scholarly journals Cell-free TXTL synthesis of infectious bacteriophage T4 in a single test tube reaction

2018 ◽  
Vol 3 (1) ◽  
Author(s):  
Mark Rustad ◽  
Allen Eastlund ◽  
Paul Jardine ◽  
Vincent Noireaux
Keyword(s):  
Self Assembly ◽  
Bacteriophage T4 ◽  
Test Tube ◽  
Great Promise ◽  
One Pot ◽  
Bottom Up ◽  
Self Assembling ◽  
Phage T4 ◽  
Biological Entities

Abstract The bottom-up construction of biological entities from genetic information provides a broad range of opportunities to better understand fundamental processes within living cells, as well as holding great promise for the development of novel biomedical applications. Cell-free transcription–translation (TXTL) systems have become suitable platforms to tackle such topics because they recapitulate the process of gene expression. TXTL systems have advanced to where the in vitro construction of viable, complex, self-assembling deoxyribonucleic acid-programmed biological entities is now possible. Previously, we demonstrated the cell-free synthesis of three bacteriophages from their genomes: MS2, ΦX174, T7. In this work, we present the complete synthesis of the phage T4 from its 169-kbp genome in one-pot TXTL reactions. This achievement, for one of the largest coliphages, demonstrates the integration of complex gene regulation, metabolism and self-assembly, and brings the bottom-up synthesis of biological systems to a new level.

scholarly journals Lipid membranes trigger misfolding and self-assembly of amyloid β 42 protein into aggregates

2019 ◽  
Author(s):  
Siddhartha Banerjee ◽  
Mohtadin Hashemi ◽  
Karen Zagorski ◽  
Yuri L. Lyubchenko
Keyword(s):  
Self Assembly ◽  
Lipid Membranes ◽  
Membrane Surface ◽  
Amyloid Β ◽  
Test Tube ◽  
Aggregation Process ◽  
Self Assembling ◽  
Nanoscale Aggregates

AbstractThe assembly of polypeptides and proteins into nanoscale aggregates is a phenomenon observed in a vast majority of proteins. Importantly, aggregation of amyloid β (Aβ) proteins is considered as a major cause for the development of Alzheimer’s disease. The process depends on various conditions and typical test-tube experiments require high protein concentration that complicates the translation of results obtained in vitro to understanding the aggregation process in vivo. Here we demonstrate that Aβ42 monomers at the membrane bilayer are capable of self-assembling into aggregates at physiologically low concentrations, and the membrane in this aggregation process plays a role of a catalyst. We applied all-atom molecular dynamics to demonstrate that the interaction with the membrane surface dramatically changes the conformation of Aβ42 protein. As a result, the misfolded Aβ42 rapidly assembles into dimers, trimers and tetramers, so the on-surface aggregation is the mechanism by which amyloid oligomers are produced and spread.

scholarly journals A New Hope: Self-Assembling Peptides with Antimicrobial Activity

Pharmaceutics ◽  
2019 ◽  
Vol 11 (4) ◽  
pp. 166 ◽  
Author(s):  
Lucia Lombardi ◽  
Annarita Falanga ◽  
Valentina Del Genio ◽  
Stefania Galdiero
Keyword(s):  
Self Assembly ◽  
Biomedical Applications ◽  
High Specificity ◽  
Antibacterial Activities ◽  
Mechanisms Of Action ◽  
Great Promise ◽  
Functional Nanomaterials ◽  
Self Assembling ◽  
Low Toxicity ◽  
Bio Compatibility

Peptide drugs hold great promise for the treatment of infectious diseases thanks to their novel mechanisms of action, low toxicity, high specificity, and ease of synthesis and modification. Naturally developing self-assembly in nature has inspired remarkable interest in self-assembly of peptides to functional nanomaterials. As a matter of fact, their structural, mechanical, and functional advantages, plus their high bio-compatibility and bio-degradability make them excellent candidates for facilitating biomedical applications. This review focuses on the self-assembly of peptides for the fabrication of antibacterial nanomaterials holding great interest for substituting antibiotics, with emphasis on strategies to achieve nano-architectures of self-assembly. The antibacterial activities achieved by these nanomaterials are also described.

scholarly journals Multiscale additive manufacturing of polymers using 3D photo-printable self-assembling ionic liquid monomers

