                    Ni, Heng, Fan, Xiao, Zhou, Feng, Guo, Galio, Lee, Jae Young, Seeman, Nadrian C., Kim, Do-Nyun, Yao, Nan, Chaikin, Paul M., and Han, Yimo. Wed .  
"Direct visualization of floppy two-dimensional DNA origami using cryogenic electron microscopy".  Netherlands.  https://doi.org/10.1016/j.isci.2022.104373.

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@article{osti_1867311,

  title        = {Direct visualization of floppy two-dimensional DNA origami using cryogenic electron microscopy},

  author       = {Ni, Heng and Fan, Xiao and Zhou, Feng and Guo, Galio and Lee, Jae Young and Seeman, Nadrian C. and Kim, Do-Nyun and Yao, Nan and Chaikin, Paul M. and Han, Yimo},

  abstractNote = {Two-dimensional (2D) DNA origami that is capable of self-assembling into complex 2D and 3D geometries pave the way for a bottom-up synthesis for various applications in nano/biotechnology. Here, we directly visualized the aqueous structure of 2D DNA origami cross-tiles and their assemblies using cryogenic electron microscopy. We uncovered flexible arms in cross-tile monomers and designated inter-tile folding. In addition, we observed the formation of clusters and stacks of DNA cross-tiles in solution, which could potentially affect the interaction and assembly of DNA origami. Finally, we quantitatively evaluated the flexibility of DNA origami in solution using finite element analysis. Our discovery has laid the foundation for investigating the dynamic structures of 2D DNA origami assemblies in solution, providing insights regarding the self-assembly and self-replication mechanisms of 2D DNA origami.},

  doi          = {10.1016/j.isci.2022.104373},

  journal      = {iScience},

  number       = 6,

  volume       = 25,

  place        = {Netherlands},

  year         = {Wed Jun 01 00:00:00 EDT 2022},

  month        = {Wed Jun 01 00:00:00 EDT 2022}

}

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Title: Direct visualization of floppy two-dimensional DNA origami using cryogenic electron microscopy

Abstract

Citation Formats

Exponential growth and selection in self-replicating materials from DNA origami rafts journal, September 2017

Multilayer DNA Origami Packed on a Square Lattice journal, November 2009

MrDNA: a multi-resolution model for predicting the structure and dynamics of DNA systems journal, March 2020

Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures journal, December 2011

Diamond family of nanoparticle superlattices journal, February 2016

Polyhedra Self-Assembled from DNA Tripods and Characterized with 3D DNA-PAINT journal, March 2014

Multilayer DNA Origami Packed on Hexagonal and Hybrid Lattices journal, January 2012

Litters of self-replicating origami cross-tiles journal, January 2019

EMAN2: An extensible image processing suite for electron microscopy journal, January 2007

Cryo-EM structure of a 3D DNA-origami object journal, November 2012

Folding DNA into Twisted and Curved Nanoscale Shapes journal, August 2009

Rapid prototyping of 3D DNA-origami shapes with caDNAno journal, June 2009

High-yield monolayer graphene grids for near-atomic resolution cryoelectron microscopy journal, December 2019

The Resolution Revolution journal, March 2014

Multivalent, multiflavored droplets by design journal, August 2018

A Bayesian View on Cryo-EM Structure Determination journal, January 2012

Complex shapes self-assembled from single-stranded DNA tiles journal, May 2012

Lipid-bilayer-assisted two-dimensional self-assembly of DNA origami nanostructures journal, August 2015

A mechanical metamaterial made from a DNA hydrogel journal, December 2012

Self-assembly of a nanoscale DNA box with a controllable lid journal, May 2009

Dynamic DNA devices and assemblies formed by shape-complementary, non-base pairing 3D components journal, March 2015

Folding DNA to create nanoscale shapes and patterns journal, March 2006

Programmable motion of DNA origami mechanisms journal, January 2015

Ordered three-dimensional nanomaterials using DNA-prescribed and valence-controlled material voxels journal, January 2020

DNA Origami with Double-Stranded DNA As a Unified Scaffold journal, July 2012

Rapid Computational Analysis of DNA Origami Assemblies at Near-Atomic Resolution journal, January 2021

Mutations in artificial self-replicating tiles: A step toward Darwinian evolution journal, December 2021

DNA Origami with Complex Curvatures in Three-Dimensional Space journal, April 2011

Three-dimensional structural dynamics of DNA origami Bennett linkages using individual-particle electron tomography journal, February 2018

