Thermal stability, structural features, and B-to-Z transition in DNA tetraloop hairpins as determined by optical spectroscopy in d(CG)(3)T(4)(CG)(3) and d(CG)(3)A(4)(CG)(3) oligodeoxynucleotides

NMR and CD data have previously shown the formation of the T(4) tetraloop hairpin in aqueous solutions, as well as the possibility of the B-to-Z transition in its stem in high salt concentration conditions. It has been shown that the stem B-to-Z transition in T(4) hairpins leads to S (south)- to N (north)-type conformational changes in the loop sugars, as well as anti to syn orientations in the loop bases. In this article, we have compared by means of UV absorption, CD, Raman, and Fourier transform infrared (FTIR), the thermodynamic and structural properties of the T(4) and A(4) tetraloop hairpins formed in 5'-d(CGCGCG-TTTT-CGCGCG)-3' and 5'-d(CGCGCG-AAAA-CGCGCG)-3', respectively. In presence of 5M NaClO(4), a complete B-to-Z transition of the stems is first proved by CD spectra. UV melting profiles are consistent with a higher thermal stability of the T(4) hairpin compared to the A(4) hairpin. Order-to-disorder transition of both hairpins has also been analyzed by means of Raman spectra recorded as a function of temperature. A clear Z-to-B transition of the stem has been confirmed in the T(4) hairpin, and not in the A(4) hairpin. With a right-handed stem, Raman and FTIR spectra have confirmed the C2'-endo/anti conformation for all the T(4) loop nucleosides. With a left-handed stem, a part of the T(4) loop sugars adopt a N-type (C3'-endo) conformation, and the C3'-endo/syn conformation seems to be the preferred one for the dA residues involved in the A(4) tetraloop.     

Proton NMR studies of 5'-d-(TC)(3) (CT)(3) (AG)(3)-3'--a paperclip triplex: the structural relevance of turns

In this study, we present the results of structural analysis of an 18-mer DNA 5'-T(1)C(2)T(3)C(4)T(5)C(6)C(7)T(8)C(9)T(10)C(11)T(12)A(13)G(14)A(15)G(16)A(17)G(18)-3' by proton nuclear magnetic resonance (NMR) spectroscopy and molecular modeling. The NMR data are consistent with characteristics for triple helical structures of DNA: downfield shifting of resonance signals, typical for the H3(+) resonances of Hoogsteen-paired cytosines; pH dependence of these H3(+) resonance; and observed nuclear Overhauser effects consistent with Hoogsteen and Watson-Crick basepairing. A three-dimensional model for the triplex is developed based on data obtained from two-dimensional NMR studies and molecular modeling. We find that this DNA forms an intramolecular "paperclip" pyrimidine-purine-pyrimidine triple helix. The central triads resemble typical Hoogsteen and Watson-Crick basepairing. The triads at each end region can be viewed as hairpin turns stabilized by a third base. One of these turns is comprised of a hairpin turn in the Watson-Crick basepairing portion of the 18-mer with the third base coming from the Hoogsteen pairing strand. The other turn is comprised of two bases from the continuous pyrimidine portion of the 18-mer, stabilized by a hydrogen-bond from a purine. This "triad" has well defined structure as indicated by the number of nuclear Overhauser effects and is shown to play a critical role in stabilizing triplex formation of the internal triads.     

On the lability of dimethylsulfoxide (DMSO) coordinated to the [Ru(II)-NO(+)] species: X-ray structures of mer-[RuCl(3)(DMSO)(2)(NO)] and mer-[RuCl(3)(CD(3)CN)(DMSO)(NO)