2019 ◽  
Vol 4 (3) ◽  
pp. 580-585 ◽  
Author(s):  
Bineh G. Ndefru ◽  
Bryan S. Ringstrand ◽  
Sokhna I.-Y. Diouf ◽  
Sönke Seifert ◽  
Juan H. Leal ◽  
...  
Keyword(s):  
Ionic Liquid ◽  
Additive Manufacturing ◽  
Self Assembly ◽  
Low Cost ◽  
Low Resolution ◽  
Top Down ◽  
Bottom Up ◽  
Cost Approach ◽  
Self Assembling ◽  
Nanoscale Features

Combining bottom-up self-assembly with top-down 3D photoprinting affords a low cost approach for the introduction of nanoscale features into a build with low resolution features.

Self Assembling Nanostructured Delivery Vehicles for Biochemically Reactive Pairs

1994 ◽  
Vol 351 ◽  
Author(s):  
Nir Kossovsky ◽  
A. Gelman ◽  
H.J. Hnatyszyn ◽  
E. Sponsler ◽  
G.-M. Chow
Keyword(s):  
Physical Properties ◽  
Self Assembly ◽  
Materials Science ◽  
Technology Development ◽  
Biological Behavior ◽  
X Ray Diffraction ◽  
Self Assembling ◽  
Transmission Electron ◽  
Carbon Ceramic

ABSTRACTIntrigued by the deceptive simplicity and beauty of macromolecular self-assembly, our laboratory began studying models of self-assembly using solids, glasses, and colloidal substrates. These studies have defined a fundamental new colloidal material for supporting members of a biochemically reactive pair.The technology, a molecular transportation assembly, is based on preformed carbon ceramic nanoparticles and self assembled calcium-phosphate dihydrate particles to which glassy carbohydrates are then applied as a nanometer thick surface coating. This carbohydrate coated core functions as a dehydroprotectant and stabilizes surface immobilized members of a biochemically reactive pair. The final product, therefore, consists of three layers. The core is comprised of the ceramic, the second layer is the dehydroprotectant carbohydrate adhesive, and the surface layer is the biochemically reactive molecule for which delivery is desired.We have characterized many of the physical properties of this system and have evaluated the utility of this delivery technology in vitro and in animal models. Physical characterization has included standard and high resolution transmission electron microscopy, electron and x-ray diffraction and ζ potential analysis. Functional assays of the ability of the system to act as a nanoscale dehydroprotecting delivery vehicle have been performed on viral antigens, hemoglobin, and insulin. By all measures at present, the favorable physical properties and biological behavior of the molecular transportation assembly point to an exciting new interdisciplinary area of technology development in materials science, chemistry and biology.

scholarly journals Thiophene Derivatives as Anticancer Agents and Their Delivery to Tumor Cells Using Albumin Nanoparticles

Molecules ◽  
2019 ◽  
Vol 24 (1) ◽  
pp. 192 ◽  
Author(s):  
Guangsheng Cai ◽  
Simiao Wang ◽  
Lang Zhao ◽  
Yating Sun ◽  
Dongsheng Yang ◽  
...  
Keyword(s):  
Tumor Cells ◽  
Cell Lines ◽  
Anticancer Agents ◽  
Drug Loading ◽  
Great Promise ◽  
Self Assembling ◽  
Laser Confocal Scanning Microscopy ◽  
Confocal Scanning ◽  
Thiophene Derivatives

A series of thiophene derivatives (TPs) were synthesized and evaluated for cytotoxicity in HepG2 and SMMC-7721 cell lines by MTT assay. TP 5 was identified as a potential anticancer agent based on its ability to inhibit tumor cell growth. Drawbacks of TPs, including poor solubility and high toxicity, were overcome through delivery using self-assembling HSA nanoparticles (NPs). The optimum conditions for TP 5-NPs synthesis obtained by adjusting the temperature and concentration of TP 5. The NPs had an encapsulation efficiency of 99.59% and drug-loading capacity of 3.70%. TP 5 was slowly released from TP 5-NPs in vitro over 120 h. HepG2 and SMMC-7721 cell lines were employed to study cytotoxicity of TP 5-NPs, which exhibited high potency. ROS levels were elevated and mitochondrial membrane potentials reversed when the two cell lines were treated with TP 5-NPs for 12 h. Cellular uptake of fluorescence-labeled TP 5-NPs in vitro was analyzed by flow cytometry and laser confocal scanning microscopy. Fluorescence intensity increased over time, suggesting that TP 5-NPs were efficiently taken up by tumor cells. In conclusion, TP 5-NPs showed great promise as an anticancer therapeutic agent.

