Laser Photofootprinting of d(C)·d(G)·d(G) Intramolecular Triplex

Abstract

Supercoiling-induced structural transition of the d(C₂₄GC₂₁,) · d(G₂₁CG₂₄) sequence in plasmid DNA in the presence of Mg²⁺ at neutral pH results in alterations of efficiencies of not only single-quantum (pyrimidine[6–4]pyrimidone adducts) but also two-quantum (alkalisensitive lesions of dG residues) photomodifications of nucleoside residues within this sequence. The generation of both types of photoreactions was achieved by the application of high-intensity laser UV radiation (intensity ～ 10¹¹ W/m², pulse duration ～ 10^?8 s, λ= 266 nm) for irradiation of a plasmid DNA The modification extent sufficient for analysis of photoreaction efficiency distributions along both strands of the insert (photofootprinting) was obtained by the action of a single nanosecond pulse of laser UV radiation. The pattern of a laser photofootprinting is consistent with the d(C) · d(G) · d(G) triplex formation in the presence of Mg²⁺ within the insert and shows some details of this triplex structure.     

DNA Interaction and Photocleavage Properties of Ru (II) Complexes [Ru(bpy)2(pibi)]2+ and [Ru(phen)2(pibi)]2+

A new asymmetry ligand pibi (pibi = 2-(pyridine-2-yl)-1-H-imidazo[4,5-f]benzo[d]imidazolone) and its ruthenium complexes with [Ru(L)₂(pibi)]²⁺ (L = bpy (2, 2′-bipyridine), phen (1, 10-phenanthroline)), have been synthesized and characterized. The binding of two complexes with calf thymus DNA has been investigated by spectroscopic and viscosity measurement. The results indicate that both complexes can bind to CT-DNA through intercalative mode. Under irradiation at 365 nm, both complexes can partly promote the photocleavage of plasmid pBR322DNA. The low singlet oxygen generation abilities of the two complexes may be the factor for the low DNA photocleavage abilities.     

Complexes of antiparallel telomeric G-quadruplex d(TTAGGG)4 with carboxymethyl tetracationic porphyrins

Porphyrins are a chemical class that is widely used in drug design. Cationic porphyrins may bind to DNA guanine quadruplexes. We report the parameters of the binding of 5,10,15,20-tetrakis(N-carboxymethyl-4-pyridinium) porphyrin (P1) and 5,10,15,20-tetrakis(N-etoxycarbonylmethyl-4-pyridinium) porphyrin (P2) to antiparallel telomeric G-quadruplex formed by d(TTAGGG)₄ sequence (TelQ). The binding constants (K _i ) and the number of binding sites (N _j ) were determined from absorption isotherms generated from the absorption spectra of complexes of P1 and P2 with TelQ. Compound P1 demonstrated a high affinity to TelQ (K _i = (40 ± 6) × 10⁶ M^?1, N ₁ = 1; K ₂ = (5.4 ± 0.4) × 10⁶ M^?1, N ₂ = 2). In contrast, the binding constants of P2-TelQ complexes (K ₁ = (3.1 ± 0.2) × 10⁶ M^?1, N ₁ = 1; K ₂ = (1.2 ± 0.2) × 10⁶ M^?1, N ₂ = 2) were one order of magnitude smaller than the corresponding values for P2-TelQ complexes. Measurements of the quantum yield and fluorescence lifetime of the drug’s TelQ complexes revealed two types of binding sites for P1 and P2 on the quadruplex oligonucleotide. We concluded that strong complexes can result from the interaction of the porphyrins with TTA loops whereas the weaker complexes are formed with G-quartets. The altered TelQ conformation detected by the circular dichroism spectra of P1-TelQ complexes can be explained by the disruption of the G-quartet. We conclude that peripheral carboxy groups contribute to the high affinity of P1 for the antiparallel telomeric G-quadruplex.     