The syntheses of nitrosyl–dimethylsulfoxide–ruthenium(II) complexes with general formula mer-[RuCl₃(L)(DMSO)(NO)] (L=DMSO or CD₃CN) is reported. The mer-[RuCl₃(DMSO)₂(NO)] (1) complex was obtained from the reaction of [RuCl₃(NO)] with the sulfoxide ligand in acetone. The mer-[RuCl₃(CD₃CN)(DMSO)(NO)] (2) compound was obtained from mer-[RuCl₃(DMSO)₂(NO)] maintained in deuterated acetonitrile. These data suggest a slow kinetic reaction due the low lability of the DMSO ligand coordinated to the {Ru^II–NO⁺} species. The crystal and molecular structures of (1) and (2) have been determined from X-ray studies. Crystal data: for (1), monoclinic, P2₁/c, a=8.8340(2) Å, b=12.0230(3) Å, c=13.7064(4) Å, β=114.546(2)°, Z=4, R1=0.0429; for (2), monoclinic, P21/n, a=10.0180(7) Å, b=9.5070(7) Å, c=13.3340(9) Å, β=102.264(4)°, Z=4, R1=0.0472. The spectroscopic characterization of (1), in solid state (infrared spectrum) and in solution (nuclear magnetic resonance and cyclic voltammetry) is also described.     

Re(CO)(3)(H(2)O)(3)(+) binding to lysozyme: structure and reactivity

The reaction of Re(CO)(3)(H(2)O)(3)(+) with hen egg white lysozyme in aqueous solution results in a single covalent adduct. Both NMR spectroscopy and single crystal X-ray diffraction show that the rhenium tricarbonyl cation binds to His15 via replacement of one of the coordinated water molecules. The formation of this adduct does not greatly affect the structure of the protein.     

Two new scorpionates vanadium haloperoxidases model complexes: synthesis and structure of VO(O2)(pzH)(HB(pz)3) and VO(O2)(pzH)(B(pz)4) (pzH = pyrazole(C3H4N2))

Using vanadate, poly(1H-pyrazol-1-yl)borate and pyrazole as starting materials, two new neutral peroxovanadium(V) complexes with poly(1H-pyrazol-1-yl)borate, VO(O(2))(pzH)(HB(pz)(3))(1) and VO(O(2))(pzH)(B(pz)(4))(2), were synthesized successfully. Both complexes were characterized by elemental analysis, IR, UV-vis and NMR spectra. And the structure of complex 1 was determined by X-ray diffraction, which is somewhat relevant for haloperoxidase enzymes. Cytotoxic effects also are discussed on 3T3 cell proliferation. In the concentration range (0.1-100mumol), both complexes have an inhibiting cellular proliferation effect. When the cells cultivated with the complexes at high dose, the toxicity effect of both complexes is more and more predominant.     

A 3p deletion syndrome in a child with both del(3)(p25-->pter) and dup(17)(q23-->qter).

A child with monosomy for the distal part of the short arm of chromosome 3 (3p25-->pter) and trisomy for the terminal portion of the long arm of chromosome 17 (17q23-->qter) is presented. This unbalanced karyotype was derived from a balanced reciprocal 3p/17q translocation in the phenotypically normal mother. Main clinical features in the proband included growth and mental retardation, hypotonia, hirsutism, micro/brachycephaly, triangular face, synophris, broad and full nose, long philtrum, narrow upper lip, low set, posteriorly turned ears, anteriorly placed anus and congenital heart defect (Tetralogy of Fallot). Most of these clinical manifestations have been constantly reported in previous cases with terminal 3p deletion.     

Familial pericentric inversion (3)(p12q24)

Summary A large kindred with a familial pericentric inversion of chromosome 3, (p12q24), was found after an investigation initiated by a young female with three spontaneous first-trimester abortions. Altogether 22 (33%) inversion carriers were discovered, 9 females and 13 males. 6 women and 9 men were included in the fertility and segregation analyses because they were all either sexually mature or past maturity. The abortion frequency was below the average European rate in both the inversion carrier group and the cytogenetically normal relative group; 6%: 3%, respectively. The mean numbers of pregnancies and live births (1.8–3.1) did not vary significantly in the two comparison groups. The segregation analysis among the inversion carriers showed a good correspondence to the theoretical 11 ratio (1613). Males and females contributed equally. No duplication/deletion syndromes have been found in the kindred; all family members are phenotypically normal. We report a balanced familial pericentric inversion with no adverse effects. This chromosome aberration could be an example of a harmless chromosome polymorphism.     

