Browsing by Subject "Self assembly"

Now showing 1 - 20 of 24

Open Access
Catalytic supramolecular self-assembled peptide nanostructures for ester hydrolysis
(Royal Society of Chemistry, 2016) Gulseren, G.; Khalily, M. A.; Tekinay, A. B.; Güler, Mustafa O.
Essential amino acids in catalytic sites of native enzymes are important in nature inspired catalyst designs. Active sites of enzymes contain the coordinated assembly of multiple amino acids, and catalytic action is generated by the dynamic interactions among multiple residues. However, catalysis studies are limited by the complex and dynamic structure of the enzyme; and it is difficult to exclusively attribute a given function to a specific residue. Minimalistic approaches involving artificial catalytic sites are promising for the investigation of the enzyme function in the absence of non-essential protein components, and self-assembling peptide nanostructures are especially advantageous in this context. Here we demonstrate the design and characterization of an enzyme-mimetic catalytic nanosystem presenting essential residues (Ser, His, Asp). The function of each residue and its combinations on the nanostructures in hydrolysis reaction was studied. The catalytic self-assembled nanostructures were used for efficient ester hydrolysis such as a model substrate (pNPA) and a natural substrate (acetylcholine) highlighting the key role of self-assembly in catalytic domain formation to test the efficiency of the de novo designed catalyst as a catalytic triad model.
Open Access
Cellular internalization of therapeutic oligonucleotides by peptide amphiphile nanofibers and nanospheres
(American Chemical Society, 2016-04) Mumcuoglu, D.; S. Ekiz, M.; Gunay, G.; Tekinay, T.; Tekinay, A. B.; Güler, Mustafa O.
Oligonucleotides are promising drug candidates due to the exceptionally high specificity they exhibit toward their target DNA and RNA sequences. However, their poor pharmacokinetic and pharmacodynamic properties, in conjunction with problems associated with their internalization by cells, necessitates their delivery through specialized carrier systems for efficient therapy. Here, we investigate the effects of carrier morphology on the cellular internalization mechanisms of oligonucleotides by using self-assembled fibrous or spherical peptide nanostructures. Size and geometry were both found to be important parameters for the oligonucleotide internalization process; direct penetration was determined to be the major mechanism for the internalization of nanosphere carriers, whereas nanofibers were internalized by clathrin- and dynamin-dependent endocytosis pathways. We further showed that glucose conjugation to carrier nanosystems improved cellular internalization in cancer cells due to the enhanced glucose metabolism associated with oncogenesis, and the internalization of the glucose-conjugated peptide/oligonucleotide complexes was found to be dependent on glucose transporters present on the surface of the cell membrane.
Open Access
Controlled enzymatic stability and release characteristics of supramolecular chiral peptide amphiphile nanofiber gels
(Elsevier B.V., 2017) Zengin, A.; Cinar, G.; Güler, Mustafa O.
Supramolecular bioarchitectures formed by assembly of achiral or chiral building blocks play important roles in various biochemical processes. Stereochemistry of amino acids is important for structural organization of peptide and protein assemblies and structure-microenvironment interactions. In this study, oppositely charged peptide amphiphile (PA) molecules with L-, D- and mixture of L- and D-amino acid conformations are coassembled into supramolecular nanofibers and formed self-supporting gels at pH 7.4 in water. The enzymatic stability of the PA nanofiber gels was studied in the presence of proteinase K enzyme, which digest a broad spectrum of proteins and peptides. The structural changes on the chiral PA nanofibers were also analyzed at different time periods in the presence of enzymatic activity. Controlled release of a model cargo molecule through the chiral PA nanofiber gels was monitored. The diffusivity parameters were measured for all gel systems. Release characteristics and the enzymatic stability of the peptide nanofiber gels were modulated depending on organization of the chiral PA molecules within the supramolecular assemblies.
Open Access
The effect of cucurbit[n]uril on the solubility, morphology, and the photophysical properties of nonionic conjugated polymers in an aqueous medium
(2010) Tuncel, D.; Artar, M.; Hanay, S. B.
