Synthesis of prebiotic molecules — Role of some carbonyl compounds in prebiotic chemistry

Methyleneaminoacetonitrile(MAAN) resulting from the interaction of formaldehyde, ammonia and hydrogen cyanide on hydrolysis under mildly alkaline conditions gives a number of amino acids and peptides. Various aldehydes react with glycine to give corresponding hydroxyalkyl amino acids, which on reduction with formic acid are converted to reduced amino acids. Formaldehyde reacts with uracil to give 5-hydroxymethyl uracil which on reduction with formic acid yields thymine. Pyrrole formed by heating serine reacts with aldehydes to form porphyrins. Clays do not seem to influence most of these reactions, except the uracil-formaldehyde — formic acid reaction which results in enhanced yield of thymine.     

The Relationship between Structure and Activity of Taurolin

Taurolin [Bis(1,1-dioxo-perhydro-1,2,4 thiadiazinyl-4)methane] is an antimicrobial compound formed by the condensation of two molecules of taurine with three of formaldehyde. It has been suggested that it releases formaldehyde in contact with bacteria. Evidence from TLC, HPLC and NMR spectroscopy indicates that taurolin is mostly hydrolysed in aqueous solution to release one molecule of formaldehyde and two monomeric molecules (1,1-dioxo-perhydro-1,2,4-thiadiazine and its carbinolamine derivative). A stable equilibrium is established. Antibacterial activity is not entirely due to adsorption of free formaldehyde but also to reaction with a masked (or latent) formaldehyde, as the activity of taurolin is greater than formaldehyde. The monomer is only slightly active by comparison.     

Effect of formaldehyde and its aminomethylol derivatives on E. coli strains with various defects of the DNA repair systems]

It was shown that aminomethylol compounds formed during reaction of formaldehyde with amino acids and formaldehyde as well exert a pronounced lethal action on E. coli strains with various defects of the DNA repair systems. The correlation between the extent of the DNA depurination caused by in vitro action of diverse aminomethylol derivatives and the inactivation of bacteria by these derivatives is revealed. The data obtained suggest that the inactivating effect of formaldehyde and its aminomethylol derivatives seems likely to be due to the formation of depurinized groups in bacterial DNA rather than to dimerization of purine bases.     

The action of products of the formaldehyde reaction with different amines on nucleic acids and their components

The kinetics and equilibrium of the reaction between nucleic acids components and the products of formaldehyde interaction with ethanolamine and different amino acids has been studied. These parameters were found to be similar for all the products used. The destabilization of the N-glycosidic bond in deoxyadenosine caused by formaldehyde derivatives of different amines was studied. The rate of the cleavage of the N-glycosidic bond under the action of formaldehyde derivatives of glycine and ethanolamine was found to be 10 times greater than that under the action of formaldehyde derivatives of other amines. It is shown that DNA preparations with different content of adenine can be obtained by adding the product of formaldehyde reaction with glycine to DNA.     

Analysis of the Reaction between Formaldehyde and Amide

The reaction between formaldehyde and acetamide which affords a model compound for an amino acid having an amide group was analyzed to investigate the role of formaldehyde as a cross-linking reagent. One of the products was isolated by Sephadex G-10 column chromatography and was identified as N-hydroxymethyl acetamide (FA) by NMR spectrometry and mass spectrometry. Another product, which could not be isolated, was estimated to be N, N-dihydroxymethyl acetamide (F₂A) by kinetic analysis and mass spectrometry. The formation of N, N′-methylene diacetamide was not observed. The mechanism of the reaction between formaldehyde and acetamide was estimated by the kinetic analyses of NMR data, and the rate constants were calculated from the data by the optimization method with a digital computer. On the other hand, formaldehyde cross-linked product was obtained in the reaction of formaldehyde with acetamide and alanine, Its decomposing reaction was analyzed with an NMR spectrometer to study the stability of the formaldehyde cross-linked product. The degradation was dominantly initiated with the release of acetamide.

Consequently, it was estimated that the C–N bond between formaldehyde and amide is so labile that amide-bound formaldehyde does not react further with amides or amines, and that the amide-formaldehyde-amine condensation product is unstable and easily decomposes by releasing the amide.     

