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Title: 3D DNA Crystals and Nanotechnology

Abstract

DNA's molecular recognition properties have made it one of the most widely used biomacromolecular construction materials. The programmed assembly of DNA oligonucleotides has been used to create complex 2D and 3D self-assembled architectures and to guide the assembly of other molecules. The origins of DNA nanotechnology are rooted in the goal of assembling DNA molecules into designed periodic arrays, i.e., crystals. Here, we highlight several DNA crystal structures, the progress made in designing DNA crystals, and look at the current prospects and future directions of DNA crystals in nanotechnology.

Authors:
 [1];  [2]
  1. Univ. of Maryland, College Park, MD (United States). Department of Chemistry and Biochemistry
  2. New York Univ. (NYU), NY (United States). Department of Chemistry
Publication Date:
Research Org.:
Univ. of Maryland, College Park, MD (United States). Department of Chemistry and Biochemistry
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1437431
Grant/Contract Number:  
SC0007991
Resource Type:
Accepted Manuscript
Journal Name:
Crystals
Additional Journal Information:
Journal Volume: 6; Journal Issue: 8; Journal ID: ISSN 2073-4352
Publisher:
MDPI
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY; DNA crystals; nanotechnology; crystal design

Citation Formats

Paukstelis, Paul, and Seeman, Nadrian. 3D DNA Crystals and Nanotechnology. United States: N. p., 2016. Web. doi:10.3390/cryst6080097.
Paukstelis, Paul, & Seeman, Nadrian. 3D DNA Crystals and Nanotechnology. United States. doi:10.3390/cryst6080097.
Paukstelis, Paul, and Seeman, Nadrian. Thu . "3D DNA Crystals and Nanotechnology". United States. doi:10.3390/cryst6080097. https://www.osti.gov/servlets/purl/1437431.
@article{osti_1437431,
title = {3D DNA Crystals and Nanotechnology},
author = {Paukstelis, Paul and Seeman, Nadrian},
abstractNote = {DNA's molecular recognition properties have made it one of the most widely used biomacromolecular construction materials. The programmed assembly of DNA oligonucleotides has been used to create complex 2D and 3D self-assembled architectures and to guide the assembly of other molecules. The origins of DNA nanotechnology are rooted in the goal of assembling DNA molecules into designed periodic arrays, i.e., crystals. Here, we highlight several DNA crystal structures, the progress made in designing DNA crystals, and look at the current prospects and future directions of DNA crystals in nanotechnology.},
doi = {10.3390/cryst6080097},
journal = {Crystals},
number = 8,
volume = 6,
place = {United States},
year = {2016},
month = {8}
}

Journal Article:
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Cited by: 7 works
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Works referenced in this record:

Crystal Structure of a Continuous Three-Dimensional DNA Lattice
journal, August 2004


Six-Helix Bundles Designed from DNA
journal, April 2005

  • Mathieu, Frederick; Liao, Shiping; Kopatsch, Jens
  • Nano Letters, Vol. 5, Issue 4
  • DOI: 10.1021/nl050084f

Addressing the Instability of DNA Nanostructures in Tissue Culture
journal, August 2014

  • Hahn, Jaeseung; Wickham, Shelley F. J.; Shih, William M.
  • ACS Nano, Vol. 8, Issue 9
  • DOI: 10.1021/nn503513p

Flexibility of DNA
journal, June 1988


DNA double-crossover molecules
journal, April 1993


Direct Evidence for Holliday Junction Crossover Isomerization
journal, April 1997

  • Li, Xiaojun; Wang, Hui; Seeman, Nadrian C.
  • Biochemistry, Vol. 36, Issue 14
  • DOI: 10.1021/bi9629586

Formulation and delivery issues for monoclonal antibody therapeutics
journal, August 2006


Design and self-assembly of two-dimensional DNA crystals
journal, August 1998

  • Winfree, Erik; Liu, Furong; Wenzler, Lisa A.
  • Nature, Vol. 394, Issue 6693
  • DOI: 10.1038/28998

