Search Menu
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information
Search Scholarly Publications

Title: Reconfigurable Two-Dimensional DNA Lattices: Static and Dynamic Angle Control

Abstract

Abstract Branched DNA motifs serve as the basic construction elements for all synthetic DNA nanostructures. However, precise control of branching orientation remains a key challenge to further heighten the overall structural order. In this study, we use two strategies to control the branching orientation. The first one is based on immobile Holliday junctions which employ specific nucleotide sequences at the branch points which dictate their orientation. The second strategy is to use angle‐enforcing struts to fix the branching orientation with flexible spacers at the branch points. We have also demonstrated that the branching orientation control can be achieved dynamically, either by canonical Watson–Crick base pairing or non‐canonical nucleobase interactions (e.g., i‐motif and G‐quadruplex). With precise angle control and feedback from the chemical environment, these results will enable novel DNA nanomechanical sensing devices, and precisely‐ordered three‐dimensional architectures.

Authors:
 [1];  [1];  [2];  [1];  [1];  [2];  [2];  [2]; ORCiD logo [1]
+ Show Author Affiliations
  1. Tsinghua University, Beijing (China)
  2. New York University (NYU), NY (United States)
Publication Date:
Research Org.:
New York Univ. (NYU), NY (United States)
Sponsoring Org.:
USDOE Office of Science (SC); National Natural Science Foundation of China (NSFC); Beijing Advanced Innovation Center for Structural Biology; Tsinghua University-Peking University; National Institute of General Medical Sciences (NIGMS); National Science Foundation (NSF); Army Research Office (ARO); US Department of the Navy, Office of Naval Research (ONR); Gordon and Betty Moore Foundation; China Postdoctoral Science Foundation
OSTI Identifier:
1976270
Alternate Identifier(s):
OSTI ID: 1829376
Grant/Contract Number:  
SC0007991; 31770926; GM-29554; CTS1120890; CCF-1117210; EFRI-1332411; CHE-1708776; W911NF-1110024; N000141110729; N000140911118; GBMF3849; 2018M631448; DESC0007991
Resource Type:
Accepted Manuscript
Journal Name:
Angewandte Chemie (International Edition)
Additional Journal Information:
Journal Name: Angewandte Chemie (International Edition); Journal Volume: 60; Journal Issue: 49; Journal ID: ISSN 1433-7851
Publisher:
Wiley
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; angle control; branching orientation; junction motif; DNA nanostructures; selfassembly

Citation Formats

Wang, Wen, Chen, Chunyu, Vecchioni, Simon, Zhang, Tianqing, Wu, Chengxian, Ohayon, Yoel P., Sha, Ruojie, Seeman, Nadrian C., and Wei, Bryan. Reconfigurable Two-Dimensional DNA Lattices: Static and Dynamic Angle Control. United States: N. p., 2021. Web. doi:10.1002/anie.202112487.
Copy to clipboard
Wang, Wen, Chen, Chunyu, Vecchioni, Simon, Zhang, Tianqing, Wu, Chengxian, Ohayon, Yoel P., Sha, Ruojie, Seeman, Nadrian C., & Wei, Bryan. Reconfigurable Two-Dimensional DNA Lattices: Static and Dynamic Angle Control. United States. https://doi.org/10.1002/anie.202112487
Copy to clipboard
Wang, Wen, Chen, Chunyu, Vecchioni, Simon, Zhang, Tianqing, Wu, Chengxian, Ohayon, Yoel P., Sha, Ruojie, Seeman, Nadrian C., and Wei, Bryan. Fri . "Reconfigurable Two-Dimensional DNA Lattices: Static and Dynamic Angle Control". United States. https://doi.org/10.1002/anie.202112487. https://www.osti.gov/servlets/purl/1976270.
Copy to clipboard
@article{osti_1976270,
title = {Reconfigurable Two-Dimensional DNA Lattices: Static and Dynamic Angle Control},
author = {Wang, Wen and Chen, Chunyu and Vecchioni, Simon and Zhang, Tianqing and Wu, Chengxian and Ohayon, Yoel P. and Sha, Ruojie and Seeman, Nadrian C. and Wei, Bryan},
abstractNote = {Abstract Branched DNA motifs serve as the basic construction elements for all synthetic DNA nanostructures. However, precise control of branching orientation remains a key challenge to further heighten the overall structural order. In this study, we use two strategies to control the branching orientation. The first one is based on immobile Holliday junctions which employ specific nucleotide sequences at the branch points which dictate their orientation. The second strategy is to use angle‐enforcing struts to fix the branching orientation with flexible spacers at the branch points. We have also demonstrated that the branching orientation control can be achieved dynamically, either by canonical Watson–Crick base pairing or non‐canonical nucleobase interactions (e.g., i‐motif and G‐quadruplex). With precise angle control and feedback from the chemical environment, these results will enable novel DNA nanomechanical sensing devices, and precisely‐ordered three‐dimensional architectures.},
doi = {10.1002/anie.202112487},
journal = {Angewandte Chemie (International Edition)},
number = 49,
volume = 60,
place = {United States},
year = {Fri Oct 01 00:00:00 EDT 2021},
month = {Fri Oct 01 00:00:00 EDT 2021}
}
Copy to clipboard
Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1002/anie.202112487
Copyright Statement
Other availability
Search WorldCat Search WorldCat to find libraries that may hold this journal
Save / Share:
Export Metadata
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.

