Characterizing the length-dependence of DNA nanotube end-to-end joining rates

Pacella, Michael S.; Mardanlou, Vahid; Agarwal, Siddharth; Patel, Anusha; Jelezniakov, Elizabeth; Mohammed, Abdul M.; Franco, Elisa; Schulman, Rebecca

doi:10.1039/C9ME00068B

Title: Characterizing the length-dependence of DNA nanotube end-to-end joining rates

Abstract

DNA nanotechnology provides a route towards the synthesis of custom nano-structured materials and circuits through hierarchical assembly processes. Although predictive kinetic models are being developed for the assembly of DNA nanostructures from small monomeric components, a general model for the hierarchical assembly of DNA nanostructures remains elusive. DNA tile nanotubes provide an ideal model system for the study of hierarchical assembly via end-to-end joining. In this study, we experimentally characterize the length-dependence of the end-to-end joining rate of DNA tile nanotubes. We then test the ability of three different models of polymer end-to-end joining to reproduce experimentally measured changes in nanotube lengths during a joining reaction using an ODE model for nanotube joining. All three models predict physically realistic joining rates that are consistent with prior measurements, with a length-independent end-to-end joining rate model providing the best fit to the experimental data. A length-independent constant joining rate is consistent with other DNA self-assembly processes across a broad range of length scales and also suggests how tractable models for hierarchical DNA nanostructure could be developed.

Authors:

^[1]; Mardanlou, Vahid ^[2]; Agarwal, Siddharth ^[2]; Patel, Anusha ^[1]; Jelezniakov, Elizabeth ^[3]; Mohammed, Abdul M. ^[4]; Franco, Elisa ^[2]; Schulman, Rebecca ^[1]

Johns Hopkins Univ., Baltimore, MD (United States)
Univ. of California, Los Angeles, CA (United States)
Baltimore Polytechnic Inst., Baltimore, MD (United States)
Ultivue, Cambridge, MA (United States)

Publication Date:: Wed Dec 11 00:00:00 EST 2019

Research Org.:: Univ. of California, Riverside, CA (United States); Johns Hopkins Univ., Baltimore, MD (United States)

Sponsoring Org.:: USDOE Office of Science (SC), Basic Energy Sciences (BES)

OSTI Identifier:: 1595293

Alternate Identifier(s):: OSTI ID: 1659414; OSTI ID: 1798464

Grant/Contract Number:: SC0010595

Resource Type:: Accepted Manuscript

Journal Name:: Molecular Systems Design & Engineering

Additional Journal Information:: Journal Volume: 5; Journal Issue: 2; Journal ID: ISSN 2058-9689

Publisher:: Royal Society of Chemistry

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES

Citation Formats


                    Pacella, Michael S., Mardanlou, Vahid, Agarwal, Siddharth, Patel, Anusha, Jelezniakov, Elizabeth, Mohammed, Abdul M., Franco, Elisa, and Schulman, Rebecca. Characterizing the length-dependence of DNA nanotube end-to-end joining rates.  United States: N. p., 2019. 
Web.  doi:10.1039/C9ME00068B.

Copy to clipboard


                    Pacella, Michael S., Mardanlou, Vahid, Agarwal, Siddharth, Patel, Anusha, Jelezniakov, Elizabeth, Mohammed, Abdul M., Franco, Elisa, & Schulman, Rebecca. Characterizing the length-dependence of DNA nanotube end-to-end joining rates.  United States.  https://doi.org/10.1039/C9ME00068B

Copy to clipboard


                    Pacella, Michael S., Mardanlou, Vahid, Agarwal, Siddharth, Patel, Anusha, Jelezniakov, Elizabeth, Mohammed, Abdul M., Franco, Elisa, and Schulman, Rebecca. Wed .  
"Characterizing the length-dependence of DNA nanotube end-to-end joining rates".  United States.  https://doi.org/10.1039/C9ME00068B.  https://www.osti.gov/servlets/purl/1595293.