Self-replication of information-bearing nanoscale patterns journal, October 2011

Programmable molecular recognition based on the geometry of DNA nanostructures journal, July 2011

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Self-assembled three-dimensional chiral colloidal architecture journal, November 2017

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Cryo-EM-the first thirty years: CRYO-ELECTRON MICROSCOPY journal, November 2011

Self-assembly of two-dimensional DNA origami lattices using cation-controlled surface diffusion journal, September 2014

3D DNA Origami Crystals journal, May 2018

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Computer Visualization of Three-Dimensional Image Data Using IMOD journal, January 1996

Crystalline Two-Dimensional DNA-Origami Arrays journal, November 2010

Scaffolded DNA Origami of a DNA Tetrahedron Molecular Container journal, June 2009

Three-Dimensional Structures Self-Assembled from DNA Bricks journal, November 2012

Self-assembly of DNA into nanoscale three-dimensional shapes journal, May 2009

Exponential growth and selection in self-replicating materials from DNA origami rafts
journal, September 2017

Multilayer DNA Origami Packed on a Square Lattice
journal, November 2009

MrDNA: a multi-resolution model for predicting the structure and dynamics of DNA systems
journal, March 2020

Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures
journal, December 2011

Diamond family of nanoparticle superlattices
journal, February 2016

Polyhedra Self-Assembled from DNA Tripods and Characterized with 3D DNA-PAINT
journal, March 2014

Multilayer DNA Origami Packed on Hexagonal and Hybrid Lattices
journal, January 2012

Litters of self-replicating origami cross-tiles
journal, January 2019

EMAN2: An extensible image processing suite for electron microscopy
journal, January 2007

Cryo-EM structure of a 3D DNA-origami object
journal, November 2012

Folding DNA into Twisted and Curved Nanoscale Shapes
journal, August 2009

Rapid prototyping of 3D DNA-origami shapes with caDNAno
journal, June 2009

High-yield monolayer graphene grids for near-atomic resolution cryoelectron microscopy
journal, December 2019

The Resolution Revolution
journal, March 2014

Multivalent, multiflavored droplets by design
journal, August 2018

A Bayesian View on Cryo-EM Structure Determination
journal, January 2012

Complex shapes self-assembled from single-stranded DNA tiles
journal, May 2012

Lipid-bilayer-assisted two-dimensional self-assembly of DNA origami nanostructures
journal, August 2015

A mechanical metamaterial made from a DNA hydrogel
journal, December 2012

Self-assembly of a nanoscale DNA box with a controllable lid
journal, May 2009

Dynamic DNA devices and assemblies formed by shape-complementary, non-base pairing 3D components
journal, March 2015

Folding DNA to create nanoscale shapes and patterns
journal, March 2006

Programmable motion of DNA origami mechanisms
journal, January 2015

Ordered three-dimensional nanomaterials using DNA-prescribed and valence-controlled material voxels
journal, January 2020

DNA Origami with Double-Stranded DNA As a Unified Scaffold
journal, July 2012

Rapid Computational Analysis of DNA Origami Assemblies at Near-Atomic Resolution
journal, January 2021

Mutations in artificial self-replicating tiles: A step toward Darwinian evolution
journal, December 2021

DNA Origami with Complex Curvatures in Three-Dimensional Space
journal, April 2011

Three-dimensional structural dynamics of DNA origami Bennett linkages using individual-particle electron tomography
journal, February 2018

Self-replication of information-bearing nanoscale patterns
journal, October 2011

Programmable molecular recognition based on the geometry of DNA nanostructures
journal, July 2011

DNA brick crystals with prescribed depths
journal, October 2014

Self-assembled three-dimensional chiral colloidal architecture
journal, November 2017

Dimensions and Global Twist of Single-Layer DNA Origami Measured by Small-Angle X-ray Scattering
journal, May 2018

Cryo-EM-the first thirty years: CRYO-ELECTRON MICROSCOPY
journal, November 2011

Self-assembly of two-dimensional DNA origami lattices using cation-controlled surface diffusion
journal, September 2014

3D DNA Origami Crystals
journal, May 2018

A primer to scaffolded DNA origami
journal, February 2011

Computer Visualization of Three-Dimensional Image Data Using IMOD
journal, January 1996

Crystalline Two-Dimensional DNA-Origami Arrays
journal, November 2010

Scaffolded DNA Origami of a DNA Tetrahedron Molecular Container
journal, June 2009

Three-Dimensional Structures Self-Assembled from DNA Bricks
journal, November 2012

Self-assembly of DNA into nanoscale three-dimensional shapes
journal, May 2009