Live‐Cell Studies of p300/CBP Histone Acetyltransferase Activity and Inhibition

Histone acetyltransferase enzymes (HATs) are important therapeutic targets, but there are few cell‐based assays available for evaluating the pharmacodynamics of HAT inhibitors. Here we present the application of a FRET‐based reporter, Histac, in live‐cell studies of p300/CBP HAT inhibition, by both genetic and pharmacologic disruption. shRNA knockdown of p300/CBP led to increased Histac FRET, thus suggesting a role for p300/CBP in the acetylation of the histone H4 tail. Additionally, we describe a new p300/CBP HAT inhibitor, C107, and show that it can also increase cellular Histac FRET. Taken together, these studies provide a live‐cell strategy for identifying and evaluating p300/CBP inhibitors.     

Importance of Translation–Replication Balance for Efficient Replication by the Self‐Encoded Replicase

In all living systems, the genetic information is replicated by the self‐encoded replicase (Rep); this can be said to be a self‐encoding system. Recently, we constructed a self‐encoding system in liposomes as an artificial cell model, consisting of a reconstituted translation system and an RNA encoding the catalytic subunit of Qβ Rep and the RNA was replicated by the self‐encoded Rep produced by the translation reaction. In this system, both the ribosome (Rib) and Rep bind to the same RNA for translation and replication, respectively. Thus, there could be a dilemma: effective RNA replication requires high levels of Rep translation, but excessive translation in turn inhibits replication. Herein, we actually observed the competition between the Rib and Rep, and evaluated the effect for RNA replication by constructing a kinetic model that quantitatively explained the behavior of the self‐encoding system. Both the experimental and theoretical results consistently indicated that the balance between translation and replication is critical for an efficient self‐encoded system, and we determined the optimum balance.     

Bacterial Alarmone,Guanosine 5′‐Diphosphate 3′‐Diphosphate (ppGpp), Predominantly Binds the β′ Subunit of Plastid‐Encoded Plastid RNA Polymerase in Chloroplasts

It's alarming : Bacterial alarmone guanosine 5′‐diphosphate 3′‐diphosphate (ppGpp), which is a key regulatory molecule that controls the stringent response, also exists in chloroplasts of plant cells. Cross‐linking experiments with 6‐thioguanosine 5′‐diphosphate 3′‐diphosphate (6‐thioppGpp) and chloroplast RNA polymerase indicate that ppGpp binds the β′ subunit of plastid‐encoded plastid RNA polymerase that corresponds to the Escherichia coli β′ subunit.

     

NIR Fluorogenic Dye as a Modular Platform for Prodrug Assembly: Real‐Time in vivo Monitoring of Drug Release

The ability to monitor drug release in vivo provides essential pharmacological information. We developed a new modular approach for the preparation of theranostic prodrugs with a turn‐ON near‐infrared (NIR) fluorescence mode of action. The prodrugs release their chemotherapeutic cargo and an active cyanine fluorophore upon reaction with a specific analyte. The prodrug platform is based on the fluorogenic dye QCy7; upon removal of a triggering substrate, the dye fluoresces, and the free drug is released. The evaluated camptothecin prodrug was activated by endogenous hydrogen peroxide produced in tumor cells in vitro and in vivo. Drug release and in vitro cytotoxicity were correlated with the emitted fluorescence. The prodrug activation was effectively imaged in real time in mice bearing tumors. The modular design of the QCy7 fluorogenic platform should allow the preparation of numerous other prodrugs with various triggering substrates and chemotherapeutic agents. We anticipate that the development of real‐time in vivo monitoring tools such as that described herein will pave the way for personalized therapy.     

2′‐Bispyrene‐Modified 2′‐O‐Methyl RNA Probes as Useful Tools for the Detection of RNA: Synthesis,Fluorescent Properties,and Duplex Stability

The synthesis and properties two series of new 2′‐O‐methyl RNA probes, each containing a single insertion of a 2′‐bispyrenylmethylphosphorodiamidate derivative of a nucleotide (U, C, A, and G), are described. As demonstrated by UV melting studies, the probes form stable complexes with model RNAs and DNAs. Significant increases (up to 21‐fold) in pyrene excimer fluorescence intensity were observed upon binding of most of the probes with complementary RNAs, but not with DNAs. The fluorescence spectra are independent of the nature of the modified nucleotides. The nucleotides on the 5′‐side of the modified nucleotide have no effect on the fluorescence spectra, whereas the natures of the two nucleotides on the 3′‐side are important: CC, CG, and UC dinucleotide units on the 3′‐side of the modified nucleotide provide the maximum increases in excimer fluorescence intensity. This study suggests that these 2′‐bispyrene‐labeled 2′‐O‐methyl RNA probes might be useful tools for detection of RNAs.     