scholarly journals Bottom-up self-assembly of heterotrimeric nanoparticles and their secondary Janus generations

2019 ◽  
Vol 10 (44) ◽  
pp. 10388-10394 ◽  
Author(s):  
Jianye Fu ◽  
Zhengying Gu ◽  
Yang Liu ◽  
Jun Zhang ◽  
Hao Song ◽  
...  
Keyword(s):  
Silica Nanoparticles ◽  
Intestinal Epithelium ◽  
Self Assembly ◽  
Bottom Up ◽  
Epithelial Monolayer ◽  
Cargo Transport ◽  
Human Intestinal Epithelium ◽  
Monolayer Model

Designed Janus silica nanoparticles can stimulate stronger phagocytosis and exhibit higher cargo transport across an in vitro epithelial monolayer model mimicking the human intestinal epithelium.

scholarly journals On the Aqueous Solution Behavior of C-Substituted 3,1,2-Ruthenadicarbadodecaboranes

Inorganics ◽  
2019 ◽  
Vol 7 (7) ◽  
pp. 91 ◽  
Author(s):  
Marta Gozzi ◽  
Benedikt Schwarze ◽  
Peter Coburger ◽  
Evamarie Hey-Hawkins
Keyword(s):  
Aqueous Solution ◽  
Aqueous Solutions ◽  
Self Assembly ◽  
Self Assembling ◽  
Vis Spectroscopy ◽  
Assembly Behavior ◽  
Biological Performance ◽  
Type 3

3,1,2-Ruthenadicarbadodecaborane complexes bearing the [C2B9H11]2− (dicarbollide) ligand are robust scaffolds, with exceptional thermal and chemical stability. Our previous work has shown that these complexes possess promising anti-tumor activities in vitro, and tend to form aggregates (or self-assemblies) in aqueous solutions. Here, we report on the synthesis and characterization of four ruthenium(II) complexes of the type [3-(η6-arene)-1,2-R2-3,1,2-RuC2B9H9], bearing either non-polar (R = Me (2–4)) or polar (R = CO2Me (7)) substituents at the cluster carbon atoms. The behavior in aqueous solution of complexes 2, 7 and the parent unsubstituted [3-(η6-p-cymene)-3,1,2-RuC2B9H11] (8) was investigated via UV-Vis spectroscopy, mass spectrometry and nanoparticle tracking analysis (NTA). All complexes showed spontaneous formation of self-assemblies (108–109 particles mL−1), at low micromolar concentration, with high polydispersity. For perspective applications in medicine, there is thus a strong need for further characterization of the spontaneous self-assembly behavior in aqueous solutions for the class of neutral metallacarboranes, with the ultimate scope of finding the optimal conditions for exploiting this self-assembling behavior for improved biological performance.

scholarly journals An investigation into the nano-/micro-architecture of electrospun poly (ε-caprolactone) and self-assembling peptide fibers

MRS Advances ◽  
2016 ◽  
Vol 1 (11) ◽  
pp. 711-716 ◽  
Author(s):  
Robabeh Gharaei ◽  
Giuseppe Tronci ◽  
Robert P. Davies ◽  
Parikshit Goswami ◽  
Stephen J. Russell
Keyword(s):  
Self Assembly ◽  
Mechanical Stability ◽  
Porous Scaffold ◽  
Fiber Formation ◽  
Peptide Sequence ◽  
Diagnostic Tools ◽  
Great Promise ◽  
Electrospinning Technique ◽  
Fibrous Scaffold ◽  
Self Assembling