Crystal structures of HM(SiPh3)(CO)3(PPh3)(M=Fe,Ru) formed from photolysis of M(CO)4PPh3 in the presence of HSiPh3

Near-UV irradiation of M(CO)₄PPh₃ (M=Fe, Ru) at 298 K in deoxygenated hydrocarbon solutions containing molecules having a Si-H bond gives clean formation of products of the formula HM(CO)₃(PPh₃)(Si

). Several isomers of such species are possible and X-ray crystallography has been used to unambiguously establish the isomer formed in the photochemical reaction. The crystal structure of the isomer of HM(SiPh₃)CO)₃(PPh₃) formed by the photochemical reaction of M(CO)₄PPh₃ with HSiPh₃ is reported for M=Fe (1) and Ru (2). Both complexes have the same geometry, a distorted octahedron with the COs meridional and the H cis to both the SiPh₃ and the PPh₃. The crystals are triclinic, space group P$\text{1}$. Crystal parameters for 2, (followed in square brackets by those for 1), are: a=12.535(3) [12.32(2)], b=14.244(3) [14.50(4)], c=10.174(3) [10.06(2)] Å, α=104.98(2) [106.3(2)], β=98.52(2) [98.2(2)], γ=71.92(2)° [72.0(2)°], V=1663.63 [1637.38] ų.     

Thermodynamic and circular dichroism studies differentiate inhibitor interactions with the stromelysin S(1)-S(3) and S(')(1)-S(')(3) subsites.

Interactions of stromelysin with a series of inhibitors representative of three chemical templates with distinct binding modes were examined. Unfolding temperatures for inhibitor complexes were 10 degrees C to 15 degrees C greater than for apo stromelysin. Minor changes in ellipticity in the far-UV CD spectra of complexes indicated that ligand-induced conformational changes were localized to the binding site and did not involve gross changes in protein folding. Isothermal titrating calorimetry of thiadiazole-containing inhibitors, which bind in the S(1)-S(3) subsites of stromelysin, indicated that the binding interaction was exothermic and only slightly favorable entropically. Near-UV CD spectra showed large positive ellipticity increases from 250 to 300 nm, consistent with an interaction between the benzene ring of the inhibitor and stromelysin residues Tyr155 and Tyr168. Interactions between stromelysin and amide-hydroxamate ligands, which bind in the S(')(1)-S(')(3) subsites, were found to be both enthalpically and entropically driven. Binding of this class of ligands resulted in modest negative ellipticity changes at 260-285 nm and positive increases at 292 nm. Stromelysin complexed to a lactam-hydroxamate inhibitor with structure extending into both the S(1)-S(3) and S(')(1)-S(')(3) subsites showed increased ellipticity at 245 nm and negative changes at 260-285 and 295 nm.     

Ternary complexes metal [Co(II), Ni(II), Cu(II) and Zn(II)]--ortho-iodohippurate (I-hip)--acyclovir. X-ray characterization of isostructural [(Co, Ni or Zn)(I-hip)(2)(ACV)(H(2)O)(3)] with stacking as a recognition factor

Four ternary metal--ortho-iodohippurate (I-hip)--acyclovir (ACV) complexes, [M(I-hip)(2)(ACV)(H(2)O)(3)] where M is Co(II) (1), Ni(II) (2), Cu (3) and Zn(II) have been obtained by reaction between the corresponding binary complexes M(II)(I-hip)(2)xnH(2)O and ACV. Three ternary complexes (M=Co, Ni and Zn) and the corresponding Zn(II)--ortho-iodohippurate binary derivative have been structurally characterized by X-ray diffraction: The studies show these three ternary complexes are isostructural and present, in solid state, an interesting stacking between the nucleobase and the aryl ring of the hippurate moiety, which probably promotes the formation of ternary complexes. Moreover, the two different ligands interact between them by means of ancillary hydrogen bonds with water molecules coordinated to the metal ion. It must be mentioned that these two recognition factors, hydrogen bonds plus stacking, could explain the reason for the isostructurality of these ternary derivatives with so different three metal ions, with diverses trends in coordination numbers and geometries. In solid state, there are two enantiomeric molecules that are related by an inversion center as the crystal-building unit (as a translational motif) for the ternary complexes.     