The effects of cucurbit[n]uril on the dissolution and the photophysical properties of nonionic conjugated polymers in water are described. For this purpose, a fluorine-based polymer, namely, poly[9,9-bis{6(N,N-dimethylamino) hexyl}fluorene-co-2,5-thienylene (PFT) was synthesized and characterized by spectroscopic techniques including 1D and 2D NMR, UV-vis, fluorescent spectroscopy, and matrix-assisted laser desorption mass spectrometry (MALDI-MS). For the first time, it was demonstrated that a nonionic conjugated polymer can be made soluble in water through an inclusion complex formation with CB8. The structure of the complex was elucidated by NMR experiments including 1H and selective 1D-NOESY. This complex emits green and is highly fluorescent with fluorescent quantum yield of 35%. In contrast, CB6 or water-soluble CB7 although they are chemically identical to CB8 do not have any effect on the dissolution and photophysical properties of PFT. By preparing a protonated version of PFT, the optical properties of PFT in methanol, protonated PFT and PFT@CB8 in water have been studied and compared. It was also observed that the morphology of the polymer PFT was affected by the presence of CB8. Thus CB8-assisted self-assembly of polymer chains leads to vesicles formation; these structures were characterized by DLS, AFM, SEM, and TEM fluorescent optical microscopy.
Open Access
Effects of temperature, pH and counterions on the stability of peptide amphiphile nanofiber structures
(Royal Society of Chemistry, 2016) Ozkan A.D.; Tekinay, A. B.; Güler, Mustafa O.; Tekin, E. D.
Peptide amphiphiles are a class of self-assembling molecules that are widely used to form bioactive nanostructures for various applications in bionanomedicine. However, peptide molecules can exhibit distinct behaviors under different conditions, suggesting that environmental variables such as temperature, pH, electrolytes and the presence of biological factors may greatly affect the self-assembly process. In this work, we used united-atom molecular dynamics simulations to understand the effects of three counterions (Na+, Ca2+ at pH 7 and Cl- at pH 2) and temperature change on the stability of the lauryl-VVAGERGD peptide amphiphile self-assembly. This molecule contains a bioactive RGD peptide sequence and has been shown to support cellular adhesion and proliferation in vitro. A 19-layered peptide nanostructure, containing 12 peptide amphiphile molecules per layer, was previously shown to exhibit optimal stability and it was used as the model nanofiber system. Peptide backbone stability was studied under increasing temperatures (300-358 K) using the number of hydrogen bonds and root-mean-square deviations of nanofiber size. At higher temperatures, fiber disintegration was observed to be dependent on the type of counter-ion used for nanofiber formation. Interestingly, rapid heating to higher temperatures could sometimes reestablish the integrity of the nanofiber backbone, possibly by allowing the system to bypass an energy barrier and assuming a more thermodynamically stable configuration. As counterion identity was observed to exhibit remarkable effects on the thermal stability of peptide nanofibers, we suggest that these behaviors should be considered while developing new materials for potential applications.
Open Access
Fabrication of supramolecular n/p-nanowires via coassembly of oppositely charged peptide-chromophore systems in aqueous media
(American Chemical Society, 2017-07) Khalily, M. A.; Bakan, G.; Kucukoz, B.; Topal, A. E.; Karatay, A.; Yaglioglu, H. G.; Dana, A.; Güler, Mustafa O.
Fabrication of supramolecular electroactive materials at the nanoscale with well-defined size, shape, composition, and organization in aqueous medium is a current challenge. Herein we report construction of supramolecular charge-transfer complex one-dimensional (1D) nanowires consisting of highly ordered mixed-stack π-electron donor-acceptor (D-A) domains. We synthesized n-type and p-type β-sheet forming short peptide-chromophore conjugates, which assemble separately into well-ordered nanofibers in aqueous media. These complementary p-type and n-type nanofibers coassemble via hydrogen bonding, charge-transfer complex, and electrostatic interactions to generate highly uniform supramolecular n/p-coassembled 1D nanowires. This molecular design ensures highly ordered arrangement of D-A stacks within n/p-coassembled supramolecular nanowires. The supramolecular n/p-coassembled nanowires were found to be formed by A-D-A unit cells having an association constant (KA) of 5.18 × 105 M-1. In addition, electrical measurements revealed that supramolecular n/p-coassembled nanowires are approximately 2400 and 10 times more conductive than individual n-type and p-type nanofibers, respectively. This facile strategy allows fabrication of well-defined supramolecular electroactive nanomaterials in aqueous media, which can find a variety of applications in optoelectronics, photovoltaics, organic chromophore arrays, and bioelectronics.
