ssDNA-amphiphile architecture used to control dimensions of DNA nanotubes

Kuang, Huihui; Gartner III, Thomas E.; Dorneles de Mello, Matheus; Guo, Jun; Zuo, Xiaobing; Tsapatsis, Michael; Jayaraman, Arthi; Kokkoli, Efrosini

doi:10.1039/c9nr03761f

Title: ssDNA-amphiphile architecture used to control dimensions of DNA nanotubes

Abstract

The ssDNA secondary structure and tail length of ssDNA-amphiphiles are used to control the length and diameter of ssDNA nanotubes.

Authors:

^[1];

^[2];

^[3]; Guo, Jun ^[1];

^[4];

^[5];

^[6];

^[5]

Institute for NanoBioTechnology; Johns Hopkins University; Baltimore; USA
Department of Chemical and Biomolecular Engineering; University of Delaware; Newark; USA
Department of Chemical Engineering and Materials Science; University of Minnesota; Minneapolis; USA
X-Ray; Science Division; Argonne National Laboratory; Argonne; USA
Institute for NanoBioTechnology; Johns Hopkins University; Baltimore; USA; Department of Chemical and Biomolecular Engineering
Department of Chemical and Biomolecular Engineering; University of Delaware; Newark; USA; Department of Materials Science and Engineering

Publication Date:: 2019-09-11

Research Org.:: Argonne National Lab. (ANL), Argonne, IL (United States). Advanced Photon Source (APS)

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

OSTI Identifier:: 1609132

Grant/Contract Number:: AC02-06CH11357

Resource Type:: Accepted Manuscript

Journal Name:: Nanoscale

Additional Journal Information:: Journal Volume: 11; Journal Issue: 42; Journal ID: ISSN 2040-3364

Publisher:: Royal Society of Chemistry

Country of Publication:: United States

Language:: English

Subject:: 59 BASIC BIOLOGICAL SCIENCES

Citation Formats


                    Kuang, Huihui, Gartner III, Thomas E., Dorneles de Mello, Matheus, Guo, Jun, Zuo, Xiaobing, Tsapatsis, Michael, Jayaraman, Arthi, and Kokkoli, Efrosini. ssDNA-amphiphile architecture used to control dimensions of DNA nanotubes.  United States: N. p., 2019. 
Web.  doi:10.1039/c9nr03761f.

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                    Kuang, Huihui, Gartner III, Thomas E., Dorneles de Mello, Matheus, Guo, Jun, Zuo, Xiaobing, Tsapatsis, Michael, Jayaraman, Arthi, & Kokkoli, Efrosini. ssDNA-amphiphile architecture used to control dimensions of DNA nanotubes.  United States.  https://doi.org/10.1039/c9nr03761f

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                    Kuang, Huihui, Gartner III, Thomas E., Dorneles de Mello, Matheus, Guo, Jun, Zuo, Xiaobing, Tsapatsis, Michael, Jayaraman, Arthi, and Kokkoli, Efrosini. Wed .  
"ssDNA-amphiphile architecture used to control dimensions of DNA nanotubes".  United States.  https://doi.org/10.1039/c9nr03761f.  https://www.osti.gov/servlets/purl/1609132.

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@article{osti_1609132,

  title        = {ssDNA-amphiphile architecture used to control dimensions of DNA nanotubes},

  author       = {Kuang, Huihui and Gartner III, Thomas E. and Dorneles de Mello, Matheus and Guo, Jun and Zuo, Xiaobing and Tsapatsis, Michael and Jayaraman, Arthi and Kokkoli, Efrosini},

  abstractNote = {The ssDNA secondary structure and tail length of ssDNA-amphiphiles are used to control the length and diameter of ssDNA nanotubes.},

  doi          = {10.1039/c9nr03761f},

  journal      = {Nanoscale},

  number       = 42,

  volume       = 11,

  place        = {United States},

  year         = {2019},

  month        = {9}

}

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To extensively control the nanofiller arrangement (location, orientation, shape) is still a bottleneck for multi-wall carbon nanotube (MWCNT) nanocomposites. Here in this paper, we demonstrate simultaneous control of alignment (orientation) and dispersion (location) of pristine, i.e., unfunctionalized MWCNT using a high molar mass (HMM) amphiphilic block copolymer (BCP). We tested whether a HMM BCP in a selective solvent (i) disperses MWCNTs (ii) by similar mechanisms to low molar mass BCPs and (iii) is melt-drawable to align the well dispersed MWCNTs. The dispersibility of MWCNTs within poly(styrene)-block-poly(2-vinylpyridine) (PS-b-P2VP) (more »« less
https://doi.org/10.1016/j.polymer.2017.08.030
Self-assembly of crystalline nanotubes from monodisperse amphiphilic diblock copolypeptoid tiles

