RNA integrity as a quality indicator during the first steps of RNP purifications : A comparison of yeast lysis methods

Background  

The completion of several genome-sequencing projects has increased our need to assign functions to newly identified genes. The presence of a specific protein domain has been used as the determinant for suggesting a function for these new genes. In the case of proteins that are predicted to interact with mRNA, most RNAs bound by these proteins are still unknown. In yeast, several protocols for the identification of protein-protein interactions in high-throughput analyses have been developed during the last years leading to an increased understanding of cellular proteomics. If any of these protocols or similar approaches shall be used for the identification of mRNA-protein complexes, the integrity of mRNA is a critical factor.     

Novel chiral three-dimensional iron(III) compound exhibiting magnetic ordering at T(c) = 40 K

The preparation and crystal structure determination of the iron(III) compound of formula [(NH(4))(2)[Fe(2)O(ox)(2)Cl(2)].2H(2)O](n) (1) (ox = oxalate dianion) are reported here. Complex 1 crystallizes in the orthorhombic system, space group Fdd2, with a = 14.956(7) A, b = 23.671(9) A, c = 9.026(4) A, and Z = 8. The structure of complex 1 consists of the chiral anionic three-dimensional network [Fe(2)O(ox)(2)Cl(2)](2-) where the iron(III) ions are connected by single oxo and bisbidentate oxalato groups. The metal-metal separations through these bridging ligands are 3.384(2) and 5.496(2) A, respectively. Ammonium cations and crystallization water molecules are located in the helical pseudohexagonal tunnels defined by iron atoms. The longest iron-iron distance in the pseudohexagonal tunnel is 15.778(2) A whereas the shortest one is 8.734(2) A. The iron atoms are hexacoordinated: a terminal chloro ligand and five oxygen atoms, that of the oxo group and four from two cis coordinated oxalate ligands, build a distorted octahedral environment around the metal atom. The Fe-O(oxo) bond distance [1.825(2) A] is significantly shorter than the Fe(III)-O(ox) [average value 2.103(4) A] and Fe(III)-Cl bond distances [2.314(2) A]. Magnetic susceptibility measurements of 1 in the temperature range 2.0-300 K reveal the occurrence of a susceptibility maximum at 195 K and a transition toward a magnetically ordered state in the lower temperature region with T(c) = 40 K. The strong antiferromagnetic coupling through the oxo bridge (J = -46.4 cm(-1), the Hamiltonian being H = -JS(A).S(B)) accounts for the susceptibility maximum whereas a weak spin canting of approximately 0.3 degrees due to the antisymmetric magnetic exchange within the chiral three-dimensional network is responsible for the magnetic ordering. The values of coercive field (H(c)) and remnant magnetization (M(r)) obtained from the hysteresis loop of 1 at 5 K are 4000 G and 0.016 micro(B).     

Reductive ring opening of dihydrodibenzothiepine and dihydrodinaphtho-oxepine and -thiepine

The 4,4′di-tert-butylbiphenyl (DTBB)-catalysed lithiation of dihydrodibenzothiepine (1) at −78 °C for 30 min followed by reaction with a carbonyl compound [^tBuCHO, Ph(CH₂)₂CHO, PhCHO, (n-C₅H₁₁)₂CO, (CH₂)₅CO, (CH₂)₇CO, (−)-menthone] at the same temperature leads, after hydrolysis with 3 M hydrochloric acid, to sulphanyl alcohols 2. If after addition of a carbonyl compound as the first electrophile [Me₂CO, (CH₂)₅CO, (−)-menthone], the resulting dianion of type II is allowed to react at room temperature for 30 min, a second lithiation takes place to give an intermediate of type III, which by reaction with a second electrophile [Me₂CO, Et₂CO, (CH₂)₅CO, ClCO₂Et], yields, after hydrolysis, difunctionalised byphenyls 4. The cyclisation of the sulphanyl alcohol 2c under acidic conditions yields the eight-membered sulphur containing heterocycle 3. The lithiation of dihydrodinaphthoheteroepines 7 and 10 with 2.2 equiv of lithium naphthalenide in THF at −78 °C followed by reaction with different electrophiles [H₂O, D₂O, ^tBuCHO, Me₂CO, Et₂CO, (CH₂)₄CO, (CH₂)₅CO] at the same temperature leads, after hydrolysis, to unsymmetrically 2,2′-disubstituted binaphthyls 9 and 12, respectively. When the lithiation is performed with an excess of lithium in the presence of a catalytic amount of DTBB (10% molar), a double reductive cleavage takes place to give the dianionic intermediate VII, which by reaction with different electrophiles [H₂O, Me₂CO, Et₂CO, (CH₂)₄CO, (CH₂)₅CO], followed by hydrolysis with water, yields symmetrically 2,2′-disubstituted binaphthyls 8 and 11. In the case of starting from (R)- or (S)-dihydrodinaphthoheteroepines 7 and 10, these methodologies allow us to prepare enantiomerically pure compounds 8, 11 and 12.     