Interactions of Hydroxyl Radicals with Tris (Hydroxymethyl) Aminomethane and Good's Buffers Containing Hydroxymethyl or Hydroxyethyl Residues Produce Formaldehyde

The production of formaldehyde from tris(hydroxymethyl) aminomethane(Tris) by interaction with hydroxyl radicals(.OH) was studied, since the reaction mixture from the Fenton reaction performed in Tris/HCl buffer was found to be color-developed by colorimetric determination of formaldehyde. The absorption spectrum of chromogens was identical to that of authentic formaldehyde. Color development, which required the presence of Tris, hydrogen peroxide and cupric ions in the Fenton reaction mixture, was inhibited by the addition of hydroxyl radical scavengers such as glucose or hyaluronic acid. These results indicated that formaldehyde was produced when Tris interacted with ·OH. With structures similar to Tris, Good's buffers were also found to produce formaldehyde by interaction with ·OH. Analysis of formaldehyde derived from these buffers may provide a simple and convenient assay for detecting ·OH generation. In evaluating effects of ·OH on the biological system in Tris/HCl buffer or certain Good's Buffers, ·OH loss may be due to interactions of ·OH with these buffers. The formaldehyde produced as a result of such interactions may affect biological systems.     

The reactions between formaldehyde,glutaraldehyde and osmium tetroxide,and their fixation effects on bovine serum albumin and on tissue blocks

Summary The reactions between osmium tetroxide and glutaraldehyde and formaldehyde were investigated. It was found that they react together to form intermediate products which then break down to form osmium black. Glutaraldehyde reacts much more rapidly with osmium tetroxide than formaldehyde. The rates of the reactions are increased by increasing the glutaraldehyde concentration or adding bovine serum albumin to the reaction mixture. The reaction rates increase with temperature. The mixtures of fixatives were also tried on tissues and the results paralleled the model experiments. The crosslinking of bovine serum albumin by osmium tetroxide, formaldehyde and glutaraldehyde singly and in mixtures was quantitatively assessed by viscosimetry, gel filtration and disc electrophoresis coupled with densitometry. The crosslinking of bovine serum albumin by pairs of fixatives was less than that produced by the most effective of the pair. After 5 min reaction osmium tetroxide was the most effective crosslinking agent according to viscosimetric experiments, but after one hour's reaction with bovine serum albumin, glutaraldehyde was revealed as the most effective crosslinking agent by gel filtration and electrophoresis.     

Pixantrone can be activated by formaldehyde to generate a potent DNA adduct forming agent

Mitoxantrone is an anti-cancer agent used in the treatment of breast and prostate cancers. It is classified as a topoisomerase II poison, however can also be activated by formaldehyde to generate drug-DNA adducts. Despite identification of this novel form of mitoxantrone-DNA interaction, excessively high, biologically irrelevant drug concentrations are necessary to generate adducts. A search for mitoxantrone analogues that could potentially undergo this reaction with DNA more efficiently identified Pixantrone as an ideal candidate. An in vitro crosslinking assay demonstrated that Pixantrone is efficiently activated by formaldehyde to generate covalent drug-DNA adducts capable of stabilizing double-stranded DNA in denaturing conditions. Pixantrone-DNA adduct formation is both concentration and time dependent and the reaction exhibits an absolute requirement for formaldehyde. In a direct comparison with mitoxantrone-DNA adduct formation, Pixantrone exhibited a 10- to 100-fold greater propensity to generate adducts at equimolar formaldehyde and drug concentrations. Pixantrone-DNA adducts are thermally and temporally labile, yet they exhibit a greater thermal midpoint temperature and an extended half-life at 37 degrees C when compared to mitoxantrone-DNA adducts. Unlike mitoxantrone, this enhanced stability, coupled with a greater propensity to form covalent drug-DNA adducts, may endow formaldehyde-activated Pixantrone with the attributes required for Pixantrone-DNA adducts to be biologically active.     

Formaldehyde as a pre-treatment for dermal collagen heterografts

The preparation, stability both in vitro and in vivo and resistance to bacterial collagenase of trypsin-purified pig dermal collagen cross-linked with a range of concentrations of formaldehyde in phosphate-buffered saline, was studied using ¹⁴C-labelled formaldehyde as a tracer. Washing in phosphate-buffered saline at 37°C produced rapid loss of formaldehyde over 6 weeks before stability was reached. After 19 weeks washing, 12–20% of the initial radioactivity remained, representing 6, 18 and 35 μmol formaldehyde/g of collagen after 21 days reaction with 0.1, 1 and 5% formaldehyde, respectively. Collagen, incorporating stable-bound formaldehyde arising from reaction with formaldehyde in concentrations of 0.5% or over, was totally resistant to bacterial collagenase.The stabilizing effect of formaldehyde cross-linking was also demonstrated by implants of fibrous pig dermal collagen in rats. After 8 weeks a significant constant amount of formaldehyde was retained in all implants. There was no net loss of mass over a 24 week period when pre-treated with 1% formaldehyde but some loss when pre-treated with 0.1% formaldehyde.     