Journal Article Sun, Jing ; Jiang, Xi ; Lund, Reidar ; ... - Proceedings of the National Academy of Sciences of the United States of America

The folding and assembly of sequence-defined polymers into precisely ordered nanostructures promises a class of well-defined biomimetic architectures with specific function. Amphiphilic diblock copolymers are known to self-assemble in water to form a variety of nanostructured morphologies including spheres, disks, cylinders, and vesicles. In all of these cases, the predominant driving force for assembly is the formation of a hydrophobic core that excludes water, whereas the hydrophilic blocks are solvated and extend into the aqueous phase. However, such polymer systems typically have broad molar mass distributions and lack the purity and sequence-defined structure often associated with biologically derived polymers. Here,more »« less
Cited by 14
https://doi.org/10.1073/pnas.1517169113
Dimension and morphology controlled fabrication of TiO{sub 2} nanotubes by electrochemical anodization method

Journal Article Tamilselvan, A. ; Balakumar, S., E-mail: balasuga@yahoo.com - AIP Conference Proceedings

We report the fabrication of titanium dioxide (TiO{sub 2}) nanotubes by electrochemical anodization of titanium foils using fluoride-based electrolytes such as ethylene glycol, diethylene glycol and glycerol. The effects of anodization voltage, time and electrolytes on the morphology and dimensions (length and pore diameter) of the tubes were investigated by scanning electron microscope (SEM). On increasing anodization voltage and time, the tube length and pore diameter were varied. In addition to this, various tubes morphologies such as circular and hexagonal structures were obtained under different electrolytic conditions. The Raman spectroscopy studies revealed the anatase phase of TiO{sub 2} nanotubes.
https://doi.org/10.1063/1.4917694

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Title: ssDNA-amphiphile architecture used to control dimensions of DNA nanotubes

Abstract

Citation Formats

Direct Observation of Time-Resolved Polymorphic States in the Self-Assembly of End-Capped Heptapeptides journal, April 2011

Thioflavin T as an Efficient Inducer and Selective Fluorescent Sensor for the Human Telomeric G-Quadruplex DNA journal, December 2012

Computer simulations of bilayer membranes: Self-assembly and interfacial tension journal, May 1998

Programming DNA Tube Circumferences journal, August 2008

Construction of DNA nanotubes with controllable diameters and patterns using hierarchical DNA sub-tiles journal, January 2016

Supramolecular Nanotube Architectures Based on Amphiphilic Molecules journal, April 2005

Moltemplate a Coarse-Grained Model Assembly Tool journal, January 2013

Hybrid lipid oligonucleotide conjugates: synthesis, self-assemblies and biomedical applications journal, January 2011

Loading and selective release of cargo in DNA nanotubes with longitudinal variation journal, March 2010

Self-assembly of DNA nanotubes with controllable diameters journal, September 2011

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

Tunable generic model for fluid bilayer membranes journal, July 2005

Nucleic acid amphiphiles: synthesis and self-assembled nanostructures journal, January 2011

Order at the Edge of the Bilayer: Membrane Remodeling at the Edge of a Planar Supported Bilayer Is Accompanied by a Localized Phase Change journal, July 2010

Role of Hydrophobicity on Self-Assembly by Peptide Amphiphiles via Molecular Dynamics Simulations journal, June 2014

Mesoscopic Simulation of Cell Membrane Damage, Morphology Change and Rupture by Nonionic Surfactants journal, August 2001

Effect of alcohol chain length on tubule formation in 1,2-bis(10,12-tricosadiynoyl)-sn-glycero-3-phosphocholine journal, November 1992

Fast Parallel Algorithms for Short-Range Molecular Dynamics journal, March 1995

Atomistic Molecular Dynamics Simulations of Peptide Amphiphile Self-Assembly into Cylindrical Nanofibers journal, March 2011

Molecular dynamics simulations of lipid bilayers journal, July 2000

pH-induced morphology-shifting of DNA-b-poly(propylene oxide) assemblies journal, January 2012

Effect of Bilayer Thickness on Membrane Bending Rigidity journal, February 2004

Irena : tool suite for modeling and analysis of small-angle scattering journal, February 2009

A Coarse Grain Model for Phospholipid Simulations journal, May 2001

Lipid Nanotubes and Microtubes: Experimental Evidence for Unsymmetrical Monolayer Membrane Formation from Unsymmetrical Bolaamphiphiles journal, July 2004

