Structural analysis of DNA interactions with biogenic polyamines and cobalt(III)hexamine studied by Fourier transform infrared and capillary electrophoresis

Biogenic polyamines, such as putrescine, spermidine, and spermine are small organic polycations involved in numerous diverse biological processes. These compounds play an important role in nucleic acid function due to their binding to DNA and RNA. It has been shown that biogenic polyamines cause DNA condensation and aggregation similar to that of inorganic cobalt(III)hexamine cation, which has the ability to induce DNA conformational changes. However, the nature of the polyamine.DNA binding at the molecular level is not clearly established and is the subject of much controversy. In the present study the effects of spermine, spermidine, putrescine, and cobalt(III)hexamine on the solution structure of calf-thymus DNA were investigated using affinity capillary electrophoresis, Fourier transform infrared, and circular dichroism spectroscopic methods. At low polycation concentrations, putrescine binds preferentially through the minor and major grooves of double strand DNA, whereas spermine, spermidine, and cobalt(III)hexamine bind to the major groove. At high polycation concentrations, putrescine interaction with the bases is weak, whereas strong base binding occurred for spermidine in the major and minor grooves of DNA duplex. However, major groove binding is preferred by spermine and cobalt(III)hexamine cations. Electrostatic attractions between polycation and the backbone phosphate group were also observed. No major alterations of B-DNA were observed for biogenic polyamines, whereas cobalt(III)hexamine induced a partial B --> A transition. DNA condensation was also observed for cobalt(III)hexamine cation, whereas organic polyamines induced duplex stabilization. The binding constants calculated for biogenic polyamines are K(Spm) = 2.3 x 10(5) M(-1), K(Spd) = 1.4 x 10(5) M(-1), and K(Put) = 1.02 x 10(5) M(-1). Two binding constants have been found for cobalt(III)hexamine with K(1) = 1.8 x 10(5) M(-1) and K(2) = 9.2 x 10(4) M(-1). The Hill coefficients indicate a positive cooperativity binding for biogenic polyamines and a negative cooperativity for cobalt(III)hexamine.     

In vitro interactions between polyamines and pectic substances

Putrescine, spermidine and spermine induce a decrease in the pH value of 1 mM polygalacturonic acid or pectin solutions; spermidine and spermine also cause the precipitation of the polymers. The association constants between polyamines and polygalacturonic acid were in the order of 10(5) for putrescine and spermidine, and 10(6) for spermine. The number of galacturonic units per binding sites are proportional to the number of positive charges on the polyamine molecule. Low affinity binding sites appear at high polyamine concentrations. Calcium ions seem to compete weakly with spermine by lowering the association constant 4- to 6-fold. Two natural pectins tested, showed that methylation of the carboxylic groups influences only the number of galacturonic units per site but not the association constant.     

Changes in the nuclear polyamine content of chick erythrocytes during embryonic development.

The polyamine content of the circulating erythrocyte population in the embryonic chick was studied during its development. Total cellular polyamine content fell dramatically between 5 and 7 days of development, paralleling the decrease in metabolic activity exhibited by these cells. Nuclei were isolated from the erythrocytes by a non-aqueous technique, which not only eliminated the polyamine loss that occurred with aqueous isolation, but also prevented redistribution of the polyamines from the cytoplasm. Nuclear spermidine and spermine contents decreased markedly between 5 and 6 days of development from 31 to 10 pmol/microgram of DNA and from 33 to 18 pmol/microgram of DNA respectively. Thereafter the spermine content remained constant, but the spermidine content continued to decline. Good correlations between spermidine and RNA contents were observed in both cells and nuclei, and similarly between spermine and RNA contents in cells, but no such correlation was observed between spermine and RNA in nuclei.     

Polyamines inhibit DNA methylation in vitro.

DNA methylase from rat liver differs from RNA methylase in response to polyamines, being inhibited rather than stimulated. With methyl-deficient DNA from rat liver as substrate, the DNA methylase is inhibited 97%, 59% and 42% respectively, by spermine, spermidine and putrescine at 1 mM concentration.     