Open Access
Heparin mimetic peptide nanofiber gel promotes regeneration of full thickness burn injury
(Elsevier Ltd, 2017) Yergoz, F.; Hastar, N.; Cimenci, C. E.; Ozkan, A. D.; Güler, Mustafa O.; Tekinay, A. B.; Tekinay, T.; Güler, Mustafa O.
Burn injuries are one of the most common types of trauma worldwide, and their unique physiology requires the development of specialized therapeutic materials for their treatment. Here, we report the use of synthetic, functional and biodegradable peptide nanofiber gels for the improved healing of burn wounds to alleviate the progressive loss of tissue function at the post-burn wound site. These bioactive nanofiber gels form scaffolds that recapitulate the structure and function of the native extracellular matrix through signaling peptide epitopes, which can trigger angiogenesis through their affinity to basic growth factors. In this study, the angiogenesis-promoting properties of the bioactive scaffolds were utilized for the treatment of a thermal burn model. Following the excision of necrotic tissue, bioactive gels and control solutions were applied topically onto the wound area. The wound healing process was evaluated at 7, 14 and 21 days following injury through histological observations, immunostaining and marker RNA/protein analysis. Bioactive peptide nanofiber-treated burn wounds formed well-organized and collagen-rich granulation tissue layers, produced a greater density of newly formed blood vessels, and exhibited increased re-epithelialization and skin appendage development with minimal crust formation, while non-bioactive peptide nanofibers and the commercial wound dressing 3M™ Tegaderm™ did not exhibit significant efficiency over sucrose controls. Overall, the heparin-mimetic peptide nanofiber gels increased the rate of repair of burn injuries and can be used as an effective means of facilitating wound healing.
Open Access
Hierarchical self-assembly of histidine-functionalized peptide amphiphiles into supramolecular chiral nanostructures
(American Chemical Society, 2017) Koc, M. H.; Ciftci, G. C.; Baday, S.; Castelletto, V.; Hamley, I. W.; Güler, Mustafa O.
Controlling the hierarchical organization of self-assembling peptide amphiphiles into supramolecular nanostructures opens up the possibility of developing biocompatible functional supramolecular materials for various applications. In this study, we show that the hierarchical self-assembly of histidine- (His-) functionalized PAs containing d- or l-amino acids can be controlled by both solution pH and molecular chirality of the building blocks. An increase in solution pH resulted in the structural transition of the His-functionalized chiral PA assemblies from nanosheets to completely closed nanotubes through an enhanced hydrogen-bonding capacity and π-π stacking of imidazole ring. The effects of the stereochemistry and amino acid sequence of the PA backbone on the supramolecular organization were also analyzed by CD, TEM, SAXS, and molecular dynamics simulations. In addition, an investigation of chiral mixtures revealed the differences between the hydrogen-bonding capacities and noncovalent interactions of PAs with d- and l-amino acids.
Open Access
Hybridization of fano and vibrational resonances in surface-enhanced infrared absorption spectroscopy of streptavidin monolayers on metamaterial substrates
(2014) Alici, K. B.
We present spectral hybridization of organic and inorganic resonant materials and related bio-sensing mechanism. We utilized a bound protein (streptavidin) and a Fano-resonant metasurface to illustrate the concept. The technique allows us to investigate the vibrational modes of the streptavidin and how they couple to the underlying metasurface. This optical, label-free, nonperturbative technique is supported by a coupled mode-theory analysis that provides information on the structure and orientation of bound proteins. We can also simultaneously monitor the binding of analytes to the surface through monitoring the shift of the metasurface resonance. All of this data opens up interesting opportunities for applications in biosensing, molecular electronics and proteomics. © 2014 IEEE.