Coarse-grained simulations of lipid bilayers journal, December 2004

Regulation of vascular smooth muscle cell autophagy by DNA nanotube-conjugated mTOR siRNA journal, October 2015

Lipid Tubule Self-Assembly: Length Dependence on Cooling Rate Through a First-Order Phase Transition journal, March 1995

Self-assembly of Surfactant-like Peptides with Variable Glycine Tails to Form Nanotubes and Nanovesicles journal, July 2002

Self-Assembly of Model Collagen Peptide Amphiphiles journal, August 2001

Effect of backbone chemistry on hybridization thermodynamics of oligonucleic acids: a coarse-grained molecular dynamics simulation study journal, January 2016

Self-organized nanotube materials and their application in bioengineering journal, August 2014

Aptamer micelles targeting fractalkine-expressing cancer cells in vitro and in vivo journal, January 2018

Programmable Shape-Shifting Micelles journal, June 2010

Enzymatic Polymerization of High Molecular Weight DNA Amphiphiles That Self-Assemble into Star-Like Micelles journal, February 2014

Modeling and Simulations of Polymers: A Roadmap journal, January 2019

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

Progress in molecular modelling of DNA materials journal, May 2014

Dexamethasone-conjugated DNA nanotubes as anti-inflammatory agents in vivo journal, July 2017

Bending Resistance and Chemically Induced Moments in Membrane Bilayers journal, December 1974

Cancer-selective antiproliferative activity is a general property of some G-rich oligodeoxynucleotides journal, December 2009

Templated Synthesis of DNA Nanotubes with Controlled, Predetermined Lengths journal, August 2010

Direct Observation of Morphological Tranformation from Twisted Ribbons into Helical Ribbons journal, July 2010

Thioflavin T as a fluorescence light-up probe for G4 formation journal, February 2014

Toward the Rational Control of Nanoscale Structures Using Chiral Self-Assembly: Diacetylenic Phosphocholines † journal, March 2003

Thioflavin T binds dimeric parallel-stranded GA-containing non-G-quadruplex DNAs: a general approach to lighting up double-stranded scaffolds journal, October 2017

Interactions of Lipid Bilayers with Supports: A Coarse-Grained Molecular Simulation Study journal, June 2008

Biological and synthetic membranes: What can be learned from a coarse-grained description? journal, November 2006

Equilibrium Structure of Simple Liquids journal, July 1970

Coarse Grained Model for Semiquantitative Lipid Simulations journal, January 2004

DNA nanotubes and helical nanotapes via self-assembly of ssDNA-amphiphiles journal, January 2015

DNA Nanotubes as Combinatorial Vehicles for Cellular Delivery journal, November 2008

Chiral Self-Assembly of Nanotubules and Ribbons from Phospholipid Mixtures journal, July 2001

Simulation Studies of Structure and Edge Tension of Lipid Bilayer Edges: Effects of Tail Structure and Force-Field journal, April 2013

Hydrophobic-Region-Induced Transitions in Self-Assembled Peptide Nanostructures † journal, April 2009

The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations journal, July 2007

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

Unraveling the Mechanism of Nanotube Formation by Chiral Self-Assembly of Amphiphiles journal, March 2011

Effective Shortening in Length of Glycolipid Nanotubes with High Axial Ratios journal, December 2003

Self-Assembly of DNA Nanotubes with Defined Diameters and Lengths journal, November 2013

PACKMOL: A package for building initial configurations for molecular dynamics simulations journal, October 2009

Optimization of lipodisk properties by modification of the extent and density of the PEG corona journal, December 2016

Controlling Lipid Micelle Stability Using Oligonucleotide Headgroups journal, February 2015

Circular dichroism and conformational polymorphism of DNA journal, January 2009

Effect of Polyethylene Glycol, Alkyl, and Oligonucleotide Spacers on the Binding, Secondary Structure, and Self-Assembly of Fractalkine Binding FKN-S2 Aptamer-Amphiphiles journal, June 2014

Shape effects of filaments versus spherical particles in flow and drug delivery journal, March 2007

Capturing intracellular oncogenic microRNAs with self-assembled DNA nanostructures for microRNA-based cancer therapy journal, January 2018

Dynamic light scattering and cryogenic transmission electron microscopy investigations on metallo-supramolecular aqueous micelles: evidence of secondary aggregation journal, November 2003

Coarse-graining DNA for simulations of DNA nanotechnology journal, January 2013

Lateral phase separation based on chirality in a polymerizable lipid and its influence on formation of tubular microstructures journal, June 1988

