Amide-Exchange-Rate-Edited NMR （AERE-NMR） Experiment： A Novel Method for Resolving Overlapping Resonances

This paper describes an amide-exchange-rate-edited （AERE） NMR method that can effectively alleviate the problem of resonance overlap for proteins and peptides. This method exploits the diversity of amide proton exchange rates and consists of two complementary experiments： （1） SEA （solvent exposed amide）-type NMR experiments to map exchangeable surface residues whose amides are not involved in hydrogen bonding, and （2） presat-type NMR experiments to map solvent inaccessibly buried residues or nonexchangeable residues located in hydrogen-bonded secondary structures with properly controlled saturation transfer via amide proton exchanges with the solvent. This method separates overlapping resonances in a spectrum into two complementary spectra. The AERE-NMR method was demonstrated with a sample of ^15N/^13C/^2H（70%） labeled ribosome-inactivating protein trichosanthin of 247 residues.     

Using polarizable POSSIM force field and fuzzy‐border continuum solvent model to calculate pKa shifts of protein residues

Our Fuzzy‐Border (FB) continuum solvent model has been extended and modified to produce hydration parameters for small molecules using POlarizable Simulations Second‐order Interaction Model (POSSIM) framework with an average error of 0.136 kcal/mol. It was then used to compute pK _a shifts for carboxylic and basic residues of the turkey ovomucoid third domain (OMTKY3) protein. The average unsigned errors in the acid and base pK _a values were 0.37 and 0.4 pH units, respectively, versus 0.58 and 0.7 pH units as calculated with a previous version of polarizable protein force field and Poisson Boltzmann continuum solvent. This POSSIM/FB result is produced with explicit refitting of the hydration parameters to the pK _a values of the carboxylic and basic residues of the OMTKY3 protein; thus, the values of the acidity constants can be viewed as additional fitting target data. In addition to calculating pK _a shifts for the OMTKY3 residues, we have studied aspartic acid residues of Rnase Sa. This was done without any further refitting of the parameters and agreement with the experimental pK _a values is within an average unsigned error of 0.65 pH units. This result included the Asp79 residue that is buried and thus has a high experimental pK _a value of 7.37 units. Thus, the presented model is capable or reproducing pK _a results for residues in an environment that is significantly different from the solvated protein surface used in the fitting. Therefore, the POSSIM force field and the FB continuum solvent parameters have been demonstrated to be sufficiently robust and transferable. © 2016 Wiley Periodicals, Inc.     

Preliminary Study on Cataractous Human Lenses Using Near-Infrared Fourier Transform Raman Spectroscopy

Raman vibrations of the fingerprint of aromatic amino acid residues were analyzed to study the changes of cataractous lens protein in the cortex and nucleus at various ages. Tryptophan content, analyzed by the quantification of I₇₅₈/I₁₄₄₈ ratio, shows the damage (modification) of tryptophan residue in the nucleus is caused primarily by the formation of cataracts, not by the aging process. Microenvironmental changes of tryptophan and tyrosine were analyzed by the intensity ratios of I₈₇₉/I₇₅₈ and I₈₂₉/I₈₅₃, respectively. The decrease of the ratio of I₈₇₉/I₇₅₈, from 0.9 to 0.6 in the nucleus and from 0.7 to 0.6 for the cortex, reveal that more buried tryptophan residues become exposed in the cortex than in the nucleus during cataractogenesis, especially for non-senile cataractous lenses. The ratio of I₈₂₉/I₈₅₃ is around 1.0 for both cortical and nuclear proteins at various ages, indicating some tyrosine residues have undergone a change in their hydrogen bonding environment. When compared to previous studies, we found that a normal (clear) lens has a higher peak at 1617 cm^?1 than at 1604 cm^?1, while a dense opaque or brunescent lens shows stronger intensity at 1604 cm^?1 than at 1617 cm^?1, suggesting the ratio of I₁₆₁₇/I₁₆₀₄ can be used to evaluate the human lens morphology.     