ABSTRACTSelf-assembling peptides (SAPs) have the ability to spontaneously assemble into ordered nanostructures enabling the manufacture of ‘designer’ nanomaterials. The reversible molecular association of SAPs has been shown to offer great promise in therapeutics via for example, the design of biomimetic assemblies for hard tissue regeneration. This could be further exploited for novel nano/micro diagnostic tools. However, self-assembled peptide gels are often associated with inherent weak and transient mechanical properties. Their incorporation into polymeric matrices has been considered as a potential strategy to enhance their mechanical stability. This study focuses on the incorporation of an 11-residue peptide, P11-8 (peptide sequence: CH3CO-Gln-Gln-Arg-Phe-Orn-Trp-Orn-Phe-Glu-Gln-Gln-NH2) within a fibrous scaffold of poly (ε-caprolactone) (PCL). In this study an electrospinning technique was used to fabricate a biomimetic porous scaffold out of a solution of P11-8 and PCL which resulted in a biphasic structure composed of submicron fibers (diameter of 100-700 nm) and nanofibers (diameter of 10-100 nm). The internal morphology of the fabric and its micro-structure can be easily controlled by changing the peptide concentration. The secondary conformation of P11-8 was investigated in the as-spun fibers by ATR-FTIR spectroscopy and it is shown that peptide self-assembly into β-sheet tapes has taken place during fiber formation and the deposition of the fibrous web.

scholarly journals Virus assembly occurs following a pH- or Ca 2+ -triggered switch in the thermodynamic attraction between structural protein capsomeres

2009 ◽  
Vol 7 (44) ◽  
pp. 409-421 ◽  
Author(s):  
Yap P. Chuan ◽  
Yuan Y. Fan ◽  
Linda H. L. Lua ◽  
Anton P. J. Middelberg
Keyword(s):  
Self Assembly ◽  
Virus Assembly ◽  
Chemical Change ◽  
Second Virial Coefficient ◽  
Direct Proof ◽  
Viral Assembly ◽  
Structural Protein ◽  
Salting Out ◽  
Self Assembling

Viral self-assembly is of tremendous virological and biomedical importance. Although theoretical and crystallographic considerations suggest that controlled conformational change is a fundamental regulatory mechanism in viral assembly, direct proof that switching alters the thermodynamic attraction of self-assembling components has not been provided. Using the VP1 protein of polyomavirus, we report a new method to quantitatively measure molecular interactions under conditions of rapid protein self-assembly. We show, for the first time, that triggering virus capsid assembly through biologically relevant changes in Ca 2+ concentration, or pH, is associated with a dramatic increase in the strength of protein molecular attraction as quantified by the second virial coefficient ( B 22 ). B 22 decreases from −2.3 × 10 −4 mol ml g −2 (weak protein–protein attraction) to −2.4 × 10 −3 mol ml g −2 (strong protein attraction) for metastable and Ca 2+ -triggered self-assembling capsomeres, respectively. An assembly-deficient mutant (VP1CΔ63) is conversely characterized by weak protein–protein repulsion independently of chemical change sufficient to cause VP1 assembly. Concomitant switching of both VP1 assembly and thermodynamic attraction was also achieved by in vitro changes in ammonium sulphate concentration, consistent with protein salting-out behaviour. The methods and findings reported here provide new insight into viral assembly, potentially facilitating the development of new antivirals and vaccines, and will open the way to a more fundamental physico-chemical description of complex protein self-assembly systems.

Evolving Reaction-Diffusion Ecosystems with Self-Assembling Structures in Thin Films

1998 ◽  
Vol 4 (1) ◽  
pp. 25-40 ◽  
Author(s):  
Jens Breyer ◽  
Jörg Ackermann ◽  
John McCaskill
Keyword(s):  
Self Assembly ◽  
Flexible Structures ◽  
Reaction Diffusion ◽  
In Vitro Evolution ◽  
Spatially Resolved ◽  
Self Assembling ◽  
Artificial Dna ◽  
Additional Stabilization ◽  
Artificial Chemistries

Recently, new types of coupled isothermal polynucleotide amplification reactions for the investigation of in vitro evolution have been established that are based on the multi-enzyme 3SR reaction. Microstructured thin-film open bioreactors have been constructed in our laboratory to run these reactions spatially resolved in flow experiments. Artificial DNA/RNA chemistries close to the in vitro biochemistry of these systems have been developed, which we have studied in computer simulations in configurable hardware (NGEN). These artificial chemistries are described on the level of individual polynucleotide molecules, each with a defined sequence, and their complexes. The key feature of spatial pattern formation provides a weak stabilization of cooperative catalytic properties of the evolving molecules. Of great interest is the step to include extended self-assembly processes of flexible structures—allowing the additional stabilization of cooperation through semipermeable, flexible, self-organizing membrane boundaries. We show how programmable matter simulations of experimentally relevant molecular in vitro evolution can be extended to include the influence of self-assembling flexible membranes.

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