Ruthenium(II)–arene complexes of diimines: Effect of diimine intercalation and hydrophobicity on DNA and protein binding and cytotoxicity

A series of half‐sandwich Ru(II)–arene complexes [Ru(η⁶‐benzene)(diimine)Cl](PF₆) ( 1 – 4 ), where diimine is 1,10‐phenanthroline ( 1 ), 5,6‐dimethyl‐1,10‐phenanthroline ( 2 ), dipyrido[3,2‐a:2′,3′‐c]phenazine ( 3 ) or 11,12‐dimethyldipyrido[3,2‐a:2′,3′‐c]phenazine ( 4 ), have been isolated and characterized using analytical and spectral methods. Complex 2 possesses a familiar pseudo‐octahedral ‘piano‐stool’ structure. The intrinsic DNA binding affinity of the complexes depends upon the diimine ligand: 3 (dppz) > 4 (11,12‐dmdppz) > 2 (5,6‐dmp) > 1 (phen). The π‐stacking interaction of extended planar ring of coordinated dppz ( 3 ) in between the DNA base pairs is more intimate than that of phen ( 1 ), and the incorporation of methyl groups on the dppz ring ( 4 ) discourages the stacking interaction leading to a lower DNA binding affinity for 4 than 3 . Docking studies show that all the complexes bind in the major groove of DNA. Interestingly, 3 shows an ability to convert supercoiled DNA into nicked circular DNA even at 20 μM concentration beyond which complete oxidative DNA degradation is observed. The protein binding affinity of the complexes decreases in the order 4 > 3 > 2 > 1 , and the higher protein binding affinity of 4 illustrates the strong involvement of methyl groups on dppz ring in hydrophobic interaction with protein. Also, 4 cleaves protein more efficiently than the other complexes in the presence of H₂O₂. It is notable that 2 , 3 and 4 display cytotoxicity against human cervical cancer cell lines (SiHa) with potency higher than the currently used drug cisplatin. Acridine orange/ethidium bromide staining studies reveal that 3 induces apoptosis in cancer cells much more efficiently than 4 .     

Density functional theory and topological analysis on the hydrogen bonding interactions in cysteine‐thymine complexes

Hydrogen bonding interactions between amino acids and nucleic acid bases constitute the most important interactions responsible for the specificity of protein binding. In this study, complexes formed by hydrogen bonding interactions between cysteine and thymine have been studied by density functional theory. The relevant geometries, energies, and IR characteristics of hydrogen bonds (H‐bonds) have been systematically investigated. The quantum theory of atoms in molecule and natural bond orbital analysis have also been applied to understand the nature of the hydrogen bonding interactions in complexes. More than 10 kinds of H‐bonds including intra‐ and intermolecular H‐bonds have been found in complexes. Most of intermolecular H‐bonds involve O (or N) atom as H‐acceptor, whereas the H‐bonds involving C or S atom usually are weaker than other ones. Both the strength of H‐bonds and the structural deformation are responsible for the stability of complexes. Because of the serious deformation, the complex involving the strongest H‐bond is not the most stable structures. Relationships between H‐bond length (ΔR_X‐H), frequency shifts (Δv), and the electron density (ρ_b) and its Laplace (?²ρ_b) at bond critical points have also been investigated. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Influence of β‐Alanine on Hairpin Polyamide Orientation in the DNA Minor Groove

Antiparallel polyamides containing 1H‐pyrrole, 1H‐imidazole, and 3‐hydroxy‐1H‐pyrrole amino acids display a preference for minor‐groove binding oriented N? C with respect to the 5′‐3′ direction of the DNA helix. We find that replacement of a central Py/Py pair with a β/β pair within a ten‐ring hairpin relaxes the orientation preference and, for some DNA sequences, causes the polyamide to prefer the opposite C? N orientation. Substitution of the achiral γ‐aminobutanoic acid (γ) with either (R)(or S)‐2‐(acetylamino)‐4‐aminobutanoic acid moderates the orientation preference of the 2‐β‐2‐hairpin.     

