Determination of haloalkane dehalogenase activity by capillary zone electrophoresis

A new sensitive method has been developed for the determination of haloalkane dehalogenase activity. The enzymatic reactions were carried out directly in thermostatted autosampler vials and the formation of product - bromide or chloride ions - was monitored by sequential capillary zone electrophoresis runs. The determinations were performed in a 75 microm fused-silica capillary using 5 mM chromate, 0.5 mM tetradecyltrimethylammonium bromide (pH 8.4) as a background electrolyte, separation voltage 15 kV (negative polarity) and indirect detection at sample wavelength 315 nm, reference wavelength 375 nm for brominated and chlorinated substrates, respectively 0.1 M beta-alanine-HCl (pH 3.50) as a background electrolyte, separation voltage 18 kV (negative polarity) and direct detection at 200 nm for brominated substrates. The temperature of capillary was in both cases 25 degrees C. The method is rapid, can be automated, and requires only small amount of enzyme preparation and substrate.     

Synthesis of 1,8-naphthalimide-based fluorescent nano-probes and their application in pH detection

Fluorescent nano-probes with particle sizes of 20 nm, 120 nm and 300 nm for proton were prepared through click reaction. The photophysical properties of the nano-probes were mainly affected by the particle size.     

Evaluation of a new linker system cleaved using samarium(II) iodide. Application in the solid phase synthesis of carbonyl compounds

A new linker design for solid phase synthesis has been developed that is cleaved under mild, neutral conditions using samarium(II) iodide. The feasibility of the linker approach has been illustrated in the solid phase synthesis of ketones and amides using an oxygen linker. Insights into the mechanism of the samarium(II) iodide cleavage reaction are described and the potential of a sequential cleavage carbon-carbon bond forming process is assessed.     

Thiazole Orange Dimers in DNA: Fluorescent Base Substitutions with Hybridization Readout

By using (S)‐2‐amino‐1,3‐propanediol as a linker, thiazole orange (TO) was incorporated in a dimeric form into DNA. The green fluorescence (λ=530 nm) of the intrastrand TO dimer is quenched, whereas the interstrand TO dimer shows a characteristic redshifted orange emission (λ=585 nm). Steady‐state optical spectroscopic methods reveal that the TO dimer fluorescence is independent of the sequential base contexts. Time‐resolved pump–probe measurements and excitation spectra reveal the coexistence of conformations, including mainly stacked TO dimers and partially unstacked ones, which yield exciton and excimer contributions to the fluorescence, respectively. The helicity of the DNA framework distorts the excitonic coupling. In particular, the interstrand TO dimer could be regarded as an excitonically interacting base pair with fluorescence readout for DNA hybridization. Finally, the use of this fluorescent readout was representatively demonstrated in molecular beacons.     

Rigid, conjugated, fluoresceinated thymidine triphosphates: syntheses and polymerase mediated incorporation into DNA analogues

Syntheses of a unique set of energy transfer dye labeled nucleoside triphosphates, compounds 1-3, are described. Attempts to prepare these compounds were only successful if the triphosphorylation reaction was performed before coupling the dye to the nucleobase, and not the other way around. Compounds were prepared as both the 2'-deoxy (a) and 2',3'-dideoxy- (b) forms. They feature progressively longer rigid conjugated linkers connecting the nucleobase and the hydroxyxanthone moiety. UV spectra of the parent nucleosides 12-14 show that as the length of the linker increases so does the absorption of the donor in the 320-330 nm region, but with relatively little red-shift of the maxima. Fluorescence spectra of the same compounds show that radiation in the 320-330 nm region results in predominant emission from the fluorescein. When the linker is irradiated at 320 nm, the only significant emission observed corresponds to the hydroxyxanthone part of the molecules at 520 nm; this corresponds to an effective Stokes' shift of 200 nm. As the absorption at 320-330 nm by the linker increases with length, so does the intensity of the fluorescein emission. A gel assay was used to gauge relative incorporation efficiencies of compounds 1-3, dTTP, ddTTP, and 6-TAMRA-ddTTP. Throughout, the thermostable polymerase TaqFS was used, as it is the one most widely applied in high throughput DNA sequencing. This assay showed that only compounds 3 were incorporated efficiently; these have the longest linkers. Of these, the 2'-deoxy nucleoside 3 a was incorporated and did not prevent the polymerase from extending the chain further. The 2',3'-dideoxy nucleoside 3 b was incorporated only about 430 times less efficiently than ddTTP under the same conditions, and caused chain termination. The implications of these studies on modified sequencing protocols are discussed.     

