7‐Iodo‐5‐aza‐7‐deazaguanine ribonucleoside: crystal structure,physical properties,base‐pair stability and functionalization

The positional change of nitrogen‐7 of the RNA constituent guanosine to the bridgehead position‐5 leads to the base‐modified nucleoside 5‐aza‐7‐deazaguanosine. Contrary to guanosine, this molecule cannot form Hoogsteen base pairs and the Watson–Crick proton donor site N3—H becomes a proton‐acceptor site. This causes changes in nucleobase recognition in nucleic acids and has been used to construct stable `all‐purine' DNA and DNA with silver‐mediated base pairs. The present work reports the single‐crystal X‐ray structure of 7‐iodo‐5‐aza‐7‐deazaguanosine, C<sub>10</sub>H<sub>12</sub>IN<sub>5</sub>O<sub>5</sub> ( 1 ). The iodinated nucleoside shows an anti conformation at the glycosylic bond and an N conformation (O4′‐endo) for the ribose moiety, with an antiperiplanar orientation of the 5′‐hydroxy group. Crystal packing is controlled by interactions between nucleobase and sugar moieties. The 7‐iodo substituent forms a contact to oxygen‐2′ of the ribose moiety. Self‐pairing of the nucleobases does not take place. A Hirshfeld surface analysis of 1 highlights the contacts of the nucleobase and sugar moiety (O—H…O and N—H…O). The concept of pK‐value differences to evaluate base‐pair stability was applied to purine–purine base pairing and stable base pairs were predicted for the construction of `all‐purine' RNA. Furthermore, the 7‐iodo substituent of 1 was functionalized with benzofuran to detect motional constraints by fluorescence spectroscopy.     

5，10，15，20-四 [4-(4''-乙基哌嗪基)苯基]卟啉的合成及其与DNA的相互作用

基于卟啉对癌细胞的特殊亲和作用和哌嗪化合物的抗肿瘤、抗病毒作用，设计并合成了具有哌嗪结构的新型卟啉化合物5，10，15，20-四[4-(4'-乙基哌嗪基)苯基]卟啉（TEPPPH₂），其结构经UV-Vis, 元素分析，¹H NMR等手段证明。采用UV-Vis光谱和荧光光谱研究了TEPPPH₂和小牛胸腺DNA 的相互作用模式和结合机理。实验发现，TEPPPH₂能嵌入到DNA的碱基对中，1个小牛胸腺DNA分子对TEPPPH₂分子的最大结合数n约为88，结合常数为8.4×10⁶mol•L^-1 。TEPPPH₂与DNA的结合数和结合常数大于已知的四（4-N-甲基吡啶基）卟啉和Ca/sal-his、Ni/sal–aln型席夫碱抗癌药物。     

Pyrrolo‐dC Metal‐Mediated Base Pairs in the Reverse Watson–Crick Double Helix: Enhanced Stability of Parallel DNA and Impact of 6‐Pyridinyl Residues on Fluorescence and Silver‐Ion Binding

Reverse Watson–Crick DNA with parallel‐strand orientation (ps DNA) has been constructed. Pyrrolo‐dC (PyrdC) nucleosides with phenyl and pyridinyl residues linked to the 6 position of the pyrrolo[2,3‐d]pyrimidine base have been incorporated in 12‐ and 25‐mer oligonucleotide duplexes and utilized as silver‐ion binding sites. Thermal‐stability studies on the parallel DNA strands demonstrated extremely strong silver‐ion binding and strongly enhanced duplex stability. Stoichiometric UV and fluorescence titration experiments verified that a single ^2pyPyrdC–^2pyPyrdC pair captures two silver ions in ps DNA. A structure for the PyrdC silver‐ion base pair that aligns 7‐deazapurine bases head‐to‐tail instead of head‐to‐head, as suggested for canonical DNA, is proposed. The silver DNA double helix represents the first example of a ps DNA structure built up of bidentate and tridentate reverse Watson–Crick base pairs stabilized by a dinuclear silver‐mediated PyrdC pair.     

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.     

