Highly sensitive and selective mercury sensor based on mismatched base pairing with dioxT

Nearest-neighbour parametrization of DNA single, double and triple mismatches at low sodium concentration

DNA mismatches, that is, base pairs different from the canonical AT and CG, are involved in numerous biological processes and can be a problem for technological applications such as PCR amplification. The nearest-neighbour (NN) model is the standard approach for predicting melting temperatures and is used in methods of secondary structure predictions and modelling of hybridization kinetics. However, despite its biological and technological importance, existing NN parameters that include DNA mismatches are incomplete, and those available were obtained from a limited set of melting temperature at high sodium concentration. To our knowledge, there is currently no NN set of parameters for up to three mismatches covering all configurations at low sodium concentrations. Here, we are applying the NN model to a large set of 4096 published melting temperatures, covering all combinations of single, double and triple mismatches. Dealing with such a large set of temperature is challenging in several ways, bringing new methodological problems. Here, optimizing a large number of 252 independent parameters has required the development of a new method where we readjust the seed parameters using the definition of the Gibbs free energy. The new parameters predict the training set within 1.1 °C and the validation set to 2.7 °C.

Thiophene-Extended Fluorescent Nucleosides as Molecular Rotor-Type Fluorogenic Sensors for Biomolecular Interactions

Fluorescent molecular rotors are versatile tools for the investigation of biomolecular interactions and the monitoring of microenvironmental changes in biological systems. They can transform invisible information into a fluorescence signal as a straightforward response. Their utility is synergistically amplified when they are merged with biomolecules. Despite the tremendous significance and superior programmability of nucleic acids, there are very few reports on the development of molecular rotor-type isomorphic nucleosides. Here, we report the synthesis and characterization of a highly emissive molecular rotor-containing thymine nucleoside (^ThexT) and its 2'-O-methyluridine analogue (2'-OMe-^ThexU) as fluorogenic microenvironment-sensitive sensors that emit vivid fluorescence via an interaction with the target proteins. ^ThexT and 2'-OMe-^ThexU may potentially serve as robust probes for a broad range of applications, such as fluorescence mapping, to monitor viscosity changes and specific protein-binding interactions in biological systems.

Enhanced duplex- and triplex-forming ability and enzymatic resistance of oligodeoxynucleotides modified by a tricyclic thymine derivative

We designed and synthesized an artificial nucleic acid, [3-(1,2-dihydro-2-oxobenzo[b][1,8]naphthyridine)]-2'-deoxy-D-ribofuranose (OBN), with a tricyclic structure in a nucleobase as a thymidine analog. Oligodeoxynucleotides (ODNs) containing consecutive OBN displayed improved duplex-forming ability with complementary single-stranded (ss) RNA and triplex-forming ability with double-stranded DNA in comparison with ODNs composed of natural thymidine. OBN-modified ODNs also displayed enhanced enzymatic resistance compared with ODNs with natural thymidine and phosphorothioate modification, respectively, due to the structural steric hindrance of the nucleobase. The fluorescence spectra of OBN-modified ODNs showed sufficient fluorescence intensity with ssDNA and ssRNA, which is an advantageous feature for fluorescence imaging techniques of nucleic acids with longer emission wavelengths than bicyclic thymine (bT).

A Disposable Electrochemical Biosensor Based on Screen-Printed Carbon Electrodes Modified with Silver Nanowires/HPMC/Chitosan/Urease for the Detection of Mercury (II) in Water

This work describes the facile preparation of a disposable electrochemical biosensor for the detection of Hg(II) in water by modifying the surface of a screen-printed carbon electrode (SPCE). The surface modification consists of the immobilization of a composite layer of silver nanowires, hydroxymethyl propyl cellulose, chitosan, and urease (AgNWs/HPMC/CS/Urease). The presence of the composite was confirmed by scanning electron microscopy (SEM) and its excellent conductivity, due chiefly to the electrical properties of silver nanowires, enhanced the sensitivity of the biosensor. Under optimum conditions, the modified SPCE biosensor showed excellent performance for the detection of Hg(II) ions, with an incubation time of 10 min and a linear sensitivity range of 5–25 µM. The limit of detection (LOD) and limit of quantitation (LOQ) were observed to be 3.94 µM and 6.50 µM, respectively. In addition, the disposable and portable biosensor exhibited excellent recoveries for the detection of Hg(II) ions in commercial drinking water samples (101.62–105.26%). The results are correlated with those obtained from inductively coupled plasma optical emission spectrometry (ICP-OES), indicating that our developed sensor is a reliable method for detection of Hg(II) in real water samples. The developed sensor device is a simple, effective, portable, low cost, and user-friendly platform for real-time detection of heavy metal ions in field measurements with potential for other biomedical applications in the future.