Empirical prediction of protein pKavalues with residue mutation

A fast, empirical method, Mut‐pKa, is presented for predicting the pK_a values of ionizable residues in proteins based on mutation. The method compares the effect of mutating each residue that may act as a hydrogen bond donor or acceptor for the ionizable residue. The energetic effect of each type of mutation, along with a desolvation measure and the overall background charge, is fit against pK_a data for histidine and carboxyl residues. A total of 214 residues from 35 different proteins were used in the dataset. Using 11 parameters for each type of ionizable residue, a root mean squared error (RMSE) of 0.78 and 1.12 pH units were obtained for carboxyl and histidines residues, respectively, using leave one out cross validation (LOOCV). The results were particularly promising for buried residues, which had RMSE values of 0.99 and 1.13 for carboxyl and histidine residues, respectively. A number of desolvation measures were tested. The simplest measure, the number of atoms surrounding the residue, was found to work best. The effect of using dynamics was also studied using short molecular dynamics runs, followed by minimization of the structures. Mut‐pKa has significantly fewer parameters than, but similar performance to, other empirical methods. Because of this and the LOOCV results, we believe the model is robust and that overfitting is not a problem. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Solvent effect on catalytic properties of the HCI-DMF-1,1,2,2-tetrachloroethane system

Ionization of 2- and 3-nitroanilines was studied in HCl-DMF-1,1,2,2-tetrachloro-ethane (TCE) solutions at 25 °C. The ionization capability of the medium and basicity constants pK _i of indicators change depending on the ratio of the components. The numerical values of pK _i are found to depend on the analytical composition of the DMF-TCE solvent. The solvent effect on pK _i is associated with a change in the solvation of the nonionized form of the indicators.Translanted fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 6, pp. 1446–1449, June, 1996.     

Triplet state sublevel spectroscopy applied to proteins

Triplet state sublevel spectroscopy using optical detection of magnetic resonance (ODMR) in zero magnetic field can be successfully employed to study (i) the environment of tryptophan (Trp) residues in a protein by observing the position and structure of phosphorescence spectra, zero field ODMR transitions and triplet state sublevel kinetics, (ii) the energy transfer among Trp residues, and (iii) whether any cysteine (Cys) residue is within van der Waals distance of any Trp residue by studying the complex of the protein with methylmercury(II) iodide (CH₃HgI) which binds to Cys residues. These studies are particularly important where crystal structure study is not possible. Study of the S₁ state often gives ambiguous results since fluorescence is always broad and shows multi-exponential decay. Our results on bacteriophage lysozyme T4 which contains three Trp residues at positions 126, 138 and 158 are presented. Measurements were facilitated by the use of a mutated enzyme containing one or two Trp-Tyr substitutions. The results indicate that (i) Trp 126 and 158 are solvent exposed, whereas Trp 138 is buried in a hydrophobic environment, (ii)S ↔S non-radiative energy transfer takes place predominantly from Trp 126 to Trp 158, and (iii) only Trp-158 undergoes a heavy atom perturbation, which affects selectively the z-sublevel (z is an out-of-plane axis of the indole plane) as a result of CH₃HgI binding to nearby Cys 97. We suggest that the Hg atom is located on the z-axis of Trp 158 in the complex. This interpretation is based on our investigations on the effect of orientation of heavy atom perturbers in some naphthalene-crown ether metal ion complexes.     

Analysis of Redox Activity of Proteins on the Carbon Screen Printed Electrodes

Direct redox activity of different proteins was investigated on the surface of carbon screen printed electrodes (SPE). The signal attributed to the electrochemical oxidation of amino acid residues (cysteine (Cys), tryptophan (Trp) and tyrosine (Tyr)) was registered at E_max from 0.6 to 0.7 V (vs. Ag/AgCl). Based on the difference in the redox behavior of L ‐tyrosine and 3‐nitro‐L ‐tyrosine, the selective electrochemical detection of native and nitrated albumins was demonstrated. It was shown that the electrochemical signal correlated with the surface density of electroactive amino acid residues on the protein molecule. A simple electrochemical method for the total protein analysis was proposed.     