Factors Affecting DNA–DNA Interstrand Cross‐Links in the Antiparallel 3′–3′ Sense: A Comparison with the 5′–5′ Directional Isomer

Reported herein is a study of the unusual 3′–3′ 1,4‐GG interstrand cross‐link (IXL) formation in duplex DNA by a series of polynuclear platinum anticancer complexes. To examine the effect of possible preassociation through charge and hydrogen‐bonding effects the closely related compounds [{trans‐PtCl(NH₃)₂}₂(μ‐trans‐Pt(NH₃)₂{NH₂(CH₂)₆NH₂}₂)]⁴⁺ (BBR3464, 1 ), [{trans‐PtCl(NH₃)₂}₂(μ‐NH₂(CH₂)₆NH₂)]²⁺ (BBR3005, 2 ), [{trans‐PtCl(NH₃)₂}₂(μ‐H₂N(CH₂)₃NH₂(CH₂)₄)]³⁺ (BBR3571, 3 ) and [{trans‐PtCl(NH₃)₂}₂{μ‐H₂N(CH₂)₃‐N(COCF₃)(CH₂)₄}]²⁺ (BBR3571‐COCF₃, 4 ) were studied. Two different molecular biology approaches were used to investigate the effect of DNA template upon IXL formation in synthetic 20‐base‐pair duplexes. In the “hybridisation directed” method the monofunctionally adducted top strands were hybridised with their complementary 5′‐end labelled strands; after 24 h the efficiency of interstrand cross‐linking in the 5′–5′ direction was slightly higher than in the 3′–3′ direction. The second method involved “postsynthetic modification” of the intact duplex; significantly less cross‐linking was observed, but again a slight preference for the 5′–5′ duplex was present. 2D [¹H, ¹⁵N] HSQC NMR spectroscopy studies of the reaction of [¹⁵N]‐ 1 with the sequence 5′‐d{TATACATGTATA}₂ allowed direct comparison of the stepwise formation of the 3′–3′ IXL with the previously studied 5′–5′ IXL on the analogous sequence 5′‐d(ATATGTACATAT)₂. Whereas the preassociation and aquation steps were similar, differences were evident at the monofunctional binding step. The reaction did not yield a single distinct 3′–3′ 1,4‐GG IXL, but numerous cross‐linked adducts formed. Similar results were found for the reaction with the dinuclear [¹⁵N]‐ 2 . Molecular dynamics simulations for the 3′–3′ IXLs formed by both 1 and 2 showed a highly distorted structure with evident fraying of the end base pairs and considerable widening of the minor groove.     

DNA interaction,cytotoxicity and molecular structure of cobalt complex of 4‐amino‐N‐(6‐chloropyridazin‐3‐yl)benzene sulfonamide in the presence of secondary ligand pyridine

Novel cobalt complex of 4‐amino‐N‐(6‐chloropyridazin‐3‐yl)benzene sulfonamide (sulfachloropyridazine) has been synthesized and characterized by elemental analysis, FT‐IR spectroscopy and magnetic susceptibility (VSM). Cobalt complex of Sulfachloropyridazine (Co‐SCP) crystallized in monoclinic space group P2₁/n with Z = 4. The structure is solved by direct method and refined to R = 0.099 for 4720 reflections with I ?4σ(I). The results of FT‐IR spectra suggest the binding of cobalt atom to the sulfonamide ligand which is in agreement with the crystal structure determination. In crystal structure, molecule is linked via, C‐H … π, C‐Cl … π and π … π intermolecular interactions. The computational studies like the optimization energy and root means square deviation compare with single crystal structure, frontier molecular orbital (Homo‐Lumo energy) and binding energy of the Co‐SCP has been carried out using DFT/B3LYP level of theory in gaseous phase. Hirshfeld surfaces and the 2D‐fingerprint analysis are performed to study the nature of interactions and their measurable contributions towards crystal packing. The interaction of the complex with DNA is investigated using viscosity measurement and absorption titration studies. The result shows the complex bind to DNA with intercalative mode with high DNA‐binding constant (K_b). Also, in vivo and in vitro cytotoxic studies are performed using S. pombe cells and brine shrimp lethality bioassay. DNA‐cleavage study shows better cleaving ability of the complex.     

