DNA-templated assembly of nanoscale wires and protein-functionalized nanogap contacts

The use of DNA to template the assembly of nanoscale wires and protein-functionalized nanogap contacts is described: Specifically, the use of DNA to template the assembly of gold nanowires between conventionally patterned gold contacts on a silicon wafer substrate. Also described is the use of DNA to template the assembly of protein-functionalized nanogap gold contacts on a silicon wafer substrate. Of particular significance is the finding that suitably modified gold nanoparticles recognize and bind selectively the protein-functionalized nanogap and are localized there.     

Role of sphingomyelin-MAPKs pathway in heat-induced apoptosis

The role of sphingomyelinase (SMase) activation and mitogen activated protein kinases (MAPKs) activation in cellular apoptosis was investigated during the hyperthermic treatment of HL-60 human leukemia cells. Treating the cells for 1 h at 43(o)C caused more than 50% of cellular apoptosis within several hours. The neutral-SMase activity in the cells treated for 1 h at 42(o)C was slightly increased but decreased in the cells treated at 43(o)C or 44(o)C for the same period whereas the acid SMase activity was slightly increased after heating the cells at 42(o)C and 43(o)C and markedly increased at 44(o)C for 1 h. Treatment of cells with inhibitors of SMase activation and ceramide formation significantly reduced the heat-induced apoptosis. Three major families of mitogen-activated protein kinases (MAPKs), i.e. ERK1/2, p38 and JNK, were activated by the hyperthermic treatment of cells. Inhibition of ERK1/2 with PD98059 exerted little effect on the heat-induced apoptosis and p38 inhibition with SB203580 slightly lessened apoptosis whereas, inhibition of JNK with SP600125 markedly suppressed the heat-induced apoptosis. These results indicate that heat-shock induced the activation of SMase, particularly acid-SMase, thereby causing apoptosis and that JNK played a pivotal role in heat-induced apoptosis in HL-60 leukemia cells.     

DNA sequencing

Determination of the sequence of DNA is one of the most important aspects of modern molecular biology. New sequencing methods currently being developed enable DNA sequence to be determined increasingly faster and more efficiently. One of the major advances in sequencing technology is the development of automated DNA sequencers. These utilize fluorescent rather than radioactive labels. A laser beam excites the fluorescent dyes, the emitted fluorescence is collected by detectors, and the information analyzed by computer. Robotic work stations are being developed to perform template preparation and purification, and the sequencing reactions themselves. Research is currently in progress to develop the technology of mass spectrometry for DNA sequencing. Success in this endeavor would mean that the gel electrophoresis step in DNA sequencing could be eliminated. A major innovation has been the application of polymerase chain reaction (PCR) technology to DNA sequence determination, which has led to the development of linear amplification sequencing (cycle sequencing). This very powerful yet technically simple method of sequencing has many advantages over conventional techniques, and may be used in manual or automated methods. Other recent innovations proposed recently to increase speed and efficiency include multiplex sequencing. This consists of pooling a number of samples and processing them as pools. After electrophoresis, the DNA is transferred to a membrane, and sequence images of the individual samples are obtained by sequential hybridizations with specific labeled oligonucleotides. Multiplex DNA sequencing has been used in conjunction with direct blotting electrophoresis to facilitate transfer of the DNA to a membrane. Chemiluminescent detection can also be used in conjunction with multiplex DNA sequencing to visualize the image on the membrane.     

