Interaction of the C14-OH group of adriamycin with DNA phosphate as spectroscopically evidenced

Monitoring the band of the antisymmetric stretching vibration of the backbone PO-2 group in DNA-anthracycline complexes demonstrates an extraordinary wavenumber shift for the adriamycin complex compared to that of daunomycin. The structures of both anthracyclines, however, are very closely related and differ only by a surplus hydroxyl group of adriamycin in the C14 position. The wavenumber shift observed for the DNA-adriamycin complex is unequivocally attributed to an additional linkage of the C14-OH of adriamycin to the phosphate group of DNA. Thus, several of the hypothetical structural models for the DNA-adriamycin complex for which a hydrogen bond between the C14 hydroxyl of the drug and DNA phosphate was postulated (S. Neidle, Cancer Treatment Rep. 61, 928 (1977); G. J. Quigley et. al., Proc. Natl. Acad. Sci. USA 77, 7204 (1980)) get the first clear-cut experimental evidence.     

Interaction of adriamycin with DNA as studied by resonance Raman spectroscopy.

Raman and resonance Raman spectra of the complex DNA-adriamycin in aqueous solution have been recorded and analysed. Calf thymus DNA was used and it is found that in the complex DNA-adriamycin the chromophore of adriamycin is intercalated in the GC sequences. The substituents on the rings give hydrogen bonding interactions with the base pairs above and below the intercalation site. It is suggested from the Raman and resonance Raman spectral modifications that the phenolic groups of the chromophore are involved in the drug-DNA intercalation, in addition to pi-pi, hydroxyl and amino group interactions.     

Interaction between poly(L-lysine48, L-histidine52) and DNA.

Poly(Lys⁴⁸, His⁵²), a random copolypeptide of L -lysine (48%) and L -histidine (52%), was used as a model protein for investigating the effects of protonation on the imidazole group of histidines on protein binding to DNA. The complexes formed between poly(Lys⁴⁸, His⁵²) and DNA were examined using absorbance, circular dichroism (CD), and thermal denaturation. Although increasing pH reduces the charges on histidine side chains in the model protein, the protein still binds the DNA with approximately one positive charge per negative charge in protein-bound regions. Nevertheless, CD and melting properties of poly(Lys⁴⁸, His⁵²)-DNA complexes still depend upon the solution pH which determines the protonation state of imidazole group of histidine side chains. At pH 7.0, the complexes show two characteristic melting bands with a t_m (46–51°C) for free base pairs and a t′_m (94°C) for protein-bound base pairs. The t′_m of the complexes is reduced to 90°C at pH 9.2, although at this pH there is still one lysine per phosphate in protein-bound regions. Presumably, the presence of deprotonated histidine residues destabilizes the native structure of protein-bound DNA. The binding of this model protein to DNA causes a red shift of the crossover point and both a red shift and a reduction of the positive CD band of DNA near 275 nm. This phenomenon is similar to that caused by polylysine binding. These effects, however, are greatly diminished when histidine side chains in the model protein are deprotonated. The structure of already formed poly(Lys⁴⁸, His⁵²)·DNA complexes can be perturbed by changing the solution pH. However, the results suggest a readjustment of the complex to accommodate charge interactions rather than a full dissociation of the complex followed by reassociation between the model protein and DNA.     

Comparison of acetate- and pyruvate-dependent fatty-acid synthesis by spinach chloroplasts

