Crystal structures of DNA:DNA and DNA:RNA duplexes containing 5-(N-aminohexyl)carbamoyl-modified uracils reveal the basis for properties as antigene and antisense molecules

Oligonucleotides containing 5-(N-aminohexyl)carbamoyl-modified uracils have promising features for applications as antigene and antisense therapies. Relative to unmodified DNA, oligonucleotides containing 5-(N-aminohexyl)carbamoyl-2′-deoxyuridine (^NU) or 5-(N-aminohexyl)carbamoyl-2′-O-methyluridine (^NU_m), respectively exhibit increased binding affinity for DNA and RNA, and enhanced nuclease resistance. To understand the structural implications of ^NU and ^NU_m substitutions, we have determined the X-ray crystal structures of DNA:DNA duplexes containing either ^NU or ^NU_m and of DNA:RNA hybrid duplexes containing ^NU_m. The aminohexyl chains are fixed in the major groove through hydrogen bonds between the carbamoyl amino groups and the uracil O4 atoms. The terminal ammonium cations on these chains could interact with the phosphate oxygen anions of the residues in the target strands. These interactions partly account for the increased target binding affinity and nuclease resistance. In contrast to ^NU, ^NU_m decreases DNA binding affinity. This could be explained by the drastic changes in sugar puckering and in the minor groove widths and hydration structures seen in the ^NU_m containing DNA:DNA duplex structure. The conformation of ^NU_m, however, is compatible with the preferred conformation in DNA:RNA hybrid duplexes. Furthermore, the ability of ^NU_m to render the duplexes with altered minor grooves may increase nuclease resistance and elicit RNase H activity.     

Preparative purification of homogenous steroid-active isozyme of horse liver alcohol dehydrogenase by affinity chromatography on an immobilized AMP-analog.

The homogeneous steroid-active isozyme, SS, of horse liver alcohol dehydrogenase was purified preparatively from a horse liver crude extract by affinity chromatography on N⁶-(6-aminohexyl)-AMP-substituted Sepharose after a batch-wise prepurification on CM-cellulose. The enzyme obtained showed only one band on agarose-gel electrophoresis and on dodecyl sulphate-gel electrophoresis; the yield was about 30 mg SS isolated from 260 g horse liver.     

Purification of pigeon liver malic enzyme by affinity chromatography

A simple and rapid method for the purification of malic enzyme (EC 1.1.1.40) from pigeon liver is described. Malic enzyme in the crude tissue extract was partially purified by heat treatment, ammonium sulfate fractionation, and DEAE-cellulose chromatography. Final purification was achieved by affinity chromatography on immobilized N⁶-(6-aminohexyl)-adenosine 2′,5′-bisphosphate. Apparently homogeneous enzyme was obtained in 2 days with 54% yield.     

Horse-liver glutathione reductase: Purification and characterization

• 1.1. Purification of horse-liver glutathione reductase was obtained by affinity chromatography on N⁶-(6-aminohexyl)-adenosine-1′5′-bisphosphate Sepharose (N⁶-2′5′-ADP-Sepharose) and Reactive Red-120-Agarose, and chromatography on DEAE-Sephadex and Sephacryl S-300.
• 2.2. The final preparation had 248 U/mg specific activity after 11,174-fold purification with 47% final recovery, and was homogeneous by SDS-electrophoresis. It showed charge heterogeneity in non-denaturing electrophoresis and chromatofocusing, with several peaks of pI between 5.7 and 6.7.
• 3.3. The enzyme was homodimeric (107,000 native MW), with S_20w = 6.31 S, and 41.22 Å of hydrodynamic radius. It showed absorption peaks at 270, 370 and 462 nm, a characteristic of flavoproteins.
• 4.4. When NADPH was substituted by deamino-NADPH or NADH the enzyme showed 69 and 8.5% activity, respectively, while with glutathione-CoA mixed disulfide the enzyme had 23% of the activity shown with GSSG. Apparent K_m values of 8.8, 680, 59, and 560 μ M were measured for NADPH, NADH, GSSG and ferrycianide, respectively.

