Macrocyclic Metal Complex-DNA Conjugates for Electrochemical Sensing of Single Nucleobase Changes in DNA

Cisplatin adducts of DNA as precursors for nanostructured catalyst materials

The synthesis and characterisation of novel metal-modified DNA precursors for fuel cell catalyst development are described. Material precursors in the form of metal-DNA complexes were prepared through the reaction of DNA with cisplatin at various loadings and spectroscopically tested to confirm the platinum binding mode and the degree of complexation. The surface morphology of the DNA-metal material was analysed by Scanning Transmission Electron Microscopy (STEM), which revealed the extent of platinum nanocluster formation, with low metal loadings leading to observation of individual platinum atoms. Electrochemical measurements showed a greater electrocatalytic activity for the hydrogen evolution reaction (HER) with increased platinum loadings, shifting the half wave potential, E _1/2, away from the glassy carbon limit towards that of a bulk Pt electrode. This is explained further by Tafel plots, from which a change in the mechanism of the apparent rate limiting step for proton reduction from a Volmer to a Heyrovsky mechanism is postulated as the platinum loading increases.

Sequential Ag+/biothiol and synchronous Ag+/Hg2+ biosensing with zwitterionic Cu2+-based metal-organic frameworks

Zwitterionic metal-organic frameworks (MOFs) of {[Cu(Cbdcp)(Dps)(H₂O)₃]·6H₂O}_n (MOF 1) and [Cu₄(Dcbb)₄(Dps)₂(H₂O)₂]_n (MOF 2) (H₃CbdcpBr = N-(4-carboxybenzyl)-(3,5-dicarboxyl)pyridinium bromide; H₂DcbbBr = 1-(3,5-dicarboxybenzyl)-4,4'-bipyridinium bromide; Dps = 4,4'-dipyridyl sulfide) quench the fluorescence of cytosine-rich DNA tagged with 5-carboxytetramethylrhodamine (TAMRA, emission at 582 nm, denoted as C-rich P-DNA-1) and yield the corresponding P-DNA-1@MOF hybrids. Exposure of these hybrids to Ag⁺ results in the release of the P-DNA-1 strands from the MOF surfaces as double-stranded, hairpin-like C-Ag^I-C (ds-DNA-1@Ag⁺) with the restoration of TAMRA fluorescence. The ds-DNA-1@Ag⁺ formed on the surface of 1 can subsequently sense biothiols cysteine (Cys), glutathione (GSH), and homocysteine (Hcy) due to the stronger affinity of mercapto groups for Ag⁺ that serves to unfold the ds-DNA-1@Ag⁺ duplex, reforming P-DNA-1, which is re-adsorbed by MOF 1 accompanied by quenching of TAMRA emission. Meanwhile, MOF 2 is also capable of co-loading a thymine-rich probe DNA tagged with 5-carboxyfluorescein (FAM, emission at 518 nm, denoted as T-rich P-DNA-2) to achieve synchronous sensing of Ag⁺ and Hg²⁺, resulting from the simultaneous yet specific ds-DNA-1@Ag⁺ and T-Hg^II-T duplex (ds-DNA-2@Hg²⁺) formation, as well as the distinctive emission wavelengths of TAMRA and FAM. Detection limits are as low as 5.3 nM (Ag⁺), 14.2 nM (Cys), 13.5 nM (GSH), and 9.1 nM (Hcy) for MOF 1, and 7.5 nM (Ag⁺) and 2.6 nM (Hg²⁺) for MOF 2, respectively. The sequential sensing of Ag⁺ and biothiols by MOF 1, and the synchronous sensing of Ag⁺ and Hg²⁺ by MOF 2 are rapid and specific, even in the presence of other mono- and divalent metal cations or other biothiols at much higher concentrations. Molecular simulation studies provide insights regarding the molecular interactions that underpin these sensing processes.

