Pentose Nucleic Acids Research Articles

Hexose nucleic acids

Abstract

Warum Pentose‐ und nicht Hexose‐Nucleinsäuren?? Teil I. Einleitung und Problemstellung, Konformationsanalyse für Oligonucleotid‐Ketten aus 2′,3′‐Dideoxyglucopyranosyl‐Bausteinen (‘Homo‐DNS’) sowie Betrachtungen zur Konformation von A‐ und B‐DNS

Why Pentose and Not Hexose Nucleic Acids? Part I. Introduction to the Problem, Conformational Analysis of Oligonucleotide Single Strands Containing 2′,3′‐Dideoxyglucopyranosyl Building Blocks (‘Homo‐DNA’), and Reflections on the Conformation of A‐ and B‐DNASummary in collaboration with Prof. Dr. C.E. Wintner, Haverford College, Haverford, PA 19041‐1392; academic guest, ETH, March and June/July, 1991.Chemical rationalization of the structure of a biomolecule can be sought through consideration of two criteria: first, the relationship between the structure and its biological function; and second, the structure's potential for constitutional self assembly. The latter criterion convers the judgment, by chemical reasoning, of the chance of its preformation, that is, a synthetic event which must have been undergone by any molecular structure in order to have been selected (or to have selected itself) to become a biomolecule. One way to further the task of rationalizing a biomolecule's structure by experimental means is the design, synthesis, and study of structural alternatives which might have become biomolecules on the basis of either criterion, but which do not, in fact, appear in Nature today.In the formation of sugar phosphates from glycolaldehyde phosphate under basic conditions, straightforward and selective formation of rac‐hexose 2,4,6‐triphosphates is observed in the absence of formaldehyde, while rac‐pentose 2,4‐diphosphates are dominant, when (0.5 equiv.) formaldehyde is present [1]. This and other observations indicate that hexose sugars should be regarded to have had a chance of preformation comparable with that of pentose sugars. Why, then, did Nature choose pentoses and not hexoses as the sugar building blocks of nucleic acids? The reason must be functional; it must be the case that pentose nucleic acids are biologically superior to potential hexose alternatives. To the extent that biological function is a consequence of molecular structure and reactivity, the origin of this superiority should be decipherable through chemical experiment, that is, through synthesis of hexose nucleic acids, systematic study of their chemical properties, and comparison of these properties with those of their natural counterparts. This has been the object of the present investigation, initiated in 1986. The paper introduces a series of papers which will describe the results of a model study, namely, the synthesis, pairing properties and structure of homo‐DNA oligonucleotides.

The cytochemical morphology of the production of antibody

The synthesis of some serum globulins appears to be the principal anabolic process of the plasma cells. If so, the syntheses of pentose nucleic acids and lipids must be quantitatively important subsidiary processes since the cytoplasmic structures associated with protein synthesis contain high concentrations of pentose nucleic acid and lipid [26]. Our observations suggest that the synthesis of complex carbohydrate may also be a quantitatively important subsidiary process with a function in the synthesis of at least some proteins. The essential basis for this suggestion is (1) the pronounced occurrence of periodic acid-Schiff positive material throughout the cytoplasm of young plasma cells, (2) its apparent progressive segregation from the nucleoprotein of the cytoplasm, and (3) its pronounced retention in Russell Bodies beyond the times of peak plasma cell proliferation and maximum antibody release [28]. In qualification of this suggestion it should be noted that (1) the positive material is only known to contain aldehyde groups after oxidation with periodic acid and that its identification as carbohydrate has not been demonstrated directly, (2) the equivalence of the positive material of different stages has not been demonstrated, (3) there is no apparent means of directly and readily distinguishing the late and presumably degenerative stages of the plasma cell from phagocytes, and (4) while the presence of a high concentration of pentose nucleic acid is indicative of an intensive synthesis of protein, high concentrations of intracellular lipid and carbohydrate are not evidence in themselves of intensive protein synthesis.

Incorporation of radioactive phosphorus into the nucleic acids of surviving rat uteri: effects of steroid hormones in vitro and in vivo.