Copy to clipboard


                    
@article{osti_1595293,

  title        = {Characterizing the length-dependence of DNA nanotube end-to-end joining rates},

  author       = {Pacella, Michael S. and Mardanlou, Vahid and Agarwal, Siddharth and Patel, Anusha and Jelezniakov, Elizabeth and Mohammed, Abdul M. and Franco, Elisa and Schulman, Rebecca},

  abstractNote = {DNA nanotechnology provides a route towards the synthesis of custom nano-structured materials and circuits through hierarchical assembly processes. Although predictive kinetic models are being developed for the assembly of DNA nanostructures from small monomeric components, a general model for the hierarchical assembly of DNA nanostructures remains elusive. DNA tile nanotubes provide an ideal model system for the study of hierarchical assembly via end-to-end joining. In this study, we experimentally characterize the length-dependence of the end-to-end joining rate of DNA tile nanotubes. We then test the ability of three different models of polymer end-to-end joining to reproduce experimentally measured changes in nanotube lengths during a joining reaction using an ODE model for nanotube joining. All three models predict physically realistic joining rates that are consistent with prior measurements, with a length-independent end-to-end joining rate model providing the best fit to the experimental data. A length-independent constant joining rate is consistent with other DNA self-assembly processes across a broad range of length scales and also suggests how tractable models for hierarchical DNA nanostructure could be developed.},

  doi          = {10.1039/C9ME00068B},

  journal      = {Molecular Systems Design & Engineering},

  number       = 2,

  volume       = 5,

  place        = {United States},

  year         = {Wed Dec 11 00:00:00 EST 2019},

  month        = {Wed Dec 11 00:00:00 EST 2019}

}

Copy to clipboard

Journal Article:

Free Publicly Available Full Text

Accepted Manuscript (DOE)

Publisher's Version of Record

https://doi.org/10.1039/C9ME00068B

Other availability

Search WorldCat to find libraries that may hold this journal

Citation Metrics:

Cited by: 2 works

Citation information provided by
Web of Science

Save / Share:

Export Metadata

Save to My Library

Works referenced in this record:

The Thermodynamics of DNA Structural Motifs
journal, June 2004

SantaLucia, John; Hicks, Donald
Annual Review of Biophysics and Biomolecular Structure, Vol. 33, Issue 1
DOI: 10.1146/annurev.biophys.32.110601.141800

Direct demonstration of actin filament annealing in vitro.
journal, June 1988

Murphy, D. B.; Gray, R. O.; Grasser, W. A.
The Journal of Cell Biology, Vol. 106, Issue 6
DOI: 10.1083/jcb.106.6.1947

Molecular engineering of chiral colloidal liquid crystals using DNA origami
journal, May 2017

Siavashpouri, Mahsa; Wachauf, Christian H.; Zakhary, Mark J.
Nature Materials, Vol. 16, Issue 8
DOI: 10.1038/nmat4909

Determining hydrodynamic forces in bursting bubbles using DNA nanotube mechanics
journal, October 2015

Hariadi, Rizal F.; Winfree, Erik; Yurke, Bernard
Proceedings of the National Academy of Sciences, Vol. 112, Issue 45
DOI: 10.1073/pnas.1424673112

Directed self-assembly of 1D microtubule nano-arrays
journal, January 2014

Bachand, M.; Bouxsein, N. F.; Cheng, S.
RSC Adv., Vol. 4, Issue 97
DOI: 10.1039/C4RA11765D

A fast parallel algorithm for thinning digital patterns
journal, March 1984

Zhang, T. Y.; Suen, C. Y.
Communications of the ACM, Vol. 27, Issue 3
DOI: 10.1145/357994.358023

Terminating DNA Tile Assembly with Nanostructured Caps
journal, September 2017

Agrawal, Deepak K.; Jiang, Ruoyu; Reinhart, Seth
ACS Nano, Vol. 11, Issue 10
DOI: 10.1021/acsnano.7b02256

Joining and Scission in the Self-Assembly of Nanotubes from DNA Tiles
journal, December 2004

Ekani-Nkodo, Axel; Kumar, Ashish; Fygenson, Deborah Kuchnir
Physical Review Letters, Vol. 93, Issue 26
DOI: 10.1103/PhysRevLett.93.268301

Assembly of Aβ Amyloid Protofibrils: An in Vitro Model for a Possible Early Event in Alzheimer's Disease ^†
journal, July 1999

Harper, James D.; Wong, Stanislaus S.; Lieber, Charles M.
Biochemistry, Vol. 38, Issue 28
DOI: 10.1021/bi9904149

