A New Synthetic Approach Towards α- and β-LNA (Locked Nucleic Acids)

Abstract

A bicyclo[2.2.1] phenyl thioglycoside was efficiently synthesised and introduced as the key synthon in a novel method for convergent synthesis of β-LNA-nucleosides as well as their α-configurated isomers. An acid-induced ring-opening reaction on the corresponding bicyclo[2.2.1] methyl furanoside is also described.     

α-Amylase Formation and Nucleic Acid Metabolism of Bacillus subtilis

The nucleic acid metabolism in washed cells of Bacillus subtilis was investigated with special reference to amylase formation of the bacterium. On incubation of the suspension of the washed cells, purines, pyrimidines and their related compounds were observed in the medium. However, in the medium of the cells incubated with a calcium chelater, where no amylase formation occurred, were detected adenosine- and guanosine-monophosphate in addition to those described above. The addition of a calcium chelater was also found to decrease the quantity of the nucleic acids being involved in the lysozyme-sensitive fraction of the bacterial cells, suggesting the possibility that the metabolism of nucleic acids in this fraction is closely related to amylase formation of the cells.     

α-cycloPNA: 1-Aminocylopentane-1-carboxylic Acid-Derived Peptide Nucleic Acid

Abstract

All four diastereoisomers of 3-thymine-1-(^tbutoxycarbonyl)aminocyclopentane- 1-carboxylic acid have been synthesised from (S)-dimethyl malate and thymine monomer 12 has been incorporated into an α-cycloPNA oligomer.     

2′-O,4′-C-Ethylene-Bridged Nucleic Acid (ENATM) for Effective Antisense Formation

Abstract

ENA^TM antisense oligonucleotides for vascular endothelial growth factor (VEGF) mRNA were synthesized and evaluated in A549 lung cancer cells. It was found that the VEGF ENA-antisense inhibited not only the expression of VEGF, but also the expression of three genes, which were found in Genbank by BLAST and Clustal W search and considered likely to bind to the VEGF ENA-antisense. These results indicate that ENA-antisense oligonucleotides act in a sequence-specific manner, and could be used as effective antisense drugs.     

Nucleic Acid Analog Peptide Containing β-Aminoalanine Modified with Nucleobases

Abstract

Oligopeptides containing N^β-(thymin-1-ylacetyl) β-aminoalanine and N^β-(cytosin-1-ylacetyl) β-aminoalanine moieties synthesized on solid phase using standard boc-chemistry showed hybridization properties with single stranded DNA and RNA, and also with double stranded DNA at pH 7.0.     

Ethyl[2-Deoxy-5-O-(4,4′-dimethoxytrityl)-α- and β-D-erythro-Pentofuranosyl] Acetates as Versatile Intermediates in Nucleic Acid Chemistry

Abstract

The title compounds (1a,b) were synthesized in three steps from 2-deoxy-D-ribose, and used in the preparation of oligonucleotide conjugates, branched oligonucleotides as well as homo-N-nucleosides.     

Isolation of Allo-isoleucic Acid (α-Hydroxy-β-methylvaleric Acid) and β-Hydroxy-β-methylvaleric Acid from Turkish Tobacco Leaves

A new method determining the activity of tannin acyl hydrolase (tannase) was made. This method was based on the change in optical density of substrate tannic acid at 310 mμ. In this method, the error of measurement was about 1~3%, and many samples could be tested at one time because of its simplicity.

The procedure was as follows; To four parts of substrate (0.350 w/v% of tannic acid dissolved in 0.05m citrate buffer, pH 5.5), one part of the enzyme solution was added.

After t minutes reaction at 30°C, 0.1 part of the mixture was added to ten parts of 90% ethanol.

The optical density of the ethanol solution at 310 mμ was measured. Tannase activity (unit/ml) was given by following equation. $u=114\times \frac{E_{t1}?E_{t2}}{t_2?t_1}$

Where E_t1 and E_t2 mean the optical density of the ethanol solution at 310 mμ prepared after t₁ and t₂ minutes reaction, and one unit of the enzyme means the amount of the enzyme which is able to hydrolyze one μ mole of the ester bond in tannic acid in one minute.

The substrate tannic acid used in this determining method was purified. It was composed of one mole of glucose and nine moles of gallic acid, and eight moles of which formed four moles of m-digallic acid.     

Photoactivatable Reagents Based on Aryl(trifluoromethyl)diazirines: Synthesis and Application for Studying Nucleic Acid–Protein Interactions

Recent data on the synthesis of photoactivatable derivatives of nucleic acids and proteins on the basis of aryl(trifluoromethyl)diazirines—analogs of nucleosides, nucleotides, oligonucleotides, as well as amino acids and peptides—are reviewed. The synthesis of bi- and polyfunctional photoactivatable reagents, including those containing a cleavable function, designed for postsynthetic modification of biopolymers is described. Data are given on the use of the photoactivatable derivatives for studying nucleic acid–protein interactions by the method of photoaffinity labeling. Special consideration is paid to the results obtained by the authors" team in cooperation with other researchers as well as graduate students of the Chemistry of Natural Products Chair, Chemical Faculty, Moscow State University and destined to solve various scientific tasks in the domain of nucleic acid–protein recognition with the use of photoaffinity crosslinking.     