New anthracene based Schiff base ligands appended Cu(II) complexes: Theoretical study,DNA binding and cleavage activities

New anthracene based Schiff base ligands L ¹ and H( L ² ), their Cu(II) complexes [Cu( L ¹ )Cl₂] ( 1 ) and [Cu( L ² )Cl] ( 2 ) , (where L ¹  = N¹,N²‐bis(anthracene‐9‐methylene)benzene‐1,2‐diamine, L ²  = (2Z,4E)‐4‐(2‐(anthracen‐9‐ylmethyleneamino)phenylimino)pent‐2‐en‐2‐ol) have been prepared and characterized by elemental analysis, NMR, FAB‐mass, EPR, FT‐IR, UV–Vis and cyclic voltammetry. The electronic structures and geometrical parameters of complexes 1 and 2 were analyzed by the theoretical B3LYP/DFT method. The interaction of these complexes 1 and 2 with CT‐DNA has been explored by using absorption, cyclic voltammetric and CD spectral studies. From the electronic absorption spectral studies, it was found that the DNA binding constants of complexes 1 and 2 are 8.7 × 10³ and 7.0 × 10⁴ M^?1, respectively. From electrochemical studies, the ratio of DNA binding constants K₊/K₂₊ for 2 has been estimated to be >1. The high binding constant values, K₊/K₂₊ ratios more than unity and positive shift of voltammetric E_1/2 value on titration with DNA for complex 2 suggest that they bind more avidly with DNA than complex 1 . The inability to affect the conformational changes of DNA in the CD spectrum is the definite evidences of electrostatic binding by the complex 1 . It can be assumed that it is the bulky anthracene unit which sterically inhibits these complexes 1 and 2 from intercalation and thereby remains in the groove or electrostatic. The complex 2 hardly cleaves supercoiled pUC18 plasmid DNA in the presence of hydrogen peroxide. The results suggest that complex 2 bind to DNA through minor groove binding.     

Sensing of Double‐Stranded DNA/RNA Secondary Structures by Water Soluble Homochiral Perylene Bisimide Dyes

A broad series of homochiral perylene bisimide (PBI) dyes were synthesized that are appended with amino acids and cationic side chains at the imide positions. Self‐assembly behavior of these ionic PBIs has been studied in aqueous media by UV/Vis spectroscopy, revealing formation of excitonically coupled H‐type aggregates. The interactions of these ionic PBIs with different ds‐DNA and ds‐RNA have been explored by thermal denaturation, fluorimetric titration and circular dichroism (CD) experiments. These PBIs strongly stabilized ds‐DNA/RNA against thermal denaturation as revealed by high melting temperatures of the formed PBI/polynucleotide complexes. Fluorimetric titrations showed that these PBIs bind to ds‐DNA/RNA with high binding constants depending on the number of the positive charges in the side chains. Thus, spermine‐containing PBIs with six positive charges each showed higher binding constants (logK_s=9.2–9.8) than their dioxa analogues (logK_s=6.5–7.9) having two positive charges each. Induced circular dichroism (ICD) of PBI assemblies created within DNA/RNA grooves was observed. These ICD profiles are strongly dependent on the steric demand of the chiral substituents of the amino acid units and the secondary structure of the DNA or RNA. The observed ICD effects can be explained by non‐covalent binding of excitonically coupled PBI dimer aggregates into the minor groove of DNA and major groove of RNA which is further supported by molecular modeling studies.     

Two New 7‐Dehydrobrefeldin A Acids from Cylindrocarpon obtusisporum,an Endophytic Fungus of Trewia nudiflora

Two new 7‐dehydrobrefeldin A acids, (2E,4R*)‐4‐hydroxy‐4‐{(1R*,2S*)‐4‐oxo‐2‐[(1E)‐6‐oxohept‐1‐en‐1‐yl]cyclopentyl}but‐2‐enoic acid ( 3 ) and (2E,4R*)‐4‐hydroxy‐4‐{(1R*,2S*)‐2‐[(1E,6S*)‐6‐hydroxyhept‐1‐en‐1‐yl]‐4‐oxocyclopentyl}but‐2‐enoic acid ( 4 ), were isolated from the endophytic fungal strain Cylindrocarpon obtusisporum (Cooke & Harkness ) Wollenw . of Trewia nudiflora, together with two known compounds, 7‐dehydrobrefeldin A ( 2 ) and brefeldin A ( 1 ). Their structures were determined on the basis of extensive 1D‐ and 2D‐NMR‐spectral analysis.     