Probing the Kinetics of β-Amyloid Self-Association
journal, June 2000

Murphy, Regina M.; Pallitto, Monica M.
Journal of Structural Biology, Vol. 130, Issue 2-3
DOI: 10.1006/jsbi.2000.4253

Guiding the folding pathway of DNA origami
journal, August 2015

Dunn, Katherine E.; Dannenberg, Frits; Ouldridge, Thomas E.
Nature, Vol. 525, Issue 7567
DOI: 10.1038/nature14860

Interactions regulating the head-to-tail directed assembly of biological Janus rods
journal, January 2017

Greene, A. C.; Bachand, M.; Gomez, A.
Chemical Communications, Vol. 53, Issue 32
DOI: 10.1039/C7CC01566F

End-to-end joining of microtubules: Kinetics in crowded solutions
journal, June 1988

Williams, R. C.; Rone, Lisa A.
Protoplasma, Vol. 145, Issue 2-3
DOI: 10.1007/BF01349360

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

Wei, Bryan; Dai, Mingjie; Yin, Peng
Nature, Vol. 485, Issue 7400
DOI: 10.1038/nature11075

Crystallization by particle attachment in synthetic, biogenic, and geologic environments
journal, July 2015

De Yoreo, J. J.; Gilbert, P. U. P. A.; Sommerdijk, N. A. J. M.
Science, Vol. 349, Issue 6247
DOI: 10.1126/science.aaa6760

Reconfigurable DNA Origami to Generate Quasifractal Patterns
journal, May 2012

Zhang, Fei; Nangreave, Jeanette; Liu, Yan
Nano Letters, Vol. 12, Issue 6
DOI: 10.1021/nl301399z

Uncovering the Self-Assembly of DNA Nanostructures by Thermodynamics and Kinetics
journal, May 2014

Wei, Xixi; Nangreave, Jeanette; Liu, Yan
Accounts of Chemical Research, Vol. 47, Issue 6
DOI: 10.1021/ar5000665

Fractal assembly of micrometre-scale DNA origami arrays with arbitrary patterns
journal, December 2017

Tikhomirov, Grigory; Petersen, Philip; Qian, Lulu
Nature, Vol. 552, Issue 7683
DOI: 10.1038/nature24655

Gigadalton-scale shape-programmable DNA assemblies
journal, December 2017

Wagenbauer, Klaus F.; Sigl, Christian; Dietz, Hendrik
Nature, Vol. 552, Issue 7683
DOI: 10.1038/nature24651

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

Rothemund, Paul W. K.
Nature, Vol. 440, Issue 7082, p. 297-302
DOI: 10.1038/nature04586

Single-Stranded Tile Stoppers for Interlocked DNA Architectures
journal, April 2016

Valero, Julián; Lohmann, Finn; Keppner, Daniel
ChemBioChem, Vol. 17, Issue 12
DOI: 10.1002/cbic.201500685

Programmable disorder in random DNA tilings
journal, November 2016

Tikhomirov, Grigory; Petersen, Philip; Qian, Lulu
Nature Nanotechnology, Vol. 12, Issue 3
DOI: 10.1038/nnano.2016.256

Directing Self-Assembly of DNA Nanotubes Using Programmable Seeds
journal, August 2013

Mohammed, Abdul M.; Schulman, Rebecca
Nano Letters, Vol. 13, Issue 9
DOI: 10.1021/nl400881w

DNA self-assembly scaled up
journal, December 2017

Zhang, Fei; Yan, Hao
Nature, Vol. 552, Issue 7683
DOI: 10.1038/d41586-017-07690-y

Studies of Thermal Stability of Multivalent DNA Hybridization in a Nanostructured System
journal, July 2009

Nangreave, Jeanette; Yan, Hao; Liu, Yan
Biophysical Journal, Vol. 97, Issue 2
DOI: 10.1016/j.bpj.2009.05.013

Geometrical self-assembly
journal, July 2011

Turberfield, Andrew J.
Nature Chemistry, Vol. 3, Issue 8
DOI: 10.1038/nchem.1097

Influence of secondary structure on kinetics and reaction mechanism of DNA hybridization
journal, April 2007

Chen, Chunlai; Wang, Wenjuan; Wang, Zhang
Nucleic Acids Research, Vol. 35, Issue 9
DOI: 10.1093/nar/gkm177

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

Woo, Sungwook; Rothemund, Paul W. K.
Nature Communications, Vol. 5, Issue 1
DOI: 10.1038/ncomms5889