In recent studies using intact chloroplasts of spinach (Spinacia oleracea L.) to investigate the accumulation of acetyl-CoA produced by the activity of either acetyl-CoA synthetase (EC 6.2.1.1) or the pyruvate-dehydrogenase complex, this product was not detectable. These results in combination with new information on the physiological levels of acetate and pyruvate in spinach chloroplasts (H.-J. Treede et al. 1986, Z. Naturforsch. 41 C, 733–740) prompted a reinvestigation of the incorporation of [1-¹⁴C] acetate and [2-¹⁴C] pyruvate into fatty acids at physiological concentrations.The K _m for the incorporation into fatty acids was about 0.1 mM for both metabolites and thus agreed with the values obtained by H.-J. Treede et al. (1986) for acetyl-CoA synthetase and the pyruvate dehydrogenase complex. However, acetate was incorporated with a threefold higher V _max. Saturation for pyruvate incorporation into the fattyacid fraction was achieved only at physiological pyruvate concentrations (<1.0 mM). The diffusion kinetics observed at higher concentrations may be the result of contamination with derivates of the labeled substrate. Competition as well as double-labeling experiments with [³H]acetate and [2-¹⁴C]pyruvate support the notion that, at least in spinach, chloroplastic acetate is the preferred substrate for fatty-acid synthesis when both substrates are supplied concurrently (P.G. Roughan et al., 1979 b, Biochem. J. 184, 565–569).Experiments with spinach leaf discs confirmed the predominance of fatty-acid incorporation from acetate. Radioactivity from [1-¹⁴C]acetate appeared to accumulate in glycerolipids while that from [2-¹⁴C]pyruvate was apparently shifted in favor of the products of prenyl metabolism.Abbreviations Chl chlorophyll - TLC thin-layer chromatography     

Improved NMR spectra of a protein–DNA complex through rational mutagenesis and the application of a sensitivity optimized isotope-filtered NOESY experiment

The NMR spectra of the complex between the DNA-binding domain of the Dead ringer protein (DRI-DBD, Gly262-Gly398) and its DNA binding site (DRI-DBD:DNA, 26 kDa) have been optimized by biochemical and spectroscopic means. First, we demonstrate the utility of a modified 2D [F1,F2] ¹³C-filtered NOESY experiment that employs a ¹J_HC versus chemical shift optimized adiabatic ¹³C inversion pulse [Zwahlen, C. et al. (1997) J. Am. Chem. Soc., 119, 6711–6721]. The new sequence is shown to be more sensitive than previously published pulse schemes (up to 40% in favorable cases) and its utility is demonstrated using two protein–DNA complexes. Second, we demonstrate that the targeted replacement of an interfacial aromatic residue in the DRI-DBD:DNA complex substantially reduces line broadening within its NMR spectra. The spectral changes are dramatic, salvaging a protein–DNA complex that was originally ill suited for structural analysis by NMR. This biochemical approach is not a general method, but may prove useful in the spectral optimization of other protein complexes that suffer from interfacial line broadening caused by dynamic changes in proximal aromatic rings.     

DNA-Carbohydrate Interaction. The Effects of Mono- and Disaccharides on the Solution Structure of Calf-Thymus DNA

Abstract

We report the interaction of calf-thymus DNA with D-glucose, D-fructose, D-galactose and sucrose in aqueous solution at physiological pH with sugar/DNA(P)(P=phosphate) molar ratios (r) of 1/10,1/5,1,5 and 10. FTIR difference spectroscopy was used to characterize the nature of sugar-DNA interaction and correlations between spectral changes and structural variations for both sugar and DNA complexes have been established.

FTIR difference spectroscopic results showed major sugar interaction (H-bonding) with the P0₂ groups of the backbone at low sugar concentrations (r= 1/10 and 1/5). Such interaction was characterized by the shift and the intensity variations of the backbone P0₂ antisymmetric stretch at 1222 cm^?1, which resulted in a major helical stability of DNA duplex. As sugar concentration increased, carbohydrate binding to DNA bases occurred. Evidence for this comes from major shiftings of the sugar O-H stretching vibrations at 3500–3200 cm^?1, and sugar C-O stretches and OH bending modes at 1450–1000 cm”. Similarly, shifting and intensity variations of several DNA in-plane vibrations at 1717 (G,T), 1663 (T,G,A,C) and 1492 cm^?1 (C,G) were observed, that are characterized by the presence of sugar-base interaction (via H₂0). The shiftings and the intensity changes of the sugar OH stretching modes at 35003200 cm^?1 are also indicative of the rearrangements of the sugar intermolecular H-bonding network, on DNA complex formation. A partial B to A conformational transition was observed for DNA molecule on sugar complexation, whereas carbohydrate binding occurred via both a- and β-anomeric structures.     