Dimeric Calixarenes: A New Family of Major‐Groove Binders

A new class of potent DNA binding agents is presented. Dimeric calix[4]arenes with cationic groups at their upper rims and flexible alkyl bridges can be synthesized from triply acyl‐protected calix[4]arene tetramines in relatively short synthetic sequences (3–5 steps). The compounds attach themselves to double‐stranded nucleic acids in a noncovalent fashion, with micro‐ to nanomolar affinities. Guanidinium headgroups with their extended hydrogen‐bonding “fingers” are more powerful than ammonium groups, and the benzylamine series is superior to the anilinium series (see below). The new ligands easily distinguish between RNA and various DNA types, and produce characteristic changes in UV/Vis, fluorescence, CD, as well as NMR spectra. Especially extended oligonucleotides of more than 100 base pairs are bound with affinities increasing from RNA (10 μM K_d)<AT‐rich (1 μM )<GC‐rich DNA double strands (100–10 nM ). Ethidium bromide displacement studies confirm this order. CE₅₀ values are remarkably low (1–4 μM ), and are more than 300 times lower than that of spermine, which is a typical backbone binder. Stoichiometries are rather high (one calixarene dimer per two BP), suggesting a potential aggregation of bound ligands inside the major groove. Most UV/Vis melting curves display an inverted shape, and start from drastically enhanced absorption intensities for the DNA complexes. DAPI displacement studies prove that up to one equivalent of calixarene dimer can be accommodated in the dye‐loaded DNA. RNA complexation by calixarene dimers is accompanied by a drastic CD spectral transition from the typical A‐form to a perfect B‐signature, providing further experimental evidence for major‐groove binding. The orientation of the ligands can be deduced from NMR titrations and is reproduced in Monte‐Carlo simulations on 1:1 complexes in water.     

Separation and recovery of nucleic acids with improved biological activity by acid‐degradable polyacrylamide gel electrophoresis

One of the fundamental challenges in studying biomacromolecules (e.g. nucleic acids and proteins) and their complexes in a biological system is isolating them in their structurally and functionally intact forms. Electrophoresis offers convenient and efficient separation and analysis of biomacromolecules but recovery of separated biomacromolecules is a significant challenge. In this study, DNAs of various sizes were separated by electrophoresis in an acid‐degradable polyacrylamide gel. Almost 100% of the nucleic acids were recovered after the identified gel bands were hydrolyzed under a mildly acidic condition and purified using anion exchange resin. Further concentration by centrifugal filtration and a second purification using ion exchange column chromatography yielded 44–84% of DNA. The second conventional (non‐degradable) gel electrophoresis confirmed that the nucleic acids recovered from acid‐degradable gel bands preserved their electrophoretic properties through acidic gel hydrolysis, purification, and concentration processes. The plasmid DNA recovered from acid‐degradable gel transfected cells significantly more efficiently than the starting plasmid DNA (i.e. improved biological activity via acid‐degradable PAGE). Separation of other types of nucleic acids such as small interfering RNA using this convenient and efficient technique was also demonstrated.     

Synthesis,characterization, DNA binding,photo-induced DNA cleavage,and antimicrobial activity of metal complexes of a Schiff base derived from bis(3-aminophenyl)malonamide

The peptide linkage Schiff base (H₂L) and its complexes have been synthesized and fully characterized by elemental analysis, UV–Vis, FTIR, ¹H-NMR, ¹³C-NMR, EPR, and FAB-mass spectra. The stoichiometry of the complexes is [ML] (where M = Cu(II), Co(II), Ni(II), Zn(II), and VO(IV)). All the complexes exhibit square-planar geometry except the vanadyl complex which has square-pyramidal geometry. Interactions of the complexes and free ligand with double-stranded calf thymus DNA (CT-DNA) are studied by UV-spectrophotometric, electrochemical, and viscosity measurements. The data suggest that all the complexes form adducts with DNA and distort the double helix by changing the base stacking. Vanadyl complex forms a weaker adduct to CT-DNA than other complexes, probably due to the square-pyramidal geometry. CT-DNA induces extensive distortion in the planarity of vanadyl complex as EPR spectral calculations reveal. The intrinsic binding constants (K _b) of [ZnL], [CuL], [CoL], and [NiL] are 1.1 × 10⁵, 1.4 × 10⁵, 0.8 × 10⁵, and 0.6 × 10⁵ M^?1, respectively. Photo-induced DNA cleavage indicates that all complexes cleave DNA effectively. Control DNA cleavage experiments using pUC19 supercoiled (SC) DNA and minor groove binder distamycin suggest major groove binding for the synthesized complexes. The antimicrobial results indicate that the complexes inhibit the growth of bacteria and fungi more than the free ligand.     