     

Characteristics of 8-substituted adenine nucleotide derivatives utilized in affinity chromatography.

Improved methods for the preparation of several 8-substituted adenine nucleotide derivatives are described. Enzymatic properties of these 8-substituted derivatives were investigated by steady state kinetic and inhibition studies. It was found that 8-(6-aminohexyl)-amino DPN⁺ and TPN⁺ exhibit relatively high affinity for most DPN⁺ and TPN⁺ dependent dehydrogenases. Preliminary nmr studies indicate that the 8-substituted adenine nucleotide derivatives may exist in slightly different ribosyl as well as glycosyl conformations from those of the natural adenine nucleotides. The chemical shift difference between geminal C₄ protons of dihydropyridine moiety of DPN⁺ and TPN⁺ changes from 0.1 to 0.2 ppm upon the 8-hexyl substitution of the natural coenzymes, indicating a strong interaction between 8-hexyl side chain of adenine moiety and the dihydropyridine moiety of these coenzyme derivatives. However, the folding and fluorescence properties of 8-(6-aminohexyl)-amino DPN⁺ and TPN⁺ as well as their reduced analogs in aqueous solutions are not significantly altered as compared to those of natural DPN⁺ and TPN⁺. Purification of glucose-6-phosphate dehydrogenase from yeast extracts and human erythrocytes using 8-(6-aminohexyl)-amino-TPN⁺ -Sepharose column is reported. Preliminary studies on the purification of various kinases using 8-substituted ADP and ATP Sepharose columns are also presented.     

General ligands in affinity chromatography. Cofactor–substrate elution of enzymes bound to the immobilized nucleotides adenosine 5′-monophosphate and nicotinamide–adenine dinucleotide

1. Two different gels have been prepared suitable for the separation of a number of enzymes, in particular NAD⁺-dependent dehydrogenases, by affinity chromatography. For both the matrix used was Sepharose 4B. For preparation (a), NAD⁺–Sepharose, 6-aminohexanoic acid has been coupled to the gel by the cyanogen bromide method and then NAD⁺ was attached by using dicyclohexylcarbodi-imide; for preparation (b), AMP–Sepharose, N⁶-(6-aminohexyl)-AMP has been coupled directly to cyanogen bromide-activated gel. 2. Affinity columns of both gels retain only the two enzymes when a mixture of bovine serum albumin, lactate dehydrogenase and glyceraldehyde 3-phosphate dehydrogenase is applied. Subsequent elution with the cofactor NAD⁺ yields glyceraldehyde 3-phosphate dehydrogenase whereas lactate dehydrogenase is eluted by applying the same molarity of the reduced cofactor. 3. The binding of both glyceraldehyde 3-phosphate dehydrogenase and lactate dehydrogenase to the gel tested, AMP–Sepharose, is strong enough to resist elution by gradients of KCl of up to at least 0.5m. A 0.0–0.15m gradient of the competitive inhibitor salicylate, however, elutes both enzymes efficiently and separately. 4. The elution efficiency of lactate dehydrogenase from AMP–Sepharose has been examined by using a series of eluents under comparable conditions of concentration etc. The approximate relative efficiencies are: 0 (lactate); 0 (lactate+semicarbazide); 0 (0.5mm-NAD⁺); 80 (lactate+NAD⁺); 95 (lactate+semicarbazide+NAD⁺); 100 (0.5mm-NADH). 5. All contaminating lactate dehydrogenase activity can be removed from commercially available crude pyruvate kinase in a single-step procedure by using AMP–Sepharose.     

Affinity chromatography of phosphofructokinase.