Ultrafast cooling reveals microsecond-scale biomolecular dynamics
journal, December 2014

Polinkovsky, Mark E.; Gambin, Yann; Banerjee, Priya R.
Nature Communications, Vol. 5, Issue 1
DOI: 10.1038/ncomms6737

Understanding the Elementary Steps in DNA Tile-Based Self-Assembly
journal, August 2017

Jiang, Shuoxing; Hong, Fan; Hu, Huiyu
ACS Nano, Vol. 11, Issue 9
DOI: 10.1021/acsnano.7b04845

Elastic properties and secondary structure formation of single-stranded DNA at monovalent and divalent salt conditions
journal, November 2013

Bosco, Alessandro; Camunas-Soler, Joan; Ritort, Felix
Nucleic Acids Research, Vol. 42, Issue 3
DOI: 10.1093/nar/gkt1089

Sensitive fluorescence-based thermodynamic and kinetic measurements of DNA hybridization in solution
journal, March 1993

Morrison, Larry E.; Stols, Lucy M.
Biochemistry, Vol. 32, Issue 12
DOI: 10.1021/bi00063a022

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

Kinetics of aggregation of synthetic β-amyloid peptide
journal, May 1992

Tomski, Sharon J.; Murphy, Regina M.
Archives of Biochemistry and Biophysics, Vol. 294, Issue 2
DOI: 10.1016/0003-9861(92)90735-F

Design and Characterization of Programmable DNA Nanotubes
journal, December 2004

Rothemund, Paul W. K.; Ekani-Nkodo, Axel; Papadakis, Nick
Journal of the American Chemical Society, Vol. 126, Issue 50
DOI: 10.1021/ja044319l

scikit-image: image processing in Python
journal, January 2014

van der Walt, Stéfan; Schönberger, Johannes L.; Nunez-Iglesias, Juan
PeerJ, Vol. 2
DOI: 10.7717/peerj.453

pH-Driven Reversible Self-Assembly of Micron-Scale DNA Scaffolds
journal, November 2017

Green, Leopold N.; Amodio, Alessia; Subramanian, Hari K. K.
Nano Letters, Vol. 17, Issue 12
DOI: 10.1021/acs.nanolett.7b02787

Length dependence of rate constants for end-to-end association and dissociation of equilibrium linear aggregates
journal, November 1983

Hill, T. L.
Biophysical Journal, Vol. 44, Issue 2
DOI: 10.1016/S0006-3495(83)84301-X

Relaxation kinetics of dimer formation by self complementary oligonucleotides
journal, December 1971

Craig, Mary E.; Crothers, Donald M.; Doty, Paul
Journal of Molecular Biology, Vol. 62, Issue 2
DOI: 10.1016/0022-2836(71)90434-7

Information-based autonomous reconfiguration in systems of interacting DNA nanostructures
journal, December 2018

Petersen, Philip; Tikhomirov, Grigory; Qian, Lulu
Nature Communications, Vol. 9, Issue 1
DOI: 10.1038/s41467-018-07805-7

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

Gerling, T.; Wagenbauer, K. F.; Neuner, A. M.
Science, Vol. 347, Issue 6229
DOI: 10.1126/science.aaa5372

Self-assembling DNA nanotubes to connect molecular landmarks
journal, December 2016

Mohammed, Abdul M.; Šulc, Petr; Zenk, John
Nature Nanotechnology, Vol. 12, Issue 4
DOI: 10.1038/nnano.2016.277

An information-bearing seed for nucleating algorithmic self-assembly
journal, March 2009

Barish, R. D.; Schulman, R.; Rothemund, P. W. K.
Proceedings of the National Academy of Sciences, Vol. 106, Issue 15
DOI: 10.1073/pnas.0808736106

Kinetics and Thermodynamics of Watson–Crick Base Pairing Driven DNA Origami Dimerization
journal, March 2016

Zenk, John; Tuntivate, Chanon; Schulman, Rebecca
Journal of the American Chemical Society, Vol. 138, Issue 10
DOI: 10.1021/jacs.5b10502

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

A Computational Approach to Edge Detection
journal, November 1986

Canny, John
IEEE Transactions on Pattern Analysis and Machine Intelligence, Vol. PAMI-8, Issue 6
DOI: 10.1109/TPAMI.1986.4767851

