Tentative study of the coding sequences without 3-base periodicity

Fourier spectra of 120 short coding sequences (<1 200 bp) show that not all coding sequences are characterized by 3-base periodicity. Statistical analysis suggests that whether a coding sequence has 3-base periodicity may be related to the composition and distribution of bases, the usage and the order of the amino acids of the encoded protein as well as the synonymous codon usage. Generally, the content of A+U is higher than that of G+C in non-period-3 sequences, inversely in period-3 sequences. In the three codon positions, the base distribution in the non-periodic-3 sequences is more uniform than in the periodic-3 sequences. The usage biases of the amino acids and the codons in non-period-3 sequences are weaker than that in period-3 sequences. All of these phenomena should be considered sufficiently in predicting the genes and exons of DNA sequences by Fourier analysis method.

Genomic organization and expression analysis of Toll-like receptor 3 in grass carp (Ctenopharyngodon idella)

Toll-like receptor 3 (TLR3) participates in the innate immune response by recognizing viral pathogens. To investigate grass carp immune system responding to GCRV (grass carp reovirus) infection, the full-length cDNA sequence and genomic organization of grass carp TLR3 (CiTLR3) was identified and characterized. The full-length genome sequence of CiTLR3 is composed of 5668 nucleotides, including five exons and four introns. The full-length of CiTLR3 cDNA is 3681 bp in length and encodes a polypeptide of 904 amino acids with an estimated molecular mass of 102,765 Da and a predicted isoelectric point of 8.35. Analysis of the deduced amino acid sequence indicated that CiTLR3 has four main structural domains, including a signal peptide sequence, 14 LRR (leucine-rich repeat) motifs, a transmembrane region and a TIR (Toll/interleukin-1 receptor) domain. It is most similar to the crucian carp (Carassius auratus) TLR3 amino acid sequence with an identity of 99%. Quantitative RT-PCR analysis showed that CiTLR3 transcripts were significantly up-regulated starting at day 1 and continued through day 7 following GCRV infection (P < 0.05). These data implied that CiTLR3 is involved in antiviral defense, provide molecular and functional information for grass carp TLR3, and implicate their role in mediating immune protection against grass carp viral diseases. (C) 2009 Elsevier Ltd. All rights reserved.

Sequence of genome segments 1, 2, and 3 of the grass carp reovirus (Genus Aquareovirus, family Reoviridae)

The genome segments 1, 2, and 3 of the grass carp reovirus (GCRV), a tentative species assigned to genus Aquareouirus, family Reouiridae, were sequenced. The respective segments 1, 2, and 3 were 3949, 3877, and 3702 nucleotides long. Conserved moths 5' (GUUAUUU) and 3' (UUCAUC) were found at the ends of each segment. Each segment contains a single ORF and the negative strand does not permit identification of consistent ORFs. Sequence analysis revealed that VP2 is the viral polymerase, while VPI might represent the viral guanyly/methyl transferase (involved in the capping process of RNA transcripts) and VP3 the NTPase/helicase (involved in the transcription and capping of viral RNAs), The highest amino acid identities (26-41%) were found with orthoreovirus proteins. Further genomic characterization should provide insight about the genetic relationships between GCRV, aquareoviruses, and orthoreoviruses, It should also permit to precise the taxonomic status of these different viruses. (C) 2000 Academic Press.

Whole-body amino acid pattern of F-4 human growth hormone gene-transgenic red common carp (Cyprinus carpio) fed diets with different protein levels

F-4 generation of human growth hormone (hGH) gene-transgenic red common carp, and the non-transgenic controls were fed for 8 weeks on purified diets with 20%, 30% or 40% protein. Analysis of whole-body amino acids showed that the proportions of lysine, leucine, phenylalanine, valine and alanine, as percentages of body protein, increased significantly, while those of arginine, glutamic acid and tyrosine decreased, with increases in dietary protein level in at least one strain of fish. Proportions of the other amino acids were unaffected by the diets. The proportions of lysine and arginine were significantly higher, while those of leucine and alanine were lower in the transgenics than in the controls in at least one diet group. Proportions of the other amino acids were unaffected by strain. The results suggest that the whole-body amino acid profile of transgenic carp, when expressed as proportions of body protein, was in general, similar to that of the non-transgenic controls. (C) 2000 Elsevier Science B.V. All rights reserved.