The behavior of mammalian phosphofructokinase on immobilized adenine nucleotides was investigated. Three different insolubilized ligands were compared using a pure rabbit muscle phosphofructokinase. N⁶-[(6-aminohexyl)-carbamoyl-methyl]-ATP-Sepharose bound at least 90 times more enzyme than either N⁶-(6-aminohexyl)-AMP-agarose or ATP-adipic acid hydrazide-Sepharose. The elution of phosphofructokinase from the ATP-Sepharose with various metabolites and combinations of metabolites was investigated. The enzyme is eluted specifically from N⁶-[(6-aminohexyl)-carbamoyl]-ATP-Sepharose with a mixture of 25 μm each of fructose 6-phosphate and ADP (±Mg²⁺). The enzyme is not eluted either with ATP (25 μm), fructose 1,6-diphosphate (1 mm), ADP (25 μm), fructose 6-phosphate (1 mm) alone, or with a mixture of fructose 1,6-diphosphate (25 μm) and ATP (25 μm). The recovery of bound enzyme was usually greater than 90%. A mixture of glucose 6-phosphate and ADP or a mixture of IDP and fructose 6-phosphate also elutes the enzyme, but the recovery with these eluants was only about 40%. It was concluded that the “dead-end” complex is the most effective in the elution. Using this method, phosphofructokinase has been prepared in an essentially homogeneous form from muscle and brain of rabbit and rat. The overall isolation procedure involves a high speed centrifugation of crude extracts which sediments phosphofructokinase as a pellet, followed with adsorption on N⁶-[(6-aminohexyl)-carbamoyl-methyl]-ATP-Sepharose and specific elution with the mixture of fructose 6-phosphate and ADP.     

Purification of cofactor-dependent enzymes by affinity chromatography

Several 8-(6-aminohexyl)-amino adenine nucleotide derivatives, including ATP, 2′,5′-ADP, 3′,5′-ADP and desulfo-CoA (CoA, reduced coenzyme A), were prepared and immobilized on Sepharose by cyanogen bromide activation. 8-(6-Aminohexyl)-amino-ATP-Sepharose was found to exhibit good affinity for both NAD⁺-dependent dehydrogenases and kinases. Sequential biospecific elutions with NADH and ATP resulted in a good separation of dehydrogenases from kinases. As many as eight different dehydrogenases and kinases could be substantially purified from both porcine muscle and mouse kidney extracts by this new procedure. 8-(6-Aminohexyl)-amino-2′,5′-ADP- and −3′,5′-ADP-Sepharose were shown to exhibit good affinity for many NADP⁺-dependent dehydrogenases from yeast extracts and CoA-dependent enzymes, respectively. Purification of citrate synthases from pig heart and Eschericia coli extracts by means of these 8-substituted adenine nucleotide affinity columns was also presented.     

Synergistic Anti-Cancer Effect of Phenformin and Oxamate

Phenformin (phenethylbiguanide; an anti-diabetic agent) plus oxamate [lactate dehydrogenase (LDH) inhibitor] was tested as a potential anti-cancer therapeutic combination. In in vitro studies, phenformin was more potent than metformin, another biguanide, recently recognized to have anti-cancer effects, in promoting cancer cell death in the range of 25 times to 15 million times in various cancer cell lines. The anti-cancer effect of phenformin was related to complex I inhibition in the mitochondria and subsequent overproduction of reactive oxygen species (ROS). Addition of oxamate inhibited LDH activity and lactate production by cells, which is a major side effect of biguanides, and induced more rapid cancer cell death by decreasing ATP production and accelerating ROS production. Phenformin plus oxamate was more effective than phenformin combined with LDH knockdown. In a syngeneic mouse model, phenformin with oxamate increased tumor apoptosis, reduced tumor size and ¹⁸F-fluorodeoxyglucose (FDG) uptake on positron emission tomography/computed tomography compared to control. We conclude that phenformin is more cytotoxic towards cancer cells than metformin. Furthermore, phenformin and oxamate have synergistic anti-cancer effects through simultaneous inhibition of complex I in the mitochondria and LDH in the cytosol, respectively.     