Monitoring of the Synthesis of Hyperbranched Poly(urea‐urethane)s by Real‐Time Attenuated Total Reflection (ATR)‐FT‐IR Spectroscopy

Summary: The reaction of 2,4‐TDI and DEA, as an A₂ + B^*B₂ polymerization system towards hyperbranched HPUs was followed using in situ ATR‐FT‐IR spectroscopy. The decrease in intensity of the NCO absorption band of the reactive isocyanate group of 2,4‐TDI along with the formation and growth of the new characteristic bands of urethane and urea groups were detected. The reactivity difference of both NH and OH groups towards the NCO group at low temperatures was proven. The rate of the reaction was found to be affected by changing the temperature, the rate of addition of the B^*B₂ monomer and the type of solvent. Moreover, the increase of the carbonyl vibration and the amide II bands of urea was very obvious during the addition of the stopper DEA. Thus, it was possible to verify the individual reaction steps of this complex polyreaction and to correlate these with the structural development of the resulting macromolecules.

Characteristic vibration bands of urethane and urea groups in the IR spectra (1 780–1 480 cm^?1) during the polymerization reaction.     

Photoactivation of Cell-Free Expressed Archaerhodopsin-3 in a Model Cell Membrane

Transmembrane receptor proteins are located in the plasma membranes of biological cells where they exert important functions. Archaerhodopsin (Arch) proteins belong to a class of transmembrane receptor proteins called photoreceptors that react to light. Although the light sensitivity of proteins has been intensely investigated in recent decades, the electrophysiological properties of pore-forming Archaerhodopsin (Arch), as studied in vitro, have remained largely unknown. Here, we formed unsupported bilayers between two channels of a microfluidic chip which enabled the simultaneous optical and electrical assessment of the bilayer in real time. Using a cell-free expression system, we recombinantly produced a GFP (green fluorescent protein) labelled as a variant of Arch-3. The label enabled us to follow the synthesis of Arch-3 and its incorporation into the bilayer by fluorescence microscopy when excited by blue light. Applying a green laser for excitation, we studied the electrophysiological properties of Arch-3 in the bilayer. The current signal obtained during excitation revealed distinct steps upwards and downwards, which we interpreted as the opening or closing of Arch-3 pores. From these steps, we estimated the pore radius to be 0.3 nm. In the cell-free extract, proteins can be modified simply by changing the DNA. In the future, this will enable us to study the photoelectrical properties of modified transmembrane protein constructs with ease. Our work, thus, represents a first step in studying signaling cascades in conjunction with coupled receptor proteins.     

Real‐Time Monitoring of Reactive Extrusion Processes by Means of In‐Line Infrared Spectroscopy and Infrared Temperature Measurement

In this paper, a possible solution for the determination of reaction kinetics in reactive extrusion processes by in‐line conversion and temperature measurement using infrared technology is proposed. As a model reaction, the activated anionic polymerization of ε‐caprolactam was used. In lab experiments, the aptitude of the used probes for the desired application is tested. The final extrusion experiments were done using a tightly intermeshing co‐rotating twin‐screw extruder. The results show that the used probes are suitable in general. In the extrusion experiments, problems occurred regarding the material exchange on the conversion measurement probe. Due to these problems, reliable conversion measurements could not be done. Several proposals are made for the improvement of this measurement system.     

Regio‐Selective Chemical‐Enzymatic Synthesis of Pyrimidine Nucleotides Facilitates RNA Structure and Dynamics Studies

Isotope labeling has revolutionized NMR studies of small nucleic acids, but to extend this technology to larger RNAs, site‐specific labeling tools to expedite NMR structural and dynamics studies are required. Using enzymes from the pentose phosphate pathway, we coupled chemically synthesized uracil nucleobase with specifically ¹³C‐labeled ribose to synthesize both UTP and CTP in nearly quantitative yields. This chemoenzymatic method affords a cost‐effective preparation of labels that are unattainable by current methods. The methodology generates versatile ¹³C and ¹⁵N labeling patterns which, when employed with relaxation‐optimized NMR spectroscopy, effectively mitigate problems of rapid relaxation that result in low resolution and sensitivity. The methodology is demonstrated with RNAs of various sizes, complexity, and function: the exon splicing silencer 3 (27 nt), iron responsive element (29 nt), Pro‐tRNA (76 nt), and HIV‐1 core encapsidation signal (155 nt).     

Conjugation and Evaluation of Triazole‐Linked Single Guide RNA for CRISPR‐Cas9 Gene Editing

The CRISPR‐Cas9 gene editing system requires Cas9 endonuclease and guide RNAs (either the natural dual RNA consisting of crRNA and tracrRNA or a chimeric single guide RNA) that direct site‐specific double‐stranded DNA cleavage. This communication describes a click ligation approach that uses alkyne–azide cycloaddition to generate a triazole‐linked single guide RNA (sgRNA). The conjugated sgRNA shows efficient and comparable genome editing activity to natural dual RNA and unmodified sgRNA constructs.     