Regioselectivity in acylation of oligosaccharides catalyzed by the metalloprotease thermolysin

Investigation of the acylation scope of carbohydrates by metalloprotease thermolysin immobilized on Celite as biocatalyst has been carried out. The reactions were performed in DMSO, a good solvent for carbohydrates, where the enzyme has previously shown its activity in transesterifications of sucrose, maltose and maltose-containing oligosaccharides. Surprisingly, no reaction was observed for glucose or the glucose-containing disaccharides, trehalose and lactose. In contrast, laurate monoesters of several sucrose-containing tri- and tetrasaccharides were synthetized through a one step transesterification using vinyl laurate as the acylating agent. Enzyme regioselectivity was accurately determined by HPLC/MS and the structure of the main regioisomers was established by a combination of NMR experiments. The preferred position of acylation in all cases was the 2-OH of the α-d-glucopyranose moiety linked 1→2 to the β-d-fructofuranose unit. These results correlate with the regioselectivity observed in the case of the disaccharide sucrose. A general carbohydrate binding motif for catalysis by thermolysin is proposed.     

Synthesis of 4-aryl-2,3,6,7-tetrahydro-1H-pyrimido[4,5-b][1,4]-diazepin-6-ones from 4,5-diamino-1H-pyrimidin-6-ones and 1-aryl-3-(dimethylamino)-1-propanones

The reaction of 1-aryl-3-(dimethylamino)-1-propanones 1 with one equivalent of 4,5-diamino-1H-pyrimidin-6-ones 2 , in acidic medium, leads to the formation of 4-aryl-2,3,6,7-tetrahydro-1H-pyrimido[4,5-b]-[1,4]diazepin-6-ones 3 . The structure elucidation of the products is based on detail nmr analysis of experiments such as ¹³C, ¹H and DEPT including selective ¹³C{¹H} decoupling experiments.     

Molecular mechanics (MM2) and conformational analysis of compounds with N?C?O units. Parametrization of the force field and anomeric effect

A molecular mechanics force field was developed for systems bearing the N? C? O unit on the basis of 6-31G* and 4-21G “ab initio” calculations with full optimization of the geometry and experimental heats of formation. The parameters used, which implicitly included the anomeric effect, provided good geometric and energetic results, both for the compounds on which the parametrization was based and for others on which the validity of the predictions was checked.     

POLYMER NETWORK-POLY(ETHYLENE GLYCOL)COMPLEXES WITH SHAPE MEMORY EFFECT

The complexes of poly(methacrylic acid-co-methyl methacrylate) network with poly(ethylene glycol) stabilized byhydrogen bonds were prepared. By introducing the poly(ethylene glycol), a large difference in storage modulus below andabove the glass transition temperature occurred and the complexes exhibited shape memory behaviors. The morphology ofcomplexes was studied by using DSC, WAXD, and DMA. The results indicate that the fixed phase of this kind of novelshape memory materials is the network, and the reversible phase is the amorphous state of PEG:PMAA complex phase. Theshape recoverability almost reaches 100%. This type of complexes can be regarded as a novel shape memory network.     