Purification and properties of a neuraminidase from Streptococcus K 6646

A neuraminidase was purified from the culture filtrate of Streptococcus 6646 (group K) by means of ammonium sulfate fractionation and successive column chromatographies on N-(p-aminophenyl)oxamic acid-substituted Sepharose derivative and p-aminophenyl-2-acetamido-2-deoxy-1-thio-β-d-glucopyranoside-substituted Sepharose derivative. The former adsorbent was found to bind a β-galactosidase and a β-N-acetylhexosaminidase in addition to the neuraminidase, and the latter adsorbent bound the β-galactosidase in addition to the β-d-N-acetylhexosaminidase. These adsorbents effectively eliminated the contaminating glycosidase activities and a 1,500-fold purification of the neuraminidase was achieved by this procedure.The neuraminidase thus purified was homogeneous by electrophoresis on polyacrylamide gel, and its molecular weight was estimated to be 110,000 by gel filtration on Biogel P-200. The activity of the purified neuraminidase was slightly stimulated by Ca²⁺, Mg²⁺, Mn²⁺, and Co²⁺, and strongly inhibited by heavy metals. The specificity of the purified neuraminidase was almost the same with Vibrio cholerae or Clostridium perfringens neuraminidase. It completely hydrolyzes sialic acid residues in neuraminyl lactose and porcine thyroglobulin, but it liberates only 50% of sialic acid residues from porcine submaxillary mucin and ganglioside GD_1a.     

Inhibition by N-(6-aminohexyl)-5-chloro-1-naphthalenesulfonamide,a calmodulin inhibitor,of dopamine release from rat brain synaptosomes

The release of preloaded [³H]dopamine by the synaptosomal fraction prepared from rat forebrain was examined in the presence and absence of N-(6-aminohexyl)-5-chloro-1-naphthalenesulfonamide (W-7), a calmodulin inhibitor. The release induced by high K⁺ was blocked by W-7 in a concentration-dependent manner after the pretreatment with and in the presence of the inhibitor. The inhibition by W-7 may specifically involve calmodulin, because little effects were seen with N-(6-aminohexyl)-naphthalenesulfonamide, an analog of W-7 with only a low affinity for calmodulin. W-7 may not affect the voltage-dependent Ca²⁺ channel of synaptosomal plasmalemma, since the inhibitor produced no change in the synaptosomal ⁴⁵Ca²⁺ uptake induced by high K⁺ depolarization. Thus, calmodulin may play a role in transmitter release and may function at the step(s) after the increase of free Ca²⁺ concentration in the cytosol of the nerve terminal. W-7 affected only to a small extent [³H]dopamine release in the presence of A23187 plus Ca²⁺.     

Affinity chromatography of Pseudomonas salicylate hydroxylase

In order to facilitate the purification of salicylate hydroxylase (salicylate 1-monooxygenase, EC 1.14.13.1) from Pseudomonas sp. RPP (ATCC 29351), an affinity chromatography procedure was developed employing immobilized salicylate as the affinity ligand. The immobilization was achieved by reacting p-aminosalicylate with the N-hydroxysuccinimide ester of Sepharose 4B-6-aminohexanoic acid. When the bacterial crude extract was chromatographed with this affinity column, salicylate hydroxylase was absorbed to the gel while the bulk of protein freely passed through. The absorbed enzyme was subsequently eluted from the affinity column by applying a 0–60 mm sodium salicylate gradient. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the enzymatically most active fraction of the affinity effluent revealed salicylate hydroxylase was by far the most predominant protein but there were also small amounts of contaminating proteins. However, a virtually homogeneous enzyme preparation was obtained when the crude extract was first fractionated with a DE-52 anion-exchange column followed by the affinity step. The enzyme preparation obtained by this two-step procedure showed a specific activity of 14.9 units/mg and an A₄₅₀:A₃₇₂:A₂₈₀ of 1.01:1:10.23. Because most of the enzymes belonging to the class of external flavoprotein monooxygenase utilize salicylate analogs as substrates and share many other common properties, there is a strong possibility that the salicylate column may be useful for the purification of other member monooxygenases.     