Versatile solid-phase synthesis of secondary amines from alcohols. Development of an N-Boc-(o-nitrobenzene)sulfonamide linker

The development of a versatile amine releasing linker based on the modified o-nitrobenzene sulfonamide protective group is described. This new N-Boc-o-nitrobenzenesulfonamide (Boc-ONBS) linker enables the elaboration on resin of primary and secondary amines by sequential substitution of the sulfonamide moiety using the Mitsunobu reaction. A 16-member array of secondary and Boc protected primary amines was then prepared using this linker.     

Effect of linker on the photosensitization of ZnO layers with CdSe quantum dots

In this work, zinc oxide (ZnO) nanoparticles (size <10 nm) were formed via precipitation in ethanolic solution. The zinc acetate and lithium hydroxide solutions in ethanol were mixed at 273 K temperatures under vigorous stirring. To study the effect of quantum dot (QD) coverage, we have prepared a colloidal suspension of capped CdSe QDs (size ~5 nm) by chemical route and anchored them to a nanoporous ZnO layer either by direct adsorption or through linker. Here a bifunctional molecule (mercaptopropionic acid, MPA, and thioglycolic acid, TGA) was previously adsorbed on the ZnO surface, which acted as a molecular cable. From TEM/SEM studies, it was observed that direct adsorption of CdSe QDs onto ZnO surface was not efficient. However, the bifunctional linker molecules particularly MPA facilitates binding of CdSe QDs to ZnO; and consequently, interparticle electron transfer is thus facilitated. The use of MPA linker despite of its long carbon chain also aids in the quenching of photoluminescence of CdSe on addition of ZnO in a more systematic manner indicating efficient charge transfer from CdSe into ZnO as compared with the without linker and with linker TGA case, respectively. Due to higher PL quenching and reduction in lifetime values, higher values of Stern–Volmer quenching constants were thus obtained for CdSe–ZnO composites with MPA as compared with TGA linker and without linker case, respectively. Nonlinear Stern–Volmer plots as observed for samples without linker case indicated heterogeneous quenching due to insufficient binding between CdSe QDs and ZnO. By means of spectroscopic (PL, UV–VIS, FTIR) and microscopic (TEM, SEM) techniques, we have demonstrated linker-dependent photosensitization mechanism of ZnO layers with CdSe QDs. Our data thus illustrate that interfacial-electron transfer kinetics in QD–linker–ZnO assemblies are almost independent of the length of alkyl-containing molecular linkers.     

Thermally activated electron transport in single redox molecules

We have studied electron transport through single redox molecules, perylene tetracarboxylic diimides, covalently bound to two gold electrodes via different linker groups, as a function of electrochemical gate voltage and temperature in different solvents. The conductance of these molecules is sensitive to the linker groups because of different electronic coupling strengths between the molecules and electrodes. The current through each of the molecules can be controlled reversibly over 2-3 orders of magnitude with the gate and reaches a peak near the redox potential of the molecules. The similarity in the gate effect of these molecules indicates that they share the same transport mechanism. The temperature dependence measurement indicates that the electron transport is a thermally activated process. Both the gate effect and temperature dependence can be qualitatively described by a two-step sequential electron-transfer process.     

Nucleic acid-templated energy transfer leading to a photorelease reaction and its application to a system displaying a nonlinear response

The photocleavage of a nitrobenzyl-type linker (NPPOC) at 405 nm wavelength was enabled by nucleic acid-templated energy transfer from a sensitizer (thioxanthenone) to the linker. This strategy was used to release profluorescent rhodamine, which facilitated monitoring of the reaction via fluorescence measurement in a nonoverlapping window with the sensitizer/photocleavage reaction. The rate acceleration of the templated reaction was greater than 20-fold over the background reaction. The templated reaction was used in conjunction with strand displacement to design four-component systems that responded to an analyte (DNA). Programming a specific hierarchical relationship among the four components enabled the design of a system that responded first positively and then negatively to increasing levels of an analyte.     

