scholarly journals DNA Origami “Quick” Refolding inside of a Micron-Sized Compartment

Molecules ◽  
2019 ◽  
Vol 25 (1) ◽  
pp. 8 ◽  
Author(s):  
Taiki Watanabe ◽  
Yusuke Sato ◽  
Hayato Otaka ◽  
Ibuki Kawamata ◽  
Satoshi Murata ◽  
...  
Keyword(s):  
Self Assembly ◽  
Average Diameter ◽  
Test Tube ◽  
Dna Origami ◽  
Bulk Solution ◽  
Dna Nanostructures ◽  
Force Microscopy ◽  
Annealing Conditions ◽  
Atomic Force ◽  
Life Phenomena

Investigations into the refolding of DNA origami leads to the creation of reconstructable nanostructures and deepens our understanding of the sustainability of life. Here, we report the refolding of the DNA origami structure inside a micron-sized compartment. In our experiments, conventional DNA origami and truss-type DNA origami were annealed and purified to remove the excess staples in a test tube. The DNA origami was then encapsulated inside of a micron-sized compartment of water-in-oil droplets, composed of neutral surfactants. The re-annealing process was then performed to initiate refolding in the compartment. The resulting 100-nm-sized DNA nanostructures were observed using atomic force microscopy (AFM), and the qualities of their structures were evaluated based on their shape. We found that the refolding of the DNA origami structure was favored inside the droplets compared with refolding in bulk solution. The refolded structures were able to fold even under “quick” one-minute annealing conditions. In addition, the smaller droplets (average diameter: 1.2 µm) appeared to be more advantageous for the refolding of the origamis than larger droplets. These results are expected to contribute to understanding the principles of life phenomena based on multimolecular polymer self-assembly in a micron-sized compartment, and for the production and maintenance of artificially designed molecules.

scholarly journals Pathway Complexity in Supramolecular Porphyrin Self-Assembly at an Immiscible Liquid|Liquid Interface

2021 ◽  
Author(s):  
Iván Robayo-Molina ◽  
Andrés F. Molina-Osorio ◽  
Luke Guinane ◽  
Syed A.M. Tofail ◽  
Micheal D. Scanlon
Keyword(s):  
Self Assembly ◽  
Immiscible Liquid ◽  
Bulk Solution ◽  
Time Resolved ◽  
Force Microscopy ◽  
Atomic Force ◽  
Aggregate Growth ◽  
High Concentrations ◽  
Thermodynamic Processes

<p>Nanostructures that are inaccessible through spontaneous thermodynamic processes may be formed by supramolecular self-assembly under kinetic control. In the past decade, the dynamics of pathway complexity in self-assembly have been elucidated through kinetic models based on aggregate growth by sequential monomer association and dissociation. Immiscible liquid|liquid interfaces are an attractive platform to develop well-ordered self-assembled nanostructures, unattainable in bulk solution, due to the templating interaction of the interface with adsorbed molecules. Here, we report time-resolved <i>in situ</i> UV/vis spectroscopic observations of the self-assembly of zinc(II) meso-tetrakis(4-carboxyphenyl)porphyrin (ZnTPPc) at an immiscible aqueous|organic interface. We show that the kinetically favoured metastable J-type nanostructures form quickly, but then transform into stable thermodynamically favoured H-type nanostructures. Numerical modelling revealed two parallel and competing cooperative pathways leading to the different porphyrin nanostructures. These insights demonstrate that pathway complexity is not unique to self-assembly processes in bulk solution, and equally valid for interfacial self-assembly. Subsequently, the interfacial electrostatic environment was tuned using a kosmotropic anion (citrate) in order to control the influence the pathway selection. At high concentrations, interfacial nanostructure formation was forced completely down the kinetically favoured pathway and only J-type nanostructures were obtained. Furthermore, we found by atomic force microscopy (AFM) and scanning electron microscopy (SEM) that the J- and H-type nanostructures obtained at low and high citric acid concentrations, respectively, are morphologically distinct, which illustrates the pathway-dependent material properties.</p>

scholarly journals Nanosized Particles Assembled by a Recombinant Virus Protein Are Able to Encapsulate Negatively Charged Molecules and Structured RNA