Subsidiary hydrogen bonding of intercalated anthraquinonic anticancer drugs to DNA phosphate

Several anthraquinone derivatives are active against different kinds of human cancer. The cancerostatic activity has been mainly attributed to their ability to bind strongly to DNA by intercalation. Here, infrared spectroscopy was used to detect further, more specific DNA interactions with the prominent anticancer drugs daunomycin, adriamycin, aclacinomycin A and mitoxantrone as well as with the cytotoxic violamycin BI. The most striking result was a significant decrease in wave number of the band arising from antisymmetric stretching vibration of the PO2- groups of DNA upon complexation with adriamycin, aclacinomycin A, violamycin BI and mitoxantrone. This became evident after separation of the contributions from conformational changes of DNA to the influence on the wave number of that band. The drug-induced shift was interpreted in terms of the formation of a hydrogen bond between the intercalated drug molecules and the PO2- moiety of DNA via the following terminal hydroxyl groups: C14-OH for adriamycin, C4-OH for both aclacinomycin A and violamycin BI and, more tentatively, the external side-chain OH of mitoxantrone. Theoretical considerations, consisting of semi-empirical CNDO/2 calculations as well as normal coordinate analyses performed with molecular model fragments, provided results confirming and rationalising the experimental findings. The capacities of the anthracyclines for restriction of the conformational flexibility of DNA differ, presumably due to variations in the spatial dimensions of the sugar moieties of the drugs. The compatibility of the present results with data obtained from current geometrical models, especially those for the DNA-daunomycin and DNA-adriamycin complexes, is discussed in detail.     

93 Spectroscopic investigation of methylene blue binding to DNA

The interaction of methylene blue (MB) with DNA has been investigated by UV absorption spectra, Fluorescence spectra and UV-melting method. Analysis of the results of the melting experiments shows that melting temperature (T _m) of the complexes increases with the [total ligand]: DNA ratio (r) at two concentrations of Na⁺ (2?mM Na⁺ and 20?mM Na⁺) providing support for conclusion that MB is a stabilizer of DNA helix structure. By contrast, the shapes of dependences of width of transition (ΔT) on r at low and high [Na⁺] are different which points to the existence of different types of binding modes of MB with DNA. UV-spectroscopy experiments and fluorescence spectra indicated that the binding modes of MB with DNA depended on r. At high r (r?>?0.25), remarkable hypochromic effect with no shift of λ _max in the absorption spectra of MB was observed. The fluorescence of MB was quenched which indicated that MB was bound to phosphate groups of DNA by electrostatic interaction. At low r ratios (r?<?0.2), the absorption spectra of MB upon increasing the concentration of DNA showed gradually decrease in the peak intensities with a red shift. This phenomenon is usually associated with molecular intercalation into the base stack of the ds-DNA. Using the Scatchard’s model, the complex formation constants for MB with DNA were determined: the binding constant K?≈?6.5?×?10⁵ and binding site size n?≈?4. Obtained data are not typical for intercalation model of ligands to DNA. Moreover, comparison between these data and our early experimental results of interaction of ethidium bromide with DNA made it possible to suggest that this binding type of MB is, more probably, semi-intercalation mode (Vardevanyan et al., 2003). This conclusion is in accordance with the analysis of the model structures of MB–DNA complexes which clearly shows the importance of solvent contributions in suggested structural form (Tong et al., 2010).     

New dinuclear copper(II) and zinc(II) complexes for the investigation of sugar–metal ion interactions

We have studied the binding interactions of biologically important carbohydrates (d-glucose, d-xylose and d-mannose) with the newly synthesized five-coordinate dinuclear copper(II) complex, [Cu₂(hpnbpda)(μ-OAc)] (1) and zinc(II) complex, [Zn₂(hpnbpda)(μ-OAc)] (2) [H₃hpnbpda = N,N′-bis(2-pyridylmethyl)-2-hydroxy-1,3-propanediamine-N,N′-diacetic acid] in aqueous alkaline solution. The complexes 1 and 2 are fully characterized both in solid and solution using different analytical techniques. A geometrical optimization was made of the ligand H₃hpnbpda and the complexes 1 and 2 by molecular mechanics (MM+) method in order to establish the stable conformations. All carbohydrates bind to the metal complexes in a 1:1 molar ratio. The binding events have been investigated by a combined approach of FTIR, UV–vis and ¹³C NMR spectroscopic techniques. UV–vis spectra indicate a significant blue shift of the absorption maximum of complex 1 during carbohydrate coordination highlighting the sugar binding ability of complex 1. The apparent binding constants of the substrate-bound copper(II) complexes have been determined from the UV–vis titration experiments. The binding ability and mode of binding of these sugar substrates with complex 2 are indicated by their characteristic coordination induced shift (CIS) values in ¹³C NMR spectra for carbon atoms C1, C2, and C3 of sugar substrates.     