Negative Cooperativity in the Molecular Recognition of Excitatory Amino-Acid Derivatives by Synthetic Allosteric 1,1′-Binaphthalene Receptors

The optically active allosteric receptors (−)-(R,R)- 3 and (+)-(R,R)- 4 were synthesized for the molecular recognition of the N-(benzyloxy)carbonyl (N-Cbz)-protected excitatory amino acids aspartic acid (Asp, 1 ) and glutamic acid (Glu, 2 ). These macrocyclic structures consist of two 1,1′-binaphthalene moieties connected by two but-2-yne-1,4-diyl (for (−)-(R,R)- 3 ) or p-xylylene (for (+)-(R,R)- 4 ) bridges between the O-atoms in the minor grooves. Each 1,1′-binaphthalene moiety contains two 2-acetamidopyridin-6-yl (CONH(py)) H-bonding sites in the major groove to bind excitatory amino-acid derivatives via two COOH█bk█⋅⋅⋅█ek█CONH(py) H-bonding arrays and additional secondary electrostatic interactions. The formation of stable complexes with 1 : 2 host-guest stoichiometry was proven by the evaluation of fluorescence binding titrations using a multiple-wavelength nonlinear least-squares curve-fitting procedure, Job plot analysis, and solubilization experiments. Complexation of the first excitatory amino-acid guest at binding site 1 reduces the affinity for the second guest at binding site 2. As measures for the negative cooperativity between the two sites, the ratios of the association constants for the first and second binding events, {K_a(1 : 1)/K_a(1 : 2)}_corr. (corrected for the statistical preference of the 1 : 1 complex formation), were found to adopt values between 1.4 and 2.4, and the Hill coefficients n_H varied between 0.49 and 0.59.     

A Study of Interaction between Flavonoids and the Parallel Quadruplex Structure [d(TGGGGT)]4 by Electrospray Ionization Mass Spectrometry

In this study, electrospray ionization mass spectrometry (ESI‐MS) was used to investigate interaction of 21 flavonoids (10 aglycones and 11 glycosides) with the parallel quadruplex structure [d(TGGGGT)]₄. Relative binding affinities of flavonoids toward [d(TGGGGT)]₄ were estimated based on the fraction of bound DNA. It was found that [d(TGGGGT)]₄ showed a binding preference to the flavonoid glycosides over flavonoid aglycones. It was deduced that glycosylation played a key role for the [d(TGGGGT)]₄‐binding properties of flavonoid glycosides. Upon collision‐induced dissociation, complexes of flavonoid/[d(TGGGGT)]₄ underwent the loss of flavonoids, suggesting an end‐stacking binding mode. The current work demonstrates that ESI‐MS is a powerful tool in the study of interaction between drugs and nucleic acids.     

Chiral differentiation of some cyclic β‐amino acids by kinetic and fixed ligand methods

Differentiation of β ‐amino acid enantiomers with two chiral centres was investigated by kinetic method with trimeric metal‐bound complexes. Four enantiomeric pairs of β ‐amino acids were studied: cis‐(1R,2S)‐, cis‐(1S,2R)‐, trans‐(1R,2R)‐ and trans‐(1S,2S)‐2‐aminocyclopentanecarboxylic acids (cyclopentane β ‐amino acids), and cis‐(1R,2S)‐, cis‐(1S,2R)‐, trans‐(1R,2R)‐, and trans‐(1S,2S)‐2‐aminocyclohexanecarboxylic acids (cyclohexane β ‐amino acids). The results showed that the choice of metal ion (Cu²⁺, Ni²⁺) and chiral reference compound (α‐ and β ‐amino acids) had an effect on the enantioselectivity. Especially, aromaticity of the reference compound was noted to enhance the enantioselectivity. The fixed‐ligand kinetic method, a modification of the kinetic method, was then applied to the same β ‐amino acids, with dipeptides used as fixed ligands. With this method, dipeptide containing an aromatic side chain enhanced the enantioselectivity. Copyright © 2009 John Wiley & Sons, Ltd.     