Insulin-like effects of polyamines spermine binding to fat cells and fat cell membranes

Two naturally occurring polyamines, spermine and spermidine, mimic the action of insulin on lipid and glucose metabolism in adipocytes. To evaluate the role of cell membranes in the action of polyamines, studies of [¹⁴C] spermine binding using an oil separation method were conducted in isolated rat adipocytes and adipose cell membranes. Spermine binding and dissociation in fat cells and fat cell membranes were rapid and complete within 3–6 min. Following a 30-min incubation of [¹⁴C] spermine with fat cell membranes, over 90% of bound [¹⁴C] spermine was dissociable while under similar conditions only 25% of bound [¹⁴C] spermine was dissociable in cells. The non-dissociable fractions in cells likely represented intracellular accumulation. Binding and stimulation of glucose oxidation were demonstrated at similar concentrations. Bound spermine was displaced by spermine, spermidine and 1,8-diaminooctane with greater efficacy than putrescine (a polyamine devoid of insulin-like properties) or insulin. Similarly, polyamines did not complete with insulin for binding to isolated adipocytes. It appears, therefore, that polyamines initiate their insulin-like effects by interacting with the cell membrane at sites which are common to biologically active polyamines and which are distinct from the insulin receptor.     

The binding of polyamines and magnesium to DNA.

1. The binding of spermine and Mg2+ to DNA has been investigated using the dye arsenazo III to measure unbound cations. 2. The apparent dissociation constant, Kd, of DNA for spermine has been found to be 7.4 +/- 3.9 x 10(-8) M and that for Mg2+, 6.5 +/- 3.3 x 10(-7) M. 3. Binding of spermine in the presence of 1 mM Mg2+ has been shown to have a Kd of about 4 x 10(-6) M. 4. Magnesium ion (2 mM) halves the concentration of spermine needed to cause DNA aggregation. 5. Spermidine binds to DNA with a similar affinity to spermine but 3,3'-iminobispropylamine and 1,5,9,13-tetra-azatridecane bind with a lower affinity. The naturally occurring polyamines thus have a higher affinity for DNA than the related polyamines which do not occur naturally. 6. Binding of spermine or spermidine to DNA alters the spectrophotometric absorbance of DNA at 260 nm.     

On the subcellular localization of the polyamines

Putrescine, spermidine and spermine were determined in the nuclear fraction of rat liver which was obtained by density gradient centrifugation in non-aqueous media, i.e. under conditions which avoid migration of water-soluble compounds. Calculations of the distribution of the polyamines between nuclear and extranuclear compartments were based on the assumption that the DNA is concentrated in the nuclei. No significant losses of the polyamines occurred during fractionation. From the polyamine determination in tissue and nuclear fraction it appeared that 16-17% of the liver spermidine and spermine, and about 8% of the putrescine content was localized in the nuclei. The spermidine/spermine-ratios in nuclei and whole tissue were not significantly different. Pretreatment of the animals with inhibitors of ornithine decarboxylase caused a decrease of putrescine exclusively in the extranuclear compartments, in agreement with a higher proportion of the inhibitors in the cytoplasm. Since the nuclear volume of rat liver corresponds to about 5% of total liver volume, the concentration of spermidine and spermine is higher in the nucleus than in extranuclear compartments. Published histochemical localizations of the polyamines suggested very low polyamine concentrations in the nuclei of non-dividing liver and HeLa cells, but dramatic polyamine accumulations in metaphase and anaphase nuclei. These results are in disagreement with previously reported autoradiographic data, subcellular localizations based on density gradient centrifugations, and with our present results. Since subcellular localization is a key issue in all attempts to clarify cellular functions of the polyamines the careful revision of the techniques involved in subcellular polyamine localizations seems imperative.     

