Barcoding Biological Reactions with DNA‐Functionalized Vesicles

Targeted vesicle fusion is a promising approach to selectively control interactions between vesicle compartments and would enable the initiation of biological reactions in complex aqueous environments. Here, we explore how two features of vesicle membranes, DNA tethers and phase‐segregated membranes, promote fusion between specific vesicle populations. Membrane phase‐segregation provides an energetic driver for membrane fusion that increases the efficiency of DNA‐mediated fusion events. The orthogonality provided by DNA tethers allows us to direct fusion and delivery of DNA cargo to specific vesicle populations. Vesicle fusion between DNA‐tethered vesicles can be used to initiate in vitro protein expression to produce model soluble and membrane proteins. Engineering orthogonal fusion events between DNA‐tethered vesicles provides a new strategy to control the spatiotemporal dynamics of cell‐free reactions, expanding opportunities to engineer artificial cellular systems.     

A molecular tweezer for lysine and arginine

Lysine and arginine play a key role in numerous biological recognition processes controlling, inter alia, gene regulation, glycoprotein targeting and vesicle transport. They are also found in signaling peptide sequences responsible, e.g. for bacterial cell wall biosynthesis, Alzheimer peptide aggregation and skin regeneration. Almost none of all artificial receptor structures reported to date are selective and efficient for lysine residues in peptides or proteins. An artificial molecular tweezer is introduced which displays an exceptionally high affinity for lysine (K(a) approximately 5000 in neutral phosphate buffer). It features an electron-rich torus-shaped cavity adorned with two peripheral anionic phosphonate groups. Exquisite selectivity for arginine and lysine is achieved by threading the whole amino acid side chain through the cavity and subsequent locking by formation of a phosphonate-ammonium/guanidinium salt bridge. This pseudorotaxane-like geometry is also formed in small basic signaling peptides, which can be bound with unprecedented affinity in buffered aqueous solution. NMR titrations, NOESY and VT experiments as well as ITC measurements and Monte Carlo simulations unanimously point to an enthalpy-driven process utilizing a combination of van der Waals interactions and substantial electrostatic contributions for a conformational lock. Since DMSO and acetonitrile compete with the amino acid guest inside the cavity, a simple change in the cosolvent composition renders the whole complexation process reversible.     

Controlled dimerization of artificial membrane receptors for transmembrane signal transduction

In biology, membrane-spanning proteins are responsible for the transmission of chemical signals across membranes, including the signal recognition-mediated conformational change of transmembrane receptors at the cell surface, and a trigger of an intracellular phosphorylation cascade. The ability to reproduce such biological processes in artificial systems has potential applications in smart sensing, drug delivery, and synthetic biology. Here, an artificial transmembrane receptors signaling system was designed and constructed based on modular DNA scaffolds. The artificial transmembrane receptors in this system are composed of three functional modules: signal recognition, lipophilic transmembrane linker, and signal output modules. Adenosine triphosphate (ATP) served as an external signal input to trigger the dimerization of two artificial receptors on membranes through a proximity effect. This effect induced the formation of a G-quadruplex, which served as a peroxidase-like enzyme to facilitate a signal output measured by either fluorescence or absorbance in the lipid bilayer vesicles. The broader utility of this modular method was further demonstrated using a lysozyme-binding aptamer instead of an ATP-binding aptamer. Therefore, this work provides a modular and generalizable method for the design of artificial transmembrane receptors. The flexibility of this synthetic methodology will allow researchers to incorporate different functional modules while retaining the same molecular framework for signal transduction.

An artificial transmbrane signal transducer was developed through the chemical input-mediated dimerization of artificial DNA transmembrane receptors and the subsequent activation of a cascade of events inside the vesicles.     

Vesicle Tubulation with Self‐Assembling DNA Nanosprings

A major goal of nanotechnology and bioengineering is to build artificial nanomachines capable of generating specific membrane curvatures on demand. Inspired by natural membrane‐deforming proteins, we designed DNA‐origami curls that polymerize into nanosprings and show their efficacy in vesicle deformation. DNA‐coated membrane tubules emerge from spherical vesicles when DNA‐origami polymerization or high membrane‐surface coverage occurs. Unlike many previous methods, the DNA self‐assembly‐mediated membrane tubulation eliminates the need for detergents or top‐down manipulation. The DNA‐origami design and deformation conditions have substantial influence on the tubulation efficiency and tube morphology, underscoring the intricate interplay between lipid bilayers and vesicle‐deforming DNA structures.     