Detection of modified tyrosines as an inflammation marker in a photo-aged skin model

Reactive nitrogen species, produced during the process of inflammation induced by various factors including UV radiation, modify amino acids in crucial proteins. It is assumed that skin tissue is more likely to be modified, as it is located at the outer layer of a body that is exposed to UV radiation on a daily basis. To investigate the influence of the modified tyrosine on UV-exposed skin, we detected the nitrotyrosine or halogenated tyrosine and dityrosine in photo-aged model mice. The back skin of mice was exposed to a dose of 10 J cm(-2) day(-1) every day for 15 weeks. Samples exhibiting typical symptoms of photo aging were provided to the immunofluorescence study. The quantification of modified proteins was accomplished through a chemical analytical method known as HPLC-tandem mass spectrometry. Analysis of the irradiated skin samples showed that all modified tyrosine except nitrotyrosine demonstrated statistically significant increases. The molecular weights of major modified proteins, confirmed as 25-50 kDa, were measured using Western blot analysis with an anti-nitrotyrosine antibody. Furthermore, the immunofluorescence study verified that the localization of myeloperoxidase conformed to that of nitrotyrosine. This result suggests that the modified tyrosine was produced during the process of inflammation by UV irradiation. In this study, we used a low dose of UV irradiation to which we are exposed in daily life. Our results suggest that UV exposure in daily life may induce the production of modified tyrosines and skin aging.     

Mass spectrometric kinetic analysis of human tyrosylprotein sulfotransferase-1 and -2

Protein tyrosine O-sulfation, a widespread post-translational modification, is mediated by two Golgi enzymes, tyrosylprotein sulfotransferase-1 and-2. These enzymes catalyze the transfer of sulfate from the universal sulfate donor 3′-phosphoadenosine-5′-phosphosulfate (PAPS) to the hydroxyl group of tyrosine residues to form tyrosine O-sulfate ester and PAP. More than 60 proteins have been identified to be tyrosine sulfated including several G protein-coupled receptors, such as CC-chemokine receptor 8 (CCR8) that is implicated in allergic inflammation, asthma, and atherogenesis. However, the kinetic properties of purified tyrosylprotein sulfotransferase (TPST)-1 and −2 have not been previously reported. Moreover, currently there is no available quantitative TPST assay that can directly monitor individual sulfation of a series of tyrosine residues, which is present in most known substrates. We chose an MS-approach to address this limitation. In this study, a liquid chromatography electrospray ionisation mass spectrometry (LC/ESI-MS)-based TPST assay was developed to determine the kinetic parameters of individual TPSTs and a mixture of both isozymes using CCR8 peptides as substrates that have three tyrosine residues in series. Our method can differentiate between mono-and disulfated products, and our results show that the K_m,app for the monosulfated substrate was 5-fold less than the nonsulfated substrate. The development of this method is the initial step in the investigation of kinetic parameters of the sequential tyrosine sulfation of chemokine receptors by TPSTs and in determining its catalytic mechanism.     

Prediction of stability changes upon single-site mutations using database-derived potentials

