Excited-State Dynamics of Thienoguanosine,an Isomorphic Highly Fluorescent Analogue of Guanosine

Thienoguanosine (^thG) is an isomorphic analogue of guanosine with promising potentialities as fluorescent DNA label. As a free probe in protic solvents, ^thG exists in two tautomeric forms, identified as the H1, being the only one observed in nonprotic solvents, and H3 keto–amino tautomers. We herein investigate the photophysics of ^thG in solvents of different polarity, from water to dioxane, by combining time-resolved fluorescence with PCM/TD-DFT and CASSCF calculations. Fluorescence lifetimes of 14.5–20.5 and 7–13 ns were observed for the H1 and H3 tautomers, respectively, in the tested solvents. In methanol and ethanol, an additional fluorescent decay lifetime (≈3 ns) at the blue emission side (λ≈430 nm) as well as a 0.5 ns component with negative amplitude at the red edge of the spectrum, typical of an excited-state reaction, were observed. Our computational analysis explains the solvent effects observed on the tautomeric equilibrium. The main radiative and nonradiative deactivation routes have been mapped by PCM/TD-DFT calculations in solution and CASSCF in the gas phase. The most easily accessible conical intersection, involving an out-of plane motion of the sulfur atom in the five-membered ring of ^thG, is separated by a sizeable energy barrier (≥0.4 eV) from the minimum of the spectroscopic state, which explains the large experimental fluorescence quantum yield.     

Determination of Anti-Parkinson Drug Pramipexole Using a Label-free Biosensor and Evaluation of its Interaction with ds-DNA

In this study, we fabricated an effective and sensitive DNA biosensor based on flower-like Pt/NiCo₂O₄ modified carbon paste electrode (FL-Pt/NiCo₂O₄/CPE) for detection of pramipexole (PPX). Spectrophotometry, differential pulse voltammetry (DPV) and docking methods were employed to evaluate the interaction of DNA-PPX. Moreover, the DPV technique was chosen to monitor the electrochemical response of guanine on the DNA biosensor. The relationship between the concentration of PPX and the oxidation signal of guanine was linear in the range of 0.4 to 310.0 μM and a limit of detection (LOD) of 0.09 μM was calculated.     

Biomolecular Release Stimulated by Electrochemical Signals at a Very Small Potential Applied

DNA release electrochemically stimulated by applying ?10 mV on the modified electrode was studied. The release process was based on the local (interfacial) pH change produced upon H₂O₂ reduction electrocatalyzed by the immobilized microperoxidase‐11. SiO₂ nanoparticles attached to the electrode surface and functionalized with trigonelline and boronic acid species changed their electrical charge from positive to negative upon the interfacial pH change, thus allowing electrostatic adsorption of negatively charged DNA on the positive interface and then its repulsion/release from the negative interface. The loaded/released DNA molecules were labeled with a fluorescent dye to allow easy detection of the released DNA molecules. The important feature of the developed system is the controlled DNA release upon applying very small electrical potential on the modified electrode.     

NMR studies on 4‐thio‐5‐furan‐modified and 4‐thio‐5‐thiophene‐modified nucleosides

Systematic NMR characterization of 4‐thio‐5‐furan‐pyrimidine nucleosides or 4‐thio‐5‐thiophene‐pyrimidine nucleosides (ribonucleosides and 2′‐deoxynucleosides) was performed. All proton and carbon signals of 4‐thio‐5‐thiophene‐ribouridine and related analogues were unambiguously assigned. The orientations of the base (4‐thiouridine or its deoxy analogue) relative to the ring (furan or thiophene) are explored by a NMR approach and further supported by X‐ray crystallographic studies. The procedures presented here would be applicable to other modified nucleosides and nucleotides. Copyright © 2016 John Wiley & Sons, Ltd.     

A novel chaotic image encryption scheme using DNA sequence operations

In this paper, we propose a novel image encryption scheme based on DNA (Deoxyribonucleic acid) sequence operations and chaotic system. Firstly, we perform bitwise exclusive OR operation on the pixels of the plain image using the pseudorandom sequences produced by the spatiotemporal chaos system, i.e., CML (coupled map lattice). Secondly, a DNA matrix is obtained by encoding the confused image using a kind of DNA encoding rule. Then we generate the new initial conditions of the CML according to this DNA matrix and the previous initial conditions, which can make the encryption result closely depend on every pixel of the plain image. Thirdly, the rows and columns of the DNA matrix are permuted. Then, the permuted DNA matrix is confused once again. At last, after decoding the confused DNA matrix using a kind of DNA decoding rule, we obtain the ciphered image. Experimental results and theoretical analysis show that the scheme is able to resist various attacks, so it has extraordinarily high security.     