DNA nanotubes self-assembled from triple-crossover tiles as templates for conductive nanowires journal, January 2004

Functional DNA Nanotube Arrays: Bottom-Up Meets Top-Down journal, August 2007

Peptide Nanotube Nematic Phase journal, April 2009

VMD: Visual molecular dynamics journal, February 1996

The role of spacers on the self-assembly of DNA aptamer-amphiphiles into micelles and nanotapes journal, January 2014

Blotting-free and lossless cryo-electron microscopy grid preparation from nanoliter-sized protein samples and single-cell extracts journal, March 2017

Sequence specificity of inter- and intramolecular G-quadruplex formation by human telomeric DNA journal, September 2007

Direct Observation of Time-Resolved Polymorphic States in the Self-Assembly of End-Capped Heptapeptides
journal, April 2011

Thioflavin T as an Efficient Inducer and Selective Fluorescent Sensor for the Human Telomeric G-Quadruplex DNA
journal, December 2012

Computer simulations of bilayer membranes: Self-assembly and interfacial tension
journal, May 1998

Programming DNA Tube Circumferences
journal, August 2008

Construction of DNA nanotubes with controllable diameters and patterns using hierarchical DNA sub-tiles
journal, January 2016

Supramolecular Nanotube Architectures Based on Amphiphilic Molecules
journal, April 2005

Moltemplate a Coarse-Grained Model Assembly Tool
journal, January 2013

Hybrid lipid oligonucleotide conjugates: synthesis, self-assemblies and biomedical applications
journal, January 2011

Loading and selective release of cargo in DNA nanotubes with longitudinal variation
journal, March 2010

Self-assembly of DNA nanotubes with controllable diameters
journal, September 2011

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

Tunable generic model for fluid bilayer membranes
journal, July 2005

Nucleic acid amphiphiles: synthesis and self-assembled nanostructures
journal, January 2011

Order at the Edge of the Bilayer: Membrane Remodeling at the Edge of a Planar Supported Bilayer Is Accompanied by a Localized Phase Change
journal, July 2010

Role of Hydrophobicity on Self-Assembly by Peptide Amphiphiles via Molecular Dynamics Simulations
journal, June 2014

Mesoscopic Simulation of Cell Membrane Damage, Morphology Change and Rupture by Nonionic Surfactants
journal, August 2001

Effect of alcohol chain length on tubule formation in 1,2-bis(10,12-tricosadiynoyl)-sn-glycero-3-phosphocholine
journal, November 1992

Fast Parallel Algorithms for Short-Range Molecular Dynamics
journal, March 1995

Atomistic Molecular Dynamics Simulations of Peptide Amphiphile Self-Assembly into Cylindrical Nanofibers
journal, March 2011

Molecular dynamics simulations of lipid bilayers
journal, July 2000

pH-induced morphology-shifting of DNA-b-poly(propylene oxide) assemblies
journal, January 2012

Effect of Bilayer Thickness on Membrane Bending Rigidity
journal, February 2004

Irena : tool suite for modeling and analysis of small-angle scattering
journal, February 2009

A Coarse Grain Model for Phospholipid Simulations
journal, May 2001

Lipid Nanotubes and Microtubes: Experimental Evidence for Unsymmetrical Monolayer Membrane Formation from Unsymmetrical Bolaamphiphiles
journal, July 2004

Coarse-grained simulations of lipid bilayers
journal, December 2004

Regulation of vascular smooth muscle cell autophagy by DNA nanotube-conjugated mTOR siRNA
journal, October 2015

Lipid Tubule Self-Assembly: Length Dependence on Cooling Rate Through a First-Order Phase Transition
journal, March 1995

Self-assembly of Surfactant-like Peptides with Variable Glycine Tails to Form Nanotubes and Nanovesicles
journal, July 2002

Self-Assembly of Model Collagen Peptide Amphiphiles
journal, August 2001

Effect of backbone chemistry on hybridization thermodynamics of oligonucleic acids: a coarse-grained molecular dynamics simulation study
journal, January 2016

Self-organized nanotube materials and their application in bioengineering
journal, August 2014

Aptamer micelles targeting fractalkine-expressing cancer cells in vitro and in vivo
journal, January 2018

Programmable Shape-Shifting Micelles
journal, June 2010

Enzymatic Polymerization of High Molecular Weight DNA Amphiphiles That Self-Assemble into Star-Like Micelles
journal, February 2014