MARKED alterations in uterine growth and physiology occur under the stimulation of estrogenic and androgenic steroids. On the assumption that desoxypentose and pentose nucleic acids (DNA and PNA) play an important part in these responses, an investigation was made in this laboratory into the effect of such steroids on the purine-pyrimidine composition of DNA and PNA extracted from uterine tissue. We have reported that compositional variations were apparently associated with the response of human and animal preparations to these steroids (Gold and Sturgis, 1954). The purpose of our present study was to determine the ability of steroid hormones to alter the rate of synthesis of uterine nucleic acids in vitro. The incorporation of P32 has been employed as an index of this synthesis. Changes in rate of incorporation associated with exposure to steroids either in vivo or in vitro may suggest one of the mechanisms whereby these hormones may bring about their profound effects on uterine growth and differentiation.

Studies of hepatic function in diabetes mellitus, portal cirrhosis and other liver diseases: A correlation of clinical, biochemical and liver needle biopsy findings I. Diabetes mellitus

In thirty-three patients the clinical and biochemical findings were correlated with histologic and histochemical observations on liver tissue obtained by needle biopsy. There were sixteen patients with diabetes mellitus, seven with portal cirrhosis but no diabetes and ten with other liver diseases. The simultaneous study of blood and liver tissue permitted a precise comparison of the corresponding constituents. Among some of the diabetic patients abnormalities of serum proteins and bromsulfalein retention were noted frequently, and abnormalities in the turbidity and flocculation tests infrequently. Focal lesions, considered to be of necrotic origin, and degenerative changes in the parenchymal cells occurred in sixteen of nineteen diabetic patients. Similar lesions were also found in the livers of three of the seven patients with portal cirrhosis and six of the ten with other liver diseases. Therefore they are not characteristic of the diabetic state. It is suggested that if these changes are diffuse they may be related to impairment of hepatic function. Our findings suggest that changes in hepatic lipids may be as dynamic in humans as they are in experimental animals. It is strongly recommended that when liver biopsies are taken for the purpose of assessing histochemically demonstrable changes, the exact conditions existing at the time should be clearly specified, including such details as the state of nutrition, obesity, diet, duration of fasting and any form of therapy. During the accumulation of lipids in the diabetic liver the neutral fats are most extensively involved. No correlation could be established between the degree of fatty metamorphosis of the liver and any other histochemical or laboratory observations. Among the diabetic patients there was a suggestive correlation between marked increases of lipids and hepatomegaly. The accumulation of lipids within the parenchymal cells was not found to antagonize the deposition of cytoplasmic glycogen to any great extent. Intranuclear glycogen, giving rise to vacuolation or “ballooning,” occurred to some degree in thirteen of the sixteen diabetic patients, in one of the seven with portal cirrhosis and in four of those with various other liver diseases. The reciprocal relationship between the amounts of nuclear and cytoplasmic glycogen reported to occur in diabetic patients was confirmed. For these studies the periodic acid-Schiff's reaction, controlled by amylase hydrolysis, was employed to verify previous reports based on Best's carmine method for glycogen. Only possibly moderate variations in nuclear desoxypentose nucleic acids were noted among the different patients. However, the DNA content of the nuclei of the parenchymal cells in any given patient was relatively constant. A similar constancy was noted for cytoplasmic pentose nucleic acids but there was a greater difference between patients. In some instances, apparently marked diminutions could be correlated with previous undernutrition. Iron was found in the parenchymal and Kupffer cells of eight of the sixteen diabetic patients. It could not be correlated with the accumulation of lipids or with previous blood transfusions. No correlations could be established between the parenchymal and mesenchymal histologic findings and abnormalities in liver function tests in the simultaneous studies on the seven patients with portal cirrhosis. The significance of intratrabecular fatty cysts in determining whether portal cirrhosis has been preceded by a fatty liver would not appear to be as great in needle biopsy material as in autopsy studies. No relationship was found to exist between the amounts of histochemically demonstrable liver lipids and the blood lipid levels or between the liver glycogen and blood sugar concentrations. In some instances uneven, regional variations in the distribution of histochemically demonstrable liver lipids and glycogen were found in different portions of the same specimens obtained by needle biopsy.

The nucleotide composition of pentose nucleic acids in different cellular fractions

The nucleotide composition of pentose nucleic acids of nucleic from rat liver and ox liver and kidney as well as of cytoplasmic fractions from rat and frog liver and kidney has been studied. While no significant differences either between organs or, with one doubtful exception, between species were found, the hepatic nuclear and cytoplasmic pentose nucleic acids of the rat did differ in composition.