More pronounced salt dependence and higher reactivity for platination of the hairpin r(CGCGUUGUUCGCG) compared with d(CGCGTTGTTCGCG)

The DNA interference pathways exhibited by cisplatin and related anticancer active metal complexes have been extensively studied. Much less is known to what extent RNA interaction pathways may operate in parallel, and perhaps contribute to both antineoplastic activity and toxicity. The present study was designed with the aim of comparing the reactivity of two model systems comprising RNA and DNA hairpins, r(CGCGUUGUUCGCG) and d(CGCGTTGTTCGCG), towards a series of platinum(II) complexes. Three platinum complexes were used as metallation reagents; cis-[PtCl(NH₃)₂(OH₂)]⁺ (1), cis-[PtCl(NH₃)(c-C₆H₁₁NH₂)(OH₂)]⁺ (2), and trans-[PtCl(NH₃)(quinoline)(OH₂)]⁺ (3). The reaction kinetics were studied at pH 6.0, 25 °C, and 1.0 mM ≤ I ≤ 500 mM. For both types of nucleic acid targets, compound 3 was found to react about 1 order of magnitude more rapidly than compounds 1 and 2. Further, all platinum compounds exhibited a more pronounced salt dependence for the interaction with r(CGCGUUGUUCGCG). Chemical and enzymatic cleavage studies revealed similar interaction patterns with r(CGCGUUGUUCGCG) after long exposure times to 1 and 2. A substantial decrease of cleavage intensity was found at residues G4 and G7, indicative of bifunctional adduct formation. Circular dichroism studies showed that platinum adduct formation leads to a structural change of the ribonucleic acid. Thermal denaturation studies revealed platination to cause a decrease of the RNA melting temperatures by 5–10 °C. Our observations therefore suggest that RNA is a kinetically competitive target to DNA. Furthermore, platination causes destabilization of RNA structural elements, which may lead to deleterious intracellular effects on biologically relevant RNA targets.Electronic supplementary material Supplementary material is available in the online version of this article at and is accessible for authorized users.     

Metal—phenoxyalkanoic acid interactions. Part 14. The crystal and molecular structures of diaquabis(4-fluorophenoxyacetato)copper(II) bis(4-fluorophenoxyacetic acid)dihydrate and tetra-μ-(4-fluorophenoxyacetato-0,0′)-bis[(2-aminopyrimidine)copper(II)]

The crystal structures of two copper(II) complexes of 4-fluorophenoxyacetic acid (4-FPAH) have been determined by X-ray diffraction. [Cu(4-FPA)₂(H₂O)₂]·2(4-FPAH)·2H₂O (1) is triclinic, space group P1 with Z = 1 in a cell of dimensions a = 14.808(2), b = 9.832(2), c = 6.847(2) Å, α = 87.77(2), β = 98.41(2), γ = 112.33(2)° and was refined to a residual of 0.038 for 1697 ‘observed’ reflections. The coordination sphere in this complex is tetragonally distorted octahedral comprising two waters [CuO, 1.940(3) Å], two unidentate carboxylate oxygens [CuO, 1.942(2) Å] and two ether oxygens [CuO, 2.471(2) Å]. Two adducted [4-FPAH] acid molecules are linked to the un-coordinated oxygens of the acid ligands by hydrogen bonds [2.547(4) Å]. [Cu₂(4-FPA)₄(2-aminopyrimidine)₂] (2) is triclinic, space group P1 with Z = 1 in a cell of dimensions a = 12.688(2), b = 11.422(2), c = 7.951(1) Å, α = 78.74(1), β = 107.51(1), γ = 75.78(1)°, and was refined to a residual of 0.042 for 2683 ‘observed’ reflections. (2) is a centrosymmetric tetracarboxylate bridged dimer with four similar CuO (equatorial) distances [1.967–1.987 Å; 1.977(3) Å mean] and the axial position occupied by the hetero nitrogen of the 2-aminopyrimidine ligand [CuN, 2.176(3) Å]. The Cu---Cu separation is 2.710(1) Å. Crystal data are also presented which confirm the isostructurality of complex (2) with [Cu₂(phenoxyacetate)₄(2-aminopyrimidine)₂], the Co^II, Mg^II and Mn^II4-fluorophenoxyacetate complexes with their phenoxyacetic and 4-chlorophenoxyacetic acid analogues, and of Cd^II4-fluorophenoxyacetate with Cd^II and Zn^II phenoxyacetates.     

