Real-Time Monitoring of RNA Synthesis in a Phospholipid-Coated Microdroplet as a Live-Cell Model

Sensitive monitoring of RNA transcription by optical amplification of cationic conjugated polymers

We reported a new strategy for sensitive monitoring in vitro RNA synthesis in real time based on fluorescence resonance energy transfer (FRET) from water-soluble conjugated polymer poly (9, 9-bis (6'-N, N, N,-trimethylammonium) hexyl) fluorene-co-alt-1,4-phenylene) bromide (PFP) to fluorogenic RNA aptamer/fluorophore (Spanich2/DFHBI and Broccoli/DFHBI) system. In this strategy, RNA of interest was transcribed accompanied by the Spanich2 or Broccoli. Then the 3, 5-difluoro-4-hydroxybenzylidene imidazolinone (DFHBI) bound to the RNA aptamer sequence and thereby induced a fluorescence signal. PFP was used as the fluorescence energy donor, and Spanich2/DFHBI was the fluorescence energy acceptor. The fluorescence signal of Spanich2/DFHBI was amplified by light-harvesting and fluorescence amplification ability of PFP via FRET. And the limit of detection (LOD) (0.29 nM) was near 10-fold lower than that of RNA aptamer/DFHBI (LOD is 2.8 nM) alone by measuring the FRET ratio, which greatly reduced the variation of background signals. Most importantly, the addition of PFP did not interfere with RNA transcription in vitro, so this method was successfully applied to sensitively monitor RNA transcription and effect of T7 RNA polymerase inhibitor in real time, supplying a sensitive and simple method to study the modulation and inhibitor of RNA polymerase in vitro.

Extrinsic stochastic factors (solute partition) in gene expression inside lipid vesicles and lipid-stabilized water-in-oil droplets: a review

The encapsulation of transcription-translation (TX-TL) machinery inside lipid vesicles and water-in-oil droplets leads to the construction of cytomimetic systems (often called 'synthetic cells') for synthetic biology and origins-of-life research. A number of recent reports have shown that protein synthesis inside these microcompartments is highly diverse in terms of rate and amount of synthesized protein. Here, we discuss the role of extrinsic stochastic effects (i.e. solute partition phenomena) as relevant factors contributing to this pattern. We evidence and discuss cases where between-compartment diversity seems to exceed the expected theoretical values. The need of accurate determination of solute content inside individual vesicles or droplets is emphasized, aiming at validating or rejecting the predictions calculated from the standard fluctuations theory. At the same time, we promote the integration of experiments and stochastic modeling to reveal the details of solute encapsulation and intra-compartment reactions.

Effect of Stearylguanidinium-Modified POPC Vesicles on the Melting Behavior of tRNA Molecules

Lipid membranes interact with biomolecules via noncovalent bonding interactions, wherein the physicochemical membrane properties are key factors in the recognition and rearrangement of biomolecule conformation. In this study, vesicles were prepared using 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and stearylguanidinium (SG) to improve the affinity between the membrane and tRNA. Membrane fluidity decreased and dehydration of the membrane surface increased with increasing SG levels, suggesting that SG molecules could make the membrane rigid and induce a liquid-ordered (lo)-like phase. The binding constant (Ka) between nucleotide and lipid was evaluated by turbidity analysis; the Ka value for POPC/SG = (86/14) was 2.9 × 10(4) M(-1) but was slightly decreased by vesicles in the lo-like phase. CD spectra of tRNA by the presence of POPC/SG vesicles showed C-G selective base cleavage in tRNA during heat denaturation. POPC/SG = (61/39) and POPC/SG = (40/60) effectively led to C-G base pair cleavage at the melting temperature of tRNA.