Kinetics of DNA Tile Dimerization
journal, May 2014

Jiang, Shuoxing; Yan, Hao; Liu, Yan
ACS Nano, Vol. 8, Issue 6
DOI: 10.1021/nn500721n

Algorithmic Self-Assembly of DNA Sierpinski Triangles
journal, December 2004

Rothemund, Paul W. K.; Papadakis, Nick; Winfree, Erik
PLoS Biology, Vol. 2, Issue 12
DOI: 10.1371/journal.pbio.0020424

Secondary structure effects on DNA hybridization kinetics: a solution versus surface comparison
journal, June 2006

Gao, Y.
Nucleic Acids Research, Vol. 34, Issue 11
DOI: 10.1093/nar/gkl422

Folding and cutting DNA into reconfigurable topological nanostructures
journal, October 2010

Han, Dongran; Pal, Suchetan; Liu, Yan
Nature Nanotechnology, Vol. 5, Issue 10
DOI: 10.1038/nnano.2010.193

Programmable self-assembly of three-dimensional nanostructures from 10,000 unique components
journal, December 2017

Ong, Luvena L.; Hanikel, Nikita; Yaghi, Omar K.
Nature, Vol. 552, Issue 7683
DOI: 10.1038/nature24648

The Intrinsic Viscosity, Translational and Rotatory Diffusion Constants of Rod‐Like Macromolecules in Solution
journal, April 1950

Riseman, Jacob; Kirkwood, John G.
The Journal of Chemical Physics, Vol. 18, Issue 4
DOI: 10.1063/1.1747672

Controlled Nucleation and Growth of DNA Tile Arrays within Prescribed DNA Origami Frames and Their Dynamics
journal, February 2014

Li, Wei; Yang, Yang; Jiang, Shuoxing
Journal of the American Chemical Society, Vol. 136, Issue 10
DOI: 10.1021/ja411446q

The rate of annealing of actin tropomyosin filaments depends strongly on the length of the filaments
journal, October 1996

Teubner, Andreas; Wegner, Albrecht
Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology, Vol. 1297, Issue 2
DOI: 10.1016/S0167-4838(96)00111-2

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

Self-Healing Materials
journal, September 2010

Hager, Martin D.; Greil, Peter; Leyens, Christoph
Advanced Materials, Vol. 22, Issue 47, p. 5424-5430
DOI: 10.1002/adma.201003036

End-to-end Joining of Taxol-stabilized GDP-containing Microtubules
journal, January 1989

Williams, R. C.; Rone, L. A.
Journal of Biological Chemistry, Vol. 264, Issue 3
DOI: 10.1016/S0021-9258(18)94238-9

Preclinical Performance Evaluation of a Robotic Endoscope for Non-Contact Laser Surgery
journal, August 2020

Kundrat, D.; Graesslin, R.; Schoob, A.
Annals of Biomedical Engineering, Vol. 49, Issue 2
DOI: 10.1007/s10439-020-02577-y

Self-healing materials
journal, September 2016

Osman, Sara
Nature Middle East
DOI: 10.1038/nmiddleeast.2016.140

Similar Records in DOE PAGES and OSTI.GOV collections:

Engineering DNA nanotubes for resilience in an E. coli TXTL system

Journal Article Klocke, Melissa A. ; Garamella, Jonathan ; Subramanian, Hari K. K. ; ... - Synthetic Biology

Abstract Deoxyribonucleic acid (DNA) nanotechnology is a growing field with potential intracellular applications. In this work, we use an Escherichia coli cell-free transcription–translation (TXTL) system to assay the robustness of DNA nanotubes in a cytoplasmic environment. TXTL recapitulates physiological conditions as well as strong linear DNA degradation through the RecBCD complex, the major exonuclease in E. coli. We demonstrate that chemical modifications of the tiles making up DNA nanotubes extend their viability in TXTL for more than 24 h, with phosphorothioation of the sticky end backbone being the most effective. Furthermore, we show that a Chi-site double-stranded DNA, an inhibitor ofmore »« less
https://doi.org/10.1093/synbio/ysy001
Modeling Damage Complexity-Dependent Non-Homologous End-Joining Repair Pathway

Journal Article Li, Yongfeng ; Reynolds, Pamela ; O'Neill, Peter ; ... - PLoS ONE