One of the purposes of studying protein stability changes upon mutations is to get information about the dominating interactions that drive folding and stabilise the native structure. With this in mind, we present a method that predicts folding free-energy variations caused by point mutations using combinations of two types of database-derived potentials, i.e. backbone torsion-angle potentials and distance potentials, describing local and non-local interactions along the chain, respectively. The method is applied to evaluate the folding free-energy changes of 344 single-site mutations introduced in six different proteins and a synthetic peptide. We found that the relative importance of local versus non-local interactions along the chain is essentially a function of the solvent accessibility of the mutated residues. For the subset of totally buried residues, the optimal potential is the sum of a distance potential and a torsion potential weighted by a factor of 0.4. This combination yields a correlation coefficient between measured and computed changes in folding free energy of 0.80. For mutations of partially buried residues, the best potential is the sum of a torsion potential and a distance potential weighted by 0.7. For fully accessible residues, the torsion potentials taken alone perform best, reaching correlation coefficients of 0.87 on all but 10 mutations; the excluded mutations seem to modify the backbone structure or to involve interactions that are atypical for the surface. These results show that the relative weight of non-local interactions along the sequence decreases as the solvent accessibility of the mutated residue increases, and vanishes at the protein surface. On the contrary, the weight of local interactions increases with solvent accessibility. The latter interactions are nevertheless never negligible, even for the most buried residues. Received: 20 May 1998 / Accepted: 3 September 1998 / Published online: 7 December 1998     

Rhodotorula aurantiaca penicillin V acylase: Active site characterization and fluorometric studies

Penicillin V acylase (PVA), a member of newly evolved Ntn-hydrolase superfamily, is a pharmaceutically important enzyme to produce 6-aminopenicillanic acid. Active site characterization of recently purified monomeric PVA from Rhodotorula aurantiaca (Ra-PVA), the yeast source, showed the involvement of serine and tryptophan in the enzyme activity. Modification of the protein with serine and tryptophan specific reagents such as PMSF and NBS showed partial loss of PVA activity and substrate protection. Ra-PVA was found to be a multi-tryptophan protein exhibiting one tryptophan, in native and, four in its denatured condition. Various solute quenchers and substrate were used to probe the microenvironment of the putative reactive tryptophan through fluorescence quenching. The results obtained indicate that the tryptophan residues of Ra-PVA were largely buried in hydrophobic core of the protein matrix. Quenching of the fluorescence by acrylamide was collisional. Acrylamide was the most effective quencher amongst all the used quenchers, which quenched 71.6% of the total intrinsic fluorescence of the protein, at a very less final concentration of 0.1 M. Surface tryptophan residues were found to have predominantly more electropositively charged amino acids around them, however differentially accessible for ionic quenchers. Denaturation led to shift in λ_max from 336, in native state, to 357 nm and more exposed to the solvent, consequently increase in fluorescence quenching with all quenchers. This is an attempt towards the conformational studies of Ra-PVA.     

THE QUENCHING OF TYROSINE AND TRYPTOPHAN FLUORESCENCE BY H2O AND D2O*

Abstract— The quantum yields and lifetimes of the fluorescence of tyrosine and tryptophan were determined in D₂O-H₂O and glycerol-H₂O solvent mixtures of varying composition from 10 vol.% to 100% H₂O at 15°C. Forboth amino acids the ratio of the quantum yields in D₂O and H₂O (i.e., q_D/q_H) was smaller than the ratio of the corresponding lifetimes (_D/_H). For tyrosine the ratio of the quantum yields in glycerol and H₂O (q_G/q_H) was also smaller than the corresponding _G/_H ratio, but for tryptophan q_G/g_HG/_H. The proximity of the q vs. plots for tyrosine in the two solvent mixtures indicates that at 15°C neither D₂O nor glycerol, in the pure state or when diluted with H₂O, quench tyrosine significantly. However, H₂O quenches tyrosine by a dynamic process, which increases both the radiative and the nonradiative rate constant. The quenching action is attributed to a tyrosine-H₂O exciplex, whose formation is independent of bulk viscosity and dielectric constant. Unlike tyrosine, tryptophan is quenched weakly by D₂O by a static process at 15°C (i.e., involving no change in), but H₂O quenches tryptophan much more efficiently by a dynamic process, which involves the nonradiative rate constant, but not the radiative constant. These results are explained on the basis of electrostatic complexation of the ammonium group to the carbon atom adjacent to the ring nitrogen with a lifetime which is longer thanin D₂O but shorter thanin H₂O, with solvent reorientation possibly also being an important factor in the quenching. This explanation is consistent with the fact that concentrated (8 M) urea increases q andof aqueous tryptophan ? 15–20%, while guanidine hydrochloride (6.4 M) has the opposite effect, i.e., it decreases q and t of tryptophan ? 15–20%, and with the fact that neither 8 M urea nor 6.4 M guanidine hydrochloride affects any fluorescence parameter of tyrosine at all.     