Evidence of common regularities in the composition of pentose nucleic acids

1. 1. The results of a survey of the nucleotide composition of pentose nucleic acids (PNA) have been presented. The material analyzed included whole tissues and various subcellular fractions derived from beef, rat and frog liver and kidney, from sea urchin eggs and embryos, and from several microorganisms. 2. 2. It appears characteristics of all preparations studied that the bases with 6-amino groups (adenine, cytosine) and those with 6-keto groups (guanine, uracil) occur in approximately equal number. 3. 3. This regularity was found only when the total PNA of the sample was analyzed. 4. 4. Some of the structural implications of the findings are discussed.

Regularities in the composition of pentose nucleic acids.

SINCE the time when they were first proposed1, certain regularities characteristic of deoxypentose nucleic acids in general, regardless of source and composition, have become well established2. The sum of total purine nucleotides equals that of the pyrimidine nucleotides, and the molar ratios of adenine to thymine and of guanine to cytosine (or its analogues) are 1. We wish to report here experimental observations which indicate that similar regularities occur in pentose nucleic acids, with uracil taking the place of thymine.

Chemical determinations of the effect of the X and Y chromosomes on the nucleic acid content of the larval salivary glands of Drosophila melanogaster

Chemical determinations of desoxypentose (DNA) and pentose (PNA) nucleic acids were carried out on mature larval salivary glands from Drosophila melanogaster which were either of normal constitution (XX or XY) or contained an extra (X XY) or lacked a Y chromosome (XO). Both DNA and PNA contents were found to be higher in the females than the males, presumably due to the additional X chromosome of the female. On a per gland basis, neither the addition nor the deficiency of a Y chromosome influenced the content of either PNA or DNA to an extent measurable by the present methods. The results are discussed with reference to the function of the heterochromatic regions, and the relation of the DNA content of the nucleus to the PNA content of the cell.

Factors affecting the incorporation of radioactive phosphate into the pentosenucleic acids of brain slices

Factors affecting the incorporation of radioactive phosphate into the pentosenucleic acids of brain slices

Biological activity of the nucleic acids.

The biological activities of the pentose (PNA) and desoxypentose nucleic acids (DNA) are discussed. Bacterial PNA inhibit certain streptococcal desoxyribonucleases. Bacterial DNA are known to act as transforming principles or heredity determinants. Methods are described for the isolation and purification of DNA from Hemophilus influenzae active as transforming principles in concentrations 3 × 10−4/γcc. The inactivation by heat, changes of pH and ionic strength, desoxyribonuclease, and formaldehyde is studied.

On the Artificial Nucleoproteins Formed from Pentose Nucleic Acids and Protamines

On the Artificial Nucleoproteins Formed from Pentose Nucleic Acids and Protamines

A mixture of methyl green and pyronin for cell fractionation studies.

A staining mixture consisting of 0.57% methyl green and 0.1 1 % pyronin B (calculated from the actual dye content) dis- solved in glycerol, 20 ml.; 2% aqueous phenol, 100 ml.; and 95% ethanol, 25 ml., was found to be optimum for differentiating cell components containing desoxypentose and pentose nucleic acids. The stain can be used for either fresh suspensions or unfixed dried smears of tissue homogenates. Nuclei are stained bright blue, and nucleoli and cytoplasmic particles, bright pink.

The incorporation of formate into pentosenucleic acids in various organs of the rat

The relative incorporation of formate into the purine ribonucleotides of various organs of the rat was greatest in the intestine, followed in order by kidney, spleen, liver, pancreas, and testis. The renewal of the PNA-adenine was greater than that of the guanine in all organs except spleen, and again there was no differentiation between the isomeric purine nucleotides. It is emphasized that, in the intestine, formate can be utilized relatively more effectively for PNA-purine synthesis than is adenine, while the reverse is true in the liver.