Fundamental photophysics of isomorphic and expanded fluorescent nucleoside analogues

Fluorescent nucleoside analogues (FNAs) are structurally diverse mimics of the natural essentially non-fluorescent nucleosides which have found numerous applications in probing the structure and dynamics of nucleic acids as well as their interactions with various biomolecules. In order to minimize disturbance in the labelled nucleic acid sequences, the FNA chromophoric groups should resemble the natural nucleobases in size and hydrogen-bonding patterns. Isomorphic and expanded FNAs are the two groups that best meet the criteria of non-perturbing fluorescent labels for DNA and RNA. Significant progress has been made over the past decades in understanding the fundamental photophysics that governs the spectroscopic and environmentally sensitive properties of these FNAs. Herein, we review recent advances in the spectroscopic and computational studies of selected isomorphic and expanded FNAs. We also show how this information can be used as a rational basis to design new FNAs, select appropriate sequences for optimal spectroscopic response and interpret fluorescence data in FNA applications.

Synthesis and application of a 19F-labeled fluorescent nucleoside as a dual-mode probe for i-motif DNAs

Because of their stable orientations and their minimal interference with native DNA interactions and folding, emissive isomorphic nucleoside analogues are versatile tools for the accurate analysis of DNA structural heterogeneity. Here, we report on a bifunctional trifluoromethylphenylpyrrolocytidine derivative (FPdC) that displays an unprecedented quantum yield and highly sensitive 19F NMR signal. This is the first report of a cytosine-based dual-purpose probe for both fluorescence and 19F NMR spectroscopic DNA analysis. FPdC and FPdC-containing DNA were synthesized and characterized; our robust dual probe was successfully used to investigate the noncanonical DNA structure, i-motifs, through changes in fluorescence intensity and 19F chemical shift in response to i-motif formation. The utility of FPdC was exemplified through reversible fluorescence switching of an FPdC-containing i-motif oligonucleotide in the presence of Ag(i) and cysteine.

A Chemodosimetric Approach for Fluorimetric Detection of Hg2+ Ions by Trinuclear Zn(II)/Cd(II) Schiff Base Complex: First Case of Intermediate Trapping in a Chemodosimetric Approach

The present work discloses the application of two fluorescent zinc and cadmium complexes (1 and 2) for sensing of Hg(II) ions through a chemodosimetric approach. The ligand under consideration in this work is a N₂O donor Schiff base ligand (E)-4-bromo-2-(((2-morpholinoethyl)imino)methyl)phenol (HL), which has been harnessed to generate complexes [Zn₃L₂(OAc)₄] (1) and [Cd₃L₂(OAc)₄] (2). X-ray single crystal diffraction studies unveil the trinuclear skeleton of complexes 1 and 2. Both complexes have been found to be highly fluorescent in nature. However, the quantum efficiency of Zn(II) complex (1) dominates over the Cd(II) analogue (2). The absorption and emission spectroscopic properties of the complexes have been investigated by density functional theory. Complexes 1 and 2 can detect Hg²⁺ ions selectively by fluorescence quenching, and it is noteworthy to mention that the mechanism of sensing is unique as well as interesting. In the presence of Hg²⁺ ions, complexes 1 and 2 are transformed to mononuclear mercuric intermediate complex (3) and finally to a trinuclear mercuric complex (4) by hydrolysis. We have successfully trapped the intermediate complex 3, and we characterized it with the aid of X-ray crystallography. Transformation of complexes 1 and 2 to intermediate complex 3 and finally to 4 has been established by UV-vis spectroscopy, fluorescence spectroscopy, ESI-MS spectroscopy, ¹H NMR spectroscopy, and X-ray crystallography. The spontaneity of the above conversion is well supported by thermodynamic aspects as reflected from density functional theoretical calculations.

Coumarin Thiourea-Based Fluorescent Turn-on Hg2+ Probe That Can Be Utilized in a Broad pH Range 1-11

A novel coumarin-thiourea conjugate was synthesized facilely. It served as a fluorescent turn-on chemosensor for selective detection of Hg²⁺ ion over other common competitive metal ions including Li⁺, Na⁺, K⁺, Ag⁺, Cu²⁺, Fe²⁺, Zn²⁺, Co²⁺, Ni²⁺, Mn²⁺, Sr²⁺, Ca²⁺, Mg²⁺, Al³⁺, Cr³⁺ and Fe³⁺ ions based on the Hg²⁺-promoted desulfurization and cyclization reactions. Addition of Hg²⁺ ion to the sensor solution in 2:8 EtOH/H₂O induced a hypsochromic shift of the UV-Vis absorption band from 360 nm to 340 nm accompanying distinct enhancement in the absorption intensity while addition of other metal ions failed to bring about substantial change in the absorption spectra. Addition of Hg²⁺ to the sensor solution also caused marked increase in the fluorescence emission intensity and most common competitive metal ions did not interfere with the selective sensing of Hg²⁺ ion by the sensor. The detection limit of Hg²⁺ ion by the probe was calculated to be 1.46 × 10^-7 M and the probe could be utilized for selective detection of Hg²⁺ ion by fluorescence turn-on mode over a broad pH range of 1-11.