Trimethylsilyloxo complexes of oxomolybdenum(V)

The complexes LMo^VIO₂X [L?=?hydrotris(3,5-dimethylpyrazol-1-yl)borate; X?=?Cl, Br, NCS, OPh, SPh, SCH₂Ph] are converted to air-stable complexes LMo^VO(OSiMe₃)X by one-electron coupled electron-electrophile transfer (CEET) reactions involving cobaltocene and the electrophilic reagent Me₃SiCl. These complexes may also be obtained from LMo^VO(OH)X by reaction with Me₃SiCl in the presence of base. LMo^VO(OSiMe₃)(SCH₂Ph) crystallises in space group P2₁/n, with a?=?8.526 (1) Å, b?=?23.141 (3) Å, c?=?16.499 (2) Å, β?=?103.75 (12)° and Z?=?4. The complex exhibits a distorted octahedral structure with a facially tridentate L ligand and mutually cis oxo [Mo=O?=?1.675 (4) Å], silyloxo [Mo–O?=?1.932 (4) Å] and thiolato [Mo–S?=?2.398 (2) Å] ligands. The detailed redox properties of LMo^VO(OR)X (R?=?SiMe₃, alkyl, aryl) differ from those of LMo^VO(OH)X. Centres [Mo^VO(OR)] are candidates for the stable "inhibited" forms of certain molybdenum enzymes formed under conditions which apparently disfavour the catalytically active [Mo^VO(OH)] centres. In the coordinating solvent pyridine (py), both LMo^VIO₂(SPh) and LMo^VO(OSiMe₃)(SPh) are reduced in one-electron steps to stable LMo^IVO(py)(SPh). LMo^IVO(py)(SR) complexes are also obtained from LMo^VIO₂(SR) (R?=?Ph, CH₂Ph, CHMe₂) via a two-electron oxygen atom transfer reaction with tertiary phosphines in pyridine. Consequently, the Mo(IV) product is accessible via a concerted two-electron step or via two one-electron steps.     

Molecular structure of the cis-syn photodimer of d(TpT) (cyanoethyl ester)

The three-dimensional structure was determined by x-ray crystallography for d(T[p](CE)T), a uv photoproduct of the cyanoethyl (CE) derivative of d(TpT), having the cis-syn cyclobutane (CB) geometry and the S-configuration at the chiral phosphorus atom. The crystals of C₂₃H₃₀N₅O₁₂P · 2H₂O belong to the orthorhombic space group P2₁2₁2₁ (Z = 4), with cell dimensions a = 11.596 Å, b = 14.834 Å, and c = 15.946 Å, containing two water molecules per asymmetric unit. The CB ring is puckered with a dihedral angle of 151°. The two pyrimidine bases are rotated by –29° from the position of direct overlap of their corresponding atoms. This represents a major distortion of DNA, since in DNA adjacent thymines are rotated by +36°. The pyrimidine rings are puckered with Cremer–Pople parameters for T[p] and in parentheses [p]T: Q: 0.24 Å (0.31 Å); θ: 123° (120°); ?: 141° (86°). These represent half-chairs designated as ⁶H₁ (T[p]) and ₆H⁵ ([p]T). The CB and pyrimidine ring conformations are interrelated, and we postulate that they execute a coupled interconversion in solution. The T[p] segment has the syn glycosyl conformation, a ²T₃ sugar pucker, and gauche^? conformation at C4′-C5′; the [p]T segment is anti, ³T₄, trans. The C5′-O5′ torsion of the [p]T unit is –124.5°, and the C3′-O3′ torsion of the T[p] unit is –152.9°. Bond angles and bond lengths involving the phosphorus atom are similar to those of other phosphotriesters. The P-O3′ and P-05′ torsion angles are –138.1° and 58.6°, respectively. Several intermolecular (but no intramolecular) hydrogen bonds are found in the crystal.     

