Intramolecular Stacking in Ternary Complexes Containing Uridine 5′-Triphosphate, 2,2′-Bipyridyl,and a Divalent Metal Ion

The stability constants of the ternary complexes containing UTP, 2,2′-bipyridyl (bipy), and Co²⁺, Ni²⁺, Cu²⁺, or Zn²⁺ (M²⁺) have been determined by potentiometric titrations (Table 1). Changes in stability are quantified by Δlog K_M = log K–log K. For the Co²⁺, Ni²⁺, Cu²⁺, and Zn²⁺ systems Δlog K_M is 0.10, ?0.13, 0.36, and 0.15, respectively. All these ternary complexes are considerably more stable than would be expected on statistical grounds; indeed, for Co²⁺, Cu²⁺, and Zn²⁺, UTP^4? binds more tightly to M (bipy)²⁺ than to M²⁺. An UV. difference spectroscopic study suggests that stacked adducts between bipyridyl and the pyrimidine moiety of uridine are formed. ¹H-NMR. studies of the bipy/uridine, bipy/UTP, and bipy/UTP/Zn²⁺ systems (Figs. 1 and 2) confirm the presence of stacking in the binary adducts and in the ternary complex. There is also evidence for the existence of the stacked protonated complex, Zn(bipy) (HUTP)^?, with the proton at the γ-phosphate group. The acidity constant of this ternary complex has been measured (Fig. 3). The observed stability enhancement of stacked adducts by the formation of a metal ion bridge is discussed (Fig. 4) and biological implications are indicated.     

Rapid PCR in a continuous flow device

Continuous flow polymerase chain reaction (CFPCR) devices are compact reactors suitable for microfabrication and the rapid amplification of target DNAs. For a given reactor design, the amplification time can be reduced simply by increasing the flow velocity through the isothermal zones of the device; for flow velocities near the design value, the PCR cocktail reaches thermal equilibrium at each zone quickly, so that near ideal temperature profiles can be obtained. However, at high flow velocities there are penalties of an increased pressure drop and a reduced residence time in each temperature zone for the DNA/reagent mixture, that potentially affect amplification efficiency. This study was carried out to evaluate the thermal and biochemical effects of high flow velocities in a spiral, 20 cycle CFPCR device. Finite element analysis (FEA) was used to determine the steady-state temperature distribution along the micro-channel and the temperature of the DNA/reagent mixture in each temperature zone as a function of linear velocity. The critical transition was between the denaturation (95 degrees C) and renaturation (55 degrees C-68 degrees C) zones; above 6 mm s(-1) the fluid in a passively-cooled channel could not be reduced to the desired temperature and the duration of the temperature transition between zones increased with increased velocity. The amplification performance of the CFPCR as a function of linear velocity was assessed using 500 and 997 base pair (bp) fragments from lambda-DNA. Amplifications at velocities ranging from 1 mm s(-1) to 20 mm s(-1) were investigated. The 500 bp fragment could be observed in a total reaction time of 1.7 min (5.2 s cycle(-1)) and the 997 bp fragment could be detected in 3.2 min (9.7 s cycle(-1)). The longer amplification time required for detection of the 997 bp fragment was due to the device being operated at its enzyme kinetic limit (i.e., Taq polymerase deoxynucleotide incorporation rate).     

Modified nucleosides in human serum.

Methylated purines and pyrimidines derived from the degradation of transfer ribonucleic acid have been shown to be excreted in abnormal amounts in the urine of patients with cancer. Recent technology developed by Gehrke and Kuo has allowed the separation and quantification of modified nucleosides in serum using reversed-phase high-performance liquid chromatography with diode-array measurement. Serum levels of ten modified nucleosides were measured in 37 normal healthy adults to establish normal values and to correlate activity with age and sex. In addition, serum levels of patients with several malignancies were measured to determine activity in these diseases. Levels of modified nucleosides in normal individuals were consistently reproducible and showed no significant variation among males versus females or with age. Patients with malignant diseases showed consistent elevations and these were highest in patients with more advanced disease. The evidence of no significant differences in the mean levels of modified nucleosides in serum with age or sex in normal adults and elevations in patients with malignancies demonstrate the potential value of modified nucleosides as cancer biomarkers.     