Ultraviolet irradiation of tobacco leaves: inhibition of tobacco mosaic virus-ribonucleic acid photoreactivation

Abstract— Short-wave (254-nm) ultraviolet irradiation of the leaves of Nicotiana tabacum var. Xanthi, n.c. inhibits their ability to photoreactivate ultraviolet-inactivated tobacco mosaic virus ribonucleic acid (TMV-RNA). The inhibition is stable in the dark; however, subsequent illumination of the leaves relaxes the inhibition. The spectral region most effective in relaxing the inhibition is the same one effective in photoreactivation. These results are consistent with the hypothesis that ultraviolet-induced lesions in cellular nucleic acids in the dark form stable complexes with agents responsible for the photoreactivation of TMV-RNA (effectively isolating the agents from the TMV-RNA) and that upon illumination these complexes dissociate (presumably with repair of the lesions). We therefore suggest that the system which photoreactivates ultraviolet-damaged TMV-RNA also photorepairs ultraviolet damage in cellular nucleic acids.     

Solution Structure of a Hexitol Nucleic Acid Duplex with Four Consecutive T⋅T Base Pairs

The structure of the hexitol nucleic acid (HNA) h(GCGCTTTTGCGC) was determined by NMR spectroscopy. This unnatural nucleic acid was developed as a mimic for A‐RNA. In solution, the studied sequence is forming a symmetric double‐stranded structure with four central consecutive T⋅T wobble pairs flanked by G⋅C Watson‐Crick base pairs. The stem regions adopt an A‐type helical structure. Discrete changes in backbone angles are altering the course of the helix axis in the internal loop region. Two H‐bonds are formed in each wobble pair, and base stacking is preserved in the duplex, explaining the stability of the duplex. This structure elucidation provides information about the influence of a (T)₄ fragment on local helix geometries as well as on the nature of the T⋅T mismatch base pairing in a TTTT tract.     

Focusing and stabilization of bis‐intercalating dye–DNA complexes for high‐sensitive CE‐LIF DNA analysis

Multiple labeling of nucleic acids by intercalative dyes is a promising method for ultrasensitive nucleic acid assays. The properties of the fast dissociation and instability of dye–DNA complexes may prevent from their wide applications in CE‐LIF nucleic acid analysis. Here, we describe an optimum CE focusing method by using appropriately paired sample and separation buffers, Tris‐glycine buffer and Tris‐glycine‐acetic acid buffer. The developed method was applied in both uncoated and polyacrylamide coated fused‐silica capillary‐based CE‐LIF analysis while the sample and separation buffers were conversely used. The complexes of intercalative dye benzoxazolium‐4‐pyridinium dimer and dsDNA were greatly focused (separation efficiency: 1.8 million theoretical plates per meter) by transient isotachophoresis mechanism in uncoated capillary, and moderately focused by transient isotachophoresis in combination of field amplified sample stacking and further stabilized by the paired buffer in polyacrylamide coated capillary. Based on the developed focusing strategy, an ultrasensitive DNA assay was developed for quantitation of calf thymus dsDNA (from 0.02 to 2.14 pM). By the use of an excitation laser power as low as 1 mW, the detection limits of calf thymus dsDNA (3.5 kb) are 7.9 fM in concentration and 2.4×10^?22 mol (150 molecules) in mass. We further demonstrate that the non‐gel sieving CE‐LIF analysis of DNA fragments can be enhanced by the same strategy. Since the presented strategy can be applied to uncoated and coated capillaries and does not require special device, it is also reasonable to extend to the applications in chip‐based CE DNA analysis.     

