Electron transfer of plurimodified DNA SAMs

A Dual Therapeutic System Based on Corrole-siRNA Conjugates

Corrole molecules are a new generation of photosensitizers (PS) due to their ease of tunability for different medical applications. Their ability to initiate cellular death using a wide range of...

Assembly, structure and thermoelectric properties of 1,1′-dialkynylferrocene ‘hinges’

Dialkynylferrocenes exhibit attractive electronic and rotational features that make them ideal candidates for use in molecular electronic applications. However previous works have primarily focussed on single-molecule studies, with limited opportunities to translate these features into devices. In this report, we utilise a variety of techniques to examine both the geometric and electronic structure of a range of 1,1′-dialkynylferrocene molecules, as either single-molecules, or as self-assembled monolayers. Previous single molecule studies have shown that similar molecules can adopt an ‘open’ conformation. However, in this work, DFT calculations, STM-BJ experiments and AFM imaging reveal that these molecules prefer to occupy a ‘hairpin’ conformation, where both alkynes point towards the metal surface. Interestingly we find that only one of the terminal anchor groups binds to the surface, though both the presence and nature of the second alkyne affect the thermoelectric properties of these systems. First, the secondary alkyne acts to affect the position of the frontier molecular orbitals, leading to increases in the Seebeck coefficient. Secondly, theoretical calculations suggested that rotating the secondary alkyne away from the surface acts to modulate thermoelectric properties. This work represents the first of its kind to examine the assembly of dialkynylferrocenes, providing valuable information about both their structure and electronic properties, as well as unveiling new ways in which both of these properties can be controlled.

Dialkynylferrocenes are interesting candidates for molecular electronics. Herein, numerous experiments are applied to probe their properties both as single-molecules and in monolayers, demonstrating unique geometric and thermoelectric properties.

Multi-Component Self-Assembled Molecular-Electronic Films: Towards New High-Performance Thermoelectric Systems

The thermoelectric properties of parallel arrays of organic molecules on a surface offer the potential for large-area, flexible, solution processed, energy harvesting thin-films, whose room-temperature transport properties are controlled by quantum interference (QI). Recently, it has been demonstrated that constructive QI (CQI) can be translated from single molecules to self-assembled monolayers (SAMs), boosting both electrical conductivities and Seebeck coefficients. However, these CQI-enhanced systems are limited by rigid coupling of the component molecules to metallic electrodes, preventing the introduction of additional layers which would be advantageous for their further development. These rigid couplings also limit our ability to suppress the transport of phonons through these systems, which could act to boost their thermoelectric output, without comprising on their impressive electronic features. Here, through a combined experimental and theoretical study, we show that cross-plane thermoelectricity in SAMs can be enhanced by incorporating extra molecular layers. We utilize a bottom-up approach to assemble multi-component thin-films that combine a rigid, highly conductive ‘sticky’-linker, formed from alkynyl-functionalised anthracenes, and a ‘slippery’-linker consisting of a functionalized metalloporphyrin. Starting from an anthracene-based SAM, we demonstrate that subsequent addition of either a porphyrin layer or a graphene layer increases the Seebeck coefficient, and addition of both porphyrin and graphene leads to a further boost in their Seebeck coefficients. This demonstration of Seebeck-enhanced multi-component SAMs is the first of its kind and presents a new strategy towards the design of thin-film thermoelectric materials.

Through an experimental and theoretical study, cross-plane thermoelectricity in Self-Assembled Monolayers (SAMs) was enhanced by adding extra molecular layers, presenting a new strategy towards the design of high thermoelectric materials.

Changes of C≡C Triple Bond Vibration that Disclosed Non-Canonical Cytosine Protonation in i-Motif-Forming Oligodeoxynucleotides

Non-canonical protonation at cytosine (C) in DNA is related to a formation of second order DNA structures such as i-motif, which has a role in gene regulation. Although the detailed structural information is indispensable for comprehension of their functions in cells, the protonation status of C in complicated environments is still elusive. To provide a reporter system of non-canonical protonation, we focused on the molecular vibration that could be monitored using the Raman spectroscopy. We prepared a cytosine derivative (^PC) with an acetylene unit as a Raman tag, and found that the Raman signal of acetylene in ^PC in oligodeoxynucleotides (ODNs) changed due to protonation at the cytosine ring which shortened an acetylene bond. The signal change in i-motif-forming ODNs was also observed in crowded environments with polyethylene glycol, evidencing protonation in i-motif DNA in complicated environments. This system would be one of tracking tools for protonation in DNA structures.

