A Far-Red Emitting Fluorescent Chemogenetic Reporter for In Vivo Molecular Imaging

Far-red emitting fluorescent labels are highly desirable for spectral multiplexing and deep tissue imaging. Here, we describe the generation of frFAST (far-red Fluorescence Activating and absorption Shifting Tag), a 14-kDa monomeric protein that forms a bright far-red fluorescent assembly with (4-hydroxy-3-methoxy-phenyl)allylidene rhodanine (HPAR-3OM). As HPAR-3OM is essentially non-fluorescent in solution and in cells, frFAST can be imaged with high contrast in presence of free HPAR-3OM, which allowed the rapid and efficient imaging of frFAST fusions in live cells, zebrafish embryo/larvae, and chicken embryos. Beyond enabling the genetic encoding of far-red fluorescence, frFAST allowed the design of a far-red chemogenetic reporter of protein–protein interactions, demonstrating its great potential for the design of innovative far-red emitting biosensors.     

A DNA Switch for Detecting Single Nucleotide Polymorphism within a Long DNA Sequence Under Denaturing Conditions

DNA detection is usually conducted under nondenaturing conditions to favor the formation of Watson–Crick base-paring interactions. However, although such a setting is excellent for distinguishing a single-nucleotide polymorphism (SNP) within short DNA sequences (15–25 nucleotides), it does not offer a good solution to SNP detection within much longer sequences. Here we report on a new detection method capable of detecting SNP in a DNA sequence containing 35–90 nucleotides. This is achieved through incorporating into the recognition DNA sequence a previously discovered DNA molecule that forms a stable G-quadruplex in the presence of 7 molar urea, a known condition for denaturing DNA structures. The systems are configured to produce both colorimetric and fluorescent signals upon target binding.     

Genetically Encoded Bioluminescent Indicator for ERK2 Dimer in Living Cells

In this study, a genetically encoded bioluminescent indicator for ERK2 dimer was developed with the split Renilla luciferase complementation method, in which the formation of ERK2 dimer induces a spontaneous emission of bioluminescence in living cells. In response to extracellular stimuli, such as epidermal growth factor (EGF) or 17β‐estradiol (E2), extracellular signal‐regulated kinase 2 (ERK2) is phosphorylated by its upstream kinase MEK, and also phosphorylates its substrates in various regions of the cell, including the nucleus. Phosphorylated ERK2 is led to form its dimer, thereby transporting itself into the nucleus. We demonstrated with the indicator that stimulation with EGF or E2 induces the formation of ERK2 dimer in living MCF‐7 cells. The dynamics of this dimer formation was examined and discussed.     

Intramolecular dimers: a new design strategy for fluorescence-quenched probes

Fluorogenic probes dual-labeled with reporter and quencher dyes use a change in fluorescence to monitor biochemical events (e.g., substrate binding or enzyme digestion). Such events change the reporter-quencher distance, which affects fluorescence. Recently, it is has been shown that static quenching through intramolecular dimers is an important mechanism that can sometimes be more efficient than F?rster resonance energy transfer (FRET).     

A Two‐Dimensional Coordination Compound as a Zinc Ion Selective Luminescent Probe for Biological Applications

A 2D coordination compound {[Cu₂(HL)(N₃)]?ClO₄}_∞ ( 1 ; H₃L=2,6‐bis(hydroxyethyliminoethyl)‐4‐methyl phenol) was synthesized and characterized by single‐crystal X‐ray diffraction to be a polymer in the crystalline state. Each [Cu₂(HL)(N₃)]⁺ species is connected to its adjacent unit by a bridging alkoxide oxygen atom of the ligand to form a helical propagation along the crystallographic a axis. The adjacent helical frameworks are connected by a ligand alcoholic oxygen atom along the crystallographic b axis to produce pleated 2D sheets. In solution, 1 dissociates into [Cu₂(HL)₂(H₃L)]?2H₂O ( 2 ); the monomer displays high selectivity for Zn²⁺ and can be used in HEPES buffer (pH 7.4) as a zinc ion selective luminescent probe for biological application. The system shows a nearly 19‐fold Zn²⁺‐selective chelation‐enhanced fluorescence response in the working buffer. Application of 2 to cultured living cells (B16F10 mouse melanoma and A375 human melanoma) and rat hippocampal slices was also studied by fluorescence microscopy.     