Functional characterization of permuted enhanced green fluorescent proteins comprising varying linker peptides

New variants of green fluorescent protein (GFP) can be engineered by circular permutation of their amino acid sequence. We characterized a series of permuted enhanced GFP (PEGFP) with new termini introduced at N144-Y145 and linkers of 1, 3, 5 and 6 residues inserted between G232 and M1, as well as a variant with an extended 7-residues linker between K238 and M1. A minimum linker length of 3 residues was necessary for a functional chromophore to be formed, and linkers exceeding 4 residues yielded almost the same fluorescence quantum yield as enhanced GFP (EGFP). PEGFP exhibited dual-wavelength absorption and fluorescence excitation with peaks at 395 and 490 nm but single-wavelength emission at 512 nm. Fluorescence emission increased with increasing pH for all excitation wavelengths with a pKa of 7.7. Between the pH values of 6 and 8 optical absorption showed an isobestic point at 445 nm. PEGFP rapidly denatured in urea between 50 and 60 degrees C. Renaturation proceeded with a short (approximately 29 s) and a longer (> 150 s) time constant. Transient transfection of HEK293 and HeLa cells revealed the expression dynamics of PEGFP to be similar to that of EGFP. Laser-scanning microscopy of HeLa cells demonstrated that the PEGFP are particularly well suited as fluorescent indicators in two-photon imaging.     

EFFICIENT FORMATION OF A CROSSLINKABLE HMT MONOADDUCT AT THE Kpn I RECOGNITION SITE

Abstract The double-stranded Kpn I linker, CGGTACCG, is readily crosslinked by 4'-hydroxymethyl-4,5',8-trimethylpsoralen (HMT). Under identical conditions, the corresponding Bam HI linker, CGGATCCG, is resistant to modification. The differential reactivity of HMT towards the two sequences is also observed with SV40 DNA where the Kpn I restriction site is ten-fold more susceptible to HMT modification than the Bam HI site. Selective reaction with the Kpn I site is attributed to preferential intercalation of HMT into the TpA sequence. The availability of crosslinked Kpn I linker has allowed us to characterize the kinetics of photoreversal. Upon irradiation at 254 nm, the diadduct reverses at a faster rate than the monoadduct, leading to an accumulation of the latter. The resultant monoadduct reforms crosslink rapidly upon irradiation at 365 nm. DNA oligomers like the Kpn I linker, which can be modified by the above protocol to contain a crosslinkable HMT monoadduct, could he exploited as photoreactive sequence-specific probes.     

Ox-SLIM: Synthesis of and Site-Specific Labelling with a Highly Hydrophilic Trityl Spin Label

The combination of pulsed dipolar electron paramagnetic resonance spectroscopy (PDS) with site-directed spin labelling is a powerful tool in structural biology. Rational design of trityl-based spin labels has enabled studying biomolecular structures at room temperature and within cells. However, most current trityl spin labels suffer either from aggregation with proteins due to their hydrophobicity, or from bioconjugation groups not suitable for in-cell measurements. Therefore, we introduce here the highly hydrophilic trityl spin label Ox-SLIM. Engineered as a short-linked maleimide, it combines the most recent developments in one single molecule, as it does not aggregate with proteins, exhibits high resistance under in-cell conditions, provides a short linker, and allows for selective and efficient spin labelling via cysteines. Beyond establishing synthetic access to Ox-SLIM, its suitability as a spin label is illustrated and ultimately, highly sensitive PDS measurements are presented down to protein concentrations as low as 45 nm resolving interspin distances of up to 5.5 nm.     

Transient violations of the second law of thermodynamics in protein unfolding examined using synthetic atomic force microscopy and the fluctuation theorem

The synthetic atomic force microscopy (AFM) method is developed to simulate a periodically replicated atomistic system subject to force and length fluctuations characteristic of an AFM experiment. This new method is used to examine the forced-extension and subsequent rupture of the alpha-helical linker connecting periodic images of a spectrin protein repeat unit. A two-dimensional potential of mean force (PMF) along the length and a reaction coordinate describing the state of the linker was calculated. This PMF reveals that the basic material properties of the spectrin repeat unit are sensitive to the state of linker, an important feature that cannot be accounted for in a one-dimensional PMF. Furthermore, nonequilibrium simulations were generated to examine the rupture event in the context of the fluctuation theorem. These atomistic simulations demonstrate that trajectories which are in apparent violation of the second law can overcome unfolding barriers at significantly reduced rupture forces.     