Site‐Specific Labeling of MicroRNA Precursors: A Structure–Activity Relationship Study

Functionalized oligoribonucleotides are essential tools in RNA chemical biology. Various synthetic routes have been developed over recent years to conjugate functional groups to oligoribonucleotides. However, the presence of the functional group on the oligoribonucleotide backbone can lead to partial or total loss of biological function. The limited knowledge concerning the positioning of functional groups therefore represents a hurdle for the development of oligoribonucleotide chemical tools. Here we describe a systematic investigation of site‐specific labeling of pre‐miRNAs to identify positions for the incorporation of functional groups, in order not to hinder their processing into active mature miRNAs.     

Test Rig for Hybrid System Emulation: New Real‐Time Transient Model Validated in a Wide Operative Range

This paper reports an entirely new simulation tool for a hybrid system emulator facility built by the Thermochemical Power Group (TPG) at the University of Genoa, Italy. This new software was developed with the following targets: real‐time performance, good stability level and high calculation reliability. In details, to obtain real‐time performance a new approach based on 0‐D technique was chosen also for components usually analysed with 1‐D or 2‐D tools (e.g. the recuperator). These are essential key aspects to operate it in hardware‐in‐the‐loop mode or to evaluate predictive results for long transient operations. This work was based on collaboration between the University of Manchester, UK and the University of Genoa, Italy. The activity was carried out with a test rig composed of the following technology: a microturbine package able to produce up to 100 kWe and modified for external connections, external pipes designed for several purposes (by‐pass, measurement or bleed), and a high temperature modular vessel necessary to emulate the dimension of an SOFC stack. The real‐time transient model of this facility was developed inside the Matlab‐Simulink environment with the following modelling approach: a library of components allows to reach a high level of flexibility and an user‐friendly approach. This model includes the machine control system as an essential device to analyse further layouts (new components in the rig) and hardware‐in‐the‐loop operations. The experimental data collected in the laboratory by TPG were used to validate the simulation tool. The results calculated with the model were satisfactory compared with experimental data considering both steady‐state and transient operations. The most important innovative aspects of this work are related to this wide validation range (not only small power steps, but the whole operative range was considered) obtaining real‐time performance and considering microturbine conditions different from standard operations (additional pressure and temperature losses and unusual thermal capacitance). The modelling simplified approach used for such a complex system is an important innovative aspect, because usually the model reliability performance is obtained with more complex (and not real‐time) tools. This work is based on an innovative modelling approach based on 0‐D tools able to operate in real‐time mode (as necessary for hardware‐in‐the‐loop tests) with an accuracy level comparable with more complex and more time consuming software. This validated tool is an important base for future calculations to study innovative hybrid system layouts. For instance, TPG is planning to analyse the option of increasing fuel cell pressure and performance with a booster system (e.g. a turbocharger).     

Multi‐phosphorylation of the Intrinsically Disordered Unique Domain of c‐Src Studied by In‐Cell and Real‐Time NMR Spectroscopy

Intrinsically disordered regions (IDRs) are preferred sites for post‐translational modifications essential for regulating protein function. The enhanced local mobility of IDRs facilitates their observation by NMR spectroscopy in vivo. Phosphorylation events can occur at multiple sites and respond dynamically to changes in kinase–phosphatase networks. Here we used real‐time NMR spectroscopy to study the effect of kinases and phosphatases present in Xenopus oocytes and egg extracts on the phosphorylation state of the “unique domain” of c‐Src. We followed the phosphorylation of S17 in oocytes, and of S17, S69, and S75 in egg extracts by NMR spectroscopy, MS, and western blotting. Addition of specific kinase inhibitors showed that S75 and S69 are phosphorylated by CDKs (cyclin‐dependent kinases) differently from Cdk1. Moreover, although PKA (cAMP‐dependent protein kinase) can phosphorylate S17 in vitro, this was not the major S17 kinase in egg extracts. Changes in PKA activity affected the phosphorylation levels of CDK‐dependent sites, thus suggesting indirect effects of kinase–phosphatase networks. This study provides a proof‐of‐concept of the use of real‐time in vivo NMR spectroscopy to characterize kinase/phosphatase effects on intrinsically disordered regulatory domains.     

Incorporation of a FRET Pair into a Riboswitch RNA to Measure Mg2+ Concentration and RNA Conformational Change in Cell

Riboswitches are natural biosensors that can regulate gene expression by sensing small molecules. Knowledge of the structural dynamics of riboswitches is crucial to elucidate their regulatory mechanism and develop RNA biosensors. In this work, we incorporated the fluorophore, Cy3, and its quencher, TQ3, into a full-length adenine riboswitch RNA and its isolated aptamer domain to monitor the dynamics of the RNAs in vitro and in cell. The adenine riboswitch was sensitive to Mg²⁺ concentrations and could be used as a biosensor to measure cellular Mg²⁺ concentrations. Additionally, the TQ3/Cy3-labeled adenine riboswitch yielded a Mg²⁺ concentration that was similar to that measured using a commercial assay kit. Furthermore, the fluorescence response to the adenine of the TQ3/Cy3-labeled riboswitch RNA was applied to determine the proportions of multiple RNA conformational changes in cells. The strategy developed in this work can be used to probe the dynamics of other RNAs in cells and may facilitate the developments of RNA biosensors, drugs and engineering.