Open Access
Ion sensing, light harvesting, energy conversion & self-assembly in rationally designed molecular constructs
(2013) Büyükçakır, Onur
In this thesis, we have constructed rationally designed functional supramolecular systems. In the first chapter, we reported two Bodipy based chemodosimeters to detect fluoride both in solution and in polymethylmethaacraylate (PMMA) matrix. In the second part, we synthesized tetrastyrl-Bodipy derivatives by condensing methyl substituents of 1,3,5,7-tetramethyl-Bodipy dyes with different aromatic aldehydes. The resulting dyes have sharp and intense emission maxima in the near-IR region and they are robust candidates for functional supramolecular systems because of their outstanding properties. In next chapter, we investigated light harvesting properties of these new generation near-IR emissive dyes. In designed light harvesters, a near-IR emissive tetrastyrl-Bodipy dye which was decorated with short wavelength Bodipy fluorophores function as antenna units. In the forth chapter, we reported a Cu(I)-diimine complex as a photosensitizer for dye-sensitized solar cells (DSSC). It was demonstrated that Cu(I) diimine complex with capability of ultrafast electron injection to TiO2 nanoparticles can be a very good candidate for replacing ruthenium based polypyridyl complexes with a much lower cost. This research potentially can generate significant impact for those working on solar energy conversion and DSSC. In the final chapter, we propose to utilize oscillations in pH to move the two components of pseudorotoxane in relation to each other and this is the first example of a pseudorotaxane in which the mobile component is shuttling autonomously.
Open Access
Nanoengineering hybrid supramolecular multilayered biomaterials using polysaccharides and self-assembling peptide amphiphiles
(Wiley-VCH Verlag, 2017) Borges, J.; Sousa, M. P.; Cinar, G.; Caridade, S. G.; Güler, Mustafa O.; Mano, J. F.
Developing complex supramolecular biomaterials through highly dynamic and reversible noncovalent interactions has attracted great attention from the scientific community aiming key biomedical and biotechnological applications, including tissue engineering, regenerative medicine, or drug delivery. In this study, the authors report the fabrication of hybrid supramolecular multilayered biomaterials, comprising high-molecular-weight biopolymers and oppositely charged low-molecular-weight peptide amphiphiles (PAs), through combination of self-assembly and electrostatically driven layer-by-layer (LbL) assembly approach. Alginate, an anionic polysaccharide, is used to trigger the self-assembling capability of positively charged PA and formation of 1D nanofiber networks. The LbL technology is further used to fabricate supramolecular multilayered biomaterials by repeating the alternate deposition of both molecules. The fabrication process is monitored by quartz crystal microbalance, revealing that both materials can be successfully combined to conceive stable supramolecular systems. The morphological properties of the systems are studied by advanced microscopy techniques, revealing the nanostructured dimensions and 1D nanofibrous network of the assembly formed by the two molecules. Enhanced C2C12 cell adhesion, proliferation, and differentiation are observed on nanostructures having PA as outermost layer. Such supramolecular biomaterials demonstrate to be innovative matrices for cell culture and hold great potential to be used in the near future as promising biomimetic supramolecular nanoplatforms for practical applications.
Open Access
A new lyotropic liquid crystalline system: oligo(ethylene oxide) surfactants with [M(H2O)n]Xm transition metal complexes
(Wiley, 2001) Çelik, Ö.; Dag, Ö.
Coordinated water molecules induce the aggregation and self-assembly of the lyotropic liquid crystalline phase formed from non-ionic surfactants CnH2n+1(CH2CH2O)mOH and transition metal aqua complexes ([Ni(H2O)6](NO3)2, [Co(H2O)6](NO3)2, [Cd(H2O)4](NO3)2, and [Co(H2O)6]Cl2) into hexagonal (see schematic representation) and/or cubic structures. While the NiII and CoII complexes undergo recrystallization and phase separation at high complex concentrations, the ZnII and CdII complexes form cubic phases above metal/surfactant molar ratios of 3.2/1 at room temperature.
Open Access
One-dimensional peptide nanostructure templated growth of iron phosphate nanostructures for lithium-ion battery cathodes
(American Chemical Society, 2016-06) Susapto, H. H.; Kudu, O. U.; Garifullin, R.; Yllmaz, E.; Güler, Mustafa O.