EXCITATION ENERGY TRANSFER IN THE CRYPTOPHYTES. FLUORESCENCE EXCITATION SPECTRA AND PICOSECOND TIME-RESOLVED EMISSION SPECTRA OF INTACT ALGAE AT 77 K

Excitation spectra of chlorophyll- a (Chl- a ) fluorescence in intact cells of Cryptomonas ovata, Chroomonas pauciplastida and Chroomonas salina were determined at 77 K. For all species the excitation spectra for emission from Chl- a associated with photosystem II (PSII) showed increased contributions by a carotenoid (493 nm) and phycobiliproteins, and decreased contributions by carotenoid (417 nm, 505 nm) and Chl- a (445 nm) as compared to excitation spectra for emission from Chl- a associated with photosystem I (PSI). Excitation spectra of C. salina and C. ovata showed an increased contribution by Chl- c ² to PSII Chl- a fluorescence emission. In all three species the absorbance band positions of Chl- a , as determined from the excitation spectra, were similar to those previously described in green plants. green algae and phycobilisome-containing organisms. Time-resolved 77 K fluorescence emission spectra of C. ovata and C. salina showed successive emission from both phycoerythrin and Chl- c ², PSII Chl- a , and PSI Chl- a. C. pauciplastida showed successive emission from phycocyanin, PSII Chl- a , and PSI Chl- a. Spectral red-shifts with time were observed for the phycobiliprotein peaks in all three species. The fluorescence decay of phycoerythrin in C. ovata and C. salina was faster than that of phycocyanin in C. pauciplastida. The results are discussed in relation to the organization of the antenna pigments of PSII and PSI in the cryptophyte algae.     

Chemoproteomic profiling of kinases in live cells using electrophilic sulfonyl triazole probes

Sulfonyl-triazoles are a new class of electrophiles that mediate covalent reaction with tyrosine residues on proteins through sulfur-triazole exchange (SuTEx) chemistry. Recent studies demonstrate the broad utility and tunability of SuTEx chemistry for chemical proteomics and protein ligand discovery. Here, we present a strategy for mapping protein interaction networks of structurally complex binding elements using functionalized SuTEx probes. We show that the triazole leaving group (LG) can serve as a releasable linker for embedding hydrophobic fragments to direct molecular recognition while permitting efficient proteome-wide identification of binding sites in live cells. We synthesized a series of SuTEx probes functionalized with a lipid kinase fragment binder for discovery of ligandable tyrosines residing in catalytic and regulatory domains of protein and metabolic kinases in live cells. We performed competition studies with kinase inhibitors and substrates to demonstrate that probe binding is occurring in an activity-dependent manner. Our functional studies led to discovery of probe-modified sites within the C2 domain that were important for downregulation of protein kinase C-alpha in response to phorbol ester activation. Our proof of concept studies highlight the triazole LG of SuTEx probes as a traceless linker for locating protein binding sites targeted by complex recognition elements in live cells.

Sulfonyl-triazole probes modified with a kinase recognition element are developed for live cell activity-based profiling to identify tyrosine sites located in catalytic and regulatory domains that are important for kinase function.     

Photoreactivation of cyclobutane dimers and (6-4) photoproducts in the epidermis of the marsupial, Monodelphis domestica

Radioimmunoassays were used to investigate the repair of cyclobutane pyrimidine dimers and pyrimidine (6-4)pyrimidone photoproducts ((6-4] photoproducts) in the epidermis of the South American opossum, Monodelphis domestica. In the absence of photoreactivating light, both types of photodamage were excised with similar kinetics, 50% of the damage remaining 8 h after UV irradiation in vivo. Exposure of UV-irradiated skin to photoreactivating light resulted in removal of most of the cyclobutane dimers and an enhanced rate of (6-4) photoproduct repair. Photoenhanced excision repair of non-dimer damage increases the range of biologically effective lesions removed by in vivo photoreactivation.     

