Proteins, nucleic acids and genetic codes.

On the basis of the previous article (Morchio and Traverso [1999]), we discuss the possible interactions between the first proteic fragments developed in the hydrophobic layer made of hydrocarbons, which would have covered the surface of the primitive seas, and the nitrogenous bases, particularly the pyrimidinic ones, which would have found in such hydrophobic layer favourable conditions to their prebiotic synthesis. These interactions would have presumably brought, on the basis of the physicochemical laws, at the moment the only ones at work, to the linkage of various bases and so to the construction of the first nucleic acid chains (most likely RNA). Interestingly enough this result would have been obtained by inserting two more bases between those hydrogen bound to the amino acids and this might have been the ground for the future "triplets". These interactions might have been particularly significant because of two important consequences: the birth of a rough genetic code and the starting of interactions of the co-operative type between bases and amino acids that would have made the growth of both proteic and nucleic acid fragments easier and faster. We conclude that the development of the genetic code was neither a "frozen accident" nor an occurrence directed by any information flow.     

Binding of bile acids, organic anions, and fatty acids by bovine intestinal Z protein.

Z protein from bovine small intestinal mucosa was purified and its binding affinities for bile acids, organic anions, and fatty acids were compared with those of bovine hepatic Z protein. Purification of Z protein from intestinal and hepatic cytosol was performed by gel filtration, chromatofocusing, and hydroxyapatite chromatography. Both purified proteins had the same molecular weight (Mr 14,000) and eluted from a chromatofocused gel at about pH 10. Binding studies were performed by the competitive displacement of 8-anilinonaphthalene-1-sulfonic acid and by equilibrium dialysis. Binding affinities for bile acids, organic anions, and fatty acids were very similar between intestinal and hepatic Z proteins. Although the real physiologic role of Z protein remains to be further elucidated, these data indicate that intestinal Z protein participates in the mechanism of intracellular bile acid transfer in enterocytes.     

E.s.r. of spin-trapped radicals in gamma-irradiated polycrystalline amino acids, N-acetyl amino acids and dipeptides

The radicals produced in several polycrystalline amino acids, N-acetyl amino acids and dipeptides by gamma-radiolysis at room temperature were investigated by spin-trapping. After irradiation in the solid state, the samples were dissolved in aqueous solutions f t-nitrosobutane and the trapped radicals identified by e.s.r. For alpha-amino acids, deamination radicals were found, and in some cases H-abstraction radicals were also observed. No decarboxylation radicals could be detected. For N-acetyl amino acids, except for N-acetylglycine, the major radical was the decarboxylation radical. For N-acetyglycine the H-abstraction radical from the glycine residue was observed. For dipeptides of the x-glycine, the radical formed by removal of H from the alpha-carbon of the carboxyl-terminal residue was always spin-trapped. Some primary deamination radicals and minor amounts of decarboxylation radicals could also be observed. For dipeptides of the type x-alanine, glycine-x and alanine-x, the decarboxylation radical was always the major spin-trapped radical. Some primary and secondary deamination radicals were also detected.     

Novel alpha-aminophosphonic acids. Design, characterization, and biological activity

Novel alpha-aminophosphonic acids are synthesized reacting 1,3-oxazolidin-2-one derivatives with formaldehyde and phosphorus trichloride. Treatment of N-(phosphonomethyl)oxazolidinones with aqueous NaOH gave the expected alpha-aminophosphonic acids. The oxidation of (2-hydroxy-1,1-dimethylethylamino)methyl phosphonic acid in the presence of CdO and water resulted in N-phosphonomethyl-2-methyl-1-propanoic acid. Their structures were proved by means of IR, 1H, 13C, and 31P NMR spectroscopy. The genotoxic, clastogenic, and antiproliferative effects of newly synthesized original aminophosphonic acids were investigated for the first time.     

Fatty acids,part 54. Some reactions of long-chain oxygenated acids with special reference to those furnishing furanoid acids

C₁₈ furanoid acids are prepared from natural oxygenated acids by palladium (II)-catalysed cyclodehydrogenation, by rearrangement of epoxides with iodopropane-sodium iodide-dimethylsulphoxide, and by dehydration of endoperoxides. Some reactions give mixed products but routes to the individual 10,13-, 9,12- and 8,11-furans are reported. The endoperoxide route leads to speculation about the biosynthesis of natural furanoid acids.     