Molecular dynamics simulation of DNA‐directed assembly of nanoparticle superlattices using patterned templates

DNA‐directed assembly is a well developed approach in constructing desired nano‐architectures. On the other hand, E‐beam lithography is widely utilized for high resolution nano‐scale patterning. Recently, a new technique combining these two methods was developed to epitaxially grow DNA‐mediated nanoparticle superlattices on patterned substrates. However, defects are observed in epitaxial layers which restricts this technique from building large‐scale superlattices for real applications. Here we use molecular dynamics simulations to study and predict defect formation on adsorbed superlattice monolayers. We demonstrate that this epitaxial growth is energetically driven by maximizing DNA hybridization between the epitaxial layer and the substrate and that the shape anisotropy of the DNA‐mediated template posts leads to structural defects. We also develop design rules to dramatically reduce defects on epitaxial layers. Ultimately, with the assist of the computational study, this technique will open the door to constructing well‐ordered, three‐dimensional novel nanomaterials. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016 , 54, 1687–1692     

Amorphous Aggregation of Amyloid Beta 1‐40 Peptide in Confined Space

The amorphous aggregation of Aβ1‐40 peptide is addressed by using micromolding in capillaries. Both the morphology and the size of the aggregates are modulated by changing the contact angle of the sub‐micrometric channel walls. Upon decreasing the hydrophilicity of the channels, the aggregates change their morphology from small aligned drops to discontinuous lines, thereby keeping their amorphous structure. Aβ1‐40 fibrils are observed at high contact angles.     

Dinuclear Ruthenium(II) Complexes That Induce and Stabilise G‐Quadruplex DNA

A series of dinuclear ruthenium(II) complexes were synthesised, and the complexes were determined to be new highly selective compounds for binding to telomeric G‐quadruplex DNA. The interactions of these complexes with telomeric G‐quadruplex DNA were studied by using circular dichroism (CD) spectroscopy, fluorescence resonance energy transfer (FRET) melting assays, isothermal titration calorimetry (ITC) and molecular modelling. The results showed that the complexes 1 , 2 and 4 induced and stabilised the formation of antiparallel G‐quadruplexes of telomeric DNA in the absence of salt or in the presence of 100 mM K⁺‐containing buffer. Furthermore, complexes 1 and 2 strongly bind to and effectively stabilise the telomeric G‐quadruplex structure and have significant selectivity for G‐quadruplex over duplex DNA. In comparison, complex 3 had a much lesser effect on the G‐quadruplex, suggesting that possession of a suitably sized plane for good π–π stacking with the G‐quadruplets is essential for the interaction of the dinuclear ruthenium(II) complexes with the G‐quadruplex. Moreover, telomerase inhibition by the four complexes and their cellular effects were studied, and complex 1 was determined to be the most promising inhibitor of both telomerase and HeLa cell proliferation.     

Solvent‐free Liquid Crystals and Liquids from DNA

As DNA exhibits persistent structures with dimensions that exceed the range of their intermolecular forces, solid‐state DNA undergoes thermal degradation at elevated temperatures. Therefore, the realization of solvent‐free DNA fluids, including liquid crystals and liquids, still remains a significant challenge. To address this intriguing issue, we demonstrate that combining DNA with suitable cationic surfactants, followed by dehydration, can be a simple generic scheme for producing these solvent‐free DNA fluid systems. In the anhydrous smectic liquid crystalline phase, DNA sublayers are intercalated between aliphatic hydrocarbon sublayers. The lengths of the DNA and surfactant are found to be extremely important in tuning the physical properties of the fluids. Stable liquid‐crystalline and liquid phases are obtained in the ?20 °C to 200 °C temperature range without thermal degradation of the DNA. Thus, a new type of DNA‐based soft biomaterial has been achieved, which will promote the study and application of DNA in a much broader context.     

High‐Energy Long‐Lived Mixed Frenkel–Charge‐Transfer Excitons: From Double Stranded (AT)n to Natural DNA

The electronic excited states populated upon absorption of UV photons by DNA are extensively studied in relation to the UV‐induced damage to the genetic code. Here, we report a new unexpected relaxation pathway in adenine–thymine double‐stranded structures (AT)_n. Fluorescence measurements on (AT)_n hairpins (six and ten base pairs) and duplexes (20 and 2000 base pairs) reveal the existence of an emission band peaking at approximately 320 nm and decaying on the nanosecond time scale. Time‐dependent (TD)‐DFT calculations, performed for two base pairs and exploring various relaxation pathways, allow the assignment of this emission band to excited states resulting from mixing between Frenkel excitons and adenine‐to‐thymine charge‐transfer states. Emission from such high‐energy long‐lived mixed (HELM) states is in agreement with their fluorescence anisotropy (0.03), which is lower than that expected for π–π* states (≥0.1). An increase in the size of the system quenches π–π* fluorescence while enhancing HELM fluorescence. The latter process varies linearly with the hypochromism of the absorption spectra, both depending on the coupling between π–π* and charge‐transfer states. Subsequently, we identify the common features between the HELM states of (AT)_n structures with those reported previously for alternating (GC)_n: high emission energy, low fluorescence anisotropy, nanosecond lifetimes, and sensitivity to conformational disorder. These features are also detected for calf thymus DNA in which HELM states could evolve toward reactive π–π* states, giving rise to delayed fluorescence.