Analogues of uracil nucleosides with intrinsic fluorescence (NIF-analogues): synthesis and photophysical properties

Uridine cannot be utilized as fluorescent probe due to its extremely low quantum yield. For improving the uracil fluorescence characteristics we extended the natural chromophore at the C5 position by coupling substituted aromatic rings directly or via an alkenyl or alkynyl linker to create fluorophores. Extension of the uracil base was achieved by treating 5-I-uridine with the appropriate boronic acid under the Suzuki coupling conditions. Analogues containing an alkynyl linker were obtained from 5-I-uridine and the suitable boronic acid in a Sonogashira coupling reaction. The uracil fluorescent analogues proposed here were designed to satisfy the following requirements: a minimal chemical modification at a position not involved in base-pairing, resulting in relatively long absorption and emission wavelengths and high quantum yield. 5-((4-Methoxy-phenyl)-trans-vinyl)-2'-deoxy-uridine, 6b, was found to be a promising fluorescent probe. Probe 6b exhibits a quantum yield that is 3000-fold larger than that of the natural chromophore (Φ 0.12), maximum emission (478 nm) which is 170 nm red shifted as compared to uridine, and a Stokes shift of 143 nm. In addition, since probe 6b adopts the anti conformation and S sugar puckering favored by B-DNA, it makes a promising nucleoside analogue to be incorporated in an oligonucleotide probe for detection of genetic material.     

A triazene-based new photolabile linker in solid phase chemistry

An extension of the T2 linker methodology by showing its applicability as a photocleavable linker is reported. Photocleavage was carried out with 355 nm UV laser irradiation (3ω Nd-YAG) in methanol/diethyl ether and is suitable for protected amino acid derivatives, as well as simple small organic molecules including resin-bound biotin. The linker is stable under a wide range of conditions with the exception of strongly acidic media.     

Novel Biodegradable Polymer with Redox‐Triggered Backbone Cleavage Through Sequential 1,6‐Elimination and 1,5‐Cyclization Reactions

In the past decade, the self‐immolative biodegradable polymer arose as a novel paradigm for its efficient degradation mechanism and vast potential for advanced biomedical applications. This study reports successful synthesis of a novel biodegradable polymer capable of self‐immolative backbone cleavage. The monomer is designed by covalent conjugations of both pendant redox‐trigger (p‐nitrobenzyl alcohol) and self‐immolative linker (p‐hydroxybenzyl alcohol) to the cyclization spacer (n‐2‐(hydroxyethyl)ethylene diamine), which serves as the structural backbone. The polymerization of the monomer with hexamethylene diisocyanate yields a linear redox‐sensitive polymer that can systemically degrade via sequential 1,6‐elimination and 1,5‐cyclization reactions within an effective timeframe. Ultimately, the polymer's potential for biomedical application is simulated through in vitro redox‐triggered release of paclitaxel from polymeric nanoparticles.     

The kinetics of helix unfolding of an azobenzene cross-linked peptide probed by nanosecond time-resolved optical rotatory dispersion

The unfolding dynamics of a 16 amino acid peptide (Ac-EACAREAAAREAACRQ-NH(2), FK-11-X) was followed using nanosecond time-resolved optical rotatory dispersion (ORD). The peptide was coupled to an azobenzene linker that undergoes subnanosecond photoisomerization and reisomerizes on a time scale of minutes. When the linker is in the trans form, the peptide favors a more helical structure (66% helix/34% disordered) and when in the cis configuration the helical content is reduced. Unfolding of FK-11-X was rapidly triggered by a 7-ns laser pulse at 355 nm, forming cis azobenzene-linked peptides that maintained the secondary structure (helical or disordered) of their trans azobenzene counterparts. The incompatibility of the instantaneous cis photoproduct with helical secondary structure drives the subsequent peptide unfolding to a new conformational equilibrium between cis helix and cis disordered structures. The kinetic results show a approximately 40% decrease in the time-dependent ORD signal at 230 nm that is best fit to a single-exponential decay with a time constant of 55 +/- 6 ns. Folding and unfolding rates for cis FK-11-X are estimated to be approximately 3.0 x 10(6) s(-)(1) (1/330 ns) and approximately 1.5 x 10(7) s(-)(1) (1/66 ns), respectively.     