Initial DNA Interactions of the Binuclear Threading Intercalator Λ,Λ‐[μ‐bidppz(bipy)4Ru2]4+: An NMR Study with [d(CGCGAATTCGCG)]2

Binuclear polypyridine ruthenium compounds have been shown to slowly intercalate into DNA, following a fast initial binding on the DNA surface. For these compounds, intercalation requires threading of a bulky substituent, containing one Ru^II, through the DNA base‐pair stack, and the accompanying DNA duplex distortions are much more severe than with intercalation of mononuclear compounds. Structural understanding of the process of intercalation may greatly gain from a characterisation of the initial interactions between binuclear Ru^II compounds and DNA. We report a structural NMR study on the binuclear Ru^II intercalator Λ,Λ‐B (Λ,Λ‐[μ‐bidppz(bipy)₄Ru₂]⁴⁺; bidppz=11,11′‐bis(dipyrido[3,2‐a:2′,3′‐c]phenazinyl, bipy = 2,2′‐bipyridine) mixed with the palindromic DNA [d(CGCGAATTCGCG)]₂. Threading of Λ,Λ‐B depends on the presence and length of AT stretches in the DNA. Therefore, the latter was selected to promote initial binding, but due to the short stretch of AT base pairs, final intercalation is prevented. Structural calculations provide a model for the interaction: Λ,Λ‐B is trapped in a well‐defined surface‐bound state consisting of an eccentric minor‐groove binding. Most of the interaction enthalpy originates from electrostatic and van der Waals contacts, whereas intermolecular hydrogen bonds may help to define a unique position of Λ,Λ‐B. Molecular dynamics simulations show that this minor‐groove binding mode is stable on a nanosecond scale. To the best of our knowledge, this is the first structural study by NMR spectroscopy on a binuclear Ru compound bound to DNA. In the calculated structure, one of the positively charged Ru²⁺ moieties is near the central AATT region; this is favourable in view of potential intercalation as observed by optical methods for DNA with longer AT stretches. Circular dichroism (CD) spectroscopy suggests that a similar binding geometry is formed in mixtures of Λ,Λ‐B with natural calf thymus DNA. The present minor‐groove binding mode is proposed to represent the initial surface interactions of binuclear Ru^II compounds prior to intercalation into AT‐rich DNA.     

A Programmed DNA Marker Based on Bis(4‐ethynyl‐1,8‐naphthalimide) and Three‐Methane‐Bridged Thiazole Orange

Two large conjugated naphthalimide derivatives with or without three‐methane‐bridged thiazole orange (TO3; i.e., compounds 1 a and 2 a , respectively) were designed and synthesized. The fluorescence of the naphthalimide group in compound 1 a at λ=532 nm initially decreased and that for the TO3 group at λ=655 nm increased sequentially upon adding Salmon testes (St) DNA. In contrast, without the TO3 group, the fluorescence intensity of compound 2 a monotonously decreased in response to the addition of DNA. The non‐monotonic change in the fluorescence for compound 1 a could be divided into two linear sections with two different wavelengths in the range of 0<R_{b/ 1 a} <1.2 and 1.2 <R_{b/ 1 a} <6.0 (R_{b/ 1 a} =[base pair]/[ 1 a ]). Thus, compound 1 a can be regarded as a programmed responding molecule for DNA, which can semi‐quantitatively determine the concentration of DNA over a large concentration range from the standard fluorescence curve of compound 1 a at different wavelengths when bound with DNA. Furthermore, the binding modes of compounds 1 a and 2 a with StDNA were studied by using CD spectroscopy and melting temperature (T_m) testing. The results showed that compound 1 a interacts with StDNA through multi‐interactions including weak intercalation, weak minor groove binding, and inter‐dye interactions, whereas compound 2 a bound with DNA through simultaneous intercalation and minor groove binding.     

Antibacterial Activities and Nuclease Properties of Two New Ternary Copper(II) Complexes with 2‐(4′‐Thiazolyl)‐benzimidazole and 2,2′‐Bipyridine/1,10‐phenanthroline