Nucleic Acid Conformation Influences Postsynthetic Suzuki-Miyaura Labeling of Oligonucleotides

Chemoselective transformations that work under physiological conditions have emerged as powerful tools to label nucleic acids in cell-free and cellular environments. However, detailed studies investigating the influence of nucleic acid conformation on the performance of such chemoselective nucleic labeling methods are less explored. Given that nucleic acids adopt complex structures, it is highly important to study the scope of the chemical modification method in the context of nucleic acid conformations. Here we report a systematic study on the effect of local conformation on the postsynthetic Suzuki-Miyaura functionalization of human telomeric (H-Telo) DNA repeat oligonucleotide (ON) sequences, which form multiple G-quadruplex (GQ) structures. 5-Iodo-2'-deoxyuridine (IdU)-modified H-Telo ONs were synthesized by the solid-phase method, and when subjected to Suzuki-Miyaura cross-coupling reaction, its efficiency was found to depend on the type of conformation and the position of IdU label in different loops of the GQ structure. IdU-labeled GQs gave better yields as compared to single-stranded random coil structures. However, the IdU-labeled duplex under different ionic conditions did not undergo the coupling reaction. Further, using this method, we directly installed an environment-sensitive fluorescent probe, which photophysically reported the formation as well as distinguished different GQ topologies of telomeric repeat. Collectively, this systematic study underscores the influence of nucleic acid conformation, which has to be taken into account when establishing postsynthetic chemoselective functionalization strategies.

Non-enzymatic DNA cleavage reaction induced by 5-ethynyluracil in methylamine aqueous solution and application to DNA concatenation

DNA can be concatenated by hybridization of DNA fragments with protruding single-stranded termini. DNA cleavage occurring at a nucleotide containing a DNA base analogue is a useful method to obtain DNA with designed protruding termini. Here, we report a novel non-enzymatic DNA cleavage reaction for DNA concatenation. We found that DNA is cleaved at a nucleotide containing 5-ethynyluracil in a methylamine aqueous solution to generate 5′-phosphorylated DNA fragment as a cleavage product. We demonstrated that the reaction can be applied to DNA concatenation of PCR-amplified DNA fragments. This novel non-enzymatic DNA cleavage reaction is a simple practical approach for DNA concatenation.

Diamondoid-modified DNA

We prepared novel C5-modified triphosphates and phosphoramidites with a diamondoid functionally linked to the nucleobase. Using primer extension experiments with different length templates we investigated whether the modified triphosphates were enzymatically incorporated into DNA and whether they were further extended. We found that all three modified nucleotides can be incorporated into DNA using a single-nucleotide incorporation experiment, but only partially using two templates that demand for multiple incorporation of the modified nucleotides. The modified phosphoramidites were introduced into oligonucleotides utilizing DNA synthesizer technology. The occurring oligonucleotide structures were examined by circular dichroism (CD) and melting temperature (T(m)) measurements and were found to adapt similar helix conformations as their unmodified counterparts.

Au-Ag template stripped pattern for scanning probe investigations of DNA arrays produced by dip pen nanolithography

We report on DNA arrays produced by dip pen nanolithography (DPN) on a novel Au-Ag micropatterned template stripped surface. DNA arrays have been investigated by atomic force microscopy (AFM) and scanning tunneling microscopy (STM) showing that the patterned template stripped substrate enables easy retrieval of the DPN-functionalized zone with a standard optical microscope permitting multi-instrument and multitechnique local detection and analysis. Moreover the smooth surface of the Au squares ( approximately 5-10 A roughness) allows AFM/STM to be sensitive to the hybridization of the oligonucleotide array with label-free target DNA. Our Au-Ag substrates, combining the retrieving capabilities of the patterned surface with the smoothness of the template stripped technique, are candidates for the investigation of DPN nanostructures and for the development of label-free detection methods for DNA nanoarrays based on the use of scanning probes.