Efficacy and site specificity of hydrogen abstraction from DNA 2-deoxyribose by carbonate radicals

The carbonate radical anion CO₃^?? is a potent reactive oxygen species (ROS) produced in vivo through enzymatic one-electron oxidation of bicarbonate or, mostly, via the reaction of CO₂ with peroxynitrite. Due to the vitally essential role of the carbon dioxide/bicarbonate buffer system in regulation of physiological pH, CO₃^?? is arguably one of the most important ROS in biological systems. So far, the studies of reactions of CO₃^?? with DNA have been focused on the pathways initiated by oxidation of guanines in DNA. In this study, low-molecular products of attack of CO₃^?? on the sugar–phosphate backbone in vitro were analyzed by reversed phase HPLC. The selectivity of damage in double-stranded DNA (dsDNA) was found to follow the same pattern C4′ > C1′ > C5′ for both CO₃^?? and the hydroxyl radical, though the relative contribution of the C1′ damage induced by CO₃^?? is substantially higher. In single-stranded DNA (ssDNA) oxidation at C1′ by CO₃^?? prevails over all other sugar damages. An approximately 2000-fold preference for 8-oxoguanine (8oxoG) formation over sugar damage found in our study identifies CO₃^?? primarily as a one-electron oxidant with fairly low reactivity toward the sugar–phosphate backbone.     

Residue Specific Ribose and Nucleobase Dynamics of the cUUCGg RNA Tetraloop Motif by MNMR 13C Relaxation

The dynamics of the nucleobase and the ribose moieties in a 14-nt RNA cUUCGg hairpin-loop uniformly labeled with ¹³C and ¹⁵N were studied by ¹³C spin relaxation experiments. R₁, R_1ρ and the ¹³C-{¹H} steady-state NOE of C₆ and C_1′ in pyrimidine and C₈ and C_1′ in purine residues were obtained at 298 K. The relaxation data were analyzed by the model-free formalism to yield dynamic information on timescales of pico-, nano- and milli-seconds. An axially symmetric diffusion tensor with an overall rotational correlation time τ_c of 2.31±0.13 ns and an axial ratio of 1.35±0.02 were determined. Both findings are in agreement with hydrodynamic calculations. For the nucleobase carbons, the validity of different reported ¹³C chemical shift anisotropy values (Stueber, D. and Grant, D. M., 2002 J. Am. Chem. Soc. 124, 10539–10551; Fiala et al., 2000 J. Biomol. NMR 16, 291–302; Sitkoff, D. and Case, D. A., 1998 Prog. NMR Spectroscopy 32, 165–190) is discussed. The resulting dynamics are in agreement with the structural features of the cUUCGg motif in that all residues are mostly rigid (0.82 < S² < 0.96) in both the nucleobase and the ribose moiety except for the nucleobase of U7, which is protruding into solution (S² = 0.76). In general, ribose mobility follows nucleobase dynamics, but is less pronounced. Nucleobase dynamics resulting from the analysis of ¹³C relaxation rates were found to be in agreement with ¹⁵N relaxation data derived dynamic information (Akke et al., 1997 RNA 3, 702–709). Electronic supplementary material Electronic supplementary material is available for this article at and accessible for authorised users.     