Structural correlations between trans- and cis-bis(diphenylphosphino)ethene,bis(diphenylphosphino)methane and their chlorogold(I) complexes

The crystal structures of trans- and cis-bis(diphenylphosphino) ethene (1, 2) have been determined by single crystal X-ray diffraction. The conformation of these free ligands is compared with structural data available in the literature for the corresponding 1:2 complexes with gold(I) chloride (4, 5). In the cis-ligand 2 the conformation of the Ph₂P-groups is such, that the molecule approaches non-crystallographic C_s symmetry with the lone pairs at phosphorus pointing towards each other. Upon addition of AuCl, rotation of one Ph₂P group around the PC bond by approximately 60° leads to a structure for 5 which allows an intramolecular Au···Au contact of 3.05(1)Å. The trans-ligand 1 undergoes little structural change upon adduct formation, but intermolecular Au···Au contacts of 3.043(1) Å are secured through aggregation. The synthesis, properties and ¹⁹⁷Au Mössbauer spectra of 1:1 and 1:2 complexes of 1 and 2 with AuCl are summarized with reference to a recent controversy in the literature.The crystal structure of bis(diphenylphosphino)- methane (3) has also been determined and the results compared with those published previously for the 1:2 complex with AuCl (7, crystallographic C₂ symmetry, Au···Au distance 3.351(2) Å). There is very little change of the ligand conformation upon coordination.     

Synthesis and characterization of technetium(V) complexes with tridentate schiff base ligands. X-ray crystal structure of chloro[N-(2-hydroxyphenyl)salicylideneiminato]oxotechnetium(V)

Five-coordinate technetium(V) complexes of the form TcO(L)Cl where L is one of the two tridentate Schiff base ligands N-(2-oxidophenyl)salicylideneiminate or N-(2-mercaptophenyl)salicylideneiminate have been synthesized and characterized. These neutral complexes precipitate from methanol upon reaction of the Schiff base ligand with TcOCl₄^?. A single crystal X-ray structure determination shows that the chloro [[N-(2-oxidophenyl)salicylideneiminato](2?)-N,O,O′]oxotechnetium(V) complex, [TcO(C₁₃H₉NO₂)Cl], formula weight 362, has a distorted square pyramidal coordination geometry with the oxo ligand in the axial position. The steric requirements of the oxo group cause the Tc atom to be displayed 0.67 Å out of the mean equatorial plane of the other four donor atoms. This complex crystallizes in the monoclinic space group P2₁/a with a = 13.423(6) Å, b = 12.570(5) Å, c = 7.769(3) Å, β = 106.53(5)°, V = 1256.7(9) ų, and Z = 4. The structure has been refined to R = 0.047 for 1775 observed reflections.     

The crystal structures and absolute configurations of the anti-tumor complexes Pt(oxalato)(1R,2R-cyclohexanediamine) and Pt(malonato)(1R,2R-cyclohexanediamine)

The absolute configurations of the anti-tumor complexes [Pt(oxalato)(trans-l-dach)] and [Pt(malonato) (trans-l-dach)] (trans-l-dach = 1R,2R-cyclohexanediamine) have been determined by X-ray anomalous scattering techniques. These complexes are particularly interesting because they show higher anti-tumor activity than the corresponding Pt complexes with other 1,2-cyclohexanediamine(dach) ligands, namely those with trans-d-dach (1S,2S-dach) or cis-dach (1R,2S-dach). The oxalato and malonato ligands are found to bind to the Pt atom in a chelating fashion, through one oxygen atom from each of the two carboxylate groups. Crystallographic details: Pt(oxalato)(trans-l-dach): space group P2₁ (monoclinic); a = 11.230(11) Å, b = 9.914(5) Å, c = 4.716(3) Å, β = 90.86(6)°; R = 4.0% for 1256 reflections. Pt(malonato)(trans-l-dach): space group P2₁ (monoclinic); a = 11.568(5) Å, b = 10.007(5) Å, c = 5.187(3) Å, β = 99.16(4)°; R = 4.8% for 1675 reflections.     