Purification of rat liver enzymes involved in the oxidation of glyoxylate

The use of Sepharose aminohexyl oxamate for the purification of glycolate oxidase and lactate dehydrogenase is described. The kinetics of both enzymes are reported in relation to their possible roles in the production of oxalate. A model is proposed in which glycolate oxidase in the peroxisomes and lactate dehydrogenase in the cytosol cooperate in the production of oxalate.     

Affinity chromatography of carbohydrate-specific immunoglobulins: coupling of oligosaccharides to sepharose.

A simple method has been developed for the coupling of oligosaccharides to Sepharose. The sugars are reacted with β-(p-aminophenyl)-ethylamine to form N-alkylglycosides which are then reduced with sodium borohydride to stable secondary amines. The derivatives are then coupled to cyanogen bromide-activated Sepharose through their arylamino groups. Yields are essentially quantitative based on starting oligosaccharides. An affinity column containing lacto-N-difucohexaose I coupled to Sepharose by this method was used for the purification of an antibody directed against this oligosaccharide. The antibody is absorbed by the gel and is specifically eluted by the free sugar.     

Substitution of carbonate by non-physiological synergistic anion modulates the stability and iron release kinetics of serum transferrin

Serum transferrin (sTf) is a bi-lobal protein. Each lobe of sTf binds one Fe³⁺ ion in the presence of a synergistic anion. Physiologically, carbonate is the main synergistic anion but other anions such as oxalate, malonate, glycolate, maleate, glycine, etc. can substitute for carbonate in vitro. The present work provides the possible pathways by which the substitution of carbonate with oxalate affects the structural, kinetic, thermodynamic, and functional properties of blood plasma sTf. Analysis of equilibrium experiments measuring iron release and structural unfolding of carbonate and oxalate bound diferric-sTf (Fe₂sTf) as a function of pH, urea concentration, and temperature reveal that the structural and iron-centers stability of Fe₂sTf increase by substitution of carbonate with oxalate. Analysis of isothermal titration calorimetry (ITC) scans showed that the affinity of Fe³⁺ with apo-sTf is enhanced by substituting carbonate with oxalate. Analysis of kinetic and thermodynamic parameters measured for the iron release from the carbonate and oxalate bound monoferric-N-lobe of sTf (Fe_NsTf) and Fe₂sTf at pH 7.4 and pH 5.6 reveals that the substitution of carbonate with oxalate inhibits/retards the iron release via increasing the enthalpic barriers.     

Effective Purification of Bioproducts by Fast Flow Affinity Chromatography

The performance of affinity adsorbents, such as HiPAC, Toyopearl, and Sepharose 4B coupled with protein A and anti-BSA, was compared. The HiPAC column, which is packed with rigid porous silica particles of 30 μm diameter, showed the highest value of D_pore/r² because of the small particle diameter and rigidity of the adsorbent particles. Further, it was operable at higher flow rates than the others. Thus, experimental data and calculation on the purification process show that fast and efficient purification is possible by use of the HiPAC column.     

Purification and characterization of folate binding proteins from rat placenta

Rat placenta contains virtually no unsaturated (i.e., apo-form) folate binding protein. However, by lowering the pH of a solubilized membrane preparation of this tissue to 3.5, the endogenous bound folate was dissociated from the protein and adsorbed to charcoal. The apo-form of the folate binding protein thus obtained was purified by affinity chromatography using pteroylglutamic acid covalently coupled to Sepharose 4B. A single protein band with an apparent M_r of 36 000 was observed by SDS-polyacrylamide gel electrophoresis of the eluate from the affinity matrix. Western blot of this preparation using a rabbit antiserum raised with the affinity eluate also identified a single 36 kDa protein band. However, peptide sequencing of the N-terminal region of the proteins in the affinity eluate established that it contained two homologous proteins. Computer alignment of the first 22 N-terminal amino acids of each rat placental protein with human, bovine milk and mouse folate binding proteins showed 50–64% identical homology and 27% homology when the eight proteins were aligned together. The affinity of both rat proteins is highest for pteroylglutamic acid (K_a = 1.6 − 109 l/mol) lower for N⁵-methyltetrahydrofolate and substantially lower for N⁵-formyltetrahydrofolate. In the dose-response range studied there was no apparent affinity for methotrexate. The folate binding proteins could be released from a preparation of placental membranes using phospholipase C indicating that these proteins belong to the class of proteins anchored to the plasma membrane by a glycosyl phosphatidylinositol adduct.     