DNA Origami as a Carrier for Circumvention of Drug Resistance
journal, August 2012

  • Jiang, Qiao; Song, Chen; Nangreave, Jeanette
  • Journal of the American Chemical Society, Vol. 134, Issue 32
  • DOI: 10.1021/ja304263n

One-Step Formation of “Chain-Armor”-Stabilized DNA Nanostructures
journal, May 2015

  • Cassinelli, Valentina; Oberleitner, Birgit; Sobotta, Jessica
  • Angewandte Chemie International Edition, Vol. 54, Issue 27
  • DOI: 10.1002/anie.201500561

DNA bending at adenine · thymine tracts
journal, April 1986

  • Koo, Hyeon-Sook; Wu, Hen-Ming; Crothers, Donald M.
  • Nature, Vol. 320, Issue 6062
  • DOI: 10.1038/320501a0

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

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


Numerical Evidence for Nucleated Self-Assembly of DNA Brick Structures
journal, June 2014


Three-Dimensional DNA Crystals as Molecular Sieves
journal, May 2006

  • Paukstelis, Paul J.
  • Journal of the American Chemical Society, Vol. 128, Issue 21
  • DOI: 10.1021/ja061322r

Enhancing DNA Crystal Durability through Chemical Crosslinking
journal, January 2016


Crystallization mechanisms in solution
journal, July 1988


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

Enzyme-catalysed assembly of DNA hydrogel
journal, September 2006

  • Um, Soong Ho; Lee, Jong Bum; Park, Nokyoung
  • Nature Materials, Vol. 5, Issue 10
  • DOI: 10.1038/nmat1741

DNA Cage Delivery to Mammalian Cells
journal, June 2011

  • Walsh, Anthony S.; Yin, HaiFang; Erben, Christoph M.
  • ACS Nano, Vol. 5, Issue 7
  • DOI: 10.1021/nn2005574

The design of a biochip: a self-assembling molecular-scale memory device
journal, January 1987

  • Robinson, Bruce H.; Seeman, Nadrian C.
  • "Protein Engineering, Design and Selection", Vol. 1, Issue 4
  • DOI: 10.1093/protein/1.4.295

Crystal-Structure-Guided Design of Self-Assembling RNA Nanotriangles
journal, February 2016

  • Boerneke, Mark A.; Dibrov, Sergey M.; Hermann, Thomas
  • Angewandte Chemie International Edition, Vol. 55, Issue 12
  • DOI: 10.1002/anie.201600233

X-ray analysis on the nanogram to microgram scale using porous complexes
journal, March 2013

  • Inokuma, Yasuhide; Yoshioka, Shota; Ariyoshi, Junko
  • Nature, Vol. 495, Issue 7442
  • DOI: 10.1038/nature11990

DNA rendering of polyhedral meshes at the nanoscale
journal, July 2015

  • Benson, Erik; Mohammed, Abdulmelik; Gardell, Johan
  • Nature, Vol. 523, Issue 7561
  • DOI: 10.1038/nature14586

Automated synthesis of gene fragments
journal, October 1981


A DNA Crystal Designed to Contain Two Molecules per Asymmetric Unit
journal, November 2010

  • Wang, Tong; Sha, Ruojie; Birktoft, Jens
  • Journal of the American Chemical Society, Vol. 132, Issue 44
  • DOI: 10.1021/ja104833t

Crystal structure of the nucleosome core particle at 2.8 Å resolution
journal, September 1997

  • Luger, Karolin; Mäder, Armin W.; Richmond, Robin K.
  • Nature, Vol. 389, Issue 6648
  • DOI: 10.1038/38444

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

Molecular structure of a left-handed double helical DNA fragment at atomic resolution
journal, December 1979

  • Wang, Andrew H. -J.; Quigley, Gary J.; Kolpak, Francis J.
  • Nature, Vol. 282, Issue 5740
  • DOI: 10.1038/282680a0

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

  • Liu, Wenyan; Zhong, Hong; Wang, Risheng
  • Angewandte Chemie International Edition, Vol. 50, Issue 1
  • DOI: 10.1002/anie.201005911