Bh3 induced conformational changes in Bcl‐Xl revealed by crystal structure and comparative analysis

Apoptosis or programmed cell death is a regulatory process in cells in response to stimuli perturbing physiological conditions. The Bcl‐2 family of proteins plays an important role in regulating homeostasis during apoptosis. In the process, the molecular interactions among the three members of this family, the pro‐apoptotic, anti‐apoptotic and BH3‐only proteins at the mitochondrial outer membrane define the fate of a cell. Here, we report the crystal structures of the human anti‐apoptotic protein Bcl‐X_L in complex with BH3‐only BID^BH3 and BIM^BH3 peptides determined at 2.0 Å and 1.5 Å resolution, respectively. The BH3 peptides bind to the canonical hydrophobic pocket in Bcl‐X_L and adopt an alpha helical conformation in the bound form. Despite a similar structural fold, a comparison with other BH3 complexes revealed structural differences due to their sequence variations. In the Bcl‐X_L‐BID^BH3 complex we observed a large pocket, in comparison with other BH3 complexes, lined by residues from helices α1, α2, α3, and α5 located adjacent to the canonical hydrophobic pocket. These results suggest that there are differences in the mode of interactions by the BH3 peptides that may translate into functional differences in apoptotic regulation. Proteins 2015; 83:1262–1272. © 2015 Wiley Periodicals, Inc.     

Adducts from mercury(I) and mercury(II) compounds with Bispyrazolylalkanes.X-Ray crystal structure of Bis(3,5-dimethylpyrazol-l-yl)methane(dicyano)-mercury(II)

The 1:1 adducts between thebis(3,5-dimethylpyrazol-1-yl)methane (L′-L′) or 2,2′-bis(pyrazol- 1-yl)propane (L″L″) ligand and HgX₂ (with X = Cl, CN or CO₂CF₃) have been obtained as well as [(L′L′)₂]Hg(ClO₄)₂ and the mercury(I) derivative (ligand)₂Hg₂(ClO₄)₂. The adducts have been characterized from analytical and spectral data (IR, proton and ¹³C NMR). Four-coordinated mercury is present in (L′L′)Hg(CN)₂, in which the metal-(NN)₂C ring adopts an asymmetric boat form. The molecular parameters are significantly different for the two independent molecules, the CHgC angles and the two Hg-N distances being 163.1(9)°and 2.55(1) plus 2.70(1) Å in the one case, and 148.2(8)° and 2.40(1) plus 2.51(1) Å, in the other; correspondingly the N-Hg-N angle, the ‘bite’ of the ligand, ranges from 79.0(5)° to 71.7(4)°, a value outside the range previously reported.     

Conformational Preferences of Heterochiral Peptides. Crystal Structures of Heterochiral Peptides Boc-(D) Val-(D) Ala-Leu-Ala-OMe and Boc-Val-Ala-Leu-(D) Ala-OMe-Enhanced Stability of β-sheet Through C-H…O Hydrogen Bonds

Abstract

The crystal structures of Boc-(D) Val-(D) Ala-Leu-Ala-OMe (vaLA) and Boc-Val-Ala-Leu-(D) Ala-OMe (VALa) have been determined. vaLA crystallises in space group P2₁2₁2₁ with a = 9.401 (4), b = 17.253 (5), c = 36.276 (9)Å, V = 5884 (3) ų, Z = 8, R = 0.086. VALa crystallises in space group P2₁ with a = 9.683 (9), b = 17.355 (7), c = 18.187 (9) Å, β = 95.84 (8)°, V = 3040(4) ų, Z = 4, R = 0.125. There are two molecules in the asymmetric unit in antiparallel β-sheet arrangement in both the structures. Several of the C^α hydrogens are in hydrogen bonding contact with the carbonyl oxygen in the adjacent strand.