NMR characterization of 1,1′‐binaphthyl‐2,2′‐diyl hydrogen phosphate binding to chiral molecular micelles

NMR spectroscopy was used to characterize the binding of the chiral compound 1,1′‐binaphthyl‐2,2′‐diyl hydrogen phosphate (BNP) to five molecular micelles with chiral dipeptide headgroups. Molecular micelles have covalent linkages between the surfactant monomers and are used as chiral mobile phase modifiers in electrokinetic chromatography. Nuclear overhauser enhancement spectroscopy (NOESY) analyses of (S)‐BNP:molecular micelle mixtures showed that in each solution the (S)‐BNP interacted predominately with the N‐terminal amino acid of the molecular micelle's dipeptide headgroup. NOESY spectra were also used to generate group binding maps for (S)‐BNP:molecular micelle mixtures. In these maps, percentages are assigned to the (S)‐BNP protons to represent the relative strengths of their interactions with a specified molecular micelle proton. All maps showed that (S)‐BNP inserted into a previously reported chiral groove formed between the molecular micelle's dipeptide headgroup and hydrocarbon chain. In the resulting intermolecular complexes, the (S)‐BNP protons nearest to the analyte phosphate group were found to point toward the N‐terminal Hα proton of the molecular micelle headgroup. Finally, pulsed field gradient NMR diffusion experiments were used to measure association constants for (R) and (S)‐BNP binding to each molecular micelle. These K values were then used to calculate the differences in the enantiomers' free energies of binding, Δ(ΔG). The NMR‐derived Δ(ΔG) values were found to scale linearly with electrokinetic chromatography (EKC) chiral selectivities from the literature. Copyright © 2010 John Wiley & Sons, Ltd.     

Chiral 1,1′-Binaphthyl Molecular Clefts for the Complexation of Excitatory Amino-Acid Derivatives

The complexation of N-benzyloxycarbonyl (Cbz) derivatives of the excitatory amino acids L -aspartic acid (Asp; 1 ), L -glutamic acid (Glu; 3 ), and, for the first time, L -kainic acid ((2S,3S,3S)-2-carboxy-4-(1-methylethenyl)pyrrolidine-3-acetic acid; Kai; 5 ) was studied in CDCl₃ with a diversity of chiral receptors consisting of a 1,1′-binaphthyl spacer with (carboxamido)pyridine (CONH(py)) functionality attached to the 6,6′-positions in the major groove. Receptors of type A possess two N-(pyridin-2-yl)carboxamide H-bonding sites (e.g. 7 ), whereas type B-receptors have two N-(pyridine-6,2-diyl)acetamide residues attached (e.g. 8 and 9 ). Complexes of excitatory amino-acid derivatives and other, achiral α,β-dicarboxylic acids with these receptors are primarily stabilized by two sets of C?O···H? N and O? H ··· N H-bonds. Optically active type-A receptors such as (R)- and (S)- 7 showed a preference for the larger Glu derivative, whereas type- B receptors such as (R)- and (S)- 8 and (R)- and (S)- 9 formed more stable complexes with the smaller Cbz-Asp. To improve the poor enantioselectivity shown by 7–9 , additional functionality was introduced at the 7,7′-positions of the 1,1′-binaphthyl spacer, and the nature of the H-bonding sites in the 6,6′-positions was varied. Screening the diversity of new racemic receptors for binding affinity, which had been shown in many examples by Cram to correlate with enantioselectivity, demonstrated that (+)- 10 and (+)- 11 formed the most stable complexes with dicarboxylic acids, and these receptors were synthesized in enantiomerically pure form. Both are type- B binders and contain additional PhCH₂O ( 10 ) and MeO ( 11 ) groups in the 7,7′-positions. By ¹H-NMR binding titrations, the complexation of (R)- and (S)- 10 and (R)- and (S)- 11 with the excitatory amino-acid derivatives was studied in CDCl₃, and association constants K_a between 10³ and 2 · 10⁵ l mol^?1 were measured for the 1:1 host-guest complexes formed. Whereas both 10 and 11 formed stable complexes, enantioselective binding was limited to the PhCH₂O-substituted receptor 10 , with the (R)-enantiomer complexing Cbz-Asp by 0.7 kcal mol^?1 more tightly than the (S)-enantiomer. The structures of the diastereoisomeric complexes were analyzed in detail by experimental methods (complexation-induced changes in ¹H-NMR chemical shifts, ¹H{¹H} nuclear Overhauser effect (NOE) difference spectroscopy) and computer modeling. These studies established that an unusual variety of interesting aromatic interactions and secondary electrostatic interactions are responsible for both the high binding affinity (? ΔG° up to 7.2 kcal mol^?1) and the enantioselection observed with (R)- and (S)- 10 . In an approach to enhance the enantioselectivity by reducing the conformational flexibility of the 1,1′-binaphthyl spacer, an additional crown-ether binding site was attached to the 2,2′-positions in the minor groove of the type- B receptors (R)- and (S)- 48 . Both the binding affinity and the enantioselectivity (Δ(ΔG°) up to 0.7 kcal mol^?1) in the complexation of the excitatory amino-acid derivatives by (R)- and (S)- 48 were not altered upon complexation of Hg(CN)₂ at the crown-ether binding site, demonstrating lack of cooperativity between the minor- and major-groove recognition sites.     