Polymers ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 858
Author(s):  
Hemalatha Mani ◽  
Yi-Cheng Chen ◽  
Yen-Kai Chen ◽  
Wei-Lin Liu ◽  
Shih-Yen Lo ◽  
...  
Keyword(s):  
Self Assembly ◽  
Rna Binding ◽  
Core Protein ◽  
Average Diameter ◽  
Virus Protein ◽  
Force Microscopy ◽  
Atomic Force ◽  
Hcv Core Protein

RNA-based molecules have recently become hot candidates to be developed into therapeutic agents. However, successful applications of RNA-based therapeutics might require suitable carriers to protect the RNA from enzymatic degradation by ubiquitous RNases in vivo. Because of their better biocompatibility and biodegradability, protein-based nanoparticles are considered to be alternatives to their synthetic polymer-based counterparts for drug delivery. Hepatitis C virus (HCV) core protein has been suggested to be able to self-assemble into nucleocapsid-like particles in vitro. In this study, the genomic RNA-binding domain of HCV core protein consisting of 116 amino acids (p116) was overexpressed with E. coli for investigation. The recombinant p116 was able to assemble into particles with an average diameter of approximately 27 nm, as visualized by electron microscopy and atomic force microscopy. Measurements with fluorescence spectroscopy, flow cytometry, and fluorescence quenching indicated that the p116-assembled nanoparticles were able to encapsulate small anionic molecules and structured RNA. This study demonstrates methods that exploit the self-assembly nature of a virus-derived protein for nanoparticle production. This study also suggests that the virus-derived protein-assembled particles could possibly be developed into potential carriers for anionic molecular drugs and structured RNA-based therapeutics.

scholarly journals Pathway Complexity in Supramolecular Porphyrin Self-Assembly at an Immiscible Liquid|Liquid Interface

2021 ◽  
Author(s):  
Iván Robayo-Molina ◽  
Andrés F. Molina-Osorio ◽  
Luke Guinane ◽  
Syed A.M. Tofail ◽  
Micheal D. Scanlon
Keyword(s):  
Self Assembly ◽  
Immiscible Liquid ◽  
Bulk Solution ◽  
Time Resolved ◽  
Force Microscopy ◽  
Atomic Force ◽  
Aggregate Growth ◽  
High Concentrations ◽  
Thermodynamic Processes

<p>Nanostructures that are inaccessible through spontaneous thermodynamic processes may be formed by supramolecular self-assembly under kinetic control. In the past decade, the dynamics of pathway complexity in self-assembly have been elucidated through kinetic models based on aggregate growth by sequential monomer association and dissociation. Immiscible liquid|liquid interfaces are an attractive platform to develop well-ordered self-assembled nanostructures, unattainable in bulk solution, due to the templating interaction of the interface with adsorbed molecules. Here, we report time-resolved <i>in situ</i> UV/vis spectroscopic observations of the self-assembly of zinc(II) meso-tetrakis(4-carboxyphenyl)porphyrin (ZnTPPc) at an immiscible aqueous|organic interface. We show that the kinetically favoured metastable J-type nanostructures form quickly, but then transform into stable thermodynamically favoured H-type nanostructures. Numerical modelling revealed two parallel and competing cooperative pathways leading to the different porphyrin nanostructures. These insights demonstrate that pathway complexity is not unique to self-assembly processes in bulk solution, and equally valid for interfacial self-assembly. Subsequently, the interfacial electrostatic environment was tuned using a kosmotropic anion (citrate) in order to control the influence the pathway selection. At high concentrations, interfacial nanostructure formation was forced completely down the kinetically favoured pathway and only J-type nanostructures were obtained. Furthermore, we found by atomic force microscopy (AFM) and scanning electron microscopy (SEM) that the J- and H-type nanostructures obtained at low and high citric acid concentrations, respectively, are morphologically distinct, which illustrates the pathway-dependent material properties.</p>

scholarly journals Effect of DNA Origami Nanostructures on hIAPP Aggregation

Nanomaterials ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 2200
Author(s):  
Marcel Hanke ◽  
Alejandro Gonzalez Orive ◽  
Guido Grundmeier ◽  
Adrian Keller
Keyword(s):  
Electrostatic Interactions ◽  
Dna Origami ◽  
Inorganic Nanoparticles ◽  
Ex Situ ◽  
Dna Nanostructures ◽  
Islet Amyloid ◽  
Force Microscopy ◽  
Double Stranded Dna ◽  
Atomic Force