Synthesis, DNA-binding and photocleavage studies of cobalt(III) mixed-polypyridyl complexes: [Co(phen)(2)(dpta)](3+) and [Co(phen)(2)(amtp)](3+)

Two novel cobalt(III) mixed-polypyridyl complexes [Co(phen)(2)(dpta)](3+) and [Co(phen)(2)(amtp)](3+) (phen=1,10-phenanthroline, dpta=dipyrido-[3,2-a;2',3'-c]- thien-[3,4-c]azine, amtp=3-amino-1,2,4-triazino[5,6-f]1,10-phenanthroline) have been synthesized and characterized. The interaction of these complexes with calf thymus DNA was investigated by spectroscopic, cyclic voltammetry, and viscosity measurements. Results suggest that the two complexes bind to DNA via an intercalative mode. Moreover, these Co(III) complexes have been found to promote the photocleavage of plasmid DNA pBR322 under irradiation at 365nm. The mechanism studies reveal that hydroxyl radical (OH()) is likely to be the reactive species responsible for the cleavage of plasmid DNA by [Co(phen)(2)(dpta)](3+) and superoxide anion radical (O(2)(-)) acts as the key role in the cleavage reaction of plasmid DNA by [Co(phen)(2)(amtp)](3+).     

The (alpha F(357)C)(3)(beta R(372)C)(3)gamma subcomplex of the F(1)-ATPase from the thermophilic Bacillus PS3 has altered ATPase activity after cross-linking alpha and beta subunits at noncatalytic site interfaces

In crystal structures of bovine MF(1), the side chains of alpha F(357) and beta R(372) are near the adenines of nucleotides bound to noncatalytic sites. To determine if during catalysis these side chains must pass through the different arrangements in which they are present in crystal structures, the catalytic properties of the (alpha F(357)C)(3)(beta R(372)C)(3)gamma subcomplex of the TF(1)-ATPase were characterized before and after cross-linking the introduced cysteines with CuCl(2). The unmodified mutant enzyme hydrolyzes MgATP at 50% the rate exhibited by wild type. Detailed comparison of the catalytic properties of the double mutant enzyme before and after cross-linking with those of the wild-type subcomplex revealed the following. Before cross-linking, the (alpha F(357)C)(3)(beta R(372)C)(3)gamma subcomplex has less tendency than wild type to release inhibitory MgADP entrapped in a catalytic site during turnover when MgATP binds to noncatalytic sites. Following cross-linking, ATPase activity is reduced 5-fold, and inhibitory MgADP entrapped in a catalytic site during turnover does not release under conditions wherein binding of ATP to noncatalytic sites of the wild-type enzyme promotes release of MgADP from the affected catalytic site. When assayed in the presence of lauryldimethylamine oxide, which prevents turnover-dependent entrapment of inhibitory MgADP in a catalytic site, ATPase activity of the cross-linked form is 47% that of the unmodified mutant enzyme. These results suggest that, during catalysis, the side chains of alpha F(357) and beta R(372) do not pass through the extremely different relative positions in which they exist at the three noncatalytic site interfaces in crystal structures.     

Hypotensive properties and acute toxicity of trans-[Ru(NH(3))(4)P(OEt)(3)(NO)](PF(6))(3), a new nitric oxide donor.