Sequence Specific Molecular Recognition and Binding of a Monocationic Bis-Imidazole Lexitropsin to the Decadeoxyribonucleotide d-[(GATCCGTATG) (CATACGGATC)]: Structural and Dynamic Aspects of Intermolecular Exchange Studied by 1H-NMR

Abstract

The non-exchangeable and imino proton NMR resonances of the non self-complementary decadeoxyribonucleotide d-[(GATCCGTATG) · (GATACGGATC)] as well as those of the 1:1 complex of the monocatonic bis-imidazole lexitropsin 1 to this sequence have been assigned by using a combination of NOE difference, COSY and NOESY techniques. Confirmation of complete annealing of the two non self-complementary decamer strands to give the duplex decadeoxyribonucleotide is obtained by the detection of ten imino protons. It is established that the sugar-base orientations of all the bases in the duplex decamer are anti. From NOE studies, it is concluded that the duplex oligomer is right-handed and adopts a conformation in solution that belongs to the B family. A population analysis reveals that the sugar moieties exist predominantly in the S-form (2′-endo-3′-exo). Addition of 1 to the DNA solution leads to doubling of the resonances for CH6(4,5), GH8(6), TH6(7) and T-CH₃(7). The base, anomeric H1′ and imino proton signals for the base sequence 5′-CCGT undergo the most marked drug-induced chemical shift changes. These results provide evidence that the lexitropsin is bound to the sequence 5′-CCGT in the minor groove of the DNA NOE measurements between the amide protons (NH1 and NH4) and the imino proton (IV and V) signals confirmed the location and orientation of 1 in the 1:1 complex, with the amino terminus oriented to C(4). The specific binding of 1 to the sequence 5′-CCGT-3′ deduced in this study is in agreement with the footprinting data obtained using the Hind III/Nci I fragment from pBR322 DNA [Kissinger et al. 1987 (13)]. Intramolecular NOEs observed between H4 and H9 of the lexitropsin suggest that the molecule is not planar, but subjected to propeller twisting, in both the free and bound forms. Furthermore, NOE measurements permit assignment of the DNA duplex in the 1:1 complex to the B-form, which is similar to that of the free DNA The [(T₇A₈T₉)· (A₁₂T₁₃A₁₄)] segment of the DNA shows better stacking, by propeller twisting, compared to the rest of the molecule in the free as well as the complex forms. The intermolecular rate of exchange of 1 between the equivalent 5′-CCGT sites, at a concentration of 12 mM, is estimated to be ～88s^?1 at 308°K with ΔG≠ of 63±5 K.J mol^?1.     

Flexibility of DNA and RNA upon Binding to Different Metal Cations. An Investigation of the B to A to Z Conformational Transition by Fourier Transform Infrared Spectroscopy

Abstract

The interaction of DNA and RNA with Cu(II), Mg(II), [Co(NH₃)₆]³⁺ [Co(NH₃)₅Cl]²⁺ chlorides and, cis- and trans-Pt(NH₃)₂Cl₂ (CIS-DDP, trans-DDP) has been studied by Fourier Transform Infrared (FT-IR) spectroscopy and a correlation between metal-base binding and conformational transitions in the sugar pucker has been established. It has been found that RNA did not change from A-form on complexation with metals, whereas DNA exhibited a B to Z transition. The marker bands for the A-form (C′₃-endo-anti conformation) were found to be near 810–816 cm^?1, while the bands at 825 and 690 cm^?1 are marker bands for the B- conformation (C′₂-endo, anti), The B to Z (C₃′-endo, syn conformation) transition is characterized by the shift of the band at 825 cm^?1 to 810–816 cm^?1 and the shift of the guanine band at 690 cm^?1 to about 600–624 cm^?1.     

Time and concentration dependence of the dicyclohexylcarbodiimide inhibition of proton movements in the cytochromebc 1 complex from yeast mitochondria reconstituted into proteoliposomes