The aggregation of human islet amyloid polypeptide (hIAPP) plays a major role in the pathogenesis of type 2 diabetes mellitus (T2DM), and numerous strategies for controlling hIAPP aggregation have been investigated so far. In particular, several organic and inorganic nanoparticles (NPs) have shown the potential to influence the aggregation of hIAPP and other amyloidogenic proteins and peptides. In addition to conventional NPs, DNA nanostructures are receiving more and more attention from the biomedical field. Therefore, in this work, we investigated the effects of two different DNA origami nanostructures on hIAPP aggregation. To this end, we employed in situ turbidity measurements and ex situ atomic force microscopy (AFM). The turbidity measurements revealed a retarding effect of the DNA nanostructures on hIAPP aggregation, while the AFM results showed the co-aggregation of hIAPP with the DNA origami nanostructures into hybrid peptide–DNA aggregates. We assume that this was caused by strong electrostatic interactions between the negatively charged DNA origami nanostructures and the positively charged peptide. Most intriguingly, the influence of the DNA origami nanostructures on hIAPP aggregation differed from that of genomic double-stranded DNA (dsDNA) and appeared to depend on DNA origami superstructure. DNA origami nanostructures may thus represent a novel route for modulating amyloid aggregation in vivo.

A Comparative Study on the Self-Assembly of Peptide TGV-9 by In Situ Atomic Force Microscopy

2020 ◽  
Vol 26 (2) ◽  
pp. 319-325
Author(s):  
Yaping Li ◽  
Na Li ◽  
Lei Wang ◽  
Qinhua Lu ◽  
Xiang Ji ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Self Assembly ◽  
The Self ◽  
Peptide Sequence ◽  
Bulk Solution ◽  
Free Standing ◽  
Atomic Lattice ◽  
Force Microscopy ◽  
Atomic Force

AbstractPrevious studies of amyloid diseases reported that the aggregating proteins share a similar conserved peptide sequence which can form the cross-β-sheet-containing nanostructures like nanofilaments. The template-assisted self-assembly (TASA) of peptides on inorganic substrates with different hydrophilicity could be an alternative approach to shed light on the fibrillization mechanism of proteins/peptides in vivo. To figure out the effect of interfaces on amyloid aggregation, we herein employed in situ atomic force microscopy (AFM) to investigate the self-assembling of a Parkinson disease-related core peptide sequence (TGV-9) on a hydrophobic liquid–solid interface via real-time observation of the dynamic fibrillization process. The results show that TGV-9 forms one-dimensional nanostructures on the surface of highly ordered pyrolytic graphite (HOPG) with three preferred growth orientations, which are consistent with the atomic lattice of HOPG, indicating an epitaxial growth or TASA. Conversely, the nanostructures formed in bulk solution can be free-standing nanofilaments, and the fibrillization mechanism is different from that on HOPG. These results could not only deepen the understanding of the protein/peptide aggregation mechanism but also benefit for the early diagnosis and clinic treatment of related diseases.

Clathrin-Inspired Coating and Stabilization of Liposomes by DNA Self-Assembly

2019 ◽  
Author(s):  
Kevin N. Baumann ◽  
Luca Piantanida ◽  
Javier García-Nafría ◽  
Diana Sobota ◽  
Kislon Voïtchovsky ◽  
...  
Keyword(s):  
Self Assembly ◽  
Mechanical Stability ◽  
Lipid Vesicles ◽  
The Self ◽  
Force Microscopy ◽  
Atomic Force ◽  
Cryo Electron Microscopy ◽  
Further Development ◽  
Liposome Surface ◽  
Dna Coating

The self-assembly of the protein clathrin on biological membranes facilitates essential processes of endocytosis in biological systems and has provided a source of inspiration for materials design by the highly ordered structural appearance. By mimicking the architecture of clathrin self-assemblies to coat liposomes with biomaterials, new classes of hybrid carriers can be derived. Here we present a method for fabricating DNA-coated liposomes by hydrophobically anchoring and subsequently growing a DNA network on the liposome surface which structurally mimics clathrin assemblies. Dynamic light scattering (DLS), ζ-potential and cryo-electron microscopy (cryo-EM) measurements independently demonstrate successful DNA coating. Nanomechanical measurements conducted with atomic force microscopy (AFM) show that the DNA coating enhances the mechanical stability of the liposomes relative to uncoated ones. Furthermore, we provide the possibility to reverse the coating process by triggering the disassembly of the DNA coating through a toehold-mediated displacement reaction. Our results describe a straightforward, versatile, and reversible approach for coating and stabilizing lipid vesicles by an interlaced DNA network. This method has potential for further development towards the ordered arrangement of tailored functionalities on the surfaces of liposomes and for applications as hybrid nanocarrier.