Dynamic spatial and structural organization in artificial cells regulates signal processing by protein scaffolding

Structural and spatial organization are fundamental properties of biological systems that allow cells to regulate a wide range of biochemical processes. This organization is often transient and governed by external cues that initiate dynamic self-assembly processes. The construction of synthetic cell-like materials with similar properties requires the hierarchical and reversible organization of selected functional components on molecular scaffolds to dynamically regulate signaling pathways. The realization of such transient molecular programs in synthetic cells, however, remains underexplored due to the associated complexity of such hierarchical platforms. In this contribution, we effectuate dynamic spatial organization of effector protein subunits in a synthetic biomimetic compartment, a giant unilamellar vesicle (GUV), by associating in a reversible manner two fragments of a split luciferase to the membrane. This induces their structural dimerization, which consequently leads to the activation of enzymatic signaling. Importantly, such organization and activation are dynamic processes, and can be autonomously regulated – thus opening up avenues toward continuous spatiotemporal control over supramolecular organization and signaling in an artificial cell.

Engineered artificial cells respond to environmental cues through a pre-programmed enzymatic machinery that induces spatio-structural organization and activation of effector proteins at the lipid membrane.     

Multivalent interaction of cyclodextrin vesicles, carbohydrate guests, and lectins: a kinetic investigation

An artificial glycocalix self-assembles when unilamellar bilayer vesicles of amphiphilic β-cyclodextrins are decorated with maltose- and lactose-adamantane conjugates by host-guest interactions. The maltose-decorated vesicles aggregate in the presence of lectin concanavalin A whereas the lactose-decorated vesicles aggregate in the presence of lectin peanut agglutinin. The kinetics of the orthogonal multivalent interfacial interactions present in this ternary system of vesicles, carbohydrates, and lectins were studied by time-dependent measurements of the optical density at 400 nm. The average vesicle and vesicle aggregate sizes were monitored by dynamic light scattering. The aggregation process was evaluated as a function of lectin concentration, vesicle concentration, and surface coverage of the vesicles by the carbohydrate-adamantane conjugates. The initial rate of vesicle aggregation scales linearly with the lectin as well as the cyclodextrin vesicle concentration. Furthermore, each lectin requires a characteristic critical density of carbohydrates at the vesicle surface. These observations allow a prediction of the response of the ternary supramolecular system at different concentrations of its components. Also, the effective binding site separation in a multivalent receptor such as a multiple binding site protein can be accurately determined. This methodology can be extended to multivalent noncovalent interactions in other ligand-receptor systems at interfaces.     

Micelle‐to‐vesicle transition induced by oligonucleotide in SDS/DEAB mixed system with a net negative charge

Sodium dodecyl sulfate (SDS)/dodecyl triethyl ammonium bromide (DEAB) mixed micelles (with SDS in excess) can transform to vesicles only when the temperature is higher than a critical value. In this study, we report for the first time that oligonucleotide can decrease the critical temperature to a much lower value and, hence, induce micelle‐to‐vesicle transition. The facilitation efficiency of oligonucleotide on vesicle formation is closely dependent on its size and base composition. Moreover, the SDS/DEAB/oligonucleotide vesicles are negatively charged and the hydrophobic interaction between oligonucleotide and SDS/DEAB mixed micelles is the driving force. As, so far, the report about the facilitation effect of oligonucleotide and DNA on vesicle formation is very limited, this study may provide some helpful information for the application of DNA/amphiphile system. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 7491–7504, 2008     

Micelle-vesicle transition of oleyldimethylamine oxide in water

We studied the effects of the degree of ionization() and the surfactant concentration (C_d) on the micelle–vesicle transition in salt-free oleyldimethylamine oxide (OlDMAO) aqueous solutions by the dynamic light scattering (DLS), the hydrogen ion titration, the small angle neutron scattering (SANS), the electrophoretic light scattering (ELS) and viscoelastic measurements. From the study of ionization effects, the micelle–vesicle transition was recognized as a change of aggregate size by the DLS measurement; however, the micelle–vesicle transition was not detected both in the ELS measurement and the hydrogen ion titration, suggesting that the electric properties of the worm-like micelles and the vesicles are very similar despite a large difference of shapes between them. From the results of the SANS, the DLS and the viscosity measurements, it was suggested that a concentration-dependent micelle–vesicle transition took place around C_p = 10 mmol kg⁻¹ for the solutions at = 0.5. In the concentration-range 10 mmol kg⁻¹ < C_d < 150 mmol kg⁻¹, the micelles and the vesicles coexisted. In the concentration region (C_d = 10–50 mmol kg⁻¹), the vesicle size increased with the surfactant concentration.     

含偶氮苯主-客体复合物的光致异构化反应对结合能与几何构象的影响

在分子尺度上构建光驱动的人工分子机器是超分子化学研究的一个热点。偶氮苯是一类具有双稳态的光致开关分子,能够完成高效、可逆的反式(E)$\to $顺式(Z)的光致异构化过程,因而可以作为人工分子机器的功能单元。本文采用密度泛函理论(DFT)和反应分子动力学(RMD)模拟,研究了含偶氮苯封端基团的互锁型超分子体系中冠醚主体与二烷基铵客体间结合强度,模拟了偶氮苯Z$\to $E异构化反应的动态过程,讨论了异构化反应对主客体分子构象的影响。在偶氮苯封端基团通过发生Z$\to $E异构化实现体系单向可控运动时,较强的主-客体间结合能力是保证互锁型超分子体系稳定的必要前提。顺式客体与主体大环氢键相互作用比反式客体更强,因此顺式复合异构体具有比反式异构体更大的结合强度。偶氮苯基团发生E$\to $Z光致异构化引入位阻效应,使得顺式复合物只能从环戊基准封端处进行脱环。主客体复合过程对偶氮苯基团的几何结构没有明显影响。偶氮苯光致异构化发生的速度快于客体脱环的速度是实现单向运动的动力学上的必要条件。在异构化反应后的500 ps内,大环会经历一个明显的结构驰豫过程。冠醚大环主体的柔性构象有助于实现在偶氮苯光致异构化发生过程中主客体间持续稳定的结合。各种超分子体系中,尽管客体组成各不相同,但是包含相似的主客体识别位点的超分子体系具有相似的结合能,显示了机械互锁型复合体系中各种功能性构建单元间主客体相互作用具有正交性。引入双稳态的偶氮苯功能基团对客体其他部分的几何结构影响很小。理论计算结果有助于理性设计更复杂的刺激响应性人工分子机器。     

Specific binding of different vesicle populations by the hybridization of membrane-anchored DNA

We demonstrate a method of heterogeneous vesicle binding using membrane-anchored, single-stranded DNA that can be used over several orders of magnitude in vesicle size, as demonstrated for large 100 nm vesicles and giant vesicles several microns in diameter. The aggregation behavior is studied for a range of DNA surface concentrations and solution ionic strengths. Three analogous states of aggregation are observed on both vesicle size scales. We explain the existence of these three regimes by a combination of DNA binding favorability, vesicle collision kinetics, and lateral diffusion of the DNA within the fluid membrane. The reversibility of the DNA hybridization allows dissociation of the structures formed and can be achieved either thermally or by a reduction in the ionic strength of the external aqueous environment. Difficulty is found in fully unbinding giant vesicles by thermal dehybridization, possibly frustrated by the attractive van der Waals minimum in the intermembrane potential when brought into close contact by DNA binding. This obstacle can be overcome by the isothermal reduction of the ionic strength of the solution: this reduces the Debye screening length, coupling the effects of DNA dehybridization and intermembrane repulsion due to the increased electrostatic repulsion between the highly charged DNA backbones.     

Analytical approaches to investigate transmitter content and release from single secretory vesicles

The vesicle serves as the primary intracellular unit for the highly efficient storage and release of chemical messengers triggered during signaling processes in the nervous system. This review highlights conventional and emerging analytical methods that have used microscopy, electrochemistry, and spectroscopy to resolve the location, time course, and quantal content characteristics of neurotransmitter release. Particular focus is on the investigation of the synaptic vesicle and its involvement in the fundamental molecular mechanisms of cell communication.     

Dynamics of DNA adsorption on and release from SDS-DDAB cat-anionic vesicles: a multitechnique study

DNA adsorption and release from cat-anionic vesicles made of sodium dodecylsulfate-dodecyldimethylammonium bromide (SDS-DDAB) in nonstoichiometric amounts was investigated by different electrochemical, spectroscopic, and biomolecular strategies. The characterization of the vesicular system was performed by dynamic light scattering, which allowed estimating both its size and distribution function(s). The interaction dynamics was followed by dielectric spectroscopy and zeta-potential, as well as by agarose gel electrophoresis, AGE. Also, circular dichroism, CD, measurements were carried out, to ascertain possible structural rearrangements of DNA, consequent to the interactions with the cat-anionic vesicles. CD demonstrates that vesicle-bound DNA retains its native conformation. The results obtained by the aforementioned techniques are consistent and indicate that binding saturation is obtained at a [DNA/vesicles] charge ratio close to 0.8, considering only the excess surface charges on the vesicles. This result is apparently in contradiction with a purely electrostatic approach and is tentatively ascribed to the distance between charges on the biopolymer and the vesicle surface, respectively. A possible interpretation is discussed. The nucleic acid can be completely retrieved from the vesicles upon addition of adequate amounts of SDS, which is the defective surfactant in the vesicular system. Precipitation of the poorly soluble SD-DDA salt results in an almost complete release of DNA.     

A DNA‐Programmed Liposome Fusion Cascade

Chemically engineered and functionalized nanoscale compartments are used in bottom‐up synthetic biology to construct compartmentalized chemical processes. Progressively more complex designs demand spatial and temporal control over entrapped species. Here, we address this demand with a DNA‐encoded design for the successive fusion of multiple liposome populations. Three individual stages of fusion are induced by orthogonally hybridizing sets of membrane‐anchored oligonucleotides. Each fusion event leads to efficient content mixing and transfer of the recognition unit for the subsequent stage. In contrast to fusion‐protein‐dependent eukaryotic vesicle processing, this artificial fusion cascade exploits the versatile encoding potential of DNA hybridization and is generally applicable to small and giant unilamellar vesicles. This platform could thus enable numerous applications in artificial cellular systems and liposome‐based synthetic pathways.     

Facilitation effect of oligonucleotide on vesicle formation from single‐chained cationic surfactant—Dependences of oligonucleotide sequence and size and surfactant structure

The interaction between DNA and surfactant has both biological and technological significances. Recently, we reported for the first time that oligo d(C)₂₅ can induce single‐chained cationic surfactant molecules to aggregate into vesicles. In this article, we studied systematically the formation of vesicles from traditional single‐chained cationic surfactant molecules in the presence of a series of oligonucleotides and found that the facilitation efficiency of oligonucleotide on vesicle formation depends on its size and base composition. Oligo d(T)_n cannot induce vesicle formation, whereas the other oligonucleotides can. Moreover, the oligonucleotide with a bigger size or with a hairpin structure favors vesicle formation more, and the increases in the size of the head group and/or the length of the alkyl group of surfactant decrease the facilitation efficiency of oligonucleotide. Since so far, there is very limited report about the vesicle formation in DNA/single‐chained cationic surfactant solution, this study could be expected to increase the efficiency and applicability for DNA/amphiphile system. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 434–449, 2009     

DNA analysis of a radiotolerant bacterium Pantoea agglomerans by FT-IR spectroscopy

A radiation tolerance strain, Pantoea agglomerans was isolated from γ-irradiated carrot samples (Daucus carota). D₁₀ determination showed that the radioresistance of this bacterium is five-fold higher than Escherichia coli, both belonging to the family of Enterobacteriaceae. DNA isolated from untreated and irradiated bacterial cells was analyzed by FT-IR spectroscopy to investigate the radiotolerance of this bacterium. At doses <5 kGy, an alteration of the interbase hydrogen networks was observed and characterized mainly by an increase of bands assigned to the carbonyl non-pairing and the free amine groups. Moderate breakage of the DNA backbone and damage of the osidic structure were also observed. Similar spectral profiles were noticed at doses ≥5 kGy, but additional increase of the band intensity of CC and CN suggests damages of nucleobases. High number of asymmetric PO₂⁻ and upper shift of symmetric PO₂⁻ are indicative of DNA strand breaks. Osidic damages were evidenced by decrease of the absorption bands ascribed to deoxyribosyl moieties and by appearance of C–OH band. DNA degradation at high irradiation doses was also noticed by electrophoresis using agarose gel. It appeared that DNA underwent covalent cross-linking, as revealed by agglomeration of DNA in the wells of agarose gel.     

Fluorescence microscopic investigation on morphological changes of giant multilamellar vesicles induced by amphiphilic additives

Adding an artificial bolaamphiphile to a dispersion of giant multilamellar vesicles (GMVs) made of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidylcholine (POPC) induced a cup-shaped deformation in GMVs accompanied by partial extrusion of the inner vesicle; thereafter, the deformed vesicles returned to their original shape. On the other hand, when the artificial bolaamphiphile together with a surfactant was added to the vesicular dispersion, these deformation and reformation dynamics were transmitted from the outer membranes in GMVs to the inner membranes until an intact inner vesicle was extruded out of the outer membrane. The microscopic aspects of these processes were investigated using amphiphiles tagged with individual fluorophores.     

Testing the applicability of artificial intelligence techniques to the subject of erythemal ultraviolet solar radiation. Part two: an intelligent system based on multi-classifier technique

The problem we address here describes the on-going research effort that takes place to shed light on the applicability of using artificial intelligence techniques to predict the local noon erythemal UV irradiance in the plain areas of Egypt. In light of this fact, we use the bootstrap aggregating (bagging) algorithm to improve the prediction accuracy reported by a multi-layer perceptron (MLP) network. The results showed that, the overall prediction accuracy for the MLP network was only 80.9%. When bagging algorithm is used, the accuracy reached 94.8%; an improvement of about 13.9% was achieved. These improvements demonstrate the efficiency of the bagging procedure, and may be used as a promising tool at least for the plain areas of Egypt.     

Determination of DNA using sodium 9,10-anthraquinone-2-sulfonate as an in situ photochemical fluorescence probe

An in situ photochemical fluorescence probe method for the determination of DNA with sodium 9,10-anthraquinone-2-sulfonate (AQS) as a photochemical fluorescence probe was developed. It was based on the conversion of AQS into an intensively fluorescent product by irradiating with UV radiation. The photochemical reaction is retarded by DNA. The determination can be carried out by measuring the fluorescence intensity at a fixed time. The calibration graph was linear in the range 0–80 ng ml⁻¹ calf thymus (CT) DNA (r = 0.9991), the limit of detection was 3.2 ng ml⁻¹ CT DNA (n = 9). The kinetic behaviour of the photochemical reaction and the effects of experimental conditions were investigated and discussed in detail. The results of absorption spectra and competitive binding experiments suggested the interaction between AQS and DNA to be intercalative.     

寡聚核苷酸/单链阳离子表面活性剂囊泡与沉淀共存(英文)

DNA(包括寡聚核苷酸)和阳离子表面活性剂可形成难溶复合物.本文通过浊度测试和透射电子显微镜观察,发现单链阳离子表面活性剂可以诱使寡聚核苷酸/单链阳离子表面活性剂沉淀转变成为寡聚核苷酸/单链阳离子表面活性剂囊泡,且寡聚核苷酸/单链阳离子表面活性剂囊泡可以与寡聚核苷酸/单链阳离子表面活性剂沉淀共存.在寡聚核苷酸/单链阳离子表面活性剂沉淀向囊泡的转变过程中,表面活性剂和沉淀之间的疏水作用力发挥了重要作用.此外,当体系温度达到寡聚核苷酸开始融解的温度后,寡聚核苷酸/单链阳离子表面活性剂体系更容易形成囊泡.因此,寡聚核苷酸的链越伸展,越易于寡聚核苷酸/单链阳离子表面活性剂囊泡的生成.据我们所知,有关寡聚核苷酸/阳离子表面活性剂囊泡的报道尚不多见.因此,考虑到DNA(包括寡聚核苷酸)/两亲分子体系在医学、生物学、药学和化学中的重要性,该研究应该有助于我们进一步了解该体系并对其进行更合理有效的应用.