α-Aminoadipic Acid and α,ɛ-Diaminopimelic Acid in Inoculated Pea Plants (Pisum sativum) and Root Nodule Bacteria (Rhizobium leguminosarum)

Observations were made on the content of α-aminoadipic acid and α-aminophimelic acid (DAP) in pea plants, nodules and Rhizobium leguminosarum, strain HT3. The preparations were purified by ion exchange chromatography, Qualitative analyses were made by paper chromatography, and quantitative analyses by means of an automatic amino acid analysator. In the whole plant and seeds the content of α-aminoadipic acid soluble in 70% ethanol varied between 10 and 80 μg/g dry weight. The shoot and red nitrogen fixing nodules contained more of this acid than roots and green inactive nodules. In the insoluble fraction of the shoot its concentration was 0.4-0.6 mg/g dry weight. α-Aminoadipic acid was not found in free living rhizobia, which again contained a considerable amount of α-aiaminopimelic acid, about 0.5 mg/g dry weight. The synthesis of DAP was intensive also in root nodules. In red nodules, which fixed molecular nitrogen, the content of DAP was 2.1 mg/g dry weight and in green inactive nodules 1.3 mg/g dry weight. It was shown that in the nodules DAP is closely connected with cell wall peptides of bacteroids. DAP could not be found in pea plants outside the nodules.     

Poly(ADP-ribose) polymerase-1: A Regulator of Protein–Nucleic Acid Interactions in Processes Responding to Genotoxic Impact

Poly(ADP-ribose) polymerase-1 (PARP-1), a nuclear protein of higher eukaryotes, specifically detects strand breaks in DNA. The enzyme is activated in the presence of such breaks and synthesizes poly(ADP-ribose) covalently bound to certain proteins, with PARP-1 itself being the main acceptor. This protein is involved in the majority of DNA-dependent processes, including replication, recombination, repair, and cell death (apoptosis and necrosis). Poly(ADP-ribosyl)ation of proteins is regarded as a mechanism which induces a signal of DNA damage and modulates the function of proteins in response to genotoxic actions. Attention in this review is focused on the role of PARP-1 and poly(ADP-ribosyl)ation in base excision repair (BER), the main process of DNA break repair. The main putative functions of PARP-1 in this process are also considered, namely, its functions as a factor initiating the BER protein complex, a temporary protector of DNA ends, a factor modulating chromatin structure through poly(ADP-ribosyl)ation of histones, and a signal in the mechanism recognizing the degree of DNA damage in the cell.     

Asymmetric Hydrolysis of (±)-α-Substituted Garboxylic Acid Esters with Microorganisms

Microorganisms that hydrolyze methyl 2-phenylpropionate (1) or reduce 4-phenyl-2-butanone (3) were screened from 250 type cultures. Several Aspergilli and two bacteria hydrolyzed ester 1, and Asp. sojae IAM 2703 preferentially hydrolyzed (R)-isomer of (±)-1, whereas Bacillus subtilis var. niger IFO 3108 and Mycobacterium smegmatis ATCC 10143 preferentially hydrolyzed (S)-isomer. The hydrolysis of the related esters of 1 with these organisms was also examined.     

Synthesis and Binding Properties of a Homopyrimidine 2′,5′-Linked Xylose Nucleic Acid (2′,5′-XNA)

Abstract

The synthesis and hybridization properties of pyrimidine 2′,5′-RNA and 2′,5′-Xylose Nucleic Acid (2′,5′-XNA) are described.     

Some X-Ray Diffraction Parameters of Liquid-Crystalline Dispersions of Nucleic Acid–Chitosan Complexes

Liquid-crystalline dispersions of nucleic acid–chitosan complexes (NA–chitosan) possess optical and X-ray diffraction properties different from those of classical cholesterics. It is possible that positive charge distribution (distance between charges, chitosan conformation, etc.) in the chitosan polymeric chain interacting with NA is a factor controlling the spatial structure of the resulting dispersions.     

How are Nucleic Acids Released in Cells from Cationic Lipid-Nucleic Acid Complexes?

Abstract

Cationic lipid-nucleic acid complexes are widely used to deliver oligonucleotides, RNA and DNA into cells. Although much has been learned about the structure and forces that hold the complex together, an understanding of the mechanism of release of the nucleic acids from the complex into cells has been lacking. Recent studies have shown that anionic liposomes with compositions similar to the cytoplasmic face of the endosomal membrane are potent agents for inducing the rapid release of oligonucleotides and DNA from cationic lipid-nucleic acid complexes. Based upon these results, we propose that after the cationic lipid/nucleic complex is internalized by endocytosis it destabilizes the endosomal membrane. This destabilization induces flip-flop of anionic lipids from the cytoplasmic facing monolayer, which laterally diffuse into the complex and form a charge neutral ion-pair with the cationic lipids. This results in displacement of the nucleic acid from the cationic lipid and subsequent release of the nucleic acid into cytoplasm of the cell. We review the data that show the proposed mechanism accounts for a variety of observations on cationic lipid/nucleic acid complex-cell interactions.     

Synthesis of (±)-Tubaic Acid

An alternative synthesis of (±)-tubaic acid (I), a key intermediate compound of rotenone synthesis, has been accomplished by the Wittig reaction.     

α-Aminoisobutyric Acid as the Constituent Amino Acid of Protein

α-Aminoisobutyric acid is the only tertiary amino acid which is reported to occur in the proteins. Nevertheless, this amino acid has not been yet isolated from the proteins. Recently we succeeded in isolating this amino acid as white prismy crystalline substance from both acid and pepsin hydrolysate of horse hind leg muscle proteins, and this crystal was identified to be α-amino-isobutyric acid by elementary analysis, properties of this derivates, etc.