Formation of tyrosine from glycine, formaldehyde and phenol under the action of a partially purified preparation of tyrosine phenol lyase: The participation of a different enzyme

In the presence of a partially purified preparation of tyrosine phenol lyase, tyrosine is formed in solutions containing glycine, formaldehyde and phenol. The enzyme preparation also catalysed the splitting of allothreonine to glycine and acetaldehyde. An enzyme which is different from tyrosine phenol lyase was shown to be responsible for this aldolase reaction. When an enzyme preparation with a higher specific activity of tyrosine phenol lyase, but without aldolase activity, was used the formation of tyrosine from glycine, formaldehyde and phenol was not observed. It is assumed that the first stage of the process is the formation of serine from glycine and formaldehyde catalysed by the enzyme responsible for the aldolase reaction. Serine in its turn is converted to tyrosine by tyrosine phenol lyase.     

Effect of formaldehyde on the efficiency of hybridization of DNA immobilized on nitrocellulose filters.

We report in this study that under certain conditions formaldehyde interacts with DNA and makes it more efficient for hybridization on nitrocellulose filters. Hybridization signals of formaldehyde-treated DNA are stronger (up to 10 fold) as compared with that of the heat- or alkali-denatured DNA. Various parameters of the DNA-formaldehyde reaction are optimized as follows: (a) 6 x SSC, 10% formaldehyde, 60 degrees C, 20-30 min, reaction volume 10-200 microliters or (b) 6 x SSC, 5% formaldehyde, 98 degrees C, 15 min, reaction volume 10-200 microliters. Treatment of agarose gels after electrophoresis with formaldehyde improved both the transfer of DNA and the efficiency of hybridization. The following conditions are recommended for gel treatment: denaturation in 0.3 N NaOH, 1 M NaCl followed by neutralization with 0.5 M phosphate buffer, pH 7.0, containing 10% formaldehyde at 60 degrees C for 20 min.     

Removal efficiency and mechanisms of formaldehyde by five species of plants in air-plant-water system

The foliar uptake and transport rates of formaldehyde as well as the abilities of leaf extracts to breakdown formaldehyde were investigated to discuss the formaldehyde removal efficiency and mechanism by five species of plants from air. Results showed that formaldehyde could be transported from air via leaves and roots to rhizosphere water. When exposed to 0.56 mg·m^?3 formaldehyde, the formaldehyde removal rate ranged from 18.64 to 38.47 μg·h^?1g^?1 FW (fresh weight). According to the mass balance in the air–plant–water system, the main mechanism of the formaldehyde loss was its breakdown in plant tissues caused by both enzymatic reaction and redox reaction. Higher oxidation potentials of the leaf-extracts of Wedelia chinensis and Desmodium motorium corresponded well to higher abilities to breakdown added formaldehyde than other plants. Based on the different abilities of fresh and boiled leaf-extracts to dissipate formaldehyde, the enzymatic reaction in Chenopodium album L. was the dominant mechanism while the redox reaction in Kochia scoparia (L.) Schrad. and Silene conoidea L. was the main formaldehyde breakdown mechanism when exposed to low-level formaldehyde in air. The redox mechanism suggested that the formaldehyde removal may be increased by an increasing level of reactive oxygen species (ROS) induced by the environmental stress.     

Formaldehyde fixation and microwave irradiation

Summary Formaldehyde is the most commonly used fixative in pathology laboratories. However, due to time pressures, this fixative is often not optimally exploited. the majority of biopsies are only partly fixed when histoprocessing is started, with adverse effects. This paper reports how formaldehyde fixation is improved, by using 1.5 min of microwave irradiation of tissue previously soaked for four hours in the fixation solution. It is argued that this beneficial effect of microwave irradiation can be attributed to the acceleration of the reaction of formaldehyde to the tissue. Formation of free formaldehyde, by the dehydration of methylene glycol present in the tissue when the irradiation starts, is also enhanced. Five different formaldehyde-containing fixatives were evaluated, using five different working protocols. Spleen was taken as a suitable tissue for these tests. The technique described leads to uniform microscopical results. It is a simple method and is suitable for use in routine laboratories.     