Aliphatic Poly(ester-carbonate)s Bearing Amino Groups and Its RGD Peptide Grafting

This article deals with (1) synthesis of novel cyclic carbonate monomer (2-oxo [1,3]dioxan-5-yl)carbamic acid benzyl ester (CAB) containing protected amino groups; (2) ring-opening copolymerization of the cyclic monomer with L-lactide (LA) to provide novel degradable poly(ester-carbonate)s with functional groups; (3) removal of the protective benzyloxycarbonyl (Cbz) groups by catalytic hydrogenation to afford the corresponding poly(ester-co-carbonate)s with free amino groups; (4) grafting of oligopeptide Gly-Arg-Gly-Asp-Ser-Tyr (GRGDSY, abbreviated as RGD) onto the copolymer pendant amino groups in the presence of 1,1'-carbonyldiimidazole (CDI).

Effect of hydroxyl and amino groups on electrochemiluminescence activity of tertiary amines at low tris(2,2 '-bipyridyl)ruthenium(II) concentrations

ECL of several amines containing different numbers of hydroxyl and amino groups was investigated. N-butyldiethanolamine is found to be more effective than 2-(dibutylamino)ethanol at gold and platinum electrodes, and is the most effective coreactant reported until now. Surprisingly, ECL intensities of monoamines, such as 2-(dibutylamino)ethanol and N-butyldiethanolamine, are much stronger than that of diamines including N,N,N',N'-tetrakis-(2-hydroxyethyl)-ethylenediamine and N,N,N',N'-tetrakis-(2-hydroxypropyl)ethlenediamine. The striking contrast between ECL signals of the investigated monoamines and diamines may result from more significant side reactions of diamines, such as the intramolecular side reactions between oxidative amine cation radicals and reductive amine free radicals.

Rare-earth metal complexes stabilized by amino-phosphine ligand. Reaction with mesityl azide and catalysis of the cycloaddition of organic azides and aromatic alkynes

Stoichiometric reactions between mesityl azide (MesN(3), Mes = 2,4,6-C6H2Me3) and amino-phosphine ligated rare-earth metal alkyl, LLn(CH2SiMe3) (2)(THF) (L = (2,6-C6H3Me2)NCH2C6H4P(C6H5)(2); Ln = Lu (1a), Sc (1b)), amide, LLu(NH(2,6-(C6H3Pr2)-Pr-i))(2)(THF) (2) and acetylide at room temperature gave the amino-phosphazide ligated rare-earth metal bis(triazenyl) complexes, [L(MesN(3))]Ln[(MesN(3))-(CH2SiMe3)](2) (Ln = Lu (3a); Sc (3b)), bis(amido) complex [L(MesN3)] Lu[NH(2,6-C6H3 Pr-i(2))](2) (4), and bis(alkynyl) complex (5) (L(MesN(3))Lu (C CPh)(2))(2), respectively. The triazenyl group in 3 coordinates to the metal ion in a rare eta(2)-mode via N-beta and N-gamma atoms, generating a triangular metallocycle. The amino-phosphazide ligand, L(MesN(3)), in 3, 4 and 5 chelates to the metal ion in a eta(3)-mode via N-alpha and N-gamma atoms. In the presence of excess phenylacetylene, complex 3a isomerized to 3', where the triazenyl group coordinates to the metal ion in a eta(3) mode via Na and Ng atoms.

Ethylene Polymerization by the New Chromium Catalysts Based on Amino-Pyrrolide Ligands

A series of amino-pyrrolide ligands (1-4a) and their derivatives aminothiophene ligand (5a), amino-indole ligand (6a) were prepared. Chromium catalysts, which were generated in situ by mixing the ligands with CrCl3(thf)(3) in toluene, were tested for ethylene polymerization. The preliminary screening results revealed that the tridentate amino-pyrrolide ligands containing soft pendant donor, 3a, 4a/CrCl3(thf)(3) systems displayed high catalytic activities towards ethylene polymerization in the presence of modified methyaluminoxane. The electronic and steric factors attached to the ligand backbone significantly affected both the catalyst activity and the polymer molecular weight. Complex 4b was obtained by the reaction of CrCl3(thf)(3) with one equivalent of the lithium salts of 4a, which was the most efficient ligand among the tested ones. The effect of polymerization parameters such as cocatalyst concentration, ethylene pressure, reaction temperature, and time on polymerization behavior were investigated in detail. The resulting polymer obtained by 4b display wax-like and possess linear structure, low molecular weight, and unimodal distribution.