A new method for side-chain conformation prediction using a Hopfield network and reproduced rotamers

We present a new side-chain prediction method based on energy minimization using a Hopfield network, focusing on the buried residues of proteins. In this method, the network is composed of automata assigned to each rotamer to restrict side-chain conformational space. We reproduced a rotamer library that enabled us to more widely cover the space for side-chain conformations than those previously produced. The accuracy of the side-chain modeling was estimated by three standards: root mean square deviations (rmsds) between the modeled and the crystal structures, the percentages of correctly predicted side-chain torsion angles, and the percentages of correctly predicted hydrogen bonds. The average rmsd for buried side chains of 21 proteins was 1.10 Å. The value was almost always improved relative to the previous works. The percentage of side-chain X₁ angles for buried residues was 87.3%. By considering the hydrogen bond energy, the average percentage of correctly predicted hydrogen bonds rose from 33% without hydrogen bond energy to 52% with the bond energy. We applied this method to homology modeling, where the protein backbone used to predict side-chain conformations deviates from the correct conformation, and could predict side-chain conformations as correctly as those using the correct backbones. © 1996 by John Wiley & Sons, Inc.     

Aromatic Cluster Sensor of Protein Folding: Near‐UV Electronic Circular Dichroism Bands Assigned to Fold Compactness

Both far‐ and near‐UV electronic circular dichroism (ECD) spectra have bands sensitive to thermal unfolding of Trp and Tyr residues containing proteins. Beside spectral changes at 222 nm reporting secondary structural variations (far‐UV range), L_b bands (near‐UV range) are applicable as 3D‐fold sensors of protein's core structure. In this study we show that both L_b(Tyr) and L_b(Trp) ECD bands could be used as sensors of fold compactness. ECD is a relative method and thus requires NMR referencing and cross‐validation, also provided here. The ensemble of 204 ECD spectra of Trp‐cage miniproteins is analysed as a training set for “calibrating” Trp?Tyr folded systems of known NMR structure. While in the far‐UV ECD spectra changes are linear as a function of the temperature, near‐UV ECD data indicate a non‐linear and thus, cooperative unfolding mechanism of these proteins. Ensemble of ECD spectra deconvoluted gives both conformational weights and insight to a protein folding?unfolding mechanism. We found that the L_b²⁹³ band is reporting on the 3D‐structure compactness. In addition, the pure near‐UV ECD spectrum of the unfolded state is described here for the first time. Thus, ECD folding information now validated can be applied with confidence in a large thermal window (5≤T≤85 °C) compared to NMR for studying the unfolding of Trp?Tyr residue pairs. In conclusion, folding propensities of important proteins (RNA polymerase II, ubiquitin protein ligase, tryptase‐inhibitor etc.) can now be analysed with higher confidence.     

Analysis of nitrated proteins and tryptic peptides by HPLC-chip-MS/MS: site-specific quantification,nitration degree,and reactivity of tyrosine residues