The hypotensive effect and the acute toxicity of trans-[Ru(NH(3))(4)P(OEt)(3)(NO)](PF(6))(3) (RuNO) were investigated in conscious animals. The approximate lethal dose of RuNO is 257.5 micromol/kg in mice i.p. and the IC(50) values evaluated for V79 culture cell cytotoxicity were higher than 2.0 mM, suggesting that the ruthenium species are significantly less toxic than Na(2)[Fe(CN)(5)(NO)] (SNP) species. The RuNO hypotensive effect measured through in-bolus intravenous administration in chronically instrumented normotensive and hypotensive adult male Wistar rats is similar to that exhibited by equivalent doses of SNP. The hypotensive effect of the ruthenium complex is fully inhibited by methylene blue and PTIO, suggesting that the RuNO effect is likely to be primarily dependent on the NO-[cGMP] pathway in the smooth muscle cells.     

Molecular structure, bioavailability and bioactivity of [Cu(o-phen)2(cnge)](NO3)2.2H2O and [Cu(o-phen)(cnge)(H2O)(NO3)2] complexes

Two Cu(II) complexes with cyanoguanidine (cnge) and o-phenanthroline, [Cu(o-phen)(2)(cnge)](NO(3))(2).2H(2)O (1) and [Cu(o-phen)(cnge)(H(2)O)(NO(3))(2)] (2), have been synthesized using different experimental techniques and characterized by elemental analyses, FTIR, diffuse and UV-vis spectra and EPR and magnetic moment measurements techniques. The crystal structures of both complexes were solved by X-ray diffraction methods. Complex (1) crystallizes in the monoclinic space group C2/c with a=12.621(5), b=31.968(3), c=15.39(1)A, beta=111.68(4) degrees, and Z=8 and complex (2) in the monoclinic space group P2(1)/n with a=10.245(1), b=13.923(2), c=12.391(2)A, beta=98.07(1) degrees, and Z=4. The environments of the copper(II) center are trigonal bipyramidal (TBP) for [Cu(o-phen)(2)(cnge)](2+) and an elongated octahedron for [Cu(o-phen)(cnge)(H(2)O)(NO(3))(2)]. Solution studies have been performed to determine the species distribution. The superoxide dismutase (SOD) activities of both complexes have also been tested in order to determine if these compounds mimic the enzymatic action of the enzyme SOD that protects cells against peroxide radicals.     

Temperature-induced conformational transition of a model elastin-like peptide GVG(VPGVG)(3) in water

The conformation of a single elastin-like peptide GVG(VPGVG)3 in liquid water is studied by computer simulations in the temperature interval between 280 and 440 K. Two main conformational states of the peptide can be distinguished: a rigid conformational state, dominating at low temperatures, and a flexible conformational state, dominating at high temperatures. A temperature-induced transition between these states occurs at about 310 K, rather close to a transition temperature seen in experiments. This transition is accompanied by the thermal breaking of the hydrogen-bonded spanning network of the hydration water via a percolation transition upon heating. This finding indicates that the H-bond clustering structure of the hydration water plays an important role in the conformational stability of biomolecules. A second important observation is the Gaussian distribution of the end-to-end distance in the high-temperature state, which supports the idea of a rubber-like elasticity of the studied elastin-like peptide. Finally our results challenge the idea of the folding of elastin-like peptides upon heating.     

Evidence for distinct membrane receptors for 1 alpha,25-(OH)(2)D(3) and 24R,25-(OH)(2)D(3) in osteoblasts