Fluorescence Quenching and Binding Interaction of l0-Methylacridinium Iodide to Nucleic Acids

Interaction of 10‐methylacridinium iodide (MAI) as fluorescence probe with nucleobases, nucleosides and nucleic acids has been studied by UV‐visible absorption and fluorescence spectroscopy. It was found that fluorescence of MAI is strongly quenched by the nucleobases, nucleosides and nucleic acids, respectively. The quenching follows the Stern‐Volmer linear equation. The fluorescence quenching rate constant (k_q) was measured to be 10^9‐10¹⁰ (L/mol)/s within the range of diffusion‐controlled rate limit, indicating that the interaction between MAI and nucleic acid and their precursors is characteristic of electron transfer mechanism. In addition, the binding interaction model of MAI to calf thymus DNA (ct‐DNA) was further investigated. Apparent hypochromism in the absorption spectra of MAI was observed when MAI binds to ct‐DNA. Three spectroscopic methods, which include (1) UV spectroscopy, (2) fluorescence quenching of MAI, (3) competitive dual‐probe method of MAI and ethidium bromide (EB), were utilized to determine the affinity binding constants (K) of MAI and ct‐DNA. The binding constants K obtained from the above methods gave consistent data in the same range (1.0–5.5) × 10⁴L/mol, which lend credibility to these measurements. The binding site number was determined to be 1.9. The influence of thermal denaturation and phosphate concentration on the binding was examined. The binding model of MAI to ct‐DNA including intercalation and outside binding was investigated.     

Stereoselection in the diels–alderase ribozyme: A molecular dynamics study

The Diels‐Alderase ribozyme is an in vitro‐evolved ribonucleic acid enzyme that catalyzes a [4 + 2] cycloaddition reaction between an anthracene diene and a maleimide dienophile. The ribozyme can in principle be used to selectively synthesize only one product enantiomer, depending on which of the two entrances to the catalytic pocket, “front” or “back”, the substrate is permitted to use. Here, we investigate stereoselection and substrate recognition in the ribozyme by means of multiple molecular dynamics simulations, performed on each of the two substrates individually in the pocket, on the reactant state, and on the product state. The results are consistent with a binding mechanism in which the maleimide likely binds first followed by the anthracene, which enters preferentially through the front door. The free energy profiles for anthracene binding indicate that the pre‐(R,R)‐enantiomer conformation is slightly preferred, in agreement with the experimentally observed small enantiomeric excess of the (R,R)‐enantiomer of the product. The reactant state is stabilized by the simultaneous presence of both substrates bound to their binding sites in the hydrophobic pocket as well as by stacking interactions between them. © 2012 Wiley Periodicals, Inc.     

Asymmetric Synthesis of All Possible Stereomers of 4‐Aminoglutamic Acid via Michael Condensation of Chiral Ni(II) Complexes of Glycine and Dehydroalanine

A new method for asymmetric synthesis of all possible stereomers of 4‐aminoglutamic acid has been developed. The method is based on asymmetric Michael condensation of the nucleophilic moiety of glycine and electrophilic moiety of dehydroalanine in their chiral Ni(II) complexes of the Schiff's bases with (S)‐ and (R)‐2‐N‐(N′‐benzylprolyl)aminobenzophenones, resulting in the formation of dimeric complexes of 4‐aminoglutamic acid. Stereoselectivity of the asymmetric condensation of the complexes exceeded 94%. The condensation of nucleophilic and electrophilic complexes in four possible combinations has resulted in the formation of dimeric complexes of all the stereomers of 4‐aminoglutamic acid: (2S,4S), (2S,4R)‐meso and (2R,4R). Optically active stereomers of 4‐aminoglutamic acid with high optical purity were isolated after decomposition of the dimeric complexes.