•Porphyrin tagged DNA is shown to be a superior electrochemical sensor for DNA detection in microfluidic systems.•DNA sequences associated with bladder cancer were reliably detected within 2 min.•A microchannel device with 20 sensors simultaneously detects different DNA sequences with a detection limit of 250 fM.Bladder cancer (BC) is one of the most difficult cancers to diagnose, and is reportedly the most expensive cancer to treat and monitor due to the lack of accurate chemical sensors; only limited methods are available, which usually are restricted to cytology and cystoscopy. Thus a system is urgently needed to detect biomarkers that give an unambiguous diagnosis on BC, as it currently is among the top five cancers occurring. Here we present a multi-sensor microchip array which efficiently detects three specific bladder cancer DNA markers simultaneously with a detection limit of 250 fM, which is well below the amount of DNA markers found in urine samples. The detection is based on the electrochemical response of a free-base porphyrin marker which is embedded in a molecular beacon; this system can easily be adapted to detect other DNA markers and developed for field applications, including point-of-care diagnostics, and gives an unambiguous readout within 20 min.

Because of their hollow interior, transmembrane channels are capable of opening up pathways for ions across lipid membranes of living cells. Here, we demonstrate ion conduction induced by a single DNA duplex that lacks a hollow central channel. Decorated with six porpyrin-tags, our duplex is designed to span lipid membranes. Combining electrophysiology measurements with all-atom molecular dynamics simulations, we elucidate the microscopic conductance pathway. Ions flow at the DNA–lipid interface as the lipid head groups tilt toward the amphiphilic duplex forming a toroidal pore filled with water and ions. Ionic current traces produced by the DNA-lipid channel show well-defined insertion steps, closures, and gating similar to those observed for traditional protein channels or synthetic pores. Ionic conductances obtained through simulations and experiments are in excellent quantitative agreement. The conductance mechanism realized here with the smallest possible DNA-based ion channel offers a route to design a new class of synthetic ion channels with maximum simplicity.

Porphyrins were attached to LNA uridine building blocks via rigid 5-acetylene or more flexible propargyl-amide linkers and incorporated into DNA strands. The systems show a greatly increased thermodynamic stability when using as little as three porphyrins in a zipper arrangement. Thermodynamic analysis reveals clustering of the strands into more ordered duplexes with both greater negative ΔΔS and ΔΔH values, and less ordered duplexes with small positive ΔΔS differences, depending on the combination of linkers used. The exciton coupling between the porphyrins is dependent on the flanking DNA sequence in the single stranded form, and on the nature of the linker between the nucleobase and the porphyrin in the double stranded form; it is, however, also strongly influenced by intermolecular interactions. This system is suitable for the formation of stable helical chromophore arrays with sequence and structure dependent exciton coupling.

We report the use of Co-porphyrins as electrochemical tags for a highly sensitive and selective genosensor. An avian influenza virus-based DNA sequence characteristic of H5N1 was detected at femtomolar levels from competing non-complementary sequences through hybridisation with the labeled DNA.

EPR spectroscopy was used to investigate both single and double stranded DNA modified with a variable number of copper(II) porphyrins. The spectra of the porphyrin–DNA complexes resemble those of the Cu(II) porphyrin building blocks, but with appreciable differences in the values for the g∥ and A∥ parameters. In addition, a significant half-field signal is observed, which is interpreted as resulting from copper–copper interactions in both the double strand (dsDNA) and the single strand DNA (ssDNA). Analysis of the EPR spectra gives evidence for cluster formation of three or more DNA strands. From the intensity ratio of the half-field and main transition, the average Cu–Cu distance is estimated to be 6.5–8.9 Å. The association of copper centres is consistent with hydrophobic porphyrin stacking, both intra- and intermolecularly, as has previously been observed with other DNA complexes using UV-vis and CD spectroscopy.

Controlled synthesis of nanoparticles with desired geometries can provide a direct approach for the formation of nanomaterials with tuneable size/shape-dependent characteristics, vastly expanding their range of applications in catalysis, electronics and optics, biology and medicine. In this report, we demonstrate the development of a microfluidics-based process for the direct synthesis (without seed-mediated growth) of silver nanoprisms in a continuous flow format using a flow focusing microreactor, coupled with UV-Vis-NIR spectroscopy for real time monitoring of optical properties of the produced nanoprisms. By adjusting microfluidic conditions, the nanomaterial's absorbance spectral position and peak broadness can be fine-tuned. TEM analysis of the produced nanoparticles quantitatively correlates the characteristics of absorbance spectra with the shape/geometry of nanoparticles. Furthermore, faster kinetics for the formation of nanoparticles has been observed in the microreactor compared to those in traditional batch reactors, and the microreactor's capability of synthesising homogenous nanoparticles over a prolonged operation time is demonstrated.

We report the analysis of a novel terpyridine based supramolecular hydrogel which shows fluorescent properties in the gel but not in the sol form; the gel forms in a narrow pH range in aqueous solutions specifically in the presence of sodium ions, and contains between 98% and 99.2% water.