Non-homologous end joining (NHEJ) is the dominant DNA double strand break (DSB) repair pathway and involves several repair proteins such as Ku, DNA-PKcs, and XRCC4. It has been experimentally shown that the choice of NHEJ proteins is determined by the complexity of DSB. In this paper, we built a mathematical model, based on published data, to study how NHEJ depends on the damage complexity. Under an appropriate set of parameters obtained by minimization technique, we can simulate the kinetics of foci track formation in fluorescently tagged mammalian cells, Ku80-EGFP and DNA-PKcs-YFP for simple and complex DSB repair, respectively, in goodmore »« less
https://doi.org/10.1371/journal.pone.0085816

Full Text Available
Self-assembly of multi-stranded RNA motifs into lattices and tubular structures

Journal Article Stewart, Jaimie Marie ; Subramanian, Hari K. K. ; Franco, Elisa - Nucleic Acids Research

Rational design of nucleic acidmolecules yields selfassembling scaffolds with increasing complexity, size and functionality. It is an open question whether design methods tailored to build DNA nanostructures can be adapted to build RNA nanostructures with comparable features. We demonstrate the formation of RNA lattices and tubular assemblies from double crossover (DX) tiles, a canonical motif in DNA nanotechnology. Tubular structures can exceed 1 m in length, suggesting that this DX motif can produce very robust lattices. Some of these tubes spontaneously form with left-handed chirality. We obtain assemblies by using two methods: a protocol where gel-extracted RNA strands are slowlymore »« less
Cited by 19
https://doi.org/10.1093/nar/gkx063

Full Text Available
Persistence Length Control of the Polyelectrolyte Layer-by-Layer Self-Assembly on Carbon Nanotubes

Journal Article Huang, S J ; Artyukhin, A B ; Wang, Y ; ... - Journal of the American Chemical Society

One-dimensional inorganic materials such as carbon nanotubes1 and semiconductor nanowires have been central to important advances in materials science in the last decade. Unique mechanical and electronic properties of these molecular-scale wires enabled a variety of applications ranging from novel composite materials, to electronic circuits, to new sensors. Often, these applications require non-covalent modification of carbon nanotubes with organic compounds, DNA and biomolecules, and polymers to change nanotube properties or to add new functionality. We recently demonstrated a versatile and flexible strategy for non-covalent modification of carbon nanotubes using layer-by-layer self-assembly of polyelectrolytes. Researchers used this technique extensively for modificationmore »« less
https://doi.org/10.1021/ja053060j

Full Text Available
Building Large DNA Bundles via Controlled Hierarchical Assembly of DNA Tubes

Journal Article Zhang, Yunlong ; Yang, Donglei ; Wang, Pengfei ; ... - ACS Nano

Structural DNA nanotechnology is capable of fabricating designer nanoscale artificial architectures. Developing simple and yet versatile assembly methods to construct large DNA structures of defined spatial features and dynamic capabilities has remained challenging. Herein, we designed a molecular assembly system where DNA tiles can assemble into tubes and then into large one-dimensional DNA bundles following a hierarchical pathway. A cohesive link was incorporated into the tile to induce intertube binding for the formation of DNA bundles. DNA bundles with length of dozens of micrometers and width of hundreds of nanometers were produced, whose assembly was revealed to be collectively determinedmore »« less
https://doi.org/10.1021/acsnano.3c01342

Similar Records

Title: Characterizing the length-dependence of DNA nanotube end-to-end joining rates

Abstract

Citation Formats

The Thermodynamics of DNA Structural Motifs journal, June 2004

Direct demonstration of actin filament annealing in vitro. journal, June 1988

Molecular engineering of chiral colloidal liquid crystals using DNA origami journal, May 2017

Determining hydrodynamic forces in bursting bubbles using DNA nanotube mechanics journal, October 2015

Directed self-assembly of 1D microtubule nano-arrays journal, January 2014

A fast parallel algorithm for thinning digital patterns journal, March 1984

Terminating DNA Tile Assembly with Nanostructured Caps journal, September 2017

Joining and Scission in the Self-Assembly of Nanotubes from DNA Tiles journal, December 2004

Assembly of Aβ Amyloid Protofibrils: An in Vitro Model for a Possible Early Event in Alzheimer's Disease † journal, July 1999