One-step synthesis of Ru(2,2 '-bipyridine)(3)Cl-2-immobilized silica nanoparticles for use in electrogenerated chemiluminescence detection

One-step synthesis of Ru (bpy)(3) Cl-2-immobilized (bpy = 2,2'-bipyridine) silica nanoparticles (Ru-silica nanoparticles) for use in electrogenerated-chemiluminescence (ECL) detection is reported. Ru-silica nanoparticles are prepared by using the Stober method. Compared with free Ru(bpy)(3)Cl-2, Ru-silica nanoparticles are seen to exhibit a red-shift of the UV-vis absorbance peak and a longer fluorescence lifetime, which are attributed to the electrostatic interaction of Ru(bpy)(3)(2+) and silica. Because silica nanoparticles are used as immobilization matrices, the surfaces of Ru-silica nanoparticles are easily modified or functionalized via the assembly of other nanoparticles, such as Au. For ECL detection, Au-colloid-modified Ru-silica nanoparticles are immobilized on a 3-mercaptopropyl-trimethoxysilane-modified indium tin oxide electrode surface by Au-S interaction; the surface concentration of electroactive Ru(bpy)(3)Cl-2 is obviously higher than that in silica films.

CE with electrochemical detection for investigation of label-free recognition of amino acid amides by guanine-rich DNA aptamers

In this work, we report a simple and effective investigation into adaptive interactions between guanine-rich DNA aptamers and amino acid amides by CE with electrochemical (EC) detection. Argininamide (Arm) and tyrosinamide (Tym) were chosen as model molecules. On a copper electrode, Arm generated a good EC signal in 60 mM NaOH at 0.7 V (vs Ag/ AgCl), while Tym. was detected well on a platinum electrode at 1. 3 V in 20 mM phosphate of pH 7.0. Based on their EC properties, the ligands themselves were used as indicators for the adaptive interactions investigated by CE-EC, making any step of labeling and/or modification of aptamers with indicators exempted. Hydrophilic ionic liquid was used as an additive in running buffer of CE to improve the sensitivity of Arm detection, whereas the additive was not used for Tym. detection due to its negative effect. Two guanine-rich DNA aptamers were used for molecular recognition of Arm and Tym. When the aptamers were incubated with ligands, they bound the model molecules with high affinity and specificity, reflected by obvious decreases in the signals of ligands but no changes in those of the control molecules. However, the ligands were hardly affected by the control ssDNAs after incubation. The results revealed the specific recognition of Arm and Tym. by the aptamers.

C-H activation motivated by N,N '-diisopropylcarbodiimide within a lutetium complex stabilized by an amino-phosphine ligand

A lutetium bis( alkyl) complex stabilized by a flexible amino phosphine ligand LLu( CH2Si(CH3)(3))(2)(THF) (L = (2,6-C6H3( CH3)(2)) NCH( C6H5) CH2P(C6H5)(2)) was prepared which upon insertion of N, N'-diisopropylcarbodiimide led to C-H activation via metalation of the ligand aryl methyl followed by reduction of the C=N double bond.

Synthesis and reactivity of rare earth metal alkyl complexes stabilized by anilido phosphinimine and amino phosphine ligands