1 alpha,25-(OH)(2)D(3) exerts its effects on chondrocytes and enterocytes via nuclear receptors (1,25-nVDR) and a separate membrane receptor (1,25-mVDR) that activates protein kinase C (PKC). 24R,25-(OH)(2)D(3) also stimulates PKC in chondrocytes, but through other membrane mechanisms. This study examined the hypothesis that osteoblasts possess distinct membrane receptors for 1 alpha,25-(OH)(2)D(3) and 24R,25-(OH)(2)D(3) that are involved in the activation of PKC and that receptor expression varies as a function of cell maturation state. 1 alpha,25-(OH)(2)D(3) stimulated PKC in well differentiated (UMR-106, MC-3T3-E1) and moderately differentiated (ROS 17/2.8) osteoblast-like cells, and in cultures of fetal rat calvarial (FRC) cells and 2T3 cells treated with rhBMP-2 to promote differentiation. 24R,25-(OH)(2)D(3) stimulated PKC in FRC and 2T3 cultures that had not been treated to induce differentiation, and in ROS 17/2.8 cells. MG63 cells, a relatively undifferentiated osteoblast-like cell line, had no response to either metabolite. Ab99, a polyclonal antibody generated to the chick enterocyte 1,25-mVDR, but not a specific antibody to the 1,25-nVDR, inhibited response to 1 alpha,25-(OH)(2)D(3). 1 alpha,25-(OH)(2)D(3) exhibited specific binding to plasma membrane preparations from cells demonstrating a PKC response to this metabolite that is typical of positive cooperativity. Western blots of these membrane proteins reacted with Ab99, and the Ab99-positive protein had an Mr of 64 kDa. There was no cross-reaction with antibodies to the C- or N-terminus of annexin II. The effect of 24,25-(OH)(2)D(3) on PKC was stereospecific; 24S,25-(OH)(2)D(3) had no effect. These results demonstrate that response to 1 alpha,25-(OH)(2)D(3) and 24R,25-(OH)(2)D(3) depends on osteoblast maturation state and suggest that specific and distinct membrane receptors are involved.     

The structure of (μ3-sulfido)(μ3-p-tolyphosphido)tris(tricarbonyliron)(2FeFe)

Compounds of the type (μ₃-S)(μ₃-RP)Fe₃(CO)₉ have been prepared by the reaction of Fe₃(CO)₁₂ with [RP(S)S]₂ or RP(S)Cl₃. In this paper we report the synthesis of (μ₃-S)(μ₃-CH₃OC₆H₄P)Fe₃(CO)₉ using Lawesson's reagents, and the three dimensional structure of (μ₃-S)(μ₃-p-CH₃C₆H₄P)Fe₃(CO)₉. This material crystallizes in the space group P2₁/n with a = 8.558(2) Å, b = 9.022(2) Å, c = 27.506(6) Å, β = 95.40(2)°, Z = 4. The cluster is a nido structure as found commonly for (μ₃-X)(μ₃-Y)Fe₃(CO)₉ complexes.     

(99m)Tc(CO)(3)-Ibritumomab tiuxetan; a novel radioimmunoimaging (RII) agent of B cell non-Hodgkin's lymphoma (NHL)

To exploit the B-lymphocyte antigen-CD20 binding capacity of the Ibritumomab tiuxetan (IBTN) monoclonal antibody (mAb) for imaging, the over-expression of B cells in non-Hodgkin's lymphoma (NHL) (a myeloproliferative disorder of the lymphatic system) was investigated. In the current investigation, we present the labeling of the IBTN with technetium-99m ((99m)Tc) through [(99m)Tc(CO)(3)](+) precursor for radioimmunoimaging (RII) of the tumor prior to its treatment with (90)Y labeled IBTN. Labeled IBTN was radiobiologically characterized in terms of radiochemical purity, in vitro stability in human plasma, immunoreactivity, binding with Raji and Ramos cells and biodistribution in a female nude mouse (FNM) model. It was observed that the reduced IBTN (rIBTN) showed more promising radiobiologic characteristics than the nonreduced IBTN. Significantly higher transchelation was seen in excess cysteine compared with histidine. The radioconjugate showed higher saturated binding affinity with CD20 antigen. Significantly higher target (tumor) to background ratios were observed 1 h post-injection (p.i.). Based on radiochemical purity, in vitro stability, immunoreactivity, binding and biodistrubtion in the FNM model, we recommend the radiolabeling of the rIBTN using tricarbonyl technique as a potential RII agent.