Works referenced in this record:

Formation of parallel four-stranded complexes by guanine-rich motifs in DNA and its implications for meiosis
journal, July 1988

  • Sen, Dipankar; Gilbert, Walter
  • Nature, Vol. 334, Issue 6180
  • DOI: 10.1038/334364a0

Designing Higher Resolution Self-Assembled 3D DNA Crystals via Strand Terminus Modifications
journal, June 2019

  • Ohayon, Yoel P.; Hernandez, Carina; Chandrasekaran, Arun Richard
  • ACS Nano, Vol. 13, Issue 7
  • DOI: 10.1021/acsnano.9b02430

Layered-Crossover Tiles with Precisely Tunable Angles for 2D and 3D DNA Crystal Engineering
journal, October 2018

  • Hong, Fan; Jiang, Shuoxing; Lan, Xiang
  • Journal of the American Chemical Society, Vol. 140, Issue 44
  • DOI: 10.1021/jacs.8b07180

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

Reconfiguration of DNA molecular arrays driven by information relay
journal, June 2017

The absence of tertiary interactions in a self-assembled DNA crystal structure: SELF-ASSEMBLED DNA CRYSTAL STRUCTURE
journal, March 2012

  • Nguyen, Nam; Birktoft, Jens J.; Sha, Ruojie
  • Journal of Molecular Recognition, Vol. 25, Issue 4
  • DOI: 10.1002/jmr.2183

Complex wireframe DNA nanostructures from simple building blocks
journal, March 2019

De Novo Design of Sequences for Nucleic Acid Structural Engineering
journal, December 1990

Revealing the structures of megadalton-scale DNA complexes with nucleotide resolution
journal, December 2020

Crossover isomer bias is the primary sequence-dependent property of immobilized Holliday junctions
journal, August 1997

  • Miick, S. M.; Fee, R. S.; Millar, D. P.
  • Proceedings of the National Academy of Sciences, Vol. 94, Issue 17
  • DOI: 10.1073/pnas.94.17.9080

Structures of helical junctions in nucleic acids
journal, May 2000

Custom-Size, Functional, and Durable DNA Origami with Design-Specific Scaffolds
journal, April 2019

  • Engelhardt, Floris A. S.; Praetorius, Florian; Wachauf, Christian H.
  • ACS Nano, Vol. 13, Issue 5
  • DOI: 10.1021/acsnano.9b01025

Engineering a 2D Protein-DNA Crystal
journal, May 2005

  • Malo, Jonathan; Mitchell, James C.; Vénien-Bryan, Catherine
  • Angewandte Chemie International Edition, Vol. 44, Issue 20
  • DOI: 10.1002/anie.200463027

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

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

A Reconfigurable DNA Accordion Rack
journal, February 2018

  • Choi, Yeongjae; Choi, Hansol; Lee, Amos C.
  • Angewandte Chemie International Edition, Vol. 57, Issue 11
  • DOI: 10.1002/anie.201709362

Biotechnological mass production of DNA origami
journal, December 2017

  • Praetorius, Florian; Kick, Benjamin; Behler, Karl L.
  • Nature, Vol. 552, Issue 7683
  • DOI: 10.1038/nature24650

Building machines with DNA molecules
journal, October 2019

Tensegrity:  Construction of Rigid DNA Triangles with Flexible Four-Arm DNA Junctions
journal, March 2004