THE BIOCHEMICAL ROLE OF NATURALLY OCCURRING POLYAMINES IN NUCLEIC ACID SYNTHESIS

1. The polyamines, putrescine, spermidine and spermine occur in free or acetylated form in a wide variety of living organisms. Putrescine is biosynthesized from ornithine or arginine; spermidine and spermine from methionine and either ornithine or arginine. 2. It is difficult to determine the intracellular distribution of polyamines since they are all very soluble in water and they are readily redistributed when cells are disrupted. Evidence suggests that a substantial proportion of the intracellular polyamines is attached to the ribosomes and that spermidine is not concentrated in the nucleus. 3. Polyamines bind strongly to both DNA and RNA. The strength of binding is:spermine > spermidine > putrescine. Polyamines stabilize the double helix of DNA, probably by forming a bridge across the narrow groove, by involving electrostatic bonding with the phosphate group. However, they do not appear to alter the overall conformation of DNA. Spermine enables single-stranded RNA to fold into a more compact configuration which is less susceptible to attack by ribonuclease. 4. Spermine and spermidine are able to stimulate the DNA primed RNA polymerase. They facilitate the removal of RNA from the DNA-RNA-enzyme complex. 5. Polyamines promote the association of ribosomal subunits and also the binding of amino acyl transfer RNA to ribosomes. They cause increased coding ambiguities in the process of translation in certain bacterial systems. 6. There is a close correlation between the intracellular concentration of spermidine and the rate of RNA synthesis both in rat liver and in Escherichia coli. Conditions which affect the rate of RNA synthesis also affect the concentration of free intracellular spermidine. 7. Bacteria usually contain putrescine and spermidine, whereas animal tissues contain spermine and spermidine. Spermidine probably fulfils the same role in both bacteria and animal tissues, but the presence of spermine, which is common to eucaryotes, is possibly associated with their more complex mechanisms for regulating RNA and protein synthesis.     

Polyamines in the lung: polyamine uptake and polyamine-linked pathological or toxicological conditions

The natural polyamines putrescine, cadaverine, spermidine, and spermine are found in all cells. These (poly)cations exert interactions with anions, e.g., DNA and RNA. This feature represents their best-known direct physiological role in cellular functions: cell growth, division, and differentiation. The lung and, more specifically, alveolar epithelial cells appear to be endowed with a much higher polyamine uptake system than any other major organ. In the lung, the active accumulation of natural polyamines in the epithelium has been studied in various mammalian species including rat, hamster, rabbit, and human. The kinetic parameters (Michaelis-Menten constant and maximal uptake) of the uptake system are the same order of magnitude regardless of the polyamine or species studied and the in vitro system used. Also, other pulmonary cells accumulate polyamines but never to the same extent as the epithelium. Although different uptake systems exist for putrescine, spermidine, and spermine in the lung, neither the nature of the carrier protein nor the reason for its existence is known. Some pulmonary toxicological and/or pathological conditions have been related to polyamine metabolism and/or polyamine content in the lung. Polyamines possess an important intrinsic toxicity. From in vitro studies with nonpulmonary cells, it has been shown that spermidine and spermine can be metabolized to hydrogen peroxide, ammonium, and acrolein, which can all cause cellular toxicity. In hyperoxia or after ozone exposure, the increased polyamine synthesis and polyamine content of the rat lung is correlated with survival of the animals. Pulmonary hypertension induced by monocrotaline or hypoxia has also been linked to the increased polyamine metabolism and polyamine content of the lung. In a small number of studies, it has been shown that polyamines can contribute to the suppression of immunologic reactions in the lung.     

Effects of organic and inorganic polyamine cations on the structure of human serum albumin

The presence of several high affinity binding sites on human serum albumin (HSA) makes it a possible target for many organic and inorganic molecules. Organic polyamines are widely distributed in living cells and their biological roles have been associated with their physical and chemical interactions with proteins, nucleic acids, and lipids. This study is designed to examine the effects of spermine, spermidine, putrescine, and cobalt [Co(III)]-hexamine cations on the solution structure of HSA using Fourier transform IR, UV-visible, and circular dichroism (CD) spectroscopic methods. The spectroscopic results show that polyamine cations are located along the polypeptide chains with no specific interaction. The order of perturbations is associated with the number of positive charges of the polyamine cation: spermine > Co(III)-hexamine > spermidine > putrescine. The overall binding constants are 1.7 x 10(4), 1.1 x 10(4), 5.4 x 10(3), and 3.9 x 10(3)M(-1), respectively. The protein conformation is altered (IR and CD data) with reductions of alpha helices from 60 to 55% for free HSA to 50-40% and with increases of beta structures from 22 to 15% for free HSA to 33-23% in the presence of polyamine cations.     