The synthesis of pentose nucleic acids in the liver of PGA-deficient megaloblastic monkeys

The synthesis of pentose nucleic acids in the liver of PGA-deficient megaloblastic monkeys

Nucleic Acid and Protein Conference

T HE second Gordon Research Conference on Acids and Proteins was held at New Hampton, New Hampshire, August 2731, 1951.2 Among the eighty-one scientists participating in the conference, twenty-three came from countries outside the United States-namely, England (11), Canada (5), Sweden (3), Denmark, Holland, Italy, and Israel. The international character of the meeting was, in large measure, due to the continued support of the Rockefeller Foundation. The main topies under discussion dealt with nucleic acid structure, physical studies on viruses and virus metabolism, effect of ionizing radiations on biological systems, and protein studies. Twenty-two papers were presented at nine sessions. The first two sessions were devoted to a symposium on the structure of nucleic acids and certain nucleotides. Erwin Chargaff (Columbia University), Maurice Stacey (University of Birmingham), Gerhard Schmidt (Boston Dispensary), Waldo Cohn (Oak Ridge National Laboratory), and Hubert S. Loring (Stanford University) discussed the subject from various points of view. Dr. Chargaff first reviewed previous work of his laboratory on the structure of desoxypentose nucleic acids, which had led to the conclusion not only that the compositions of these compounds deviate in most cases very considerably from that postulated by the classical tetranucleotide hypothesis, but also that they differ from each other in a manner characteristic for the species (but not the tissue) from which they have been isolated. On the other hand, certain remarkable regularities in the relative proportions of the nitrogenous constituents were observed. Thus, all desoxypentose nucleic acids so far examined possess a purine-to-pyrimidine ratio of unity, and the same holds for the ratio of guanine to cytosine. The ATtype contains adenine and thymine, whereas the GCtype contains guanine and cytosine as major components. It was found that all the purines can be removed, yielding polymers composed of pyrimidine nucleotides (apurinic acids). In the instance of pentose nucleic acids (PNA), a branched structure with a polyguanylic acid chain as the backbone was considered. In the subsequent discussion, R. G. Wyatt confirmed Chargaff's general conclusions on the basis of his own analyses. He found that desoxypentose 1 Publication No. 8 of the Department of Biophysics. 2 For a report on the first Nucleic Acid and Protein Conference see E. R. Blout and P. M. Doty, Science, 112, 639 (1950). nucleic acids (DNA) from various animal tissues contain a small amount of 5-methyleytosine, the amount being characteristic of the species serving as the source. In contrast, the DNAs of several insect viruses were found to be free of methylcytosine. The nature of the linkages present in desoxypentose nucleic acids was discussed by M. Stacey, who pointed out that polynucleotide chains may be either straight or branched. They may be ruptured by various means, including ultrasonic waves and ion exchange resins. Upon chain rupture, RCHO-groups are set free, resulting in a positive Feulgen reaction, and the release of purine residues may be followed by the Dische reaction. Steric effects may arise from interaction between base (purine, pyrimidine) groups, leading to a partial stripping of the side branches from the main chain. The possibility of cross-linking by amino and enolic hydroxyl groups was considered. In the discussion, Chargaff pointed out that nucleic acids may also be considered as a form of polysaccharide. DNA, in contrast to PNA, does not appear to be highly branched, and it is possible that links other than phosphoric acid ester bonds are involved in the polymer DNA-structure. Stacey mentioned that D. 0. Jordan's work indicates some degree of branching in DNA. The enzymatic hydrolysis of ribonucleic acids, with particular reference to its bearing on the concepts of their structure, was discussed by G. Schmidt, who employed prostate phosphatase, an enzyme of high activity toward PNA. The hypothesis that PNA consists of a purine polynucleotide and a pyrimidine polynucleotide, which are linked together only at one point, was considered untenable on the basis of the results obtained by the enzymatic hydrolysis of PNA by ribonuclease and phosphatase. The action of ribonuclease leads to the conclusion that the core of PNA consists largely of purine nucleotides. PNA represents a highly branched structure, from which the ribonuclease removes terminal pyrimidine nucleotide residues. Studies on the structure of various nucleotides isolated from nucleic acids were described by W. Cohn and H. S. Loring. Dr. Cohn reported the discovery of new nucleotides from previously known nucleic acids from the work of his group on ion exchange adsorption columns. In addition to the separation of isomeric forms of adenylic, guanylic, cytodylic, and uridylic acids from yeast PNA, a fifth desoxypentose