Unusual DNA conformation at low pH revealed by NMR: parallel-stranded DNA duplex with homo base pairs
journal, November 1992

  • Robinson, Howard; Van der Marel, Gijs A.; Van Boom, Jacques H.
  • Biochemistry, Vol. 31, Issue 43
  • DOI: 10.1021/bi00158a014

Functionalizing Designer DNA Crystals with a Triple-Helical Veneer
journal, March 2014

  • Rusling, David A.; Chandrasekaran, Arun Richard; Ohayon, Yoel P.
  • Angewandte Chemie International Edition, Vol. 53, Issue 15
  • DOI: 10.1002/anie.201309914

DNA Crystals as Vehicles for Biocatalysis
journal, May 2014

  • Geng, Chun; Paukstelis, Paul J.
  • Journal of the American Chemical Society, Vol. 136, Issue 22
  • DOI: 10.1021/ja502356m

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


Synthesis from DNA of a molecule with the connectivity of a cube
journal, April 1991

  • Chen, Junghuei; Seeman, Nadrian C.
  • Nature, Vol. 350, Issue 6319
  • DOI: 10.1038/350631a0

A nanomechanical device based on the B–Z transition of DNA
journal, January 1999

  • Mao, Chengde; Sun, Weiqiong; Shen, Zhiyong
  • Nature, Vol. 397, Issue 6715
  • DOI: 10.1038/16437

A DNA Dodecamer Containing an Adenine Tract Crystallizes in a Unique Lattice and Exhibits a New Bend
journal, June 1993

  • DiGabriele, Anna D.; Steitz, Thomas A.
  • Journal of Molecular Biology, Vol. 231, Issue 4
  • DOI: 10.1006/jmbi.1993.1349

Encapsulation of a Nerve Agent Detoxifying Enzyme by a Mesoporous Zirconium Metal–Organic Framework Engenders Thermal and Long-Term Stability
journal, June 2016

  • Li, Peng; Moon, Su-Young; Guelta, Mark A.
  • Journal of the American Chemical Society, Vol. 138, Issue 26
  • DOI: 10.1021/jacs.6b03673

The Thermal Stability of DNA Fragments With Tandem Mismatches at a d(CXYG)d(CY'X'G) Site
journal, February 1996


DNA polymorphism in crystals: three stable conformations for the decadeoxynucleotide d(GCATGCATGC)
journal, May 2016

  • Thirugnanasambandam, Arunachalam; Karthik, Selvam; Artheswari, Gunanithi
  • Acta Crystallographica Section D Structural Biology, Vol. 72, Issue 6
  • DOI: 10.1107/S2059798316006306

HELIX: a new modular nucleic acid crystallization screen
journal, May 2014


Characterization and thermodynamic properties of quadruplex/duplex competition
journal, August 2002


Stabilisation of self-assembled DNA crystals by triplex-directed photo-cross-linking
journal, January 2016

  • Abdallah, Hatem O.; Ohayon, Yoel P.; Chandrasekaran, Arun Richard
  • Chemical Communications, Vol. 52, Issue 51
  • DOI: 10.1039/C6CC03695C

DNA Origami as an In Vivo Drug Delivery Vehicle for Cancer Therapy
journal, June 2014


Kinetics of quadruplex to duplex conversion
journal, November 2015


Cellular processing and destinies of artificial DNA nanostructures
journal, January 2016

  • Lee, Di Sheng; Qian, Hang; Tay, Chor Yong
  • Chemical Society Reviews, Vol. 45, Issue 15
  • DOI: 10.1039/C5CS00700C

Molecular Configuration in Sodium Thymonucleate
journal, April 1953

  • Franklin, Rosalind E.; Gosling, R. G.
  • Nature, Vol. 171, Issue 4356
  • DOI: 10.1038/171740a0

A DNA decamer with a sticky end: the crystal structure of d-CGACGATCGT
journal, April 1997

  • Qiu, Hangxia; Dewan, John C.; Seeman, Nadrian C.
  • Journal of Molecular Biology, Vol. 267, Issue 4
  • DOI: 10.1006/jmbi.1997.0918