A planar and uncharged copper(II)-picolinic acid chelate: Its intercalation to duplex DNA by experimental and theoretical studies and electrochemical sensing application

Using an external redox-active molecule as a DNA hybridization indicator is still a popular strategy in electrochemical DNA biosensors because it is label-free and the multi-site binding can enhance the response signal. A planar and uncharged transition metal complex, Cu(PA)₂ (PA = picolinic acid) with excellent electrochemical activity has been synthesized and its interaction with double-stranded DNA (dsDNA) is studied by experimental electrochemical methods and theoretical molecular docking technology. The experimental results reveal that the copper complex interacts with dsDNA via specific intercalation, which is verified by the molecular docking result. The surface-based voltammetric analysis demonstrates that the planar Cu(PA)₂ can effectively accumulate within the electrode-confined hybridized duplex DNA rather than the single-stranded probe DNA. Based on this phenomenon, the Cu(PA)₂ is utilized as an electrochemical hybridization indicator for the detection of oligonucleotides. The sensing assays show that upon incubation in Cu(PA)₂ solution, the probe electrode does not display any Faraday signal, but the hybridized one has a pair of strong redox peaks corresponding to the electrochemistry of Cu(PA)₂, showing excellent hybridization indicating function of Cu(PA)₂ without background interference. The signal intensity of Cu(PA)₂ is dependent on the concentrations of the target oligonucleotide ranging from 1 fM to 100 nM with an experimental detection limit of 1.0 fM. Due to the specific intercalation of Cu(PA)₂ with dsDNA, the biosensor also exhibits good ability to recognize oligonucleotide with different base mismatching degree.

Ultrasensitive Electrochemical Biosensor Developed by Probe Lengthening for Detection of Genomic DNA in Human Serum

As an alternative to most of the reported nucleic acid amplification-based electrochemical DNA biosensors used for detection of trace levels of genomic DNA, we herein present a novel detection concept. The proposed system involves the conversion of two short double-stranded DNAs (dsDNAs), labeled with a thiol-tag or biotin-tag, into a single integrated dsDNA containing thiol and biotin at both terminals in the presence of target DNA through ligase chain reaction (LCR) and followed by the immobilization of these integrated dsDNAs on a bovine serum albumin (BSA)-modified gold electrode surface. Owing to rapid depletion of the two short dsDNAs via LCR, the integrated dsDNAs were generated in an exponential manner so that this sensoring approach offered a limit of detection of 25 yoctomoles (15 copies in 50 μL sample volumes), a high discrimination of single-base mismatch and a wide linear concentration range (across 6 orders of magnitude) for target DNA. Significantly, the proposed sensor, which has simplicity in operation and ease of miniaturization, detected the target of interest in total nucleic acid extracts derived from clinical serum samples with excellent results, thereby demonstrating its considerable diagnostic potential in fields ranging from virus detection to the diagnosis of genetic diseases.

Chemistries for DNA Nanotechnology

The predictable nature of DNA interactions enables the programmable assembly of highly advanced 2D and 3D DNA structures of nanoscale dimensions. The access to ever larger and more complex structures has been achieved through decades of work on developing structural design principles. Concurrently, an increased focus has emerged on the applications of DNA nanostructures. In its nature, DNA is chemically inert and nanostructures based on unmodified DNA mostly lack function. However, functionality can be obtained through chemical modification of DNA nanostructures and the opportunities are endless. In this review, we discuss methodology for chemical functionalization of DNA nanostructures and provide examples of how this is being used to create functional nanodevices and make DNA nanostructures more applicable. We aim to encourage researchers to adopt chemical modifications as part of their work in DNA nanotechnology and inspire chemists to address current challenges and opportunities within the field.