The cytochromebc ₁ complex was isolated from yeast mitochondria solubilized with the detergent dodecyl maltoside and reconstituted into proteoliposomes to measure electrogenic proton pumping. Optimal respiratory control ratios of 4.0, obtained after addition of the uncoupler CCCP, and H⁺/e ^– ratios of 1.6 were obtained when the proteoliposomes were prepared with egg yolk phosphatidylcholine supplemented with cardiolipin. Moreover, it was critical to remove excess dodecyl maltoside in the final concentrated preparation prior to reconstitution to prevent loss of enzymatic activity. The rate of electrogenic proton pumping, the respiratory control ratios, and the H⁺/e ^– ratios were decreased by incubation of the cytochromebc ₁ complex with dicyclohexylcarbodiimide (DCCD) in a time and concentration dependent manner. Maximum inhibitions were observed when 50 nmol DCCD per nmol of cytochromeb were incubated for 30 min at 12°C with the intact cytochromebc ₁ complex. Under these same conditions maximum labeling of cytochromeb with [¹⁴C] DCCD was reported in a previous study [Beattieet al. (1984).J. Biol. Chem. 259, 10562–10532] consistent with a role for cytochromeb in electrogenic proton movements.     

Über O-Demethylierung und Decarboxylierung von Benzoesäuren in pflanzlichen Zellsuspensionskulturen

Summary Various benzoic acids ¹⁴C-labelled in para and meta methoxyl groups as well as (O-methyl-¹⁴C) p-methoxy cinnamic acid were tested for O-demethylation in cell suspension cultures of Phaseolus aureus Roxb. and Glycine max Merr. On the basis of ¹⁴CO₂-formation and product analyses the O-demethylation reactions were shown to be specific for para methoxyl groups. A vanillate-O-demethylase known from microbial sources seemed to be absent in the plant cell cultures.In this and in an earlier publication (Berlin et al., 1971) some twenty ¹⁴C-labelled aromatic compounds were tested for catabolic reactions in the cell cultures, and here we report on the product analyses and the general pattern of distribution of radioactivity. Finally, some indications for compartmentalisation in connection with catabolic studies of aromatic compounds in plant cell cultures are discussed.Decarboxylation of substituted benzoic acids in the cell cultures is restricted to aromatic acids possessing a hydroxyl group in the para position. Only trace amounts of labelled CO₂ were released from (carboxyl-¹⁴C)-anisic acid. This acid, however, was nearly quantitatively demethylated to p-hydroxybenzoic acid, which itself was decarboxylated to a considerable extent after being fed to cell suspension cultures. Similar differences in respect to decarboxylation were observed with syringic acid produced by demethylation of trimethoxybenzoic acid and syringic acid applied directly to the cell cultures.     

A Renaissance Man: In Memoriam of Jon Widom (1955–2011)

Abstract

Assignment of the ¹H and ³¹P resonances of a decamer DNA duplex, d(CGCTTAAGCG)₂ was determined by two-dimensional COSY, NOESY and ¹H- ³¹P Pure Absorption phase Constant time (PAC) heteronuclear correlation spectroscopy. The solution structure of the decamer was calculated by an iterative hybrid relaxation matrix method combined with NOESY-distance restrained molecular dynamics. The distances from the 2D NOESY spectra were calculated from the relaxation rate matrix which were evaluated from a hybrid NOESY volume matrix comprising elements from the experiment and those calculated from an initial structure. The hybrid matrix-derived distances were then used in a restrained molecular dynamics procedure to obtain a new structure that better approximates the NOESY spectra. The resulting partially refined structure was then used to calculate an improved theoretical NOESY volume matrix which is once again merged with the experimental matrix until refinement is complete. J_H3′-P coupling constants for each of the phosphates of the decamer were obtained from ¹H-³¹P J-resolved selective proton flip 2D spectra. By using a modified Karplus relationship the C4′-C3′-03′-P torsional angles (?) were obtained. Comparison of the ³¹P chemical shifts and J_H3′-P coupling constants of this sequence has allowed a greater insight into the various factors responsible for ³¹P chemical shift variations in oligonucleotides. It also provides an important probe of the sequence-dependent structural variation of the deoxyribose phosphate backbone of DNA in solution. These correlations are consistent with the hypothesis that changes in local helical structure perturb the deoxyribose phosphate backbone. The variation of the ³¹P chemical shift, and the degree of this variation from one base step to the next is proposed as a potential probe of local helical conformation within the DNA double helix. The pattern of calculated ? and ζ torsional angles from the restrained molecular dynamics refinement agrees quite well with the measured J_H3′-P coupling constants. Thus, the local helical parameters determine the length of the phosphodiester backbone which in turn constrains the phosphate in various allowed conformations.     

