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.     

A massively parallel electrochemical approach to the miniaturization of organic micro- and nanostructures on surfaces

This paper describes a simple and convenient strategy for reducing the dimensions of organic micro-and nanostructures on metal surfaces. By varying electrochemical desorption conditions, features patterned by dip-pen nanolithography or micro contact printing and made of linear alkanethiols or selenols can be gradually desorbed in a controlled fashion. The process is referred to as electrochemical whittling because the adsorbate desorption is initiated at the exterior of the feature and moves inward as a function of time. The whittling process and adsorbate desorption were studied as a function of substrate morphology, adsorbate head and tail groups, and electrolyte solvent and salt. Importantly, one can independently address different nanostructures made of different adsorbates and effect their miniaturization based upon ajudicious selection of adsorbate, applied potential, and supporting electrolyte. Some of the physical and chemical origins of these observations have been elucidated.     

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.     

Cs+ -selective membrane electrodes based on ethylene glycol-functionalized polymeric microspheres

A new strategy for improving the robustness of membrane-based ion-selective electrodes (ISEs) is introduced based on the incorporation of microsphere-immobilized ionophores into plasticized polymer membranes. As a model system, a Cs⁺-selective electrode was developed by doping ethylene glycol-functionalized cross-linked polystyrene microspheres (P-EG) into a plasticized poly(vinyl chloride) (PVC) matrix containing sodium tetrakis-[3,5-bis(trifluoromethyl)phenyl] borate (TFPB) as the ion exchanger. Electrodes were evaluated with respect to Cs⁺ in terms of sensitivity, selectivity, and dynamic response. ISEs containing P-EG and TFPB that were plasticized with 2-nitrophenyl octyl ether (NPOE) yielded a linear range from 10⁻¹ to 10⁻⁵ M Cs⁺, a slope of 55.4 mV/decade, and a lower detection limit (log a_Cs) of −5.3. In addition, these membranes also demonstrated superior selectivity over Li⁺, Na⁺, and alkaline earth metal ion interferents when compared to analogous membranes plasticized with bis(2-ethylhexyl) sebacate (DOS) or membranes containing a lipophilic, mobile ethylene glycol derivative (ethylene glycol monooctadecyl ether (U-EG)) as ionophore.     

A two-color-change, nanoparticle-based method for DNA detection

Herein, we describe the detailed synthesis of Ag/Au core-shell nanoparticles, the surface-functionalization of these particles with thiolated oligonucleotides, and their subsequent use as probes for DNA detection. The Ag/Au core-shell nanoparticles retain the optical properties of the silver core and are easily functionalized with thiolated oligonucleotides due to the presence of the gold shell. As such, the Ag/Au core-shell nanoparticles have optical properties different from their pure gold counterparts and provide another “color” option for target DNA-directed colorimetric detection. Size-matched Ag/Au core-shell and pure gold nanoparticles perform nearly identically in DNA detection and melting experiments, but with distinct optical signatures. Based on this observation, we report the development of a two-color-change method for the detection and simultaneous validation of single-nucleotide polymorphisms in a DNA target using Ag/Au core-shell and pure gold nanoparticle probes.     

Synthesis of digitoxigenin by remote functionalization

Treatment of a 21-hydroxy-20-keto steroid with the mixed anhydride of trifluoroacetic acid—diethylphosphonoacetic acid leads directly to cardenolides by an intramolecular Horner-Emmons reaction. Photolysis of 3β-acetoxy-5β,14α-card-20(22)-enolide and iodobenzenedichloride in benzene solution then yields 3β-acetoxy-5β-carda-14,20(22)-dienolide (β-anhydrodigitoxigenin acetate).     

The use of discharge lamps as directly modulated atom reservoirs for selective line modulation in atomic emission spectrometry

A simple method is described for selectively modulating the atomic or ionic resonance lines emitted by an excitation source. A modified discharge lamp with a cylindrical hollow cathode is used to generate a modulated atom cloud. The emission from the excitation source is then imaged through the modulated atom cloud within the cylindrical cathode lamp, to yield a selectively modulated signal. The ability of the system to reduce spectral interferences in inductively-coupled plasma emission spectrometry is assessed and discussed.     

Isomer-specific spectroscopy and conformational isomerization energetics of o-, m-, and p-ethynylstyrenes

The infrared and ultraviolet spectroscopy of o-, m-, and p-ethynylstyrene isomers (oES, mES, and pES) were studied by a combination of methods, including resonance-enhanced two-photon ionization (R2PI), UV-UV hole-burning spectroscopy (UVHB), resonant ion-dip infrared spectroscopy (RIDIRS), and rotationally resolved fluorescence excitation spectroscopy. In addition, the newly developed method of stimulated emission pumping-population transfer spectroscopy (SEP-PTS) was used to determine the energy threshold to conformational isomerization in m-ethynylstyrene. The S(1) <-- S(0) origin transitions of oES and pES occur at 32 369 and 33 407 cm(-1), respectively. In mES, the cis and trans conformations are calculated to be close in energy. In the R2PI spectrum of mES, the two most prominent peaks (32672 and 32926 cm(-1)) were confirmed by UVHB spectroscopy to be S(1) <-- S(0) origins of these two conformers. The red-shifted conformer was identified as the cis structure by least-squares fitting of the rotationally resolved fluorescence excitation spectrum of the origin band. There are also two possible conformations in oES, but transitions due to only one were observed experimentally, as confirmed by UVHB spectroscopy. Density functional theory calculations (B3LYP/6-31+G) predict that the cis-ortho conformer, in which the substituents point toward each other, is about 8 kJ/mol higher in energy than the trans-ortho isomer, and should only be about 5% of the room temperature population of oES. Ground-state infrared spectra in the C-H stretch region (3000-3300 cm(-1)) of each isomer were obtained with RIDIRS. In all three structural isomers, the acetylenic C-H stretch fundamental was split by Fermi resonance. Infrared spectra were also recorded in the excited electronic state, using a UV-IR-UV version of RIDIR spectroscopy. In all three isomers the acetylenic C-H stretch fundamental was unshifted from the ground state, but no Fermi resonance was seen. The first observed and last unobserved transitions in the SEP-PT spectrum were used to place lower and upper bounds on the barrier to cis --> trans isomerization in m-ethynylstyrene of 990-1070 cm(-1). Arguments are given for the lack of a kinetic shift in the measurement. The analogous trans --> cis barrier is in the same range (989-1065 cm(-1)), indicating that the relative energies of the zero-point levels of the two isomers are (E(ZPL)(cis) - E(ZPL)(trans))= -75 to +81 cm(-1). Both the barrier heights and relative energies of the minima are close to those determined by DFT (Becke3LYP/6-31+G) calculations.