Diamond Quantum Devices in Biology

The currently available techniques for molecular imaging capable of reaching atomic resolution are limited to low temperatures, vacuum conditions, or large amounts of sample. Quantum sensors based on the spin‐dependent photoluminescence of nitrogen‐vacancy (NV) centers in diamond offer great potential to achieve single‐molecule detection with atomic resolution under ambient conditions. Diamond nanoparticles could also be prepared with implanted NV centers, thereby generating unique nanosensors that are able to traffic into living biological systems. Therefore, this technique might provide unprecedented access and insight into the structure and function of individual biomolecules under physiological conditions as well as observation of biological processes down to the quantum level with atomic resolution. The theory of diamond quantum sensors and the current developments from their preparation to sensing techniques have been critically discussed in this Minireview.     

Methylene-azaphosphirane as a reactive intermediate

Reaction of the transient phosphinidene complexes R-P=W(CO)5 with N-substituted-diphenylketenimines leads unexpectedly to the novel 2-aminophosphindoles, as confirmed by an X-ray crystal structure determined for one of the derivatives. Experimental evidence for a methylene-azaphosphirane intermediate was found by using the iron-complexed phosphinidene iPr2N-P=Fe(CO)4, which affords the 2-aminophosphindole together with the novel methylene-2,3-dihydro-1H-benzo[1,3]azaphosphole. Analysis of the reaction pathways with DFT indicates that the initially formed methylene-azaphosphirane yields both phosphorus heterocycles by way of a [1,5]- or [1,3]-sigmatropic shift, respectively, followed by a H-shift. Strain underlies both rearrangements, which causes these remarkably selective conversions that can be tuned by changing the substituents.     

Characterization of the monovalent ion position and hydrogen-bond network in guanine quartets by DFT calculations of NMR parameters

Conformational stability of G-quartets found in telomeric DNA quadruplex structures requires the coordination of monovalent ions. Here, an extensive Hartree-Fock and density functional theory analysis of the energetically favored position of Li+, Na+, and K+ ions is presented. The calculations show that at quartet-quartet distances observed in DNA quadruplex structures (3.3 A), the Li+ and Na+ ions favor positions of 0.55 and 0.95 A outside the plane of the G-quartet, respectively. The larger K+ ion prefers a central position between successive G-quartets. The energy barrier separating the minima in the quartet-ion-quartet model are much smaller for the Li+ and Na+ ions compared with the K+ ion; this suggests that K+ ions will not move as freely through the central channel of the DNA quadruplex. Spin-spin coupling constants and isotropic chemical shifts in G-quartets extracted from crystal structures of K+- and Na+-coordinated DNA quadruplexes were calculated with B3LYP/6-311G(d). The results show that the sizes of the trans-hydrogen-bond couplings are influenced primarily by the hydrogen bond geometry and only slightly by the presence of the ion. The calculations show that the R(N2N7) distance of the N2-H2...N7 hydrogen bond is characterized by strong correlations to both the chemical shifts of the donor group atoms and the (h2)J(N2N7) couplings. In contrast, weaker correlations between the (h3)J(N1C6') couplings and single geometric factors related to the N1-H1...O6=C6 hydrogen bond are observed. As such, deriving geometric information on the hydrogen bond through the use of trans-hydrogen-bond couplings and chemical shifts is more complex for the N1-H1...O6=C6 hydrogen bond than for the N2-H2...N7 moiety. The computed trans-hydrogen-bond couplings are shown to correlate with the experimentally determined couplings. However, the experimental values do not show such strong geometric dependencies.     

Strategies for "wiring" redox-active proteins to electrodes and applications in biosensors, biofuel cells, and nanotechnology

In this tutorial review the basic approaches to establish electrochemical communication between redox-active proteins and electrodes are elucidated and examples for applications in electrochemical biosensors, biofuel cells and nanotechnology are presented. The early stage of protein electrochemistry is described giving a short overview over electron transfer (ET) between electrodes and proteins, followed by a brief introduction into experimental procedures for studying proteins at electrodes and possible applications arising thereof. The article starts with discussing the electrochemistry of cytochrome c, the first redox-active protein, for which direct reversible ET was obtained, under diffusion controlled conditions and after adsorption to electrodes. Next, examples for the electrochemical study of redox enzymes adsorbed on electrodes and modes of immobilization are discussed. Shortly the experimental approach for investigating redox-active proteins adsorbed on electrodes is outlined. Possible applications of redox enzymes in electrochemical biosensors and biofuel cells working by direct ET (DET) and mediated ET (MET) are presented. Furthermore, the reconstitution of redox active proteins at electrodes using molecular wire-like units in order to "wire" the proteins to the electrode surface and possible applications in nanotechnology are discussed.     