A sequential injection method for the determination of piroxicam in pharmaceutical formulations using europium sensitized fluorescence

A simple, selective and sensitive luminescence method for the assay of piroxicam (PX) in pharmaceutical formulation is developed. The method is based on the luminescence sensitization of europium (Eu³⁺) by complexation with PX. The signal for PX–EU is monitored at λ_ex=358 nm and λ_em=615 nm. Optimum conditions for the formation of the complex in methanol were 0.01 M TRIS buffer and 0.2 mM of Eu³⁺ which allows the determination of 100–2000 ppb of pX in batch method and 100–1000 ppb with limit of detection (LOD) = 23.0 ppb using sequential injection analysis (SIA). The relative standard deviations of the method range between 2 and 3% indicating excellent reproducibility of the method. The proposed method was successfully applied for he assay of PX in pharmaceutical formulations (Feldene capsules and tablets). Average recoveries of 101.0±0.3 and 98.8±2.7% were obtained for capsules in methanol using batch and sequential injection (SI) methods, respectively.     

Optical and electrical properties of three-dimensional interlinked gold nanoparticle assemblies

The optical and electrical properties of 11-20 nm thick films composed of approximately 4 nm gold nanoparticles (Au-NPs) interlinked by six organic dithiol or bis-dithiocarbamate derivatives were compared to investigate how these properties depend on the core of the linker molecule (benzene or cyclohexane) and its metal-binding substituents (thiol or dithiocarbamate). Films prepared with the thiol-terminated linker molecules, (1,4-bis(mercaptomethyl)benzene, 1,4-bis(mercaptomethyl)cyclohexane, 1,4-bis(mercaptoacetamido)benzene, and 1,4-bis(mercaptoacetamido)cyclohexane), exhibit thermally activated charge transport. The activation energies lie between 59 and 71 meV. These films show distinct plasmon absorption bands with maxima between 554 and 589 nm. In contrast, the film prepared with 1,4-cyclohexane-bis(dithiocarbamate) has a significantly red-shifted plasmon band ( approximately 626 nm) and a pronounced absorbance in the near infrared. The activation energy for charge transport is only 14 meV. These differences are explained in terms of the formation of a resonant state at the interface due to overlap of the molecular orbital and metal wave function, leading to an apparent increase in NP diameter. The film prepared with 1,4-phenylene-bis(dithiocarbamate) exhibits metallic properties, indicating the full extension of the electron wave function between interlinked NPs. In all cases, the replacement of the benzene ring with a cyclohexane ring in the center of the linker molecule leads to a 1 order of magnitude decrease in conductivity. A linear relationship is obtained when the logarithm of conductivity is plotted as a function of the number of nonconjugated bonds in the linker molecules. This suggests that nonresonant tunneling along the nonconjugated parts of the molecule governs the electron tunneling decay constant (beta(N)(-)(CON)), while the contribution from the conjugated parts of the molecule is weak (corresponding to resonant tunneling). The obtained value for beta(N)(-)(CON) is approximately 1.0 (per non-conjugated bond) and independent of the nanoparticle-binding group. Hence, the molecules can be viewed as consisting of serial connections of electrically insulating (nonconjugated) and conductive (conjugated) parts.     

Cluster Linker Approach: Preparation of a Luminescent Porous Framework with NbO Topology by Linking Silver Ions with Gold(I) Clusters

A cluster‐based luminescent porous metal–organic framework has been constructed through a “cluster linker” approach. The luminescent gold(I) cluster, prefunctionalized with pyrazinyl groups, was used as a cluster linker, similar to an organic linker, to connect silver ions in order to form a 3D framework. 1D channels with 1.1 nm diameter were observed in the framework. The cluster with its intrinsic luminescence was incorporated into a porous framework to give a luminescent bifunctional NbO net. This MOF shows solvatochromic behavior, and the interactions between solvent molecules and silver ions inside the channels account for the changes in absorption and emission spectra.