An analysis of the observed conformational feature of D-chiral amino acid residues in oligopeptides, using coordinates of 123 crystal structures selected from the 1998 release of CSD has been carried out. This shows that all the residues except D-isoleucine prefer both extended and α_L conformation though the frequence of occurence may not be equal. In addition to this, D-leucine, valine, proline and phenylalanine have assumed α_R conformations in solid state. D-leucine has a strong preference for helical conformation in linear peptides whereas they prefer an extended conformation in cyclic peptides.     

Crystal and molecular structure of bis(tricyclohexylphosphine)silver(I)nitrate and bis(tricyclohexylphosphine)silver(I)perchlorate; correlation of the structures with the silver-phosphorus coupling constants

Two (1:2) silver monophosphine complexes have been studied by X-ray diffraction methods and in solution by P NMR spectroscopy. Both are monomeric and tricoordinated in the solid state but one of them, the perchlorate compound, is probably associated as a dimer species in solution from the lower ¹J(¹⁰⁷Ag³¹P) value when compared to the nitrate analogue. Previous structural correlations found in other silver-phosphine complexes have been confirmed for these new compounds. Thus, larger PAgP bond angles are associated with shorter AgP bond distances, longer Aganion bond distances and lower Lewis basicity of the anions. Selected structural data are: PAgP bond angle of 139.04(9)°, AgP bond lengths of 2.440(3) and 2.445(3) Å for the nitrate complex and 147.34(3)°, 2.429(1) Å and 2.432(1) Å, for the perchlorate one. J(¹⁰⁷Ag³¹P) is 457 Hz and 447 Hz, respectively. The complexes are triclinic, Z = 2, with the parameters: a = 9.258(2), b = 9.828(2), c = 23.385(5) Å, α = 94.73(2)°, β = 96.35(2)°, γ = 116.42(1)° (nitrate) and a = 9.505(2), b = 9.790(2), c = 23.667(6) Å, α= 99.03(2) β = 95.44(2) γ = 115.97(1)° (perchlorate).     

Synthesis,characterization, DNA interaction,and cytotoxicity of novel Pd(II) and Pt(II) complexes

Four complexes [Pd(L)(bipy)Cl]·4H₂O (1), [Pd(L)(phen)Cl]·4H₂O (2), [Pt(L)(bipy)Cl]·4H₂O (3), and [Pt(L)(phen)Cl]·4H₂O (4), where L = quinolinic acid, bipy = 2,2’-bipyridyl, and phen = 1,10-phenanthroline, have been synthesized and characterized using IR, ¹H NMR, elemental analysis, and single-crystal X-ray diffractometry. The binding of the complexes to FS-DNA was investigated by electronic absorption titration and fluorescence spectroscopy. The results indicate that the complexes bind to FS-DNA in an intercalative mode and the intrinsic binding constants K of the title complexes with FS-DNA are about 3.5?×?10⁴ M^?1, 3.9?×?10⁴ M^?1, 6.1?×?10⁴ M^?1, and 1.4?×?10⁵ M^?1, respectively. Also, the four complexes bind to DNA with different binding affinities, in descending order: complex 4, complex 3, complex 2, complex 1. Gel electrophoresis assay demonstrated the ability of the Pt(II) complexes to cleave pBR322 plasmid DNA.     