Interactions of tetracationic porphyrins with DNA and their effects on DNA cleavage

The interaction of tetracationic porphyrins with DNA was studied using UV-Vis absorption, fluorescence spectroscopy and viscometry, and the particle sizes were determined. Аs cationic porphyrins, two isomer porphyrins, 3,3',3″,3‴-(5,10,15,20-Porphyrintetrayl)tetrakis(1-methylpyridinium) (TMPyP3) and 4,4',4″,4‴-(5,10,15,20-Porphyrintetrayl)tetrakis(1-methylpyridinium) (TMPyP4), were studied. They differ in the position of NCH₃⁺ group in phenyl ring of the porphyrins and hence, in degree of freedom of rotation of the phenyl rings about the central macrocycle. It was found that intercalated complexes are formed at DNA/porphyrin molar ratios (R) of 2.2 and 3.9 for TMPyP3 и TMPyP4, respectively. Decreasing R up to 0.4 and 0.8 for TMPyP3 и TMPyP4, respectively, leads mainly to formation of outside complexes due to π-π stacking between the porphyrin chromophores interacting electrostatically with phosphate framework of DNA. Each type of the obtained complexes was characterized using Scatchard approach. It was ascertained that the affinity of TMPyP4 to DNA is stronger than TMPyP3, meanwhile the wedge effect of the latter is higher. The differences between the porphyrin isomers become more evident at irradiation of their complexes with DNA. It was established that irradiation of the intercalated complexes results in DNA fragmentation. In the case of TMPyP4, DNA fragments of different size are formed. The irradiation of the outside DNA/porphyrin complexes leads to cleavage of DNA (TMPyP3 and TMPyP4) and partial destruction of the complex due to photolysis of the porphyrin (TMPyP3).

Rationalisation of a mechanism for sensing single point variants in target DNA using anthracene-tagged base discriminating probes

The fluorescence sensing mechanism for identifying single base changes in target DNA strands has been established through detailed biophysical measurements.

Direct Readout of Single Nucleobase Variations in an Oligonucleotide

Direct, low-cost, label-free, and enzyme-free identification of single nucleobase is a great challenge for genomic studies. Here, this study reports that wild-type aerolysin can directly identify the difference of four types of single nucleobase (adenine, thymine, cytosine, and guanine) in a free DNA oligomer while avoiding the operations of additional DNA immobilization, adapter incorporation, and the use of the processing enzyme. The nanoconfined space of aerolysin enables DNA molecules to be limited in the narrow pore. Moreover, aerolysin exhibits an unexpected capability of detecting DNA oligomers at the femtomolar concentration. In the future, by virtue of the high sensitivity of aerolysin and its high capture ability for DNA oligomers, aerolysin will play an important role in the studies of single nucleobase variations and open up new avenues for a broad range of nucleic-acid-based sensing and disease diagnosis.

Ferrocene conjugated oligonucleotide for electrochemical detection of DNA base mismatch

We describe the synthesis, binding, and electrochemical properties of ferrocene-conjugated oligonucleotides (Fc-oligos). The key step for the preparation of Fc-oligos contains the coupling of vinylferrocene to 5-iododeoxyuridine via Heck reaction. The Fc-conjugated deoxyuridine phosphoramidite was used in the Fc-oligonucleotide synthesis. We show that thiol-modified Fc-oligos deposited onto gold electrodes possess potential ability in electrochemical detection of DNA base mismatch.

Rotaxanes composed of dibenzo-24-crown-8 and macrocyclic transition metal complexing tetraimine units

New rotaxanes, composed of dibenzo-24-crown-8 and the axle containing two tetraazamacrocyclic Ni and/or Cu units, adopt either folded or extended conformations and di-Ni-rotaxanes exhibit a shuttling effect of DB24C8.

Synthesis, magnetism and spectral studies of six defective dicubane tetranuclear {M4O6} (M = NiII, CoII, ZnII) and three trinuclear CdII complexes with polydentate Schiff base ligands

Six defective dicubane face-shared and three trinuclear complexes are synthesized. The magnetic behaviors of Ni^II/Co^II complexes and fluorescence properties of Zn^II and Cd^II are studied.

A Cu(ii) MOF with a flexible bifunctionalised terpyridine as an efficient catalyst for the single-pot hydrocarboxylation of cyclohexane to carboxylic acid in water/ionic liquid medium

A bifunctionalised terpyridine based Cu(ii) MOF for efficient hydrocarboxylation of cyclohexane to cyclohexanecarboxylic acid in an ionic liquid medium.