Chemotherapy of cancer

Dr. Gilbert H. Mudge: The chemotherapy of malignant disease has been discussed with particular emphasis on the biology of cancer and the mechanisms of action of various chemotherapeutic agents. The metabolism of nucleic acids has been stressed because of their undoubtedly important role in the biologic reactions under consideration. Nucleic acids arc found in all living cells and may be divided into two main groups. The desoxypentose nucleic acids occur mainly within nuclei while the pentose nucleic acids are found chiefly within the cytoplasm. Their physical and chemical properties are briefly reviewed. Present evidence strongly indicates that nucleic acids represent the chemical basis of chromosomes and as such play a central role in the mitotic activity of both normal and malignant cells. The nitrogen mustards are unquestionably of great use in the treatment of certain types of malignancy. Their pharmacologic action is reviewed in relationship to chemical structure. These compounds react rapidly with a variety of chemical groupings. A careful analysis of minimally effective concentrations reveals mitotic activity to be the cell function most sensitive to their action. The evidence is reviewed which suggests a specific effect upon nucleoproteins. The analogues of folic acid represent another group of agents employed in the treatment of malignancy. Their use has permitted precise definition of the role of folic acid in hematopoiesis as well as in nucleic acid metabolism. Studies with aminopterin have revealed that it blocks intermediary reactions leading to the synthesis of nuclear proteins and that the metabolic block is competitive in type. The probable site of this block is discussed in relationship to the action of the citrovorum factor. A different aspect of cancer chemotherapy is discussed in relationship to the action of 8-azaguanine. This antimetabolite has a marked effect upon certain tumors but no effect upon others. In this instance it has been possible to demonstrate that the specificity of the drug action can be correlated with the metabolism of the tumor. Thus normal tissue and resistant tumors can inactivate the drug while sensitive tumors contain low concentrations of the inactivating enzyme. It is emphasized that the successful development and employment of chemotherapeutic agents for the treatment of cancer will depend upon further knowledge of the specific metabolic abnormalities of the malignant cell. The subtle differences in the biochemical makeup of different tumors makes it extremely improbable that any single drug will ever become a panacea for all cancers.

Nucleic acid content in relation to cell size in the mature larval salivary gland of Drosophila melanogaster

1. 1. The content of desoxypentose (DNA) and pentose (PNA) nucleic acids was determined in mature larval salivary glands of Drosophila melanogaster. Use of a stock giving giant and normal-sized larvae permitted the quantities (expressed on a per cell basis) to be related to different cell sizes. 2. 2. A micromodification of the Schneider method was developed which allows determination of samples consisting of 18 pairs of salivary glands (approximately 5400 cells) containing a total of 10–20 μg. N, 1–2 μg. DNA, and 10–20 μg. PNA. Data from some experiments using perchloric acid as the extraction medium are also included. Details of the extraction procedure and comparison of the nucleic acid values obtained from sugar determinations, phosphorus, and ultraviolet absorption are given. A discussion of the validity of the measurements is also included. 3. 3. The results obtained show that there is an increase of PNA per cell with doubling of cell size but no measurable increase of DNA. The increase in the PNA content is, however, not as great as that previously (1) found for nitrogen and alanylglycine peptidase in comparable material. 4. 4. The absolute values of DNA (284 μμg.) and PNA (2250–3600 μμg.) found per cell are compared with those found by others in related types and sizes of cells. In addition, the changes in DNA and PNA with cell size are correlated with similar measurements made elsewhere on materials undergoing various types of growth.

183. The nucleic acid of normal and tumour tissues. Part II. The preparation and composition of pentosenucleic acids from the fowl sarcomata, rous no. 1 and duran-reynals “D.”

183. The nucleic acid of normal and tumour tissues. Part II. The preparation and composition of pentosenucleic acids from the fowl sarcomata, rous no. 1 and duran-reynals “D.”

Separation of deoxypentose and pentose nucleic acids.

CRUDE preparations of deoxypentose nucleic acids are almost invariably contaminated with pentose nucleic acids. This admixture renders many studies of the chemical and biological specificity of nucleic acids difficult. A preliminary separation must be carried out before the exact determination of the constituent purines and pyrimidines becomes possible1. Only in a few cases (sperm, thymus and, possibly, spleen) will suitable washing of the biological material, prior to its extraction, sufficiently depress the extent of contamination of the nucleic acid specimens2–4.