Liposome membrane can induce self-cleavage of RNA that models the core fragments of hammerhead ribozyme

The hammerhead ribozyme (HHR) is one of smallest catalytic RNAs, composed of a catalytic core and three stems; it undergoes self-cleavage in the presence of divalent magnesium ions (Mg(2+)) or other cations. It is hypothesized that the function and metabolism of RNAs might be regulated via interaction with lipid membranes in the prebiotic world. Using synthetic RNAs that model the core fragment of hammerhead ribozyme-like assembly (HHR-a), we investigated the enhancement of the self-cleavage reaction of HHR-a induced by the liposomes, both in the absence and presence of Mg(2+). The HHR-a activity was enhanced by 1,2-dioleoyl-sn-glycero-3-phosphoethanolamine (DOPE)/1,2-dioleoyl-sn-glycero-3-phosphocholine (DPPC) = 8/2 liposome with Mg(2+), while other liposomes did not so significant. In the presence of DOPE/DPPC = 8/2 liposome, the HHR-a activity was observed without Mg(2+), revealed by the conformational change of the HHR inhibitor complex induced by the interaction with the liposome. The UV resonance Raman spectroscopy analysis investigated the interaction between lipid molecules and nucleobases, suggesting that the ethanolamine group of DOPE molecules are assumed to act as monovalent cations alternative to Mg(2+), depending on the liposome membrane characteristics.

Droplet microfluidics for the study of artificial cells

In this review, we describe recent advances in droplet-based microfluidics technology that can be applied in studies of artificial cells. Artificial cells are simplified models of living cells and provide valuable model platforms designed to reveal the functions of biological systems. The study of artificial cells is promoted by microfluidics technologies, which provide control over tiny volumes of solutions during quantitative chemical experiments and other manipulations. Here, we focus on current and future trends in droplet microfluidics and their applications in studies of artificial cells.

Compartmentalization and separation of aqueous reagents in the water droplets of water-in-oil high internal phase emulsions

We have compartmentalized aqueous reagents and indicator species within the micrometer-sized water droplets of mixed high internal phase emulsions (HIPEs). Mass transport of the reagents across the micrometer-thickness oil films separating the water droplets followed by reaction with the indicator species produces a visible color change which provides a simple method to measure the trapping times of the reagents. Trapping times have been measured for an uncharged reagent (hydrogen peroxide) and charged reagents (HCl and NaClO) in different HIPEs. The trapping times are discussed in terms of a model in which the transferring species partitions from the water to the oil film followed by a rate-determining step of diffusion across the oil film. Rather surprisingly, it is found that trapping times are of similar orders of magnitude for both uncharged and charged aqueous species transferring across liquid oil films.

ON-OFF switching of transcriptional activity of large DNA through a conformational transition in cooperation with phospholipid membrane

We report that structural transitions of DNA cause the ON-OFF switching of transcriptional activity in cooperation with phospholipid membrane in a reconstituted artificial cell. It has been shown that long DNA of more than 20-30 kilo base-pairs exhibits a discrete conformational transition between a coiled state and highly folded states in aqueous solution, depending on the presence of various condensing agents such as polyamine. Recently, we reported a conformational transition of long DNA through interplay with phospholipid membrane, from a folded state in aqueous phase to an extended coil state on a membrane surface, in a cell-sized water-in-oil microdroplet covered by phosphatidylethanolamine monolayer (Kato, A.; Shindo, E.; Sakaue, T.; Tsuji, A.; Yoshikawa, K. Biophys. J. 2009, 97, 1678-1686). In this study, to elucidate the effects of these conformational changes on the biologically important function of DNA, transcription, we investigated the transcriptional activity of DNA in a microdroplet. Transcriptional activity was evaluated at individual DNA molecule level by a method we developed, in which mRNA molecules are labeled with fluorescent oligonucleotide probes. Transcription proceeded on almost all of the DNA molecules with a coiled conformation in the aqueous phase. In the presence of a tetravalent amine, spermine, the DNA had a folded conformation, and transcription was completely inhibited. When the Mg(2+) concentration was increased, DNA was adsorbed onto the inner surface of the membrane and exhibited an extended conformation. The transcription experiments showed that this conformational transition recovered transcriptional activity; transcription occurred on DNA molecules that were on the membrane.