The poly dA helix: a new structural motif for high performance DNA-based molecular switches
journal, March 2009

  • Chakraborty, Saikat; Sharma, Suruchi; Maiti, Prabal K.
  • Nucleic Acids Research, Vol. 37, Issue 9
  • DOI: 10.1093/nar/gkp133

How sequence defines structure: A crystallographic map of DNA structure and conformation
journal, May 2005

  • Hays, F. A.; Teegarden, A.; Jones, Z. J. R.
  • Proceedings of the National Academy of Sciences, Vol. 102, Issue 20
  • DOI: 10.1073/pnas.0409455102

Tunable, colorimetric DNA-based pH sensors mediated by A-motif formation
journal, January 2012

  • Saha, Sonali; Chakraborty, Kasturi; Krishnan, Yamuna
  • Chemical Communications, Vol. 48, Issue 19
  • DOI: 10.1039/c2cc16347k

Circuits and programmable self-assembling DNA structures
journal, September 2002

  • Carbone, A.; Seeman, N. C.
  • Proceedings of the National Academy of Sciences, Vol. 99, Issue 20
  • DOI: 10.1073/pnas.202418299

The Flexibility of DNA Double Crossover Molecules
journal, June 2003


Two DNA nanomachines map pH changes along intersecting endocytic pathways inside the same cell
journal, May 2013

  • Modi, Souvik; Nizak, Clément; Surana, Sunaina
  • Nature Nanotechnology, Vol. 8, Issue 6
  • DOI: 10.1038/nnano.2013.92

Post-Assembly Stabilization of Rationally Designed DNA Crystals
journal, July 2015

  • Zhao, Jiemin; Chandrasekaran, Arun Richard; Li, Qian
  • Angewandte Chemie International Edition, Vol. 54, Issue 34
  • DOI: 10.1002/anie.201503610

5'-CGA sequence is a strong motif for homo base-paired parallel-stranded DNA duplex as revealed by NMR analysis.
journal, June 1993

  • Robinson, H.; Wang, A. H.
  • Proceedings of the National Academy of Sciences, Vol. 90, Issue 11
  • DOI: 10.1073/pnas.90.11.5224

Molecular structure of the G.A base pair in DNA and its implications for the mechanism of transversion mutations.
journal, April 1986

  • Brown, T.; Hunter, W. N.; Kneale, G.
  • Proceedings of the National Academy of Sciences, Vol. 83, Issue 8
  • DOI: 10.1073/pnas.83.8.2402

Gene synthesis machines: DNA chemistry and its uses
journal, October 1985


Cations Mediate B-DNA Conformational Heterogeneity
journal, November 2000

  • Sines, Chad C.; McFail-Isom, Lori; Howerton, Shelley B.
  • Journal of the American Chemical Society, Vol. 122, Issue 45
  • DOI: 10.1021/ja002244p

A Highly Efficient 24-Condition Matrix for the Crystallization of Nucleic Acid Fragments
journal, May 1996

  • Berger, I.; Kang, C.; Sinha, N.
  • Acta Crystallographica Section D Biological Crystallography, Vol. 52, Issue 3
  • DOI: 10.1107/S0907444995013564

Self-Assembled DNA Crystals: The Impact on Resolution of 5′-Phosphates and the DNA Source
journal, January 2013

  • Sha, Ruojie; Birktoft, Jens J.; Nguyen, Nam
  • Nano Letters, Vol. 13, Issue 2
  • DOI: 10.1021/nl304550c

Photo-Cross-Linking-Assisted Thermal Stability of DNA Origami Structures and Its Application for Higher-Temperature Self-Assembly
journal, September 2011

  • Rajendran, Arivazhagan; Endo, Masayuki; Katsuda, Yousuke
  • Journal of the American Chemical Society, Vol. 133, Issue 37
  • DOI: 10.1021/ja204546h

Interlocked mismatch-aligned arrowhead DNA motifs
journal, July 1999


Probing the role of sequence in the assembly of three-dimensional DNA crystals: Three-Dimensional DNA Crystals
journal, August 2015