Effect of polyamines on mitochondrial F1-ATPase catalyzed reactions

The effect of polyamines on F1-ATPase catalyzed reactions has been studied through the use of submitochondrial particles and F1-ATPase. ATP degradation catalyzed by submitochondrial particles and F1-ATPase was inhibited by spermine and spermidine. Spermine's inhibition was much greater than spermidine's effect. In contrast, P1-ATP exchange and succinate dependent ATP synthesis catalyzed by submitochondrial particles were both stimulated by spermine. The inhibition of ATPase activity by polyamines probably occurs through polyamine's replacement of Mg2+ on ATP, for the following reasons. (a) The ATPase activity inhibited by spermine was partially recovered when Mg2+ was added. (b) Spermine bound to ATP and phospholipids but not to F1-ATPase; yet spermine inhibited the ATPase reaction catalyzed by F1-ATPase, a protein free of phospholipid. (c) The binding of spermine to ATP was inhibited by Mg2+. The ATP content in polyamine-deficient cells definitely was lower than that in normal cells. On the basis of these results, the possible role of spermine in keeping the ATP concentration at a high level is discussed.     

Activation of phosphatidylinositol-4-phosphate kinase in rat liver plasma membranes by polyamines

The formation of phosphatidylinositol 4,5-bisphosphate (PIP2) from endogenous substrate in rat liver plasma membranes was stimulated approximately 3-fold by 1 mM spermine, with half-maximal effect at 0.2 mM polyamine. This effect of spermine was due to enhancement of phosphatidylinositol-4-phosphate kinase activity rather than to a decrease in degradation of PIP2 formed or the substrate phosphatidylinositol 4-phosphate (PIP). The stimulation of phosphatidylinositol-4-phosphate kinase by spermine decreased to half at physiological ionic strength, and was not affected appreciably by variations in the concentration of ATP and MgCl2. Among several di- and polyamines only spermine and spermidine were effective. Although spermine may cause aggregation of membrane vesicles, thereby potentially increasing substrate availability for phosphatidylinositol-4-phosphate kinase, our results do not support such an explanation for the enhancement in enzyme activity. Phosphatidylinositol kinase activity, contrary to phosphatidylinositol-4-phosphate kinase, was not stimulated appreciably by spermine.     

Excretion of acetylated and free polyamines by polyamine depleted Chinese hamster ovary cells

1. Cultured Chinese hamster ovary cells (CHO) and their ornithine decarboxylase deficient mutant cells (C55.7) were found to excrete small amounts of N8-acetylspermidine and free polyamines, putrescine and spermidine into the culture medium. 2. The concentration of N8-acetylspermidine in the control cells was 2-3% of that of spermidine. In the medium, however, the amount of N8-acetylspermidine was about 2-fold that of spermidine and 2- to 3-fold higher than the intracellular amount. N1-acetylspermidine or acetylated spermine were never detected in the cells or in the media. 3. Confluent CHO cells treated with 2 mM difluoromethylornithine stopped the excretion when the intracellular spermidine concentration had decreased to 20% of control while there was no decrease in spermine concentration. At low cell density, neither polyamine depleted CHO cells nor the C55.7 cells excreted any polyamines into the culture media.     

Methylglyoxal bis(guanylhydrazone) elimination of polyamine effects on protein synthesis

The effect of methylglyoxal bis(guanylhydrazone) (MGBG), a structural analog of polyamines, on protein synthesis has been studied in the presence and absence of spermidine. The spermidine stimulation of polyphenylalanine- and MS2 RNA-directed RNA replicase synthesis in an Escherichia coli cell-free system and of globin synthesis in a rabbit reticulocyte cell-free system disappeared with the addition of MGBG. The spermidine reduction of misincorporation of leucine during polyphenylalanine synthesis in both E. coli and wheat germ cell-free systems was also disturbed by MGBG. MGBG noncompetitively interfered with polyamine stimulation of polyphenylalanine and globin synthesis, suggesting that MGBG could bind to both RNA and the complex of RNA and polyamine. MGBG was preferentially bound to ribosomal RNA among ribosomal RNA, poly(U), and calf thymus DNA, and strongly inhibited the amount of polyamine bound to ribosomal RNA. These results suggest that MGBG elimination of polyamine effects on protein synthesis may occur through the disturbance of polyamine binding to ribosomal RNA.     