Coordination chemistry of 7,9-disubstituted 6-oxopurine metal compounds. 4. Platinum(II) coordination at N(1). Molecular and crystal structure of [(ethylenediamine)bis(7,9-dimethylhypoxanthine)platinum(II)] hexafluorophosphate

The preparation and molecular and crystal structure of the complex [(ethylenediamine)bis(7,9,-dimethylhypoxanthine)platinum(II)] hexafluorophosphate, [Pt(C₂H₈N₂)(C₇H₈N₄O)₂] (PF₆)₂, are reported. The complex crystallizes in the monoclinic system, space group C2/c, with a = 12.334(2)Å, b = 10.256(2)Å, c = 22.339(3)Å, β = 101.31(1)°, V = 2771.0ų, Z = 4, D_measd = 2.087(3) g cm^?3, D_calc = 2.094 g cm^?3. Intensities for 3992 symmetry-averaged reflections were collected in the θ-2o scan mode on an automated diffractometer employing graphite-monochromatized MoKα radiation. The structure was solved by standard heavy-atom Patterson and Fourier methods. Full matrix least-squares refinement led to a final R value of 0.051. Both the ethylenediamine chelate and the PF₆^? anion are disordered. The primary coordination sphere about the Pt(II) center is approximately square planar with the bidentate ethylenediamine ligand and the N(1) atoms [Pt(II) ? N(1) = 2.020(5)Å] of two 7,9-dimethylhypoxanthine bases (related by a crystallographic twofold axis of symmetry) occupying the four coordination sites. The exocyclic O(6) carbonyl oxygen atoms of the two 7,9-dimethylhypoxanthine ligands participate in intracomplex hydrogen bonding with the amino groups of the ethylenediamine chelate [N(ethylenediamine) ? O(6) = 2.89( )Å]. The observed Pt ? O(6) intramolecular distances of 3.074(6)Å are similar to those found in other Pt(II) N(1)-bound 6-oxopurine complexes and in several Pt(II) N(3)-bound cytosine systems.     

Molecular mechanical studies of base-pair opening in d(CGCGC):d(GCGCG), dG5·dC5, d(TATAT):d(ATATA), and dA5·dT5 in the B and Z forms of DNA

Molecular mechanical energy refinement of double-helical pentanucleotide tetra-phosphates, d(CGCGC):d(GCGCG), dG₅·dC₅, d(TATAT):d(ATATA), and dA₅ ·dT₅ geometries, are presented in order to examine the energy required to open the Nl(purine) …? N3(pyrimidine) distance (base-pair opening) of a Watson-Crick base pair from its normal value of 3 Å to a value of 6 Å. The structural consequences of forcing base-pair opening is sequence dependent. For both dA₅ ·dT₅ and d(TATAT):d(ATATA), forcing the Nl (AdeKN3 (Thy) distance of the central base pair to a value of 6 Å slides the bases perpendicular to the helix axis forming a low-energy non-Watson-Crick base pair having an adenine amine hydrogen …? thymine carbonyl oxygen hydrogen bond. The two GC sequences behave differently from both AT sequences and differently from each other. Forcing the Nl(Gua) …? N3(Cyt) distance to 6 Å leads to unconventional structures in which hydrogen bonds are formed between the separated bases and the bases above or below them. These structures appear to be trapped in true local minima 6–10 kcal/mol higher in energy than the Watson-Crick structures. Preliminary simulations on d(CGCGC):d(GCGCG) in the Z geometry suggest the reason the Z form may be more refractory to proton exchange than the B form, consistent with experimental observations.     