Probing the Kinetics of β-Amyloid Self-Association journal, June 2000

Guiding the folding pathway of DNA origami journal, August 2015

Interactions regulating the head-to-tail directed assembly of biological Janus rods journal, January 2017

End-to-end joining of microtubules: Kinetics in crowded solutions journal, June 1988

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

Crystallization by particle attachment in synthetic, biogenic, and geologic environments journal, July 2015

Reconfigurable DNA Origami to Generate Quasifractal Patterns journal, May 2012

Uncovering the Self-Assembly of DNA Nanostructures by Thermodynamics and Kinetics journal, May 2014

Fractal assembly of micrometre-scale DNA origami arrays with arbitrary patterns journal, December 2017

Gigadalton-scale shape-programmable DNA assemblies journal, December 2017

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

Single-Stranded Tile Stoppers for Interlocked DNA Architectures journal, April 2016

Programmable disorder in random DNA tilings journal, November 2016

Directing Self-Assembly of DNA Nanotubes Using Programmable Seeds journal, August 2013

DNA self-assembly scaled up journal, December 2017

Studies of Thermal Stability of Multivalent DNA Hybridization in a Nanostructured System journal, July 2009

Geometrical self-assembly journal, July 2011

Influence of secondary structure on kinetics and reaction mechanism of DNA hybridization journal, April 2007

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

Ultrafast cooling reveals microsecond-scale biomolecular dynamics journal, December 2014

Understanding the Elementary Steps in DNA Tile-Based Self-Assembly journal, August 2017

Elastic properties and secondary structure formation of single-stranded DNA at monovalent and divalent salt conditions journal, November 2013

Sensitive fluorescence-based thermodynamic and kinetic measurements of DNA hybridization in solution journal, March 1993

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

Kinetics of aggregation of synthetic β-amyloid peptide journal, May 1992

Design and Characterization of Programmable DNA Nanotubes journal, December 2004

scikit-image: image processing in Python journal, January 2014

pH-Driven Reversible Self-Assembly of Micron-Scale DNA Scaffolds journal, November 2017

Length dependence of rate constants for end-to-end association and dissociation of equilibrium linear aggregates journal, November 1983

Relaxation kinetics of dimer formation by self complementary oligonucleotides journal, December 1971

Information-based autonomous reconfiguration in systems of interacting DNA nanostructures journal, December 2018

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

Self-assembling DNA nanotubes to connect molecular landmarks journal, December 2016

An information-bearing seed for nucleating algorithmic self-assembly journal, March 2009

Kinetics and Thermodynamics of Watson–Crick Base Pairing Driven DNA Origami Dimerization journal, March 2016

Biotechnological mass production of DNA origami journal, December 2017

A Computational Approach to Edge Detection journal, November 1986

Kinetics of DNA Tile Dimerization journal, May 2014

Algorithmic Self-Assembly of DNA Sierpinski Triangles journal, December 2004

Secondary structure effects on DNA hybridization kinetics: a solution versus surface comparison journal, June 2006

Folding and cutting DNA into reconfigurable topological nanostructures journal, October 2010

Programmable self-assembly of three-dimensional nanostructures from 10,000 unique components journal, December 2017

The Intrinsic Viscosity, Translational and Rotatory Diffusion Constants of Rod‐Like Macromolecules in Solution journal, April 1950

Controlled Nucleation and Growth of DNA Tile Arrays within Prescribed DNA Origami Frames and Their Dynamics journal, February 2014

The rate of annealing of actin tropomyosin filaments depends strongly on the length of the filaments journal, October 1996

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

Self-Healing Materials journal, September 2010

End-to-end Joining of Taxol-stabilized GDP-containing Microtubules journal, January 1989

Preclinical Performance Evaluation of a Robotic Endoscope for Non-Contact Laser Surgery journal, August 2020

Self-healing materials journal, September 2016

The Thermodynamics of DNA Structural Motifs
journal, June 2004

Direct demonstration of actin filament annealing in vitro.
journal, June 1988

Molecular engineering of chiral colloidal liquid crystals using DNA origami
journal, May 2017

Determining hydrodynamic forces in bursting bubbles using DNA nanotube mechanics
journal, October 2015