Two new complexes: [Cu(TBZ)(bipy)Cl]Cl·H₂O ( 1 ) and [Cu(TBZ)(phen)Cl]Cl·H₂O ( 2 ) [TBZ=2‐(4′‐thiazolyl)‐ benzimidazole, phen=1,10‐phenanthroline and bipy=2,2′‐bipyridine] have been synthesized and characterized by elemental analysis, molar conductivity, IR, and UV‐vis methods. Complex 2 , structurally characterized by single‐crystal X‐ray crystallography, crystallizes in the monoclinic space group P2₁/c in a unit cell of a=0.85257(12) nm, b=2.5358(4) nm, c=1.15151(13) nm, β=118.721(8)°, V=2.183.2(5) nm³, Z=4, D_c=1.624 g·cm⁻³, µ=1.367 mm⁻¹. The complexes, free ligands and chloride copper(II) salt were each tested for their ability to inhibit the growth of two gram‐positive (B. subtilis and S. aureus) and two gram‐negative (Salmonella and E. coli) bacteria. The complexes showed good antibacterial activities against the microorganisms. The interaction between the complexes and calf thymus DNA in aqueous solution was investigated adopting electronic absorption spectroscopy, fluorescence spectroscopy, viscosity measurements and cyclic voltammetry. Results suggest that the two complexes can bind to DNA by intercalative mode. In addition, the result of agarose gel electrophoresis suggested that the complexes can cleave the plasmid DNA at physiological pH and room temperature. Mechanistic studies with different inhibiting reagents reveal that hydroxyl radicals, and a singlet oxygen‐like copper‐oxo species are all involved in the DNA scission process mediated by the complexes.     

Some divalent metal(II) complexes of novel potentially tetradentate Schiff base N,N′‐bis(2‐carboxyphenylimine)‐2,5‐thiophenedicarboxaldhyde: Synthesis,spectroscopic characterization and bioactivities

A novel tetradentate dianionic Schiff base ligand, N ,N ′‐bis(2‐carboxyphenylimine)‐2,5‐thiophenedicarboxaldhyde (H₂L) and some first row d‐transition metal chelates (Co(II), Cu(II), Ni(II) and Zn(II)) were synthesized and characterized using various physicochemical and spectroscopic methods. The spectroscopic data suggested that the parent Schiff base ligand coordinates through both deprotonated carboxylic oxygen and imine nitrogen atoms. The free Schiff base and its metal chelates were screened for their antimicrobial activities for various pathogenic bacteria and fungi using the agar well diffusion method. The antibacterial and antifungal activities of all the newly synthesized compounds are significant compared to the standard drugs ciprofloxacin and nystatin. The antioxidant activities of the compounds were determined by reduction of 1,1‐diphenyl‐2‐picrylhydrazyl and compared with that of vitamin C as a standard. DNA binding ability of the novel Schiff base and its complexes was investigated using absorption spectroscopy, fluorescence spectroscopy, viscosity measurements and thermal denaturation. The obtained results clearly demonstrate that the binding affinity with calf thymus DNA follows the order: Cu(II) complex > Ni(II) complex > Zn(II) complex > Co(II) complex >H₂L. Furthermore, the DNA cleavage activity of the newly synthesized ligand and its metal complexes was investigated using supercoiled plasmid DNA (pUC18) gel electrophoresis.     

Synthesis,spectroscopic/electrochemical characterization and DNA interaction study of novel ferrocenyl‐substituted porphyrins

We report the synthesis and characterization of two new meso‐ferrocenylporphyrins, with the ferrocenyl unit attached at the para position of a C₆F₄ group by a C? N bond with ? NH(CH₂)₂NH? ( 2a ) and ? NH(CH₂)₄NH? ( 2b ) spacers. Compounds 2a and 2b were characterized through elemental analyses, electrospray ionization high‐resolution mass spectrometry, ¹H NMR, UV–visible and fluorescence spectroscopies, electrochemistry and spectroelectrochemistry. The free base porphyrin 2 was included for comparison purposes. The binding ability of 2 and the porphyrin derivatives 2a and 2b with calf thymus DNA was determined using UV–visible and fluorescence spectroscopies. The results suggest that the interaction of these systems most probably occurs through π‐stacking by non‐classical modes involving the partial insertion of the C₆F₅ ring between adjacent base pairs on DNA and possible hydrogen interaction with the aliphatic ? NH(CH₂)_nNH? (n = 2 or 4) groups with calf thymus DNA. Moreover, we also demonstrate that porphyrins generate singlet oxygen species and show good photostability after irradiation.     