A programmable switch based on a DNA hairpin loop is functionalised with a rigid or flexible porphyrin or FAM and TAMRA FRET pair, which provides insight into the restructuring of the hairpin as well as porphyrin–porphyrin coupling. The switch contains five discrete states which can be accessed independently and followed by real-time spectroscopy, opening the way to a quinary computing code.

Oligonucleotides have recently gained increased attraction as a supramolecular scaffold for the design and synthesis of functional molecules on the nanometre scale. This tutorial review focuses on the recent progress in this highly active field of research with an emphasis on covalent modifications of DNA; non-covalent interactions of DNA with molecules such as groove binders or intercalators are not part of this review. Both terminal and internal modifications are covered, and the various points of attachment (nucleobase, sugar moiety or phosphodiester backbone) are compared. Using selected examples of the recent literature, the diversity of the functionalities that have been incorporated into DNA strands is discussed.

A more flexible nucleotide building block for the synthesis of new DNA based porphyrin–zipper arrays is described. Changing the rigid acetylene linker between the porphyrin substituent and the 2′-deoxyuridine to a more flexible propargyl amide containing linkage leads in part to an increased duplex stability. The CD spectra reveal different electronic interactions between the porphyrins depending on the type of linker used. Molecular modelling suggests large variation of the relative orientation of the porphyrins within the major groove of the DNA. The porphyrins can be metallated post-synthetically with different metals as shown with zinc, cobalt and copper. The spectroscopic features do not alter drastically upon metallation apart from the CD spectra, and the stability of the metal complex is highly dependent on the nature of the metal. As shown by CD spectroscopy, the zinc porphyrin is rapidly demetallated at high temperatures. Globular structure determination using SAXS indicates that a molecular assembly comprised of a two to four helical bundle dominates in solution at higher concentrations (≥50 μM) which is not observed by spectroscopy at lower concentrations (≤1 μM).

The efficiencies of DNA-templated acyl transfer reactions between a thioester modified oligonucleotide and a series of amine and thiol based nucleophiles are directly compared. The reactivity of the nucleophile, reaction conditions (solvent, buffer, pH) and linker length all play important roles in determining the efficiency of the transfer reaction. Careful optimisation of the system enables the use of DNA-templated synthesis to form stable peptide-like bonds under mild aqueous conditions close to neutral pH.

A series of ruthenium(II) and rhodium(III) porphyrin complexes with diphenyl phenylacetylene phosphine (dpap) was synthesised and fully characterised by UV-vis, 1H NMR and 31P{1H} NMR spectroscopy, and in most cases also by single-crystal X-ray diffraction. The substitution pattern of the porphyrin was varied with increasing meso-phenyl substitution, from octa-ethyl porphyrin (OEP), through diphenyl di-ethyl porphyrin (DPP), to tetraphenyl porphyrin (TPP) and 3,5-di-tbutyl tetraphenyl porphyrin (tbTPP). The dpap readily displaces the CO ligand from the parent Ru(CO)(porphyrin) and the iodide from the Rh(I)(porphyrin) to give bis-phosphine complexes M(dpap)2(porphyrin). The UV-vis spectra reveal that some of the complexes are partially dissociated at concentrations of 10−6 M, and the association constants were estimated to be in the range of 106 to 107 M−1 for the first, and 104 to 106 M−1 for the second binding event. The 1H NMR chemical shifts of the complexes vary greatly despite the fact that they display very similar geometries in the solid state, and no correlation could be discerned between the crystal structures and the spectroscopic parameters in solution.

We present a novel nanoparticle building block system based on the interactions between short synthetic oligonucleotides and peptides. Gold nanoparticles coated with DNA-binding peptides can be attached to self-organized oligonucleotide templates to formulate well-ordered structures of nanoparticles. By regulating the amount of DNA-binding peptide attached to the nanoparticle surface and using specifically designed oligonucleotides, the nanoparticle assembly can be controlled to form dimers, trimers, and adjustable-length nanoparticle chains as well as more complex structures.

A diphenyl porphyrin substituted nucleotide was incorporated site specifically into DNA, leading to helical stacked porphyrin arrays in the major groove of the duplexes. The porphyrins show an electronic interaction which is significantly enhanced compared to the analogous tetraphenyl porphyrin (TPP) as shown in the large exciton coupling of the porphyrin B-band absorbance. Analogous to the TPP–DNA, an induced helical secondary structure is observed in the single strand porphyrin–DNA. The modified DNA can be hybridised to an immobilised complementary strand leading to fluorescent beads.

Highly efficient composite films, consisting of silica coated and functionalised silver nanoprisms (SNPs), are presented as a low-cost material to reduce thermal radiation flux with low impact on daylight transmission compared to similar solutions. The SNPs are covalently embedded in a poly(methyl methacrylate) (PMMA) matrix which prevents both leaking of the SNPs and aggregation within the matrix, thus enabling the formation of stable thin films with controllable dispersion. The cast thin films show absorbance in the IR region above 700 nm and a figure of merit of around 1, which is achieved with very thin films and low material consumption.