  • Saoji, Maithili; Zhang, Daoning; Paukstelis, Paul J.
  • Biopolymers, Vol. 103, Issue 11
  • DOI: 10.1002/bip.22688

Logical computation using algorithmic self-assembly of DNA triple-crossover molecules
journal, September 2000

  • Mao, Chengde; LaBean, Thomas H.; Reif, John H.
  • Nature, Vol. 407, Issue 6803
  • DOI: 10.1038/35035038

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

Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid
journal, April 1953

  • Watson, J. D.; Crick, F. H. C.
  • Nature, Vol. 171, Issue 4356
  • DOI: 10.1038/171737a0

DNA Nanotechnology Based on i-Motif Structures
journal, May 2014

  • Dong, Yuanchen; Yang, Zhongqiang; Liu, Dongsheng
  • Accounts of Chemical Research, Vol. 47, Issue 6
  • DOI: 10.1021/ar500073a

Structure of a B-DNA dodecamer: conformation and dynamics.
journal, April 1981

  • Drew, H. R.; Wing, R. M.; Takano, T.
  • Proceedings of the National Academy of Sciences, Vol. 78, Issue 4
  • DOI: 10.1073/pnas.78.4.2179

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 brick crystals with prescribed depths
journal, October 2014

  • Ke, Yonggang; Ong, Luvena L.; Sun, Wei
  • Nature Chemistry, Vol. 6, Issue 11
  • DOI: 10.1038/nchem.2083

G-Wires: Self-Assembly of a Telomeric Oligonucleotide, d(GGGGTTGGGG), into Large Superstructures
journal, September 1994


A robust DNA mechanical device controlled by hybridization topology
journal, January 2002

  • Yan, Hao; Zhang, Xiaoping; Shen, Zhiyong
  • Nature, Vol. 415, Issue 6867
  • DOI: 10.1038/415062a

Nucleic acid junctions and lattices
journal, November 1982


Construction, Analysis, Ligation, and Self-Assembly of DNA Triple Crossover Complexes
journal, March 2000

  • LaBean, Thomas H.; Yan, Hao; Kopatsch, Jens
  • Journal of the American Chemical Society, Vol. 122, Issue 9
  • DOI: 10.1021/ja993393e

The Nucleic Acid Database: new features and capabilities
journal, October 2013

  • Coimbatore Narayanan, Buvaneswari; Westbrook, John; Ghosh, Saheli
  • Nucleic Acids Research, Vol. 42, Issue D1
  • DOI: 10.1093/nar/gkt980

Matthews coefficient probabilities: Improved estimates for unit cell contents of proteins, DNA, and protein-nucleic acid complex crystals
journal, September 2003

  • Kantardjieff, Katherine A.; Rupp, Bernhard
  • Protein Science, Vol. 12, Issue 9
  • DOI: 10.1110/ps.0350503

Toward Larger DNA Origami
journal, September 2014

  • Marchi, Alexandria N.; Saaem, Ishtiaq; Vogen, Briana N.
  • Nano Letters, Vol. 14, Issue 10
  • DOI: 10.1021/nl502626s

Crystal structure of a yeast TBP/TATA-box complex
journal, October 1993

  • Kim, Youngchang; Geiger, James. H.; Hahn, Steven
  • Nature, Vol. 365, Issue 6446
  • DOI: 10.1038/365512a0

Nucleic Acid Conformation: Crystal Structure of a Naturally Occurring Dinucleoside Phosphate (UpA)
journal, September 1971

  • Seeman, Nadrian C.; Sussman, Joel L.; Berman, Helen M.
  • Nature New Biology, Vol. 233, Issue 37
  • DOI: 10.1038/newbio233090a0

Sequence-specific recognition of double helical nucleic acids by proteins.
journal, March 1976

  • Seeman, N. C.; Rosenberg, J. M.; Rich, A.
  • Proceedings of the National Academy of Sciences, Vol. 73, Issue 3
  • DOI: 10.1073/pnas.73.3.804

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