锆基纤维素手性固定相直接拆分萘普生衍生物

萘普生是一种消炎镇痛药 ,其 S对映体的抗炎作用是 R构型的 2 8倍 ,萘普生及其衍生物的拆分具有重要意义 .手性固定相 HPLC直接拆分 [1～ 4 ] 是最简便的分析方法 .氧化锆是近年来备受关注的色谱载体 [5,6 ] .Carr等 [7] 对碱性药物快速拆分表明氧化锆在手性分离Scheme1　 Structuresof chiral naproxen and its derivatives中的独特选择性 .萘普生及其衍生物在锆基手性固定相上的分离未见文献报道 .本组利用自制的球形氧化锆制备了涂敷型纤维素 -三 ( 3,5 -二甲基苯基氨基甲酸酯 ) -Zr O2 手性固定相 ( CDMPC- Zr O2 - CSP) ,在正…     

Manganese,cobalt and nickel complexes with a novel 17-membered macrocycle containing an N5 donor set

Summary The synthesis of a new macrocycle containing phenanthroline and pyridine subunits is described. The reaction of 2,9-bis(hydrazone)-1,10-phenanthroline with 2,6-bis-(bromomethyl) pyridine in the presence of Mn^II, Co^II or Ni^II ion templates leads to the isolation, in high yield, of the seven-coordinate complexes [M(L³)Br₂] (L³ = 4,5, 6,7,8,9-phenanthrolino-14,15,16-pyridino-1,2,5,8,11,12,15 heptaazacycloheptadecane,2,10-diene). The compounds were characterized by physical measurements, which indicated that in all the complexes the ligand is acting as a pentadentate N₅ chelating agent.     

Molecular nitrides containing group 4 and 5 metals: single and double azatitanocubanes

Treatment of [[Ti(eta(5)-C(5)Me(5))(micro-NH)](3)(micro(3)-N)] (1) with the imido complexes [Ti(NAr)Cl(2)(py)(3)] (Ar=2,4,6-C(6)H(2)Me(3)) and [Ti(NtBu)Cl(2)(py)(3)] in toluene affords the single azatitanocubanes [[Cl(2)(ArN)Ti]( micro(3)-NH)(3)[Ti(3)(eta(5)-C(5)Me(5))(3)(micro(3)-N)]].(C(7)H(8)) (2.C(7)H(8)) and [[Cl(2)Ti](micro(3)-N)(2)(micro(3)-NH)[Ti(3)(eta(5)-C(5)Me(5))(3)(micro(3)-N)]] (3), respectively. Similar reactions of complex 1 with the niobium and tantalum imido derivatives [[M(NtBu)(NHtBu)Cl(2)(NH(2)tBu)](2)] (M=Nb, Ta) in toluene give the single azaheterometallocubanes [[Cl(2)(tBuN)M](micro(3)-N)(micro(3)-NH)(2)[Ti(3)(eta(5)-C(5)Me(5))(3)(micro(3)-N)]] (M=Nb (4), Ta (5)), both complexes react with 2,4,6-trimethylaniline to yield the analogous species [[Cl(2)(ArN)M](micro(3)-N)(micro(3)-NH)(2)[Ti(3)(eta(5)-C(5)Me(5))(3)(micro(3)-N)]].(C(7)H(8)) (Ar=2,4,6-C(6)H(2)Me(3), M=Nb (6.C(7)H(8)), Ta (7.C(7)H(8))). Also the azaheterodicubanes [M[micro(3)-N)(2)(micro(3)-NH)](2)[Ti(3)(eta(5)-C(5)Me(5))(3)(micro(3)-N)](2)].2C(7)H(8) [M=Ti (8.2C(7)H(8)), Zr (9.2C(7)H(8))], and [M[(micro(3)-N)(5)(micro(3)-NH)][Ti(3)(eta(5)-C(5)Me(5))(3)(micro(3)-N)](2)].2 C(7)H(8) (Nb (10.2C(7)H(8)), Ta (11.2C(7)H(8))) were prepared from 1 and the homoleptic dimethylamido complex [M(NMe(2))(x)] (x=4, M=Ti, Zr; x=5, M=Nb, Ta) in toluene at 150 degrees C. X-ray crystal structure determinations were performed for 6 and 10, which revealed a cube- and double-cube-type core, respectively. For complexes 2 and 4-7 we observed and studied by DNMR a rotation or trigonal-twist of the organometallic ligands [[Ti(eta(5)-C(5)Me(5))(micro-NH)](3)(micro(3)-N)] (1) and [(micro(3)-N)(micro(3)-NH)(2)[Ti(3)(eta(5)-C(5)Me(5))(3)(micro(3)-N)]](1-). Density functional theory calculations were carried out on model complexes of 2, 3, and 8 to establish and understand their structures.