Dynamic light-scattering analysis of the electrostatic interaction of hexahistidine-tagged cytochrome P450 enzyme with semiconductor quantum dots.

Currently, there is great interest in the development of methods suitable for determining the stoichiometry of biomolecules attached to nanoparticles. We describe the use of the dynamic light-scattering technique (DLS) to determine the stoichiometry of the protein cytochrome P450(BSbeta) attached to CdS and CdSe quantum dots (QDs). The enzyme-conjugated QDs have different diffusion characteristics compared to the QD and enzyme precursors, expressed in their size, scattering intensity as well as zeta-potential values. The significant enhancement of the scattering intensity of QDs observed upon conjugation with the P450(BSbeta) due to the refractive-index increment and the systematic variation in zeta potential resulting from charge neutralization of the anionic QDs by the cationic histidine-tagged P450(BSbeta) have been used for stoichiometry determination.     

Chemical Biological Sensors Based on Advances in Conducting Electroactive Polymers

Advances in conducting electroactive polymers (CEPs) have driven the design of novel chemical and biochemical sensors. The redox properties of CEPs have been intensely studied for more than two decades with emphasis on their synthesis and characterization. Little attention has been paid to the importance of mechanism in sensor designs. However, in order to design robust and stable sensors, it is important to understand how the polymer structure, morphology, adhesion properties and microenvironment affect sensor performance. This work describes how chemical and biological sensors have been designed, fabricated, characterized and tested based on the fundamental understanding in CEPs. The use of photopolymerized conducting polymers in sensor designs is described. Four focus areas are presented in which the electronic properties of CEPs have enabled the design of novel sensors for organics, nucleic acids, biological molecules, vapors and metal ions.     

Biomolecule-functionalized carbon nanotubes: applications in nanobioelectronics.

Carbon nanotubes (CNTs) revealing metallic or semiconductive properties depending on the folding modes of the nanotube walls represent a novel class of nanowires. Different methods to separate semiconductive CNTs from conductive CNTs have been developed, and synthetic strategies to chemically modify the side walls or tube ends by molecular or biomolecular components have been reported. Tailoring hybrid systems consisting of CNTs and biomolecules (proteins and DNA) has rapidly expanded and attracted substantial research effort. The integration of biomaterials with CNTs enables the use of the hybrid systems as active field-effect transistors or biosensor devices (enzyme electrodes, immunosensors, or DNA sensors). Also, the integration of CNTs with biomolecules has allowed the generation of complex nanostructures and nanocircuitry of controlled properties and functions. The rapid progress in this interdisciplinary field of CNT-based nanobioelectronics and nanobiotechnology is reviewed by summarizing the present scientific accomplishments, and addressing the future goals and perspectives of the area.     

Recent Advances in Electropolymerized Conducting Polymers in Amperometric Biosensors

Conducting electroactive polymers (CPs) are materials discovered just over 20 years ago which have aroused considerable interest on account of their electronic conducting properties and unique chemical and biochemical properties. Consequently, they have numerous (bio)analytical and technological applications. CPs are easily synthesized and deposited onto the conductive surface of a given substrate from monomer solutions by electrochemical polymerization with precise electrochemical control of their formation rate and thickness. Coating electrodes with CPs under mild conditions opens up enormous possibilities for the immobilization of biomolecules and bioaffinity or biorecognizing reagents, the improvement of their electrocatalytic properties, rapid electron transfer and direct communication to produce a range of analytical signals and new analytical applications. Co-immobilization of other molecules (enzymatic co-factors or charge-transfer mediators) by entrapment within electropolymerized films or by covalent binding on these films permits straightforward fabrication of reagentless biosensors. The characteristics of CPs and their uses, mainly in amperometric biosensors, are reviewed. The most recent applications and lines of research related to CP films are summarized in the different sections of the paper, and probable future trends are discussed.