Template-directed synthesis of nanomaterials can provide benefits such as small crystalline size, high surface area, large surface-to-volume ratio, and structural stability. These properties are important for shorter distance in ion/electron movement and better electrode surface/electrolyte contact for energy storage applications. Here nanostructured FePO4 cathode materials were synthesized by using peptide nanostructures as a template inspired by biomineralization process. The amorphous, high surface area FePO4 nanostructures were utilized as a cathode for lithium-ion batteries. Discharge capacity of 155 mAh/g was achieved at C/20 current rate. The superior properties of biotemplated and nanostructured amorphous FePO4 are shown compared to template-free crystalline FePO4.
Open Access
Polymer/clay nanocomposites through multiple hydrogen-bonding interactions
(John Wiley and Sons Inc., 2015) Aydin, M.; Uyar, Tamer; Tasdelen, M. A.; Yagci Y.
An 2-ureido-4[1H]pyrimidinone (UPy) motif with self-association capability (through quadruple hydrogen bonds) was successfully anchored onto montmorillonite clay layers. Polymer/clay nanocomposites were prepared by specific hydrogen bonding interactions between surface functionalized silica nanoclays and UPy-bonded supramolecular poly(ethylene glycol) or poly(É-caprolactone). The mixed morphologies including intercalated layers with a non-uniform separation and exfoliated single layers isolated from any stack were determined by combined X-ray diffraction and transmission electron microscopic measurements. Thermal analyses showed that all nanocomposites had higher decomposition temperatures and thermal stabilities compared with neat polymer. The differential scanning calorimetric data implied that the crystallinity of polymers did not show essential changes upon introduction of organomodified UPy clays.
Open Access
Probing nanoscale domains of J-Aggregates deposited on a mica surface
(American Chemical Society, 2004) Özçelik, S.; Demir, M. M.; Birkan, B.
J-aggregates of 1,1′,3,3′-tetraethyl-5,5′,6,6′- tetrachlorobenzimidazolocarbocyanine (TTBC) were deposited on a mica surface and probed by atomic force microscopy operated at tapping mode in air. Optical spectra showed that J-aggregates were formed in aqueous solutions. Atomic force microscopy images revealed that J-aggregates deposited on mica surfaces mainly present single domains with a mean height of 2.00 ± 0.25 nm and an average diameter of 100 ± 20 nm. Quantitative analysis of the morphology of images indicated that the single domain of J-aggregates exhibits very uniform height and diameter distributions with polydispersity indices of 1.02 and 1.04, respectively. Based on the results, we propose a two-dimensional nanostructure in which TTBC J-aggregates could be arranged in a monolayer.
Open Access
Selective adhesion and growth of vascular endothelial cells on bioactive peptide nanofiber functionalized stainless steel surface
(Elsevier, 2011) Ceylan, Hakan; Tekinay, Ayse B.; Güler, Mustafa O.
Metal-based scaffolds such as stents are the most preferred treatment methods for coronary artery disease. However, impaired endothelialization on the luminal surface of the stents is a major limitation occasionally leading to catastrophic consequences in the long term. Coating the stent surface with relevant bioactive molecules is considered to aid in recovery of endothelium around the wound site. However, this strategy remains challenging due to restrictions in availability of proper bioactive signals that will selectively promote growth of endothelium and the lack of convenience for immobilization of such signaling molecules on the metal surface. In this study, we developed self-assembled peptide nanofibers that mimic the native endothelium extracellular matrix and that are securely immobilized on stainless steel surface through mussel-inspired adhesion mechanism. We synthesized Dopa-conjugated peptide amphiphile and REDV-conjugated peptide amphiphile that are self-assembled at physiological pH. We report that Dopa conjugation enabled nanofiber coating on stainless steel surface, which is the most widely used backbone of the current stents. REDV functionalization provided selective growth of endothelial cells on the stainless steel surface. Our results revealed that adhesion, spreading, viability and proliferation rate of vascular endothelial cells are remarkably enhanced on peptide nanofiber coated stainless steel surface compared to uncoated surface. On the other hand, although vascular smooth muscle cells exhibited comparable adhesion and spreading profile on peptide nanofibers, their viability and proliferation significantly decreased. Our design strategy for surface bio-functionalization created a favorable microenvironment to promote endothelial cell growth on stainless steel surface, thereby providing an efficient platform for bioactive stent development for long term treatment of cardiovascular diseases. © 2011 Elsevier Ltd.