scholarly journals Morphometric characterization of fibrinogen's αC regions and their role in fibrin self-assembly and molecular organization

Nanoscale ◽  
2017 ◽  
Vol 9 (36) ◽  
pp. 13707-13716 ◽  
Author(s):  
Anna D. Protopopova ◽  
Rustem I. Litvinov ◽  
Dennis K. Galanakis ◽  
Chandrasekaran Nagaswami ◽  
Nikolay A. Barinov ◽  
...  
Keyword(s):  
Atomic Force Microscopy ◽  
Self Assembly ◽  
Molecular Organization ◽  
Microscopy Imaging ◽  
Force Microscopy ◽  
Atomic Force ◽  
Atomic Force Microscopy Imaging ◽  
Morphometric Characterization

High-resolution atomic force microscopy imaging reveals the role of fibrinogen αC regions in the early stages of fibrin self-assembly.

Self-assembly layer-by-layer fabrication using porphyrin dye anion and polycation

2009 ◽  
Vol 13 (07) ◽  
pp. 774-778 ◽  
Author(s):  
Byung-Soon Kim ◽  
Young-A Son
Keyword(s):  
Ultrathin Films ◽  
Self Assembly ◽  
Film Surface ◽  
Layer By Layer ◽  
Preparation Technique ◽  
Force Microscopy ◽  
Atomic Force ◽  
Diallyldimethylammonium Chloride ◽  
Afm Analysis ◽  
Progressive Growth

In this study, self-assembled alternating film using poly(diallyldimethylammonium chloride) (PDDAC) and meso-tetrakis(4-carboxyphenyl)porphyrin (MTCP) was prepared as a multilayer deposition on glass substrate. This preparation technique for dye deposition may provide new feasibilities to achieve the manufacture of ultrathin films for nanotechnology application. The deposition films were characterized by UV-vis spectrophotometer and Atomic Force Microscopy (AFM) analysis. The results of UV-vis spectra showed that the absorbance characteristic of the multilayer films linearly increased with an increased number of PDDAC and MTCP bilayers. AFM analysis showed the film surface was relatively uniform and the progressive growth of layers was determined.

Preparation of Cellulose Nanofibrils by High-Pressure Homogenizer and Zein Composite Films

2013 ◽  
Vol 829 ◽  
pp. 534-538 ◽  
Author(s):  
Alireza Shakeri ◽  
Sattar Radmanesh
Keyword(s):  
Atomic Force Microscopy ◽  
High Pressure ◽  
Food Packaging ◽  
Cellulose Nanofibrils ◽  
Composite Films ◽  
Average Diameter ◽  
Nanocomposite Films ◽  
Force Microscopy ◽  
Atomic Force ◽  
High Pressure Homogenizer

Cellulose nanofibrils ( NF ) have several advantages such as biodegradability and safety toward human health. Zein is a biodegradable polymer with potential use in food packaging applications. It appears that polymer nanocomposites are one of the most promising applications of zein films. Cellulose NF were prepared from starting material Microcrystalline cellulose (MCC) by an application of a high-pressure homogenizer at 20,000 psi and treatment consisting of 15 passes. Methods such as atomic force microscopy were used for confirmation of nanoscale size production of cellulose. The average diameter 45 nm were observed. Zeincellulose NF nanocomposite films were prepared by casting ethanol suspensions of Zein with different amounts of cellulose NF in the 0% to 5%wt. The nanocomposites were characterized by using Fourier transform infrared spectroscopy ( FTIR ), Atomic force microscopy ( AFM ) and X-ray diffraction ( XRD ) analysis. From the FTIR spectra the various groups present in the Zein blend were monitored. The homogeneity, morphology and crystallinity of the blends were ascertained from the AFM and XRD data, respectively. The thermal resistant of the zein nanocomposite films improved as the nanocellulose content increased. These obtained materials are transparent, flexible and present significantly better physical properties than the corresponding unfilled Zein films.

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