Synthesis,crystal structures and DNA/human serum albumin binding of ternary Cu(II) complexes containing amino acids and 6‐(pyrazin‐2‐yl)‐1,3,5‐triazine‐2,4‐diamino

Two water‐soluble 6‐(pyrazin‐2‐yl)‐1,3,5‐triazine‐2,4‐diamino (pzta)‐based Cu(II) complexes, namely [Cu(l ‐Val)(pzta)(H₂O)]ClO₄ ( 1 ) and [Cu(l ‐Thr)(pzta)(H₂O)]ClO₄ ( 2 ) (l ‐Val: l ‐valinate; l ‐Thr: l ‐threoninate), were synthesized and characterized using elemental analyses, molar conductance measurements, spectroscopic methods and single‐crystal X‐ray diffraction. The results indicated that the molecular structures of the complexes are five‐coordinated and show a distorted square‐pyramidal geometry, in which the central copper ions are coordinated to N,N atoms of pzta and N,O atoms of amino acids. The interactions of the complexes with DNA were investigated using electronic absorption, competitive fluorescence titration, circular dichroism and viscosity measurements. These studies confirmed that the complexes bind to DNA through a groove binding mode with certain affinities (K_b = 4.71 × 10³ and 1.98 × 10³ M^?1 for 1 and 2 , respectively). The human serum albumin (HSA) binding properties of the complexes were also evaluated using fluorescence and synchronous fluorescence spectroscopies, indicating that the complexes could quench the intrinsic fluorescence of HSA in a static quenching process. The relevant thermodynamic parameters revealed the involvement of van der Waals forces and hydrogen bonds in the formation of complex–HSA systems. Finally, molecular docking technology was also used to further verify the interactions of the complexes with DNA/HSA.     

Solution Structure of a RNA Decamer Duplex,Containing 9‐[2‐O‐(β‐D‐ribofuranosyl)‐β‐D‐ribofuranosyl]adenine,a Special Residue in Lower Eukaryotic Initiator tRNAs

The solution structure of the self‐complementary deca‐ribonucleotide 5′‐r(GCGA*AUUCGC)‐3′ containing 9‐[2‐O‐(β‐D ‐ribofuranosyl)‐β‐D ‐ribofuranosyl]adenine (A*), a modified nucleotide that occurs in lower eukaryotic methionine initiator tRNAs (tRNAs_i^Met), was determined by NMR spectroscopy. Unexpectedly, the modification has no effect on the thermal stability of the duplex. However, the extra ribose moiety is in the C(3′)‐endo conformation and takes up a well‐defined position in the minor groove, which is in agreement with its position in tRNAs_i^Met as determined by X‐ray crystallography. Molecular‐dynamics simulations on the RNA duplex in H₂O show that the position of the extra ribofuranose moiety seems to be stabilized by bridged H‐bonds (mediated by two H₂O molecules) to the backbone of the complementary chain.     

Synthesis,characterization, DNA interaction,apoptosis and molecular docking of Cu(II) and Mn(II) complexes with endo‐norbornene‐cis‐5,6‐dicarboxylic acid

Two new novel complexes, [Cu₄(Endc)₄(phen)₄]⋅7(H₂O)⋅2(O) and [Mn₂(Endc)₂(phen)₂(H₂O)₂]⋅(H₂O) (phen =1,10‐phenanthroline, H₂Endc = endo ‐norbornene‐cis ‐5,6‐dicarboxylic acid), were synthesized and structurally characterized using IR and ¹H NMR spectroscopies, elemental analysis and single‐crystal X‐ray diffractometry. Their reactivity with calf thymus DNA and HeLa cell DNA was measured using UV absorption and fluorescence spectroscopies. The results indicated that these complexes can bind to DNA with different binding affinity. Gel electrophoresis assay demonstrated the ability of the complexes to cleave pBR322 plasmid DNA. Apoptotic study showed that the complexes exhibit significant cancer cell inhibitory rates. Eventually, the complexes can suitably dock with a special DNA (PDB ID: 1AIO).     

Formation of a Thymine‐HgII‐Thymine Metal‐Mediated DNA Base Pair: Proposal and Theoretical Calculation of the Reaction Pathway