Effects of Polyamines on Proline Endopeptidase Activity in Rat Brain

The in vitro effects of polyamines on the activity of proline endopeptidase (PEPase) in rat brain cytosol, which contains an endogenous PEPase inhibitor, have been studied. Of the three amines tested (spermine, spermidine, and putrescine), spermine and spermidine markedly enhanced the enzyme activity in brain cytosol. At 6.25 mM spermine or 25 mM spermidine, a 13- or 14-fold enhancement of the enzyme activity was observed. When Mg2+ was used, an approximately fourfold enhancement of the enzyme activity was observed at 50 mM. The enhancement produced by spermine or spermidine was unaffected by Mg2+ up to 50 mM. The activity of purified PEPase was only slightly affected by each polyamine, but it was inhibited 50% by 50 mM Mg2+. On the other hand, 50% inhibition of the enzyme produced by the purified PEPase inhibitor (Mr 7,000: Ki 0.67 mM) was completely restored by addition of 0.7 mM spermine, 3.5 mM spermidine, or 28 mM putrescine. This restoration of inhibition by polyamines was reversed by increasing the inhibitor concentration. These data suggest that polyamines effectively reverse the inhibition of PEPase by its endogenous inhibitor by the reversible formation of a kinetically significant complex. The possible functions of polyamines in the regulation of PEPase in vivo are discussed.     

Depletion of intracellular putrescine and spermidine by alpha-difluromethylornithine does not inhibit proliferation of 9L rat brain tumor cells.

Incubation of 9L rat brain tumor cells with 25 mM DL-α-difluoromethylornithine inhibits cell proliferation, while treatment with 10 mM and 1 mM do not. All three concentrations cause equal degrees of depletion of intracellular putrescine and spermidine content, but have no effect on spermine content. These observations show that 9L cells can continue to proliferate in spite of significant polyamine depletion and leads one to question the role of polyamines in 9L cell replication. These observations also suggest that inhibition of 9L cell proliferation by 25 mM DL-α-difluormethylornithine is probably not due to its effect on ornithine decarboxylase or on intracellular polyamine content.     

Ultrastructural changes in vitro of rat liver nucleoli in response to polyamines

Summary Structural alterations of the nucleoli of rat liver cells were noted when these nuclei were isolated with spermidine or spermine rather than magnesium. When 5–10 mM spermidine or spermine were used to isolate the nuclei, the nucleoli were a) larger, b) contained numerous and sometimes large lacunae, and c) were less aggregated and had prominent chromatin caps. These chromatin caps gave the nucleolus a ring-shaped appearance in the light microscope. These findings, coupled with physiological data that indicate that polyamines enhance nucleolar RNA polymerase activity (Russell et al., 1971), suggest that spermidine and spermine may be involved in the control of ribosomal RNA synthesis. To our knowledge, this is the first instance of the direct stimulation of ribosomal RNA synthesis during nuclear isolation.Supported by USPHS Grant NS-07934.     

DNA condensation by polyamines: a laser light scattering study of structural effects.

Polyamines such as spermidine and spermine are abundant in living cells and are believed to aid in the dense packaging of cellular DNA. DNA condensation is a prerequisite for the transport of gene vectors in living cells. To elucidate the structural features of polyamines governing DNA condensation, we studied the collapse of lambda-DNA by spermine and a series of its homologues, H2N(CH2)3NH(CH2)n=2-12NH(CH2)3NH2 (n = 4 for spermine), using static and dynamic light scattering techniques. All polyamines provoked DNA condensation; however, their efficacy varied with the structural geometry of the polyamine. In 10 mM sodium cacodylate buffer, the EC50 values for DNA condensation were comparable (4 +/- 1 microM) for spermine homologues with n = 4-8, whereas the lower and higher homologues provoked DNA condensation at higher EC50 values. The EC50 values increased with an increase in the monovalent ion (Na+) concentration in the buffer. The slope of a plot of log [EC50(polyamine4+)] against log [Na+] was approximately 1.5 for polyamines with even number values of n, whereas the slope value was approximately 1 for compounds with odd number values of n. Dynamic light scattering measurements showed the presence of compact particles with hydrodynamic radii (Rh) of about 40-50 nm for compounds with n = 3-6. Rh increased with further increase in methylene chain length separating the secondary amino groups of the polyamines (Rh = 60-70 nm for n = 7-10 and >100 nm for n = 11 and 12). Determination of the relative binding affinity of polyamines to DNA using an ethidium bromide displacement assay showed that homologues with n = 2 and 3 as well as those with n > 7 had significantly lower DNA binding affinity compared to spermine and homologues with n = 5 and 6. These data suggest that the chemical structure of isovalent polyamines exerts a profound influence on their ability to recognize and condense DNA, and on the size of the DNA condensates formed in aqueous solution.