Open Access
Self-assembled one-dimensional soft nanostructures
(Royal Society of Chemistry, 2010) Toksoz, S.; Acar, H.; Güler, Mustafa O.
The self-assembly process is a bottom-up approach and is the spontaneous aggregation of many different subunits into well-defined functional structures with varying properties. Self-assembly is an attractive method to develop one-dimensional nanostructures and is controlled by many factors including temperature, pH and electrolyte addition. Novel self-assembled one-dimensional nanostructures are finding applications in regenerative medicine and electronics as well as in fabrication of nanoscale electronic, mechanic, magnetic, optical, and combinatorial devices. Their utility comes from their high ratio of surface area to volume, and their quantum-confinement effects. This paper reviews one-dimensional self-assembled organic nanostructures classified according to the noncovalent forces acting on their formation.
Open Access
Self-assembled peptide nanofiber templated ALD growth of TiO2 and ZnO semiconductor nanonetworks
(Wiley - V C H Verlag GmbH & Co. KGaA, 2016) Garifullin, R.; Eren, H.; Ulusoy, T. G.; Okyay, Ali Kemal; Bıyıklı, Necmi; Güler, Mustafa O.
Here peptide amphiphile (PA) nanofiber network is exploited as a three‐dimensional soft template to construct anatase TiO2 and wurtzite ZnO nanonetworks. Atomic layer deposition (ALD) technique is used to coat the organic nanonetwork template with TiO2and ZnO. ALD method enables uniform and conformal coatings with precisely controlled TiO2 and ZnO thickness. The resulting semiconducting metal oxide nanonetworks are utilized as anodic materials in dye‐sensitized solar cells. Effect of metal oxide layer thickness on device performance is studied. The devices based on thin TiO2 coatings (<10 nm) demonstrate considerable dependence on material thickness, whereas thicker (>17 nm) ZnO‐based devices do not show an explicit correlation.
Open Access
Self-assembled peptide nanostructures for functional materials
(Institute of Physics Publishing, 2016) Ekiz, M. S.; Cinar, G.; Khalily, M. A.; Güler, Mustafa O.
Nature is an important inspirational source for scientists, and presents complex and elegant examples of adaptive and intelligent systems created by self-assembly. Significant effort has been devoted to understanding these sophisticated systems. The self-assembly process enables us to create supramolecular nanostructures with high order and complexity, and peptide-based self-assembling building blocks can serve as suitable platforms to construct nanostructures showing diverse features and applications. In this review, peptide-based supramolecular assemblies will be discussed in terms of their synthesis, design, characterization and application. Peptide nanostructures are categorized based on their chemical and physical properties and will be examined by rationalizing the influence of peptide design on the resulting morphology and the methods employed to characterize these high order complex systems. Moreover, the application of self-assembled peptide nanomaterials as functional materials in information technologies and environmental sciences will be reviewed by providing examples from recently published high-impact studies.
Open Access
Solventless acid-free synthesis of mesostructured titania: nanovessels for metal complexes and metal nanoclusters
(Wiley - V C H Verlag GmbH & Co. KGaA, 2003) Dag, Ö.; Soten, I.; Çelik, Ö.; Polarz, S.; Coombs, N.; Ozin, G. A.
A new and highly reproducible method to obtain mesostructured titania materials is introduced in this contribution. The meso-structured titania is obtained by employing self-assembled structures of non-ionic alkyl-poly(ethylene oxide) surfactants as templates. The materials are produced without additional solvents such as alcohols, or even water. Only the titanium(iv) ethoxide and the surfactant (C12EO10) are needed. Water, in the form of that attached to the surfactant and from the atmosphere, induces growth of titania nanoclusters in the synthesis sol. It is indicated that these nanoclusters interact with the surfactant EO-head groups to form a new titanotropic amphiphile. The new amphiphiles self-assemble into titanium nanocluster-surfactant hybrid lyotropic phases, which are transformed to the final mesostructured materials by further condensation of the titania network. The titania materials can be obtained also with noble-metal particles immobilized in the mesostructured framework. It is seen that when different metal salts are used as the metal precursors, different interactions with the titania walls are found. The materials are characterized by X-ray diffraction (XRD), polarization optical microscopy (POM), transmission electron microscopy (TEM), UV-vis spectroscopy, and micro-Raman analysis.