Infrared studies of deoxyribonucleic acids, their consituents and analogues. II. Deoxyribonucleic acids with different base composition

The base composition of DNA from microorganisms varies over a wide range of guanine + cytosine (G-C) content. We have examined the infrared spectra of a number of DNA samples isolated from different microorganisms and have found marked differences in their infrared spectra. These differences have been related to the G-C content of the investigated DNA samples. A comparison between the infrared spectra of nucleosides, synthetic polynucleotides, apurinic acid, and apyrimidinic acid has permitted a more extensive assignment of infrared bands to distinct base residues. The relative intensity of the absorption bands at 1485 and 1505 cm.^?1 depends on the G-C content of the deuterated DNA sample. On the basis of these results a new method for the determination of the G-C content in DNA has been developed from the results. Its advantage is that the measurement is rapid and the DNA samples are not changed by the procedure.     

Bile acids. 38. Conversion of 5 -cholestane-3 ,7 -diol to allo bile acids by the rat

5alpha-[4-(14)C, 3alpha-(3)H]Cholestane-3beta,7alpha-diol was prepared from individual samples of 5alpha-[3alpha-(3)H]cholestane-3beta,7alpha-diol and 5alpha-[4-(14)C]cholestane-3beta,7alpha-diol, each derived from 3beta-acetoxycholest-5-en-7-one. Bile was collected for 11 days from adult male rats, with cannulated bile ducts, that had received intraperitoneally 0.90-0.92 mg of the doubly labeled diol. Bile from the first 10 hr, containing 63% of the administered (14)C and 6% of the (3)H, was hydrolyzed, and the bile acids were separated by acetic acid partition chromatography. Allochenodeoxycholic and allocholic acids contained at least 20.6% and 48.6%, respectively, of the (14)C retained in the biliary acids. Small amounts of (14)C (2.5% and 1.9%, respectively) were present in the 3beta isomers of these acids, but the tritium content totaled more than half of that found in the bile acid fraction. No evidence was obtained for presence of the extensive quantities of the allomuricholates.     

Synthesis of alpha-, beta- and cyclic spaglumic acids.

A short, one-pot synthesis of alpha- and beta-spaglumic acids (N-acetyl-L-aspartyl-L-glutamic acids, NAAGA) has been developed based on ultrasound-promoted acetylation of aspartic acid, followed by dehydration, condensation with glutamic acid dibenzyl ester and hydrogenolysis. The alpha- and beta-peptides were separated by anion-exchange chromatography. The alpha-peptide shows a remarkable tendency to cyclize during methylation with diazomethane and yields cyclic N-acetylaspartylglutamic acid dimethyl ester, which could be hydrolysed to the hitherto unreported diketopiperazine dicarboxylic acid, cyclic spaglumic acid (cyclic NAAGA).     

Stereochemistry of nucleic acids and their constituents. IV. Allowed and preferred conformations of nucleosides,nucleoside mono-, di-, tri-, tetraphosphates,nucleic acids and polynucleotides

A uniform notation and convention is suggested to describe the torsional angles in nucleic acids and their derivatives. The torsional angle χ, relating the stereochemistry of the base with respect to the sugar, shows more variation for the β-purine glycosides than for the β-pyrimidine glycosides. This variation is attributed to the fact that the β-purine derivatives may form intramolecular O(5′)-H…N(3) hydrogen bonding. The χ values for the α-purine and α-pyrimidine glycosides show preference for the –syn-clinal (or anti) conformation. The mode of puckering of the sugar also influences the χ value. The various possible conformations for the furanose ring are described by the torsional angles τ₀ τ₁, τ₂, τ₃, τ₄, about the five ring bonds. From an analysis of the torsional angles (ω, ?, ψ, ψ′, ?′, ω′) about the sugar phosphate bonds in the x-ray structures of the known nucleosides, nucleotides, phosphodiesters, nucleic acids, and related compounds, and from a consideration of molecular models, it is found that the possible conformations for the backbone of helical nucleic acids is strikingly limited. Most importantly, the preferred conformation of the nucleotide unit in poly nucleotides and nucleic acids turns out to be the same as that found for the nucleotide in the crystal structure. It is observed that base “stacking” is a consequence of the restricted backbone conformation. The torsional angles are illustrated in the form of conformational “wheels”. Interrelation between the torsion angles about successive pairs of sugar-phosphate bonds are presented in the form of conformational maps: ω,?; ?,ψ; ψ.ψ′; ψ′,?′; ?′,ω′; ω′,ω. The ω′,ω map shows the perferred conformations about the inter-nucleotide bonds of right- and left-handed helices and the possible conformations of phosphodiesters. The preferred conformation of the pyrophosphate and triphosphate is that in which the phosphate oxygens display a staggered arrangement when viewed along the P–P axis. A plausible structure and conformation for the ATPM^2? backbound complex is presented. This structure differs from that proposed by SzentGyorgi in that the metal (only transition metals are considered here) is not bound to the NH₂ nitrogen of adenine, but rather is simultaneously bound to N(7) of the ring and three phosphates (α, β, γ), or N(7) of the ring and two phosphates (β, γ). The remaining metal coordination may be satisfied by solvent–metal or enzyme–metal bonds.