2-(3,5-Dibromo-4-hydroxyphenyl)imidazo[4,5-<Emphasis Type="Italic">f</Emphasis>][1,10]phenanthrolinoruthenium(II) complexes: synthesis,characterization, cytotoxicity,apoptosis, DNA-binding and antioxidant activity

A new ligand DBHIP and its two ruthenium(II) complexes [Ru(dmb)₂(DBHIP)](ClO₄)₂ (1) and [Ru(dmp)₂(DBHIP)](ClO₄)₂ (2) have been synthesized and characterized. The cytotoxicity of DBHIP and complexes 1 and 2 has been assessed by MTT assay. The apoptosis studies were carried out with acridine orange/ethidium bromide (AO/EB) staining methods. The binding behaviors of these complexes to calf thymus DNA (CT-DNA) were studied by absorption titration, viscosity measurements, thermal denaturation and photoactivated cleavage. The DNA-binding constants of complexes 1 and 2 were determined to be 8.64 ± 0.16 × 10⁴ (s = 1.34) and 2.79 ± 0.21 × 10⁴ (s = 2.17) M⁻¹. The results suggest that these complexes interact with DNA through intercalative mode. The studies on the mechanism of photocleavage demonstrate that superoxide anion radical (O₂ ^•–) and singlet oxygen (¹O₂) may play an important role in the DNA cleavage. The experiments on antioxidant activity show that these compounds also exhibit good antioxidant activity against hydroxyl radical (OH^•).     

Complexes of hybrid ligands. Synthesis of mixed-ligand,phosphino-alkoxide complexes of Pd2+: the crystal and molecular structure of the complex Ph2 PCH2C(CF3 )2OPdCl(PPh2Me)

The hybrid, bidentate, diarylphosphino-alkoxide ligand PPh₂CH₂C(CF₃)₂O⁻, L¹, gives the Pd²⁺ bis- complex Pd(L¹)₂, from which the chloride-bridged dinuclear complex [(L¹)Pd(μ-Cl)₂Pd(L¹)] is made by reaction with PdCl₂(PhCN)₂. Cleavage of the dinuclear complex with monodentate ligands L² then gives Pd(L¹)Cl(L²) (L² =PPh₃, PPh₂Me, PPhMe₂, PMe₃, SMe₂, or pyridine); NMR data show that PR₃ is cis to the phosphine site in L¹ in these complexes, but SMe₂ or pyridine are probably trans.A complete crystal and molecular structural determination has been made for cis-Pd(L¹)Cl(PPh₂Me). Crystals are monoclinic, space group P2₁/c, a = 10.821(1), b = 14.600(1), c = 18.674(2) Å, β = 101.25(1)°, V = 2893 ų, Z = 4. Least-squares refinement on F of 361 variables using 3977 observations converged at a conventional agreement factor R = 0.025. The complex is square-planar, with the two phosphines cis; the 5-membered chelate ring is in a dissymmetric envelope conformation. The PdP bonds differ in length, with that to the unidentate phosphine, 2.259(1) Å, being significantly longer than that to the phosphine on the chelating ligand, 2.231(1) Å.     

Crystal structure of cyclo(Pro-Gly)3: Li complex: A model for ion transport by cyclo(Pro-Gly)3

The crystal structure of cyclo(Pro-Gly)₃ (PG3) complex with LiSCN (C₂₂H₃₀N₇O₆SLi) has been solved by x-ray diffraction. The crystals belong to the space group R3 in the hexagonal setting with unit cell parameters of a = 12.581(1), c = 29.705(3) Å, V = 4072.0 ų, Z = 6, M_r = 527.53, D_c = 1.23 g/cm³. The crystal structure was solved by direct methods using the program SHELXS-86 and refined to an R value of 5.3% for 1645 reflections (I > 2σI). There are two conformers in the crystal structure. One conformer has three carbonyls on one side and three on the other side of the peptide plane. The other conformer has all six of the carbonyls on the same side of the peptide plane. Both of these conformers bind independently to a Li ion. Based on the conformers of the Li complex and other reported ion complexes formed by PG3, we propose a model for the transport of ions across the lipid membrane. The features of the model are as follows: (1) PG3 forms a hexameric stack in a lipid bilayer when complexing and transporting metal ions. (2) It undergoes a conformational flipping in order pass the ion along the channel. The energy required for the conformational change involved in the flipping of the PG3 molecule may be provided by the applied potential during ion transport. © 1994 John Wiley & Sons, Inc.