A contribution to pharmaceutical biology of freshwater sponges

In vitro anti-tumour and anti-radical activities of the acetone extract of the freshwater sponge Ochridaspongia rotunda were the subject of this study. The extract was found to be highly cytotoxic to human lung tumour cell line A-549 reaching IC₅₀ value of 5.01 ± 0.21 μg/mL. Indeed, it displayed only 2-fold less anti-tumour activity than doxorubicin (IC₅₀ value 2.42 ± 0.13 μg/mL) used as a positive control. The same extract was also found to be almost 37-fold more selective against A-549 vs. MRC-5 (normal) lung cells, in difference to weak selectivity of doxorubicin (less than 3-fold). Its profound anti-DPPH radical activity comparable to that of quercetin (IC₅₀ values 3.68 ± 0.19 and 3.14 ± 0.09 μg/mL, respectively) coupled with no signs of genotoxicity in the comet assay (MRC-5 cell line, vs. doxorubicin) has actually implicated the importance of this animal bioresource in searching for pharmaceutically useful bioactive compounds of natural origin.     

Fabrication of Defined Polydopamine Nanostructures by DNA Origami‐Templated Polymerization

A versatile, bottom‐up approach allows the controlled fabrication of polydopamine (PD) nanostructures on DNA origami. PD is a biosynthetic polymer that has been investigated as an adhesive and promising surface coating material. However, the control of dopamine polymerization is challenged by the multistage‐mediated reaction mechanism and diverse chemical structures in PD. DNA origami decorated with multiple horseradish peroxidase‐mimicking DNAzyme motifs was used to control the shape and size of PD formation with nanometer resolution. These fabricated PD nanostructures can serve as “supramolecular glue” for controlling DNA origami conformations. Facile liberation of the PD nanostructures from the DNA origami templates has been achieved in acidic medium. This presented DNA origami‐controlled polymerization of a highly crosslinked polymer provides a unique access towards anisotropic PD architectures with distinct shapes that were retained even in the absence of the DNA origami template.     

Antibunching in the emission of a single tetrachromophoric dendritic system

The photophysics of a dendrimer containing four chromophores are investigated at the single-molecule level. First, the multichromophoric character of single dendrimers' absorption is probed by modulating the linear polarization of the excitation beam. Subsequently, using circular polarization, the same dendrimers are excited, and their fluorescence transients are recorded. Using pulsed excitation in combination with the classical Hanbury-Brown and Twiss coincidence setup the presented data demonstrate that efficient singlet-singlet annihilation ensures that always only one photon is emitted even when several excitations are generated in an individual multichromophoric molecule.     

Viscoelastic shear properties of in vivo breast lesions measured by MR elastography

Elastography is a technique to assess the viscoelastic properties of tissue by measuring an acoustic wave propagating though the object. Here, the technique is applied in the course of standard MR mammography to 15 patients with different pathologies (six breast cancer cases, six fibroadenoma cases and three mastopathy cases). Low-frequency mechanical waves are coupled longitudinally into the tissue in order to obtain sufficient wave amplitude throughout the entire breast. This leads to the presence of a substantial fraction of compressional waves, which contribute to the total displacement field. It is shown theoretically that the correct evaluation of these contributions from the compressional wave is rather difficult due to the almost incompressible nature of tissue. To overcome this problem, it is proposed to apply the curl-operator to the measured displacement field in order to completely remove contributions from the compressional wave. Results from simulations and a breast phantom demonstrate the feasibility of the technique. The in vivo results show a good separation between breast cancer and benign fibroadenoma utilizing the shear modulus. Breast cancer appears on average 2.2 (P<.001) times stiffer. All breast cancer cases showed a good delineation to the surrounding breast tissue with an average elevation of a factor of 3.3 (P< 1.4 x 10(-6)). The results as obtained for the shear viscosity do not indicate to be useful for separating benign from malignant lesions.     

Self-poisoning of crystal nuclei in hard-rod liquids

We report a Monte Carlo study of the pathway for crystal nucleation in a fluid of hard, colloidal rods. In the earliest stages of nucleation, a lamellar crystallite forms. Subsequent thickening of this lamella is hampered by the fact that the top and bottom surfaces of this crystallite are preferentially covered by rods that align parallel to the surface. As a consequence, subsequent growth of individual crystals is stunted. Experimental evidence for such stunted crystal growth has recently been reported by Maeda and Maeda in experiments on suspensions of colloidal rods [Phys. Rev. Lett. 90, 018303 (2003)]]. The simulations suggest that, in experiments, the growth of multilayer colloidal crystals can be selectively enhanced by the application of an external aligning field.