Kinetic mechanism of human glutathione-dependent formaldehyde dehydrogenase

Formaldehyde, a major industrial chemical, is classified as a carcinogen because of its high reactivity with DNA. It is inactivated by oxidative metabolism to formate in humans by glutathione-dependent formaldehyde dehydrogenase. This NAD(+)-dependent enzyme belongs to the family of zinc-dependent alcohol dehydrogenases with 40 kDa subunits and is also called ADH3 or chi-ADH. The first step in the reaction involves the nonenzymatic formation of the S-(hydroxymethyl)glutathione adduct from formaldehyde and glutathione. When formaldehyde concentrations exceed that of glutathione, nonoxidizable adducts can be formed in vitro. The S-(hydroxymethyl)glutathione adduct will be predominant in vivo, since circulating glutathione concentrations are reported to be 50 times that of formaldehyde in humans. Initial velocity, product inhibition, dead-end inhibition, and equilibrium binding studies indicate that the catalytic mechanism for oxidation of S-(hydroxymethyl)glutathione and 12-hydroxydodecanoic acid (12-HDDA) with NAD(+) is random bi-bi. Formation of an E.NADH.12-HDDA abortive complex was evident from equilibrium binding studies, but no substrate inhibition was seen with 12-HDDA. 12-Oxododecanoic acid (12-ODDA) exhibited substrate inhibition, which is consistent with a preferred pathway for substrate addition in the reductive reaction and formation of an abortive E.NAD(+).12-ODDA complex. The random mechanism is consistent with the published three-dimensional structure of the formaldehyde dehydrogenase.NAD(+) complex, which exhibits a unique semi-open coenzyme-catalytic domain conformation where substrates can bind or dissociate in any order.     

A new enzymo-chemical method for simultaneous assay of methanol and formaldehyde

A new enzymo-chemical method for the simultaneous assay of methanol and formaldehyde in mixtures is described which exploits alcohol oxidase (AO) and aldehyde-selective reagent, 3-methyl-2-benzothiazolinone hydrazone (MBTH). The enzyme is used for methanol oxidation to formaldehyde and MBTH plays a double role: 1) at the first step of reaction, it forms a colorless azine adduct with pre-existing and enzymatically formed formaldehyde and masks it from oxidation by AO; 2) at the second step of reaction, non-enzymatic oxidation of azine product to cyanine dye occurs in the presence of ferric ions in acid medium. Pre-existing formaldehyde content is assayed by colorimetric reaction with MBTH without treating samples by AO, and methanol content is determined by a gain in a colored product due to methanol-oxidising reaction. Possibility of differential assay of methanol and formaldehyde by the proposed method has been proved for model solutions as well as for real samples of industrial waste and technical formaline. A threshold sensitivity of the assay method for both analytes is near 1 microM that responds to 30-32 ng analyte in 1 ml of reaction mixture and is 3.2-fold higher when compared to the chemical method with the use of permanganate and chromotropic acid. Linearity of the calibration curve is reliable (p < 0.0001) and standard deviation for parallel measurements for real samples does not exceed 7%. The proposed method, in contrast to the standard chemical approach, does not need the use of aggressive chemicals (concentrated sulfuric, phosphoric, chromotropic acids, permanganate), it is more simple in fulfillment and can be used for industrial wastes control and certification of formaline-contained stuffs.     

Prebiotic ribose synthesis: A critical analysis

The discovery of catalytic ability in RNA has given fresh impetus to speculations that RNA played a critical role in the origin of life. This question must rest on the plausibility of prebiotic oligonucleotide synthesis, rather than on the properties of the final product. Many cliams have been published to support the idea that the components of RNA were readily available on the prebiotic earth. In this article, the literature cited in support of the prebiotic availability of one subunit, D-ribose, is reviewed to determine whether it justifies the claim.Polymerization of formaldehyde (the formose reaction) has been the single reaction cited for prebiotic ribose synthesis. It has been conducted with different catalysts: numerous basic substances, neutral clays and heat, and various types of radiation. Ribose has been identified (yields are uncertain, but unlikely to be greater than 1%) in reactions run with concentrated (0.15 M or greater) formaldehyde. It has been claimed in reactions run at lower concentration, but characterization has been inadequate, and experimental details have not been provided.The complex sugar mixture produced in the formose reaction is rapidly destroyed under the reaction conditions. Nitrogenous substances (needed for prebiotic base synthesis) would interfere with the formose reaction by reacting with formaldehyde, the intermediates, and sugar products in undesirable ways.The evidence that is currently available does not support the availability of ribose on the prebiotic earth, except perhaps for brief periods of time, in low concentration as part of a complex mixture, and under conditions unsuitable for nucleoside synthesis.     