Quinolinone and pyridopyrimidinone inhibitors of DNA-dependent protein kinase

8-Substituted 2-morpholin-4-yl-quinolin-4-ones and 9-substituted 2-morpholin-4-yl-pyrido[1,2-a]pyrimidin-4-ones with selected aryl and heteroaryl groups as the substituent have been synthesised as potential inhibitors of DNA-dependent protein kinase. A multiple-parallel approach, employing Suzuki cross-coupling methodology, was utilised in the preparation of 8-substituted 2-morpholin-4-yl-quinolin-4-ones. For this purpose 8-bromo-2-morpholin-4-yl-quinolin-4-one was required as an intermediate. This compound was obtained by adapting a literature route in which thermal cyclocondensation of (2-bromoanilino)-morpholin-4-yl-5-methylene-2,2-dimethyl[1,3]dioxane-4,6-dione afforded 8-bromo-2-morpholin-4-yl-quinolin-4-one. A multiple-parallel approach, employing Suzuki cross-coupling methodology, was also utilised to prepare 9-substituted 2-morpholin-4-yl-pyrido[1,2-a]pyrimidin-4-ones using 9-hydroxy-2-morpholin-4-yl-pyrido[1,2-a]pyrimidin-4-one O-trifluoromethanesulfonate as an intermediate. 8-Substituted 2-morpholin-4-yl-quinolin-4-ones and 9-substituted 2-morpholin-4-yl-pyrido[1,2-a]pyrimidin-4-ones were both inhibitors of DNA-dependent protein kinase. When the substituent was dibenzothiophen-4-yl, dibenzofuran-4-yl or biphen-3-yl, IC50 values in the low nanomolar range were observed. Interestingly, the pyridopyrimidinones and quinolinones were essentially equipotent with the corresponding 8-substituted 2-morpholin-4-yl-chromen-4-ones previously reported (I. R. Hardcastle, X. Cockcroft, N. J. Curtin, M. Desage El-Murr, J. J. J. Leahy, M. Stockley, B. T. Golding, L. Rigoreau, C. Richardson, G. C. M. Smith and R. J. Griffin, J. Med. Chem., 2005, 48, 7829-7846).     

Spin‐State Ordering on One Sub‐lattice of a Mononuclear Iron(III) Spin Crossover Complex Exhibiting LIESST and TIESST

The two‐step spin crossover in mononuclear iron(III) complex [Fe(salpm)₂]ClO₄ ? 0.5 EtOH ( 1 ) is shown to be accompanied by a structural phase transition as concluded from ⁵⁷Fe Mössbauer spectroscopy and single crystal X‐ray diffraction, with spin‐state ordering on just one of two sub‐lattices in the intermediate magnetic and structural phase. The complex also exhibits thermal‐ and light‐induced spin‐state trapping (TIESST and LIESST), and relaxation from the LIESST and TIESST excited states occurs via the broken symmetry intermediate phase. Two relaxation events are evident in both experiments, that is, two T(LIESST) and two T(TIESST) values are recorded. The change in symmetry which accompanies the TIESST effect was followed in real time using single crystal diffraction. After flash freezing at 15 K the crystal was warmed to 40 K at which temperature superstructure reflections were observed to appear and disappear within a 10 000 s time range. In the frame of the international year of crystallography, these results illustrate how X‐ray diffraction makes it possible to understand complex ordering phenomena.     

Metabolic profiling of rodent biological fluids via 1H NMR spectroscopy using a 1 mm microlitre probe

The application of a 1 mm TXI (1H/13C/15N) microlitre NMR probe with z-gradient for metabolic profiling of biofluids is described. The probe was used to provide spectral profiles for rat blood plasma using only approximately 2 microl of fluid with a range of solvent suppression techniques. Using a similar amount of fluid, spectra were obtained from rat and mouse cerebrospinal fluid, demonstrating that the probe could be used to profile rodents metabolically via biofluids previously inaccessible to NMR analysis without the need for termination.     

Soft-triple resonance solid-state NMR experiments for assignments of U-13C, 15N labeled peptides and proteins

The process of obtaining sequential resonance assignments for heterogeneous polypeptides and large proteins by solid-state NMR (ssNMR) is impeded by extensive spectral degeneracy in these systems. Even in these challenging cases, the cross peaks are not distributed uniformly over the entire spectral width. Instead, there exist both well-resolved single resonances and distinct groups of resonances well separated from the most crowded region of the spectrum. Here, we present a series of new triple resonance experiments that exploit the non-uniform clustering of resonances in heteronuclear correlation spectra to obtain additional resolution in the more crowded regions of a spectrum. Homonuclear and heteronuclear dipolar recoupling sequences are arranged to achieve directional transfer of coherence between neighboring residues in the peptide sequence. A frequency-selective (soft) pulse is applied to select initial polarization from a limited (and potentially) well-resolved region of the spectrum. The pre-existing resolution of one or more spins is thus utilized to obtain additional resolution in the more crowded regions of the spectrum. A new protocol to utilize these experiments for sequential resonance assignments in peptides and proteins is also demonstrated.