Directed self-assembly of 1D microtubule nano-arrays
journal, January 2014

A fast parallel algorithm for thinning digital patterns
journal, March 1984

Terminating DNA Tile Assembly with Nanostructured Caps
journal, September 2017

Joining and Scission in the Self-Assembly of Nanotubes from DNA Tiles
journal, December 2004

Assembly of Aβ Amyloid Protofibrils: An in Vitro Model for a Possible Early Event in Alzheimer's Disease ^†
journal, July 1999

Probing the Kinetics of β-Amyloid Self-Association
journal, June 2000

Guiding the folding pathway of DNA origami
journal, August 2015

Interactions regulating the head-to-tail directed assembly of biological Janus rods
journal, January 2017

End-to-end joining of microtubules: Kinetics in crowded solutions
journal, June 1988

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

Crystallization by particle attachment in synthetic, biogenic, and geologic environments
journal, July 2015

Reconfigurable DNA Origami to Generate Quasifractal Patterns
journal, May 2012

Uncovering the Self-Assembly of DNA Nanostructures by Thermodynamics and Kinetics
journal, May 2014

Fractal assembly of micrometre-scale DNA origami arrays with arbitrary patterns
journal, December 2017

Gigadalton-scale shape-programmable DNA assemblies
journal, December 2017

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

Single-Stranded Tile Stoppers for Interlocked DNA Architectures
journal, April 2016

Programmable disorder in random DNA tilings
journal, November 2016

Directing Self-Assembly of DNA Nanotubes Using Programmable Seeds
journal, August 2013

DNA self-assembly scaled up
journal, December 2017

Studies of Thermal Stability of Multivalent DNA Hybridization in a Nanostructured System
journal, July 2009

Geometrical self-assembly
journal, July 2011

Influence of secondary structure on kinetics and reaction mechanism of DNA hybridization
journal, April 2007

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

Ultrafast cooling reveals microsecond-scale biomolecular dynamics
journal, December 2014

Understanding the Elementary Steps in DNA Tile-Based Self-Assembly
journal, August 2017

Elastic properties and secondary structure formation of single-stranded DNA at monovalent and divalent salt conditions
journal, November 2013

Sensitive fluorescence-based thermodynamic and kinetic measurements of DNA hybridization in solution
journal, March 1993

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

Kinetics of aggregation of synthetic β-amyloid peptide
journal, May 1992

Design and Characterization of Programmable DNA Nanotubes
journal, December 2004

scikit-image: image processing in Python
journal, January 2014

pH-Driven Reversible Self-Assembly of Micron-Scale DNA Scaffolds
journal, November 2017

Length dependence of rate constants for end-to-end association and dissociation of equilibrium linear aggregates
journal, November 1983

Relaxation kinetics of dimer formation by self complementary oligonucleotides
journal, December 1971

Information-based autonomous reconfiguration in systems of interacting DNA nanostructures
journal, December 2018

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

Self-assembling DNA nanotubes to connect molecular landmarks
journal, December 2016

An information-bearing seed for nucleating algorithmic self-assembly
journal, March 2009

Kinetics and Thermodynamics of Watson–Crick Base Pairing Driven DNA Origami Dimerization
journal, March 2016

Biotechnological mass production of DNA origami
journal, December 2017

A Computational Approach to Edge Detection
journal, November 1986

Kinetics of DNA Tile Dimerization
journal, May 2014

Algorithmic Self-Assembly of DNA Sierpinski Triangles
journal, December 2004

Secondary structure effects on DNA hybridization kinetics: a solution versus surface comparison
journal, June 2006

Folding and cutting DNA into reconfigurable topological nanostructures
journal, October 2010

Programmable self-assembly of three-dimensional nanostructures from 10,000 unique components
journal, December 2017

The Intrinsic Viscosity, Translational and Rotatory Diffusion Constants of Rod‐Like Macromolecules in Solution
journal, April 1950

Controlled Nucleation and Growth of DNA Tile Arrays within Prescribed DNA Origami Frames and Their Dynamics
journal, February 2014

The rate of annealing of actin tropomyosin filaments depends strongly on the length of the filaments
journal, October 1996

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

Self-Healing Materials
journal, September 2010

End-to-end Joining of Taxol-stabilized GDP-containing Microtubules
journal, January 1989

Preclinical Performance Evaluation of a Robotic Endoscope for Non-Contact Laser Surgery
journal, August 2020

Self-healing materials
journal, September 2016