A reaction mechanism that describes the substitution of two imino protons in a thymine:thymine (T:T) mismatched DNA base pair with a Hg^II ion, which results in the formation of a (T)N3‐Hg^II‐N3(T) metal‐mediated base pair was proposed and calculated. The mechanism assumes two key steps: The formation of the first Hg^II? N3(T) bond is triggered by deprotonation of the imino N3 atom in thymine with a hydroxo ligand on the Hg^II ion. The formation of the second Hg^II? N3(T) bond proceeds through water‐assisted tautomerization of the remaining, metal‐nonbonded thymine base or through thymine deprotonation with a hydroxo ligand of the Hg^II ion already coordinated to the thymine base. The thermodynamic parameters ΔG_R=?9.5 kcal mol^?1, ΔH_R=?4.7 kcal mol^?1, and ΔS_R=16.0 cal mol^?1 K^?1 calculated with the ONIOM (B3LYP:BP86) method for the reaction agreed well with the isothermal titration calorimetric (ITC) measurements by Torigoe et al. [H. Torigoe, A. Ono, T. Kozasa, Chem. Eur. J. 2010 , 16, 13218–13225]. The peculiar positive reaction entropy measured previously was due to both dehydration of the metal and the change in chemical bonding. The mercury reactant in the theoretical model contained one hydroxo ligand in accord with the experimental pK_a value of 3.6 known for an aqua ligand of a Hg^II center. The chemical modification of T:T mismatched to the T‐Hg^II‐T metal‐mediated base pair was modeled for the middle base pair within a trinucleotide B‐DNA duplex, which ensured complete dehydration of the Hg^II ion during the reaction.     

Photophysical and Duplex‐DNA‐Binding Properties of Distamycin Dimers Based on 4,4′‐ and 2,2′‐Dialkoxyazobenzenes as the Core

Distamycin‐based tetrapeptide ( 1 ) was covalently tethered to both ends of the central dihydroxyazobenzene moiety at either the 2,2′ or 4,4′ positions. This afforded two isomeric, distamycin–azobenzene–distamycin systems, 2 (para) and 3 (ortho), both of them being photoisomerizable. Illumination of these conjugates in solution at approximately 360 nm induced photoisomerization and the time course of the process was followed by UV/Vis and ¹H NMR spectroscopy. The kinetics of the thermal reversion at various temperatures of cis to trans isomers of the conjugates obtained after photoillumination were also examined. This afforded the respective thermal‐activation parameters. Both the molecular architecture and the location of the substituent around the core azobenzene determined the rate and activation‐energy barrier for the cis‐to‐trans back‐isomerization of these conjugates in solution. Duplex–DNA binding of the conjugates and the changes in DNA‐binding efficiency upon photoisomerization was also examined by CD spectroscopy, thermal denaturation studies, and a Hoechst displacement assay. The conjugate 2 showed higher DNA‐binding affinity and a greater change in the DNA‐binding efficiency upon photoisomerization compared with its 2,2′‐disubstituted counterpart. The experimental findings were substantiated by using molecular‐docking studies involving each conjugate with a model duplex d[(GC(AT)₁₀CG)]₂ DNA molecule.     

Synthesis,Antibacterial Activities and Nuclease Properties of Ternary Copper(II) Complex Containing 2‐(2′‐Pyridyl)benzothiazole and Glycinate

A new ternary complex [Cu(PBT)(Gly)(H₂O)]ClO₄ (PBT=2‐(2′‐pyridyl)benzothiazole, and Gly=glycinate) has been synthesized and characterized by elemental analysis, molar conductivity, and IR methods. The complex, structurally characterized by single‐crystal X‐ray crystallography, shows a slightly distorted square‐pyramidal coordination geometry in which two nitrogen atoms of PBT and the carboxylate oxygen atom O and the amino nitrogen atom N of Gly bind at the basal plane, a water molecule is coordinated at the apical position. The complex, Cu(ClO₄)₂ and free PBT were each tested for their ability to inhibit the growth of two Gram(?) (Escherichia coil, Salmonella) and two Gram(+) (Bacillus subtilis, Staphylococcus aureus) microorganisms. The complex showed good antibacterial activities against the microorganisms compared with free PBT and Cu(ClO₄)₂. The interaction between the complex and calf thymus DNA in aqueous solution was investigated using electronic spectroscopy, fluorescence spectroscopy, circular dichroic spectroscopy, and viscosity measurements. Results suggest that the complex could bind to DNA by an intercalative mode. In addition, the result of agarose gel electrophoresis showed that the complex can cleave the plasmid DNA by hydroxyl radicals and singlet oxygen‐like species under the condition of physiological pH and room temperature.     