Anilido phosphinimino ancillary ligand H2L1 reacted with one equivalent of rare earth metal trialkyl [Ln{CH2Si(CH3)(3)}(3)(thf)(2)] (Ln = Y, Lu) to afford rare earth metal monoalkyl complexes [L(1)LnCH(2)Si(CH3)(3)(THF)] (1a: Ln = Y; 1b: Ln = Lu). In this process, deprotonation of H2L1 by one metal alkyl species was followed by intramolecular C-H activation of the phenyl group of the phosphine moiety to generate dianionic species L-1 with release of two equivalnts of tetramethylsilane. Ligand L-1 coordinates to Ln(3+) ions in a rare C,N,N tridentate mode. Complex 1a reacted readily with two equivalents of 2,6-diisopropylaniline to give the corresponding bis-amido complex [(HL1)LnY(NHC(6)H(3)iPr(2)-2,6)(2)] (2) selectively, that is, the C-H activation of the phenyl group is reversible. When 1a was exposed to moisture, the hydrolyzed dimeric complex [{(HL1)Y(OH)}(2)](OH)(2) (3) was isolated. Treatment of [Ln{CH2Si(CH3)(3)}(3)-(thf)(2)] with amino phosphine ligands HL2-R gave stable rare earth metal bisalkyl complexes [(L2-R)Ln{CH2Si(CH3)(3)}(2)(thf)] (4a: Ln=Y, R=Me; 4b: Ln=Lu, R=Me; 4c: Ln=Y, R=iPr; 4d: Ln=Y, R=iPr) in high yields. No proton abstraction from the ligand was observed. Amination of 4a and 4c with 2,6-diisopropylaniline afforded the bis-amido counterparts [(L2-R)Y(NHC(6)H(3)iPr(2)-2,6)(2)(thf)] (5a: R=Me; 5b: R=iPr).

Rare earth metal bis(alkyl) complexes bearing amino phosphine ligands: Synthesis and catalytic activity toward ethylene polymerization

Reactions of neutral amino phosphine compounds HL1-3 with rare earth metal tris(alkyl)s, Ln(CH2SiMe3)(3)(THF)(2), afforded a new family of organolanthanide complexes, the molecular structures of which are strongly dependent on the ligand framework. Alkane elimination reactions between 2-(CH3NH)-C6H4P(Ph)(2) (HL1) and Lu(CH2SiMe3)(3)(THF)(2) at room temperature for 3 h generated mono(alkyl) complex (L-1)(2)Lu(CH2SiMe3)(THF) (1). Similarly, treatment of 2-(C6H5CH2NH)-C6H4P(Ph)(2) (HL2) with Lu(CH2SiMe3)(3)(THF)(2) afforded (L-2)(2)Lu(CH2SiMe3)(THF) (2), selectively, which gradually deproportionated to a homoleptic complex (L-2)(3)Lu (3) at room temperature within a week. Strikingly, under the same condition, 2-(2,6-Me2C6H3NH)-C6H4P(Ph)(2) (HL3) swiftly reacted with Ln(CH2SiMe3)(3)(THF)(2) at room temperature for 3 h to yield the corresponding lanthanide bis(alkyl) complexes L(3)Ln(CH2SiMC3)(2)(THF)(n) (4a: Ln = Y, n = 2; 4b: Ln = Sc, n = 1; 4c: Ln = Lu, n = 1; 4d: Ln = Yb, n = 1; 4e: Ln = Tm, n = 1) in high yields. All complexes have been well defined and the molecular structures of complexes 1, 2, 3 and 4b-e were confirmed by X-ray diffraction analysis. The scandium bis(alkyl) complex activated by AlEt3 and [Ph3C][B(C6F5)(4)], was able to catalyze the polymerization of ethylene to afford linear polyethylene.

Structural diversity of lanthanide-amino acid complexes under near physiological pH conditions and their recognition of single-stranded DNA

We reported here four structures of lanthanide-amino acid complexes obtained under near physiological pH conditions and their individual formula can be described as [Tb-2(DL-Cys)(4)(H2O)(8)]Cl-2 (1), [Eu-4(mu(3)-OH)(4)(L-Asp)(2)(L-HAsp)(3)(H2O)(7)] Cl center dot 11.5H(2)O (2), [Eu-8-(L-HVal) (16)(H2O)(32)]Cl-24 center dot 12.5H(2)O (3), and [Tb-2(DL-HVal)(4)(H2O)(8)]Cl-6 center dot 2H(2)O (4). These complexes showed diverse structures and have shown potential application in DNA detection. We studied the interactions of the complexes with five single-stranded DNA and found different fluorescence enhancement, binding affinity and binding stoichiometry when the complexes are bound to DNA.