Structure and DNA binding characteristics of the three‐Cys2His2 domain of mouse testis zinc finger protein

The C‐terminal three‐Cys₂His₂ zinc‐finger domain (TZD) of mouse testis zinc‐finger protein binds to the 5′‐TGTACAGTGT‐3′ at the Aie1 (aurora‐C) promoter with high specificity. Interestingly, the primary sequence of TZD is unique, possessing two distinct linkers, TGEKP and GAAP, and distinct residues at presumed DNA binding sites at each finger, especially finger 3. A K_d value of ～10^?8 M was obtained from surface plasmon resonance analysis for the TZD‐DNA complex. NMR structure of the free TZD showed that each zinc finger forms a typical ββα fold. On binding to DNA, chemical shift perturbations and the R₂ transverse relaxation rate in finger 3 are significantly smaller than those in fingers 1 and 2, which indicates that the DNA binding affinity in finger 3 is weaker. Furthermore, the shift perturbations between TZD in complex with the cognate DNA and its serial mutants revealed that both ADE7 and CYT8, underlined in 5′‐ATATGTACAGTGTTAT‐3′, are critical in specific binding, and the DNA binding in finger 3 is sequence independent. Remarkably, the shift perturbations in finger 3 on the linker mutation of TZD (GAAP mutated to TGEKP) were barely detected, which further indicates that finger 3 does not play a critical role in DNA sequence‐specific recognition. The complex model showed that residues important for DNA binding are mainly located on positions ?1, 2, 3, and 6 of α‐helices in fingers 1 and 2. The DNA sequence and nonsequence‐specific bindings occurring simultaneously in TZD provide valuable information for better understanding of protein–DNA recognition. Proteins 2010. © 2010 Wiley‐Liss, Inc.     

Activity of the pentose phosphate pathway during lignification

Summary We did this work to see if there is a correlation between lignin synthesis and the activity of the pentose phosphate pathway. Excision of the third internode of the stem of Coleus blumei Benth. followed by incubation on sucrose and indoleacetic acid led to extensive formation of tracheids. During this lignification we determined the activities of glucose-6-phosphate dehydrogenase and fructose-1,6-diphosphate aldolase, and the extent to which [1-¹⁴C]-,[3,4-¹⁴C]-, and [6-¹⁴C]glucose labelled CO₂ and the major cellular components. The results indicate that the pentose phosphate pathway was active during lignification, and that the activity of this pathway relative to glycolysis increased at the onset of lignification. Explants of storage tissue of Helianthus tuberosus L. were cultured under conditions which caused extensive lignification. ¹⁴CO₂ production from [1-¹⁴C]-, [3,4-¹⁴C]-, and [6-¹⁴C]glucose indicated activity of the pentose phosphate pathway during tracheid formation. We suggest that lignification is accompanied by appreciable activity of the pentose phosphate pathway and that this could provide the reducing power for lignin synthesis.Abbreviations NADP nicotinamide-adenine dinucleotide phosphate - IAA indoleacetic acid     

DNA Binding,Antioxidant Activity,and DNA Damage Protection of Chiral Macrocyclic Mn(III) Salen Complexes

We are reporting the synthesis, characterization, and calf thymus DNA binding studies of novel chiral macrocyclic Mn(III) salen complexes S‐1 , R‐1 , S‐2 , and R‐2 . These chiral complexes showed ability to bind with DNA, where complex S‐1 exhibits the highest DNA binding constant 1.20 × 10⁶ M^?1. All the compounds were screened for superoxide and hydroxyl radical scavenging activities; among them, complex S‐1 exhibited significant activity with IC₅₀ 1.36 and 2.37 μM, respectively. Further, comet assay was used to evaluate the DNA damage protection in white blood cells against the reactive oxygen species wherein complex S‐1 was found effective in protecting the hydroxyl radicals mediated plasmid and white blood cells DNA damage. Chirality 24:1063–1073, 2012.© 2012 Wiley Periodicals, Inc.