The reaction products and pathways of protein nitration were studied with bovine serum albumin (BSA) and ovalbumin (OVA) nitrated by liquid tetranitromethane (TNM) or by gaseous nitrogen dioxide and ozone (NO₂ + O₃). Native and nitrated proteins were enzymatically digested with trypsin, and the tryptic peptides were analyzed by high-performance liquid chromatography and tandem mass spectrometry (HPLC-MS/MS) using a chip cube nano-flow system (Agilent). Upon nitration by TNM, up to ten of 17 tyrosine residues in BSA and up to five of ten tyrosine residues in OVA could be detected in nitrated form. Upon nitration by NO₂ + O₃, only three nitrated tyrosine residues were found in BSA. The nitration degrees of individual nitrotyrosine residues (ND_Y) were determined by site-specific quantification and compared to the total protein nitration degrees (ND) determined by photometric detection of HPLC-DAD. The slopes of the observed linear correlations between ND_Y and ND varied in the range of ~0.02–2.4 for BSA and ~0.2–1.6 for OVA. They provide information about the relative rates of nitration or reaction probabilities for different tyrosine residues. In BSA, the tyrosine residue Y₁₆₁ was by far most reactive against NO₂ + O₃ and one of the four most reactive positions with regard to nitration by TNM. In OVA, all except one tyrosine residue detected in nitrated form exhibited similar reactivities. The observed nitration patterns show how the site selectivity of protein nitration depends on the nitrating agent, reaction conditions, and molecular structure of the protein (primary, secondary, and tertiary).     

Salicylaldimine-bridged dinuclear cyclopalladated complexes: Synthesis,characterization and BSA binding studies

Salicylaldimine-bridged dinuclear cyclopalladated complexes were synthesized by the reactions of cyclopalladated chloro dimers [Pd{(4-R)C₆H₃CH=N-C₆H₃–2,6-i-Pr₂}(μ-Cl)]₂ (R = H; OMe) with salen-based bridging ligands. The complexes were characterized by FTIR, NMR spectroscopy, elemental analysis and X-ray crystallography. The binding interaction of cyclopalladated complexes to bovine serum albumin (BSA) was investigated by UV–vis, fluorescence and synchronous fluorescence spectroscopy. The experimental results showed that these Pd (II) complexes could bind to BSA with high affinity and quench its intrinsic fluorescence by a static or combined process. Also the interaction of Pd complexes with BSA affected the conformation of the tryptophan and tyrosine residues.     

Amide-Bond Syntheses Catalyzed by Penicillin Acylase

The enzymatic synthesis of amide bonds catalyzed by penicillin acylase is investigated both in H₂O solution and in organic solvents containing reverse micelles. The specificity of the reaction is rather high on the side of the acyl component, practically only phenylacetic acid gives sizeable yields. On the contrary, a variety of amino-acid esters, dipeptides, and tripeptides can be used as amino component, e.g., serine methyl ester, methionine ethyl ester, tyrosine ethyl ester, Gly–Asp, Ala–Tyr, Gly–Tyr–Gly etc. However, Many other amino-acid residues do not react, and the possible reasons for this are discussed. Yields varyin rang the 10–80%. A. systematic study to optimize yields by varying the solvent composition is presented for one model reaction. The enzyme is also able to couple certain D-amino-acid residues (e.g. D-methionine ethyl ester or Gly-D -Asp) though at lower rate. Reverse micelles formed by the cationic surfactant cetyltrimethylammonium bromide (CTAB) in CHCl₃/isooctane are used to host penicillin acylase and to perform amide synthesis in which the product is perferentially soluble in the organic solvent mixture. The reaction is studied as a function of pH and certain micellar parameters, e. g. w_o (w_o = [H₂O]/[CTAB]). A new membrane enzyme reactor is utilized to separate the product from the enzyme-containing micelles. The adavantges and the limits of this approach are discussed.     

Effect of Solvent and Protonation/Deprotonation on Electrochemistry,Spectroelectrochemistry and Electron‐Transfer Mechanisms of N‐Confused Tetraarylporphyrins in Nonaqueous Media