Porphyrins were attached to LNA uridine building blocks via rigid 5-acetylene or more flexible propargyl-amide linkers and incorporated into DNA strands. The systems show a greatly increased thermodynamic stability when using as little as three porphyrins in a zipper arrangement. Thermodynamic analysis reveals clustering of the strands into more ordered duplexes with both greater negative ΔΔS and ΔΔH values, and less ordered duplexes with small positive ΔΔS differences, depending on the combination of linkers used. The exciton coupling between the porphyrins is dependent on the flanking DNA sequence in the single stranded form, and on the nature of the linker between the nucleobase and the porphyrin in the double stranded form; it is, however, also strongly influenced by intermolecular interactions. This system is suitable for the formation of stable helical chromophore arrays with sequence and structure dependent exciton coupling.

A programmable switch based on a DNA hairpin loop is functionalised with a rigid or flexible porphyrin or FAM and TAMRA FRET pair, which provides insight into the restructuring of the hairpin as well as porphyrin–porphyrin coupling. The switch contains five discrete states which can be accessed independently and followed by real-time spectroscopy, opening the way to a quinary computing code.

A more flexible nucleotide building block for the synthesis of new DNA based porphyrin–zipper arrays is described. Changing the rigid acetylene linker between the porphyrin substituent and the 2′-deoxyuridine to a more flexible propargyl amide containing linkage leads in part to an increased duplex stability. The CD spectra reveal different electronic interactions between the porphyrins depending on the type of linker used. Molecular modelling suggests large variation of the relative orientation of the porphyrins within the major groove of the DNA. The porphyrins can be metallated post-synthetically with different metals as shown with zinc, cobalt and copper. The spectroscopic features do not alter drastically upon metallation apart from the CD spectra, and the stability of the metal complex is highly dependent on the nature of the metal. As shown by CD spectroscopy, the zinc porphyrin is rapidly demetallated at high temperatures. Globular structure determination using SAXS indicates that a molecular assembly comprised of a two to four helical bundle dominates in solution at higher concentrations (≥50 μM) which is not observed by spectroscopy at lower concentrations (≤1 μM).

The efficiencies of DNA-templated acyl transfer reactions between a thioester modified oligonucleotide and a series of amine and thiol based nucleophiles are directly compared. The reactivity of the nucleophile, reaction conditions (solvent, buffer, pH) and linker length all play important roles in determining the efficiency of the transfer reaction. Careful optimisation of the system enables the use of DNA-templated synthesis to form stable peptide-like bonds under mild aqueous conditions close to neutral pH.

A diphenyl porphyrin substituted nucleotide was incorporated site specifically into DNA, leading to helical stacked porphyrin arrays in the major groove of the duplexes. The porphyrins show an electronic interaction which is significantly enhanced compared to the analogous tetraphenyl porphyrin (TPP) as shown in the large exciton coupling of the porphyrin B-band absorbance. Analogous to the TPP–DNA, an induced helical secondary structure is observed in the single strand porphyrin–DNA. The modified DNA can be hybridised to an immobilised complementary strand leading to fluorescent beads.

Oligonucleotides have recently gained increased attraction as a supramolecular scaffold for the design and synthesis of functional molecules on the nanometre scale. This tutorial review focuses on the recent progress in this highly active field of research with an emphasis on covalent modifications of DNA; non-covalent interactions of DNA with molecules such as groove binders or intercalators are not part of this review. Both terminal and internal modifications are covered, and the various points of attachment (nucleobase, sugar moiety or phosphodiester backbone) are compared. Using selected examples of the recent literature, the diversity of the functionalities that have been incorporated into DNA strands is discussed.

We report the use of Co-porphyrins as electrochemical tags for a highly sensitive and selective genosensor. An avian influenza virus-based DNA sequence characteristic of H5N1 was detected at femtomolar levels from competing non-complementary sequences through hybridisation with the labeled DNA.

Controlled synthesis of nanoparticles with desired geometries can provide a direct approach for the formation of nanomaterials with tuneable size/shape-dependent characteristics, vastly expanding their range of applications in catalysis, electronics and optics, biology and medicine. In this report, we demonstrate the development of a microfluidics-based process for the direct synthesis (without seed-mediated growth) of silver nanoprisms in a continuous flow format using a flow focusing microreactor, coupled with UV-Vis-NIR spectroscopy for real time monitoring of optical properties of the produced nanoprisms. By adjusting microfluidic conditions, the nanomaterial's absorbance spectral position and peak broadness can be fine-tuned. TEM analysis of the produced nanoparticles quantitatively correlates the characteristics of absorbance spectra with the shape/geometry of nanoparticles. Furthermore, faster kinetics for the formation of nanoparticles has been observed in the microreactor compared to those in traditional batch reactors, and the microreactor's capability of synthesising homogenous nanoparticles over a prolonged operation time is demonstrated.

We report the analysis of a novel terpyridine based supramolecular hydrogel which shows fluorescent properties in the gel but not in the sol form; the gel forms in a narrow pH range in aqueous solutions specifically in the presence of sodium ions, and contains between 98% and 99.2% water.