The ability to discriminate between epigenetic variants in DNA is a necessary tool if we are to increase our understanding of the roles that they play in various biological processes and medical conditions. Herein, it is demonstrated how a simple two-step fluorescent probe assay can be used to differentiate all three major epigenetic variants of cytosine at a single locus site in a target strand of DNA.

The direct incorporation of macrocyclic cyclidene complexes into DNA via automated synthesis results in a new family of metal-functionalized DNA derivatives that readily demonstrate their utility through the ability of one redox-active copper(II)-containing strand to distinguish electrochemically between all four canonical DNA nucleobases at a single site within a target sequence of DNA.

A [2]rotaxane, whose thread component comprises a central dibenzylammonium group and 9-alkoxyanthracene stoppers and is hosted by a 24-dibenzo-8-crown bead, undergoes an efficient photocatenation step resulting in a [2]rotaxane-to-[2]catenane topology interconversion via a fully reversible [4π+4π] photocyclomerization of terminal anthracene groups.

The field of synthetic biology includes studies that aim to develop new materials and devices from biomolecules. In recent years, much work has been carried out using a range of biomolecular chassis including α-helical coiled coils, β-sheet amyloids and even viral particles. In this work, we show how hybrid bionanoparticles can be produced from a viral M13 bacteriophage scaffold through conjugation with DNA primers that can template a polymerase chain reaction (PCR). This unprecedented example of a PCR on a virus particle has been studied by flow aligned linear dichroism spectroscopy, which gives information on the structure of the product as well as a new protototype methodology for DNA detection. We propose that this demonstration of PCR on the surface of a bionanoparticle is a useful addition to ways in which hybrid assemblies may be constructed using synthetic biology.Keywords: bacteriophage; linear dichroism; M13; nanoparticle; PCR; shear flow;

A new series of chiral ureas containing one or two redox-active ferrocene units was synthesised and studied in order to investigate the effect of planar chirality and central chirality on electrochemical chiral sensing. Binding of chiral carboxylate anions in organic solvents through H-bond formation caused a negative shift in the potentials of the ferrocene/ferrocenium (Fc/Fc+) couples of the receptors, demonstrating their use as electrochemical sensors in solution. While the presence of two ferrocene units gave no marked improvement in the chiral sensing capabilities of these systems, the introduction of planar chirality, in addition to central chirality, switched the enantiomeric binding preference of the system and also caused an interesting change in the appearance of some voltammograms, with unusual two-wave behaviour observed upon binding a protected prolinate guest.

Photoirradiation of a hydrogen-bonded molecular complex comprising acyclic components, namely, a stoppered thread (1) with a central barbiturate motif and an optimized doubly anthracene-terminated acyclic Hamilton-like receptor (2b), leads to an interlocked architecture, which was isolated and fully characterized. The sole isolated interlocked photoproduct (Φ = 0.06) is a [2]rotaxane, with the dimerized anthracenes assuming a head-to-tail geometry, as evidenced by NMR spectroscopy and consistent with molecular modeling (PM6). A different behavior was observed on irradiating homologous molecular complexes 1⊂2a, 1⊂2b, and 1⊂2c, where the spacers of 2a, 2b, and 2c incorporated 3, 6, and 9 methylene units, respectively. While no evidence of interlocked structure formation was observed following irradiation of 1⊂2a, a kinetically labile rotaxane was obtained on irradiating the complex 1⊂2c, and ring slippage was revealed. A more stable [2]rotaxane was formed on irradiating 1⊂2b, whose capture is found to be fully reversible upon heating, thereby resetting the system, with some fatigue (38%) after four irradiation–thermal reversion cycles.

Interlocked structures containing the classic Hamilton barbiturate binding motif comprising two 2,6-diamidopyridine units are reported for the first time. Stable [2]-rotaxanes can be accessed either through hydrogen-bonded preorganization by a barbiturate thread followed by a Cu+-catalyzed “click” stoppering reaction or by a Cu2+-mediated Glaser homocoupling reaction.

Examples of organometallic compounds as nucleoside analogues are rare within the field of medicinal bioorganometallic chemistry. We report on the synthesis and properties of two chiral ferrocene derivatives containing a nucleobase and a hydroxyalkyl group. These so-called ferronucleosides show promising anticancer activity, with cytostatic studies on five different cancer cell lines indicating that both functional groups are required for optimal activity.

A method for probing the strength of B–N dative bonds is reported. The activation parameters for nitrogen inversion in a series of azetidines tethered to boronate esters have been quantified by VT-NMR and the measured barriers correlated with data obtained by 11B NMR, X-ray crystallography and MP2 calculations.

Rates of pyramidal motion in an aziridine are controlled by reversible trans to cis photoisomerisation of an azobenzene unit attached to the ring nitrogen atom. The dynamics of the inversion process and activation parameters are derived by variable temperature NMR, and are supported by ab initio calculations.

Modified DNA strands undergo a reversible light-induced reaction involving the intramolecular photodimerization of two appended anthracene tags. The photodimers exhibit markedly different binding behavior toward a complementary strand that depends on the number of bases between the modified positions. By preforming the duplex, photochromism can be suppressed, illustrating dual-mode gated behavior.

The design, synthesis and electrochemical behaviour of an oligomer consisting of linked thymine-functionalised ferrocene units are reported, which, as a so-called form of ferrocene nucleic acid (FcNA), acts as a structural mimic of DNA.