A series of N‐confused free‐base meso‐substituted tetraarylporphyrins was investigated by electrochemistry and spectroelectrochemistry in nonaqueous media containing 0.1 M tetra‐n‐butylammonium perchlorate (TBAP) and added acid or base. The investigated compounds are represented as (XPh)₄NcpH₂, in which “Ncp” is the N‐confused porphyrin macrocycle and X is a OCH₃, CH₃, H, or Cl substituent on the para position of each meso‐phenyl ring of the macrocycle. Two distinct types of UV/Vis spectra are initially observed depending upon solvent, one corresponding to an inner‐2H form and the other to an inner‐3H form of the porphyrin. Both forms have an inverted pyrrole with a carbon inside the cavity and a nitrogen on the periphery of the π‐system. Each porphyrin undergoes multiple irreversible reductions and oxidations. The first one‐electron addition and first one‐electron abstraction are located on the porphyrin π‐ring system to give π‐anion and π‐cation radicals with a potential separation of 1.52 to 1.65 V between the two processes, but both electrogenerated products are unstable and undergo a rapid chemical reaction to give new electroactive species, which were characterized in the present study. The effect of the solvent and protonation/deprotonation reactions on the UV/Vis spectra, redox potentials and reduction/oxidation mechanisms is discussed with comparisons made to data and mechanisms for the structurally related free‐base corroles and porphyrins.     

Capillary liquid chromatography with off-line mid-IR and Raman micro-spectroscopic detection: analysis of chlorinated pesticides at ppb levels

A flow-through microdispenser was used as a solvent elimination interface, allowing vibrational spectroscopic detection in capillary liquid chromatography in addition to standard UV detection. Using a flow-through microdispenser, robust and stable deposition of picoliter-sized droplets on a CaF₂ plate window was achieved. The CaF₂ window was placed on a thermostated sample holder (80 °C) mounted on a computerized x, y stage for achieving fast solvent evaporation and enabling recording of the chromatogram as a trace of deposited material. The dried residues that were formed had diameters of a few tens of micrometers and were analysed by mid-IR and Raman micro-spectroscopy. Conditions were optimized for high sensitivity of measurement and maintaining chromatographic resolution during the deposition step. Due to the destruction-free character of Raman and FTIR spectroscopy, these techniques could be applied sequentially to interrogate the same deposits. To test the usefulness of the methodology for environmental analysis, the determination and unambiguous identification of chlorinated pesticides (chlortoluron, diuron, atrazine, and terbuthylazine) in river water was used as an example, obtaining limits of identification of 2 ng analyte on-column and precision of approximately 10% RSD. The application of the developed method to spiked real river samples demonstrated the identification power of the proposed method as, in addition to the four previously studied pesticides, two additional pesticides (simazine and isoproturon) could also be detected and identified.     

2‐Phenanthrenyl–DNA: Synthesis,Pairing, and Fluorescence Properties

Three 2′‐phenanthrenyl‐C‐deoxyribonucleosides with donor (phenNH₂), acceptor (phenNO₂), or no (phenH) substitution on the phenanthrenyl core were synthesized and incorporated into oligodeoxyribonucleotides. Duplexes containing either one or three consecutive phenR residues, which were located opposite each other, were formed. Within these residues, the phenR residues are expected to recognize each other through interstrand stacking interactions, in much the same way as described previously for biphenyl DNA. The thermal, thermodynamic, and fluorescence properties of such duplexes were determined by UV melting analysis and fluorescence spectroscopy. Depending on the nature of the substituent, the thermal stability of single‐modified duplexes can vary between ?2.7 to +11.3 °C in T_m and that of triple‐modified duplexes from +7.8 to +11.1 °C. Van′t Hoff analysis suggested that the observed higher thermodynamic stability in phenH‐ and phenNO₂‐containing duplexes is of enthalpic origin. A single phenH or phenNO₂ residue in a bulge position also stabilizes a corresponding duplex. If a phenNO₂ residue is placed in a bulge position next to a base mismatch this can lead, in a sequence‐dependent manner, to duplex destabilization. The phenNO₂ residue was found to be a highly efficient (10–100‐fold) quencher of phenH and phenNH₂ fluorescence if placed in the opposite position to the fluorophores. When phenH and phenNH₂ residues were placed opposite each other, efficient quenching of phenH and enhancement of phenNH₂ fluorescence was found, which is an indicator for electron‐ or energy‐transfer processes between the aromatic units.