Metal‐Ion‐Mediated Tuning of Duplex DNA Binding by Bis(2‐(2‐pyridyl)‐1H‐benzimidazole)

Studies of double‐stranded‐DNA binding have been performed with three isomeric bis(2‐(n‐pyridyl)‐1H‐benzimidazole)s (n=2, 3, 4). Like the well‐known Hoechst 33258, which is a bisbenzimidazole compound, these three isomers bind to the minor groove of duplex DNA. DNA binding by the three isomers was investigated in the presence of the divalent metal ions Mg²⁺, Co²⁺, Ni²⁺, Cu²⁺, and Zn²⁺. Ligand–DNA interactions were probed with fluorescence and circular dichroism spectroscopy. These studies revealed that the binding of the 2‐pyridyl derivative to DNA is dramatically reduced in the presence of Co²⁺, Ni²⁺, and Cu²⁺ ions and is abolished completely at a ligand/metal‐cation ratio of 1:1. Control experiments done with the isomeric 3‐ and 4‐pyridyl derivatives showed that their binding to DNA is unaffected by the aforementioned transition‐metal ions. The ability of 2‐(2‐pyridyl)benzimidazole to chelate metal ions and the conformational changes of the ligand associated with ion chelation probably led to such unusual binding results for the ortho isomer. The addition of ethylenediaminetetraacetic acid (EDTA) reversed the effects completely.     

Stabilization of G‐Quadruplex DNA with Platinum(II) Schiff Base Complexes: Luminescent Probe and Down‐Regulation of c‐myc Oncogene Expression

The interactions of a series of platinum(II) Schiff base complexes with c‐myc G‐quadruplex DNA were studied. Complex [PtL ^1a ] ( 1 a ; H₂L ^1a =N,N′‐bis(salicylidene)‐4,5‐methoxy‐1,2‐phenylenediamine) can moderately inhibit c‐myc gene promoter activity in a cell‐free system through stabilizing the G‐quadruplex structure and can inhibit c‐myc oncogene expression in cultured cells. The interaction between 1 a and G‐quadruplex DNA has been examined by ¹H NMR spectroscopy. By using computer‐aided structure‐based drug design for hit‐to‐lead optimization, an in silico G‐quadruplex DNA model has been constructed for docking‐based virtual screening to develop new platinum(II) Schiff base complexes with improved inhibitory activities. Complex [PtL ³ ] ( 3 ; H₂L ³ = N,N′‐bis{4‐[1‐(2‐propylpiperidine)oxy]salicylidene}‐4,5‐methoxy‐1,2‐phenylenediamine) has been identified with a top score in the virtual screening. This complex was subsequently prepared and experimentally tested in vitro for its ability to stabilize or induce the formation of the c‐myc G‐quadruplex. The inhibitory activity of 3 (IC₅₀=4.4 μM ) is tenfold more than that of 1 a . The interaction between 1 a or 3 with c‐myc G‐quadruplex DNA has been examined by absorption titration, emission titration, molecular modeling, and NMR titration experiments, thus revealing that both 1 a and 3 bind c‐myc G‐quadruplex DNA through an external end‐stacking mode at the 3’ terminal face of the G‐quadruplex. Such binding of G‐quadruplex DNA with 3 is accompanied by up to an eightfold increase in the intensity of photoluminescence at λ_max=652 nm. Complex 3 also effectively down‐regulated the expression of c‐myc in human hepatocarcinoma cells.     

Synthesis and spectral characterization of N‐[2‐(4‐halophenoxy)‐3‐(3‐chlorophenyl)‐3, 4‐dihydro‐2H‐1,3,2‐λ5‐benzoxazaphosphinin‐2‐yliden]‐N‐substituted amines by the Staudinger reaction

The synthesis of the title compounds was accomplished in four steps. The synthetic route involves the preparation of Schiff's base by reacting salicylaldehyde with m‐chloroaniline in EtOH. The Schiff's base was then reduced with NaBH₄/MeOH. In the second step, PCl₃ was reacted with p‐chlorophenol/p‐bromophenol in THF in the presence of Et₃N to obtain P(III) dichloride derivatives. The reduced Schiff's base and dichloride derivatives were reacted in equimolar quantities in the presence of Et₃N in THF to get the cyclized product. Alkyl azides were prepared by reacting alkyl bromides with sodium azide, and then alkyl azides were treated with the cyclized product to obtain the title compounds. The structure of these novel compounds was elucidated by elemental analysis, IR, ¹H, ¹³C, ³¹P NMR, and mass spectroscopy. © 2010 Wiley Periodicals, Inc. Heteroatom Chem 21:499–504, 2010; View this article online at wileyonlinelibrary.com . DOI 10.1002/hc.20639