Large scale isolation,purification, and partial characterization of the intermediate filament-specific,Ca2+-activated proteinase from porcine kidney and Ehrlich ascites tumor cells: A comparative study

The Ca²⁺-activated, neutral thiol proteinase specific for intermediate filament subunit proteins was isolated at large scale from the postribosomal supernatant of a low-ionic-strength extract of porcine kidney and Ehrlich ascites tumor (EAT) cells, respectively. The purification procedure encompassed DEAE-Sephacel ion exchange chromatography of the material precipitating between 23 and 55% (NH₄)₂SO₄ saturation, followed by hyroxylapatite chromatography and activated thiol Sepharose 4B covalent chromatography. On the average, 25 mg of 62% pure enzyme was obtained from 500 g frozen kidney and 55 mg of 51% pure enzyme from 500 g EAT cells within a week. Both enzyme preparations were free of Ca²⁺-independent proteolytic activities and indistinguishable with respect to their physicochemical and functional properties; their catalytic properties were indistinguishable from those of enzyme purified to homogeneity on arginine methylester Sepharose 4B. Because of this identity, porcine kidney proves to be an inexpensive source for the Ca²⁺-activated proteinase which had previously been isolated and purified at small scale from EAT cells (W. J. Nelson and P. Traub, (1983) J. Biol. Chem.257, 5544–5553). Despite a 38% protein contamination, the partially purified enzyme from porcine kidney is useful for the in vitro study of structure-function relationships of intermediate filaments and their subunit proteins. During affinity chromatography of the partially purified proteinase from EAT cells on arginine methylester Sepharose 4B, a 100-kDa protein was purified which has a high affinity for arginine residues. It also occurs in porcine kidney, although at a considerably lower concentration. Its cellular localization and function remain to be determined.     

Studies on purification of a lectin from fruiting bodies of the edible shiitake mushroom Lentinus edodes

A lectin, with a specificity for N-acetylgalactosamine and N-acetylglucosamine and a molecular weight of 43 kDa, was isolated from fruiting bodies of the edible shiitake mushroom Lentinus edodes. The purification procedure entailed extraction with aqueous buffer, ammonium sulfate precipitation, gel filtration on Sephadex G-100 and affinity chromatography on N-acetylgalactosamine-agarose. The lectin was unique in that it was tenaciously bound on anion exchangers including DEAE-cellulose, DEAE-Sepharose, DEAE-Sephadex, Q-Sepharose, Dowex and PEI-cellulose and also on hydroxyapatite and phenyl Sepharose. It was largely unadsorbed on cation exchangers including CM-cellulose, CM-Sepharose, SP-Sepharose and Amberlite, and also on protein G-Sepharose, Red Sepharose and Affi-gel Blue gel, wheat germ lectin-Sepharose and p-aminophenyl-d-glucopyranoside agarose.     

Purification and Properties of Oxalate Oxidase from NaCl Stressed Grain Sorghum Seedlings

The effect of NaCl stress on molecular and biochemical properties of oxalate oxidase (OXO) was studied in leaves of grain sorghum hybrid (var CSH-14) seedlings. There was no effect on molecular weight and number of subunits of the enzyme but it showed some important changes in its kinetic parameters such as K_m for oxalate and V_max. Optimum pH (5.8), activation energy (5.084 kcal mole^?1), time of incubation (6 min) and K_m for oxalate (1.21×10^t-4M) were increased, while V_max (0.182 mmole min^?1) decreased and no change in optimum temperature was observed. This showed that substrate affinity and maximum activity of the enzyme was adversely affected. The specific activity of oxalate oxidase was increased in seedlings grown in a NaCl containing medium compared to normal, which reveals the increased de novo synthesis of the enzyme to sustain oxalate degradation.