Determination of formaldehyde by the Hantzsch reaction: interference by naturally occurring compounds

The quantitation of formaldehyde, a product of many drug oxidations, can be determined by a simple and sensitive assay which employs the Hantzsch reaction. The present study demonstrates that both oxaloacetate and acetoacetate in the presence of Mg²⁺ interfere with the Hantzsch reaction by interacting with formaldehyde, making the aldehyde unavailable for the condensation reaction with acetylacetone. This can lead to errors when trying to quantitate either the disappearance or the formation of formaldehyde in metabolic studies utilizing tissue slices, homogenates, or subcellular fractions containing mitochondria.     

Reaction of formaldehyde with the histidine residues of proteins

Imidazoles or imidazoles substituted in the 2 or 4(5) position but with the ring nitrogen free, give a positive Pauly reaction. N-Methylimidazole does not react. In the presence of formaldehyde, all imidazole compounds give a negative Pauly reaction. In agreement with nmr studies, it is concluded that formaldehyde reacts with the imidazole ring nitrogen in acid solution to form N-hydroxymethyl derivatives.The Pauly color yield of various proteins (chymotrypsin, TPCK-chymotrypsin, lysozyme, ribonuclease, and reduced ribonuclease) is reduced 90–95% when the reaction is performed in the presence of formaldehyde. The color yield in water is essentially accounted for by the known reactive histidine and tyrosine content. In the presence of formaldehyde the color yield can be interpreted as arising from the known tyrosine content. It is therefore concluded that the histidine residues of the proteins examined have reacted with formaldehyde to form N-hydroxymethyl derivatives.In contrast to the Pauly color yield of chymotrypsin (A_M, 52 720) which can be accounted for by the contribution of its two histidine and three reactive tyrosine residues, the color yield of TPCK-chymotrypsin (A_M, 47 685) is higher than would be expected on the basis of the reported site of reaction of TPCK with chymotrypsin. The experimental molar extinction coefficient should be close to that calculated (A_M, 31 300) for its presumed one reactive histidine and three tyrosine residues. That it is not is in agreement with a previous report from our laboratories suggesting that His-57 is not the only site of reaction of TPCK with chymotrypsin.     

Amino acids as catalysts of the binding reaction of formaldehyde with adenine residue in polyadenylic acid

Binding of formaldehyde and amino acids (Gly, Lys and Leu) with poly(A), poly(G), and poly(C) has been investigated in comparison with treatment with formaldehyde alone. It was found that in the case of poly(A) amino acids were found to catalyze the N-hydroxymethylation reaction on exocyclic amino groups of adenine. For example, at 20 degrees C and pH 6.0 the rate of this reaction increased about 10 fold in the presence of glycine.     

Immunocytochemical localization of nerve growth factor: effects of fixation

The fixation dependence of immunocytochemically demonstrable nerve growth factor (NGF) was investigated. Several commonly used fixation methods have been employed, including buffered formaldehyde, Bouin's fluid, and chloroform-methanol, as well as freezing and cryostat sectioning. The immunostaining technique was an immunoenzyme bridge procedure on either paraffin sections or frozen sections. Of those methods tested, fixation for 1 hr in a buffered formaldehyde appeared to provide optimal preservation and localization of immunoreactive material. Using this method, reaction product was localized in granules of the granular tubule cells of the male mouse submandibular gland. Prolonged fixation in buffered formaldehyde resulted in a diffuse background staining and loss of granule immunoreactivity. In frozen sections and in tissues fixed with either Bouin's solution, chloroform-methanol, or buffered paraformaldehyde-glutaraldehyde increased cytoplasmic background staining and loss of granule immunoreactivity were observed. It was concluded that, for the localization of NGF at the light microscopic level, a brief (1 hr) buffered formaldehyde fixation is optimal.