EXCISION OF CYCLOBUTANE DIMERS IN GENOMIC AND EPISOMAL DNA IN HUMAN CELLS

Abstract Direct determination has been made of cyclobutyl pyrimidine dimer induction and excision repair in an episomal SV40 DNA population in vivo . Maintaining SV40-transformed human (GM637) cells in confluent culture results in amplification of a mutant SV40 episome to high copy number. T4 endonuclease V was used to quantify the induction and repair of cyclobutane dimers in the SV40 episome and genomic DNA of the same cells. Differences in both parameters were observed cyclobutane dimers were induced at 1.5–2-fold greater frequency in episomal DNA and excised at a reduced rate compared to genomic DNA in the host cells.     

An annulene-fused cyclopentadienide. A photochromic cyclopentadienodimethyldihydropyrene where the fused cyclopentadienide group resembles benzene in its effect on the dihydropyrene-metacyclophanediene valence isomerization

The synthesis of the green cyclopentadiene-fused dimethyldihydropyrene 12 was achieved in 36% yield in 7 steps from the parent dihydropyrene 3. Reaction of 12 with KH or LiCH(2)SiMe(3) gave the [14]annulene-fused cyclopentadienide anion quantitatively. In the (1)H NMR spectra, the internal methyl protons of 12 at delta -3.9, change dramatically on formation of anion 5, becoming deshielded to delta -1.82. This is caused by the reduction in diatropicity of the [14]annulene ring on fusion to the 6pi-cyclopentadienide ring. The anion is also a photochromic switch. Irradiation of the closed form 5 with visible light opens it to the open form 5', which reverts to the closed form 5 either with UV light or thermally. The switching behavior is between that of the parent 3/3' and the benzannelated system 4/4' and suggests that in its effect on the photoswitching, cyclopentadienide is behaving chemically similar to benzene.     

Excited-state characters and dynamics of [W(CO)(5)(4-cyanopyridine)] and [W(CO)(5)(piperidine)] studied by picosecond time-resolved IR and resonance Raman spectroscopy and DFT calculations: roles of W --> L and W --> CO MLCT and LF excited states revised

The characters, dynamics, and relaxation pathways of low-lying excited states of the complexes [W(CO)(5)L] [L = 4-cyanopyridine (pyCN) and piperidine (pip)] were investigated using theoretical and spectroscopic methods. DFT calculations revealed the delocalized character of chemically and spectroscopicaly relevant molecular orbitals and the presence of a low-lying manifold of CO pi-based unoccupied molecular orbitals. Traditional ligand-field arguments are not applicable. The lowest excited states of [W(CO)(5)(pyCN)] are W --> pyCN MLCT in character. They are closely followed in energy by W --> CO MLCT states. Excitation at 400 or 500 nm populates the (3)MLCT(pyCN) excited state, which was characterized by picosecond time-resolved IR and resonance Raman spectroscopy. Excited-state vibrations were assigned using DFT calculations. The (3)MLCT(pyCN) excited state is initially formed highly excited in low-frequency vibrations which cool with time constants between 1 and 20 ps, depending on the excitation wavelength, solvent, and particular high-frequency nu(CO) or nu(CN) mode. The lowest excited states of [W(CO)(5)(pip)] are W --> CO MLCT, as revealed by TD-DFT interpretation of a nanosecond time-resolved IR spectrum that was measured earlier in a low-temperature glass (Johnson, F. P. A.; George, M. W.; Morrison, S. L.; Turner, J. J. J. Chem. Soc., Chem. Commun. 1995, 391-393). MLCT(CO) excitation involves transfer of electron density from the W atom and, to a lesser extent, the trans CO to the pi orbitals of the four cis CO ligands. Optical excitation into MLCT(CO) transition of either complex in fluid solution triggers femtosecond dissociation of a W-N bond, producing [W(CO)(5)(solvent)]. It is initially vibrationally excited both in nu(CO) and anharmonicaly coupled low-frequency modes. Vibrational cooling occurs with time constants of 16-22 ps while the intramolecular vibrational energy redistribution from the v = 1 nu(CO) modes is much slower, 160-220 ps. No LF excited states have been found for the complexes studied in a spectroscopically relevant range up to 6-7 eV. It follows that spectroscopy, photophysics, and photochemistry of [W(CO)(5)L] and related complexes are well described by an interplay of close-lying MLCT(L) and MLCT(CO) excited states. The high-lying LF states play only an indirect photochemical role by modifying potential energy curves of MLCT(CO) states, making them dissociative.