  • Liu, Dage; Wang, Mingsheng; Deng, Zhaoxiang
  • Journal of the American Chemical Society, Vol. 126, Issue 8
  • DOI: 10.1021/ja031754r

The Holliday junction in an inverted repeat DNA sequence: Sequence effects on the structure of four-way junctions
journal, April 2000

  • Eichman, B. F.; Vargason, J. M.; Mooers, B. H. M.
  • Proceedings of the National Academy of Sciences, Vol. 97, Issue 8
  • DOI: 10.1073/pnas.97.8.3971

Atomic Force Microscopic Measurement of the Interdomain Angle in Symmetric Holliday Junctions
journal, April 2002

  • Sha, Ruojie; Liu, Furong; Seeman, Nadrian C.
  • Biochemistry, Vol. 41, Issue 19
  • DOI: 10.1021/bi020001z

Conformational distributions of a four-way DNA junction revealed by time-resolved fluorescence resonance energy transfer
journal, December 1993

Designed Two-Dimensional DNA Holliday Junction Arrays Visualized by Atomic Force Microscopy
journal, June 1999

  • Mao, Chengde; Sun, Weiqiong; Seeman, Nadrian C.
  • Journal of the American Chemical Society, Vol. 121, Issue 23
  • DOI: 10.1021/ja9900398

The structure of the holliday junction, and its resolution
journal, October 1988

A Holliday recombination intermediate is twofold symmetric.
journal, July 1988

  • Churchill, M. E.; Tullius, T. D.; Kallenbach, N. R.
  • Proceedings of the National Academy of Sciences, Vol. 85, Issue 13
  • DOI: 10.1073/pnas.85.13.4653

DNA Gridiron Nanostructures Based on Four-Arm Junctions
journal, March 2013

Symmetric Holliday Junction Crossover Isomers
journal, May 1994

  • Zhang, Siwei; Seeman, Nadrian C.
  • Journal of Molecular Biology, Vol. 238, Issue 5
  • DOI: 10.1006/jmbi.1994.1327

DNA-Templated Self-Assembly of Protein Arrays and Highly Conductive Nanowires
journal, September 2003

Nucleic acid junctions and lattices
journal, November 1982

Design of immobile nucleic acid junctions
journal, November 1983

Fluorescence-Force Spectroscopy Maps Two-Dimensional Reaction Landscape of the Holliday Junction
journal, October 2007

Crystal structure of a four-stranded intercalated DNA: d(C4)
journal, November 1994

  • Chen, Liqing; Cai, Li; Zhang, Xiaohua
  • Biochemistry, Vol. 33, Issue 46
  • DOI: 10.1021/bi00250a005

From molecular to macroscopic via the rational design of a self-assembled 3D DNA crystal
journal, September 2009

  • Zheng, Jianping; Birktoft, Jens J.; Chen, Yi
  • Nature, Vol. 461, Issue 7260
  • DOI: 10.1038/nature08274

DNA nanotechnology
journal, November 2017

A Reconfigurable DNA Accordion Rack
journal, February 2018

  • Choi, Yeongjae; Choi, Hansol; Lee, Amos C.
  • Angewandte Chemie, Vol. 130, Issue 11
  • DOI: 10.1002/ange.201709362

A Two-Dimensional DNA Array: The Three-Layer Logpile
journal, September 2009

  • Malo, Jonathan; Mitchell, James C.; Turberfield, Andrew J.
  • Journal of the American Chemical Society, Vol. 131, Issue 38
  • DOI: 10.1021/ja9042593

Atomic force microscopy of parallel DNA branched junction arrays
journal, September 2000

Macromolecular Design, Nucleic Acid Junctions, and Crystal Formation
journal, August 1985

Engineering a 2D Protein-DNA Crystal
journal, May 2005

  • Malo, Jonathan; Mitchell, James C.; Vénien-Bryan, Catherine
  • Angewandte Chemie, Vol. 117, Issue 20
  • DOI: 10.1002/ange.200463027

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

  • Douglas, Shawn M.; Dietz, Hendrik; Liedl, Tim
  • Nature, Vol. 459, Issue 7245
  • DOI: 10.1038/nature08016

Hierarchical self-assembly of DNA into symmetric supramolecular polyhedra
journal, March 2008

    Sort by:
    [ × clear filter / sort ]

    Similar Records in DOE PAGES and OSTI.GOV collections: