MaxSynBio: Avenues Towards Creating Cells from the Bottom Up

A large German research consortium mainly within the Max Planck Society (“MaxSynBio”) was formed to investigate living systems from a fundamental perspective. The research program of MaxSynBio relies solely on the bottom‐up approach to synthetic biology. MaxSynBio focuses on the detailed analysis and understanding of essential processes of life through modular reconstitution in minimal synthetic systems. The ultimate goal is to construct a basic living unit entirely from non‐living components. The fundamental insights gained from the activities in MaxSynBio could eventually be utilized for establishing a new generation of biotechnological processes, which would be based on synthetic cell constructs that replace the natural cells currently used in conventional biotechnology.     

Novel method for measuring the adhesion energy of vesicles

Adhering vesicles with osmotically stabilized volume are studied with Monte Carlo simulations and optical microscopy. The simulations are used to determine the dependence of the adhesion area on the vesicle volume, the surface area, the bending rigidity, the adhesion energy per membrane area, and the adhesion potential range. The simulation results lead to a simple functional expression that is supplemented by a correction term for gravity effects. The obtained equation provides a new tool to analyze optical microscopy data and, thus, to measure the adhesion energy per area by analyzing the geometry of the adhering vesicle. The method can be applied in the weak and ultra-weak adhesion regime, where the adhesion energy per area is below 10(-6) J/m(2). By comparing the shapes of adhering vesicles with different reduced volumes, the bending rigidity can be estimated as well. The new approach is applied to experimental data for lipid vesicles on (i) an untreated and (ii) a monolayer-coated glass surface, providing ultra-weak and weak adhesion strength, respectively.     

Synergy in lipofection by cationic lipid mixtures: superior activity at the gel-liquid crystalline phase transition

Some mixtures of two cationic lipids including phospholipid compounds (O-ethylphosphatidylcholines) as well as common, commercially available cationic lipids, such as dimethylammonium bromides and trimethylammonium propanes, deliver therapeutic DNA considerably more efficiently than do the separate molecules. In an effort to rationalize this widespread "mixture synergism", we examined the phase behavior of the cationic lipid mixtures and constructed their binary phase diagrams. Among a group of more than 50 formulations, the compositions with maximum delivery activity resided unambiguously in the solid-liquid crystalline two-phase region at physiological temperature. Thus, the transfection efficacy of formulations exhibiting solid-liquid crystalline phase coexistence is more than 5 times higher than that of formulations in the gel (solid) phase and over twice that of liquid crystalline formulations; phase coexistence occurring at physiological temperature thus appears to contribute significantly to mixture synergism. This relationship between delivery activity and physical property can be rationalized on the basis of the known consequences of lipid-phase transitions, namely, the accumulation of defects and increased disorder at solid-liquid crystalline phase boundaries. Packing defects at the borders of coexisting solid and liquid crystalline domains, as well as large local density fluctuations, could be responsible for the enhanced fusogenicity of mixtures. This study leads to the important conclusion that manipulating the composition of the lipid carriers so that their phase transition takes place at physiological temperature can enhance their delivery efficacy.     

Drag of a Solid Particle Trapped in a Thin Film or at an Interface: Influence of Surface Viscosity and Elasticity

We propose a theoretical model for the motion of a spherical particle entrapped in a thin liquid film or in a monolayer of insoluble surfactant at the air/water interface. Both surface shear and dilational viscosity, surface diffusion, and elasticity of the film are taken into consideration. The drag force acting on the particle is analytically calculated and asymptotic expressions of the problem are provided. The relevance of the model is discussed by comparing the calculated "viscoelastic" drag, gamma(vel), to the one predicted by Saffman's theory, gamma(S), for cylindrical inclusions in membranes. Numerical analyses are performed to evaluate the contributions of the surface viscosity and the diffusion coefficient of the layer on the hydrodynamical resistance experienced by the particle. Copyright 2000 Academic Press.     

Quantum dot-conjugated hybridization probes for preliminary screening of siRNA sequences

In the present study, we describe the design and fabrication of quantum dot-conjugated hybridization probes and their application to the development of a comparatively simple and rapid procedure for the selection of highly effective small-interfering RNA (siRNA) sequences for RNA interference (RNAi) in mammalian cells, for example, siRNAs with high accessibility and affinity to the respective mRNA target. A single-stranded siRNA was conjugated with a quantum dot and used as a hybridization probe. The target mRNA was amplified in the presence of Cy5-labeled nucleotides, and Cy5-mRNA served as a hybridization sample. The formation of siRNA/mRNA duplexes during a comparatively short hybridization time (1 h) was used as a criterion for the selection of highly effective, target-specific siRNA sequences. The accessibility and affinity of the siRNA sequence for the target mRNA site were determined by fluorescence resonance energy transfer (FRET) between a quantum dot (donor) and a fluorescent dye molecule (Cy5, acceptor) localized at an appropriate distance from each other when hybridization occurred. The FRET signal was observed only when there was high accessibility between an antisense siRNA and a sense mRNA and did not appear in the case of mismatch siRNAs. Moreover, the amplitude of the FRET signal significantly correlated with the specific effect of siRNA on the expression of the target mRNA and protein, determined in native cells by RT-PCR and immunoblot analysis, respectively.     

Single quantum dot-micelles coated with silica shell as potentially non-cytotoxic fluorescent cell tracers

The present study describes a stabilization of single quantum dot (QD) micelles by hydrophobic silica precursors and an extension of the silica layer to form a silica shell around the micelle. The obtained product consists of up to 92% of single nanocrystals (CdSe, CdSe/ZnS, or CdSe/ZnSe/ZnS quantum dots) in the silica micelles, coated with silica shell. The thickness of silica shell could vary, starting from 3 to 4 nm. Increasing the shell thickness increases the photoluminescent characteristics of QDs in aqueous solution. The silica-shelled single CdSe/ZnS QD micelles possess a high quantum yield in aqueous solution, a controlled small size, sharp photoluminescence spectra (fwhm approximately 30 nm), an absence of aggregation, and a high transparency. The presence of a hydrophobic layer between the QD and silica shell ensures an incorporation of other hydrophobic molecules (with interesting properties) in the close proximity of nanocrystal. Thus, it is possible to combine the characteristics of hybrid material with the priority of small size. The nanoparticles are amino functionalized and ready for conjugation. A comparatively good biocompatibility is demonstrated. The nanoparticles show ability for intracellular delivery and are noncytotoxic during long-term incubation with viable cells in the absence of light exposure, which makes them appropriate for cell tracing and drug delivery.     

Polymerization of cyclic acetals. II. Synthesis of amphiphilic block copolymers

The sequential copolymerization of 1,3,6-trioxacyclooctane (TOC) and 1,3-dioxolane (DOL) (B) with various vinyl monomers (A) was investigated. Under appropriate conditions amphiphilic block copolymers of the type AB and ABA were formed. The reaction mixtures and the isolated polymers were analyzed by GPC (double detection—IR and UV at 254 nm), IR, ¹H-, and ¹³C-NMR spectroscopy. Block copolymers with chosen molecular weights and low polydispersity could be obtained only by sequential copolymerization of p-methoxystyrene on “living” TOC. In the polymerization of DOL with α-methylstyrene and i-butyl vinyl ether (IBVE) transfer reactions take place to a larger degree.     

Quantum dot-based western blot technology for ultrasensitive detection of tracer proteins

The present study describes two quantum dot-based Western blotting protocols for ultrasensitive detection of "tracer" proteins in cell lysates.     

A problem for diffusion with relaxation in polymers

A nonlinear problem for penetrant diffusion with relaxation in polymers is considered. A numerical approach to solving this type of problems is developed. The proposed numerical scheme based on a finite element domain approximation and a time difference method can be used for numerical simulation of the considered penetrant diffusion in 2-D and 3-D domains. A numerical procedure and a corresponding computer code are created and tested for some examples in 1-D and 2-D domains.