The synthesis and in-depth characterisation including X-ray crystallography of a new hydroxy derivative of bis(2-pyridylcarbonyl)amine Hbpca, namely N-(3-hydroxypicolinoyl)picolinamide (Hbpca-OH), as well as two ferrocenyl derivatives of Hbpca-OH, namely 2-(picolinoylcarbamoyl)pyridin-3-yl ferrocenoate (HL1) and bis(2-(picolinoylcarbamoyl)pyridin-3-yl) 1,1′-ferrocenoate (H2L2), is reported. HL1 and H2L2 were complexed with five different transition metal cations, namely Fe2+, Zn2+, Ni2+, Cu2+ and Cu+, to give ten complexes with varying stoichiometries, which were characterised by different analytical methods including 1H NMR, ESI-MS, IR spectroscopy and microanalysis. The metal complexation was also confirmed by electrochemical measurements for all complexes except Zn(L1)2 and FeL2, for which the changes in formal redox potentials of ferrocene ΔE°′ observed were not significant enough. Furthermore, two X-ray structures of CuII complexes, namely [Cu2I2L12] and [Cu2I2L2]n, were determined. Both structures contain an extremely rare CuII–I2–CuII bridge. Finally, a small antiferromagnetic coupling in [Cu2I2L2]n was observed.

Single nucleotide polymorphisms within a sequence of a gene associated with prostate cancer were identified using oligodeoxynucleotide probe sequences bearing internal anthracene fluorophores proximal to the SNP site. Depending upon the nature of the synthesised target sequences, probe–target duplex formation could lead to enhanced or attenuated fluorescence emission from the anthracene, enabling detection of a proximal base–pair as either matching or mismatching.

A fluorescent DNA probe containing an anthracene group attached via an anucleosidic linker can identify all four DNA bases at a single site as well as the epigenetic modification C/5-MeCvia a hybridisation sensing assay.

Four organometallic nucleobases have been prepared and characterized, each consisting of a disubstituted ferrocene unit connected through either a conjugated or saturated linker group to adenine or thymine nucleobases. Their assembly behavior has been studied in the solid state via X-ray crystallography, revealing intermolecular H-bonded arrays. The electrode potentials in DCM are strongly dependent upon the nature of the linker group between the ferrocene unit and the nucleobase.

A chiral ferrocene-based boronic acid interacts with (R)- and (S)-Binol to form two complexes that exhibit significantly different ferrocene-based electrode potentials. This difference in redox behavior can be exploited to demonstrate in principle how high levels of enantiomeric excess in a mixture of enantiomers can be quantified and read-out using an electrochemical method.

A novel organometallic receptor binds anions in solution and in the solid state, with complexes stabilised through a series of C–H⋯X interactions, as evidenced by 1H NMR spectroscopy, X-ray crystallography and computational models.

The molecular motion associated with atomic inversion at an aziridine nitrogen can be essentially halted by metal complexation; addition of a second chemical input that decomplexes the metal from the aziridine restores fast inversion (k = 40 s–1 at 303 K).

A novel anthracene-tagged oligonucleotide can discriminate between a fully-matched DNA target sequence and one with a single mismatching base-pair through a remarkable difference in fluorescence emission intensity upon duplex formation.

Ferrocene-containing amidopyridine receptors bind carboxylic acids and the amino acid phenylalanine in acetonitrile via a novel proton transfer process that enables guests to be electrochemically sensed by positive shifts in the ferrocene-centred redox potentials.

A new series of chiral ureas containing one or two redox-active ferrocene units was synthesised and studied in order to investigate the effect of planar chirality and central chirality on electrochemical chiral sensing. Binding of chiral carboxylate anions in organic solvents through H-bond formation caused a negative shift in the potentials of the ferrocene/ferrocenium (Fc/Fc+) couples of the receptors, demonstrating their use as electrochemical sensors in solution. While the presence of two ferrocene units gave no marked improvement in the chiral sensing capabilities of these systems, the introduction of planar chirality, in addition to central chirality, switched the enantiomeric binding preference of the system and also caused an interesting change in the appearance of some voltammograms, with unusual two-wave behaviour observed upon binding a protected prolinate guest.

The design, synthesis and electrochemical behaviour of an oligomer consisting of linked thymine-functionalised ferrocene units are reported, which, as a so-called form of ferrocene nucleic acid (FcNA), acts as a structural mimic of DNA.

A fluorescent DNA probe containing an anthracene group attached via an anucleosidic linker can identify all four DNA bases at a single site as well as the epigenetic modification C/5-MeCvia a hybridisation sensing assay.

The molecular motion associated with atomic inversion at an aziridine nitrogen can be essentially halted by metal complexation; addition of a second chemical input that decomplexes the metal from the aziridine restores fast inversion (k = 40 s–1 at 303 K).

A novel organometallic receptor binds anions in solution and in the solid state, with complexes stabilised through a series of C–H⋯X interactions, as evidenced by 1H NMR spectroscopy, X-ray crystallography and computational models.

Rates of pyramidal motion in an aziridine are controlled by reversible trans to cis photoisomerisation of an azobenzene unit attached to the ring nitrogen atom. The dynamics of the inversion process and activation parameters are derived by variable temperature NMR, and are supported by ab initio calculations.

A [2]rotaxane, whose thread component comprises a central dibenzylammonium group and 9-alkoxyanthracene stoppers and is hosted by a 24-dibenzo-8-crown bead, undergoes an efficient photocatenation step resulting in a [2]rotaxane-to-[2]catenane topology interconversion via a fully reversible [4π+4π] photocyclomerization of terminal anthracene groups.

A method for probing the strength of B–N dative bonds is reported. The activation parameters for nitrogen inversion in a series of azetidines tethered to boronate esters have been quantified by VT-NMR and the measured barriers correlated with data obtained by 11B NMR, X-ray crystallography and MP2 calculations.