Modeling and Simulations of Polymers: A Roadmap
journal, January 2019

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

Progress in molecular modelling of DNA materials
journal, May 2014

Dexamethasone-conjugated DNA nanotubes as anti-inflammatory agents in vivo
journal, July 2017

Bending Resistance and Chemically Induced Moments in Membrane Bilayers
journal, December 1974

Cancer-selective antiproliferative activity is a general property of some G-rich oligodeoxynucleotides
journal, December 2009

Templated Synthesis of DNA Nanotubes with Controlled, Predetermined Lengths
journal, August 2010

Direct Observation of Morphological Tranformation from Twisted Ribbons into Helical Ribbons
journal, July 2010

Thioflavin T as a fluorescence light-up probe for G4 formation
journal, February 2014

Toward the Rational Control of Nanoscale Structures Using Chiral Self-Assembly: Diacetylenic Phosphocholines ^†
journal, March 2003

Thioflavin T binds dimeric parallel-stranded GA-containing non-G-quadruplex DNAs: a general approach to lighting up double-stranded scaffolds
journal, October 2017

Interactions of Lipid Bilayers with Supports: A Coarse-Grained Molecular Simulation Study
journal, June 2008

Biological and synthetic membranes: What can be learned from a coarse-grained description?
journal, November 2006

Equilibrium Structure of Simple Liquids
journal, July 1970

Coarse Grained Model for Semiquantitative Lipid Simulations
journal, January 2004

DNA nanotubes and helical nanotapes via self-assembly of ssDNA-amphiphiles
journal, January 2015

DNA Nanotubes as Combinatorial Vehicles for Cellular Delivery
journal, November 2008

Chiral Self-Assembly of Nanotubules and Ribbons from Phospholipid Mixtures
journal, July 2001

Simulation Studies of Structure and Edge Tension of Lipid Bilayer Edges: Effects of Tail Structure and Force-Field
journal, April 2013

Hydrophobic-Region-Induced Transitions in Self-Assembled Peptide Nanostructures ^†
journal, April 2009

The MARTINI Force Field: Coarse Grained Model for Biomolecular Simulations
journal, July 2007

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

Unraveling the Mechanism of Nanotube Formation by Chiral Self-Assembly of Amphiphiles
journal, March 2011

Effective Shortening in Length of Glycolipid Nanotubes with High Axial Ratios
journal, December 2003

Self-Assembly of DNA Nanotubes with Defined Diameters and Lengths
journal, November 2013

PACKMOL: A package for building initial configurations for molecular dynamics simulations
journal, October 2009

Optimization of lipodisk properties by modification of the extent and density of the PEG corona
journal, December 2016

Controlling Lipid Micelle Stability Using Oligonucleotide Headgroups
journal, February 2015

Circular dichroism and conformational polymorphism of DNA
journal, January 2009

Effect of Polyethylene Glycol, Alkyl, and Oligonucleotide Spacers on the Binding, Secondary Structure, and Self-Assembly of Fractalkine Binding FKN-S2 Aptamer-Amphiphiles
journal, June 2014

Shape effects of filaments versus spherical particles in flow and drug delivery
journal, March 2007

Capturing intracellular oncogenic microRNAs with self-assembled DNA nanostructures for microRNA-based cancer therapy
journal, January 2018

Dynamic light scattering and cryogenic transmission electron microscopy investigations on metallo-supramolecular aqueous micelles: evidence of secondary aggregation
journal, November 2003

Coarse-graining DNA for simulations of DNA nanotechnology
journal, January 2013

Lateral phase separation based on chirality in a polymerizable lipid and its influence on formation of tubular microstructures
journal, June 1988

DNA nanotubes self-assembled from triple-crossover tiles as templates for conductive nanowires
journal, January 2004

Functional DNA Nanotube Arrays: Bottom-Up Meets Top-Down
journal, August 2007

Peptide Nanotube Nematic Phase
journal, April 2009

VMD: Visual molecular dynamics
journal, February 1996

The role of spacers on the self-assembly of DNA aptamer-amphiphiles into micelles and nanotapes
journal, January 2014

Blotting-free and lossless cryo-electron microscopy grid preparation from nanoliter-sized protein samples and single-cell extracts
journal, March 2017

Sequence specificity of inter- and intramolecular G-quadruplex formation by human telomeric DNA
journal, September 2007

Functional DNA Nanotube Arrays: Bottom-Up Meets Top-Down
journal, August 2007

Programmable Shape-Shifting Micelles
journal, June 2010

Direct Observation of Time-Resolved Polymorphic States in the Self-Assembly of End-Capped Heptapeptides
journal, April 2011