Preparation and properties of poly-9-vinyladenine

Poly-9-vinyladenine was prepared by reaction of poly-6-chloro-9-vinylpurine with ammonia and poly-1-vinyluracil by hydrolysis of poly-L -vinyl-2-ethoxy-4-pyrimidinone. In aqueous solutions poly-9-vinyladenine shows hypochromism in the ultraviolet spectrum and forms a complex with polyuridylic acid as detected by a further decrease in the ultraviolet absorption. Under the same conditions, poly-9-vinyladenine and poly-L -vinyluracil interact with formation of higher aggregates.     

Template specific inhibitor of mammalian DNA polymerases.

A study of the inhibition of mouse cellular DNA polymerases by poly-nucleotides and their vinyl analogs is presented. Poly(dT)-directed poly(dA) synthesis by representatives of all three classes of cellular DNA polymerase could be completely inhibited by poly(9-vinyladenine), although higher concentrations were required in the case of the gamma class enzyme. Studies on the mechanism of the inhibition using the alpha class DNA polymerase and different templates showed that the enzyme activity was inhibited in all cases where base-pairing between the vinyl polymer and the template occurred; poly(9-vinyladenine) did not interfere with the replication of templates to which it does not bind. The inhibition occurred shortly after addition of poly(9-vinyladenine) to ongoing reactions, yet the enzyme was not displaced from the template - primer complex.     

Spectroscopic study of the interaction between poly-(9-vinyladenine) and single or multistrand RNA.

The interaction between poly(9-vinyladenine) (PVAd) and poly[r(U)] was investigated by means of uv, CD, 1H-, and 31P-nmr spectroscopies. The interaction was dependent on the molecular weight of PVAd determined by uv and CD spectroscopies. Based on imino proton nmr, it was clearly found that PVAd formed the complex with poly[r(U)] by complementary hydrogen bonding. The interaction of PVAd with double- and triple-stranded helices of RNA was also investigated by uv melting behavior and 31P-nmr spectroscopy. The results suggested that PVAd could not interact with the double-stranded poly[r(A)].poly[r(U)] but did with the triple-stranded RNA.     

NMR studies of complex formation between the modified oligonucleotide d(T*TCTGT) covalently linked to an acridine derivative and its complementary sequence d(GCACAGAA)

The oligodeoxynucleotide d(TTCTGT) was covalently attached to the 9-amino group of 2-methoxy-6-chloro-9-aminoacridine (Acr) through its 3'-phOsphate via a pentamethylene linker (m5). In order to avoid its hydrolysis by nucleases inside the cel., one of its phosphates (TpT) was substituTed with a neopentyl group. Complex formation between each of the two purified isomers and the complementary strand d(GCACAGAA) was investigated by nuclear magnetic resonance. The COSY and NOESY connectivities allowed us to assign all the proton resonances of the bases, the sugars (except the overlapping 5'-5' resonances), the acridine, and the pentamethylene chain. Structural information derived from the relative intensity of COSY and NOESY maps revealed that the duplex d(T*TCTGT).d(GCACAGAA) adopts a B-type conformation and that the deoxyriboses preferentially adopt a 2'-endo conformation. The NOE connectivities observed between the protons of the bases or the sugars and the protons of the dye show the intercalation of the acridine between the base pairs. NOE connectivities as well as imino proton resonances show that, at room temperature, the C7 base and the G8 base belonging to two different duplexes are paired. The pseudoaxial and pseudoequatorial isomers were assigned, and the differences in stability of their complex with the complementary strand are discussed.     

Isolation and some properties of 11- and 9-Gla prothrombins from normal plasma.

The relationship of prothrombin structure to function with respect to gamma-carboxyglutamic acid (Gla) residues can be effectively evaluated by characterizing the behavior of prothrombin isomers differing in Gla content. In addition to the isolation of a whole spectrum of Gla-deficient, 0- to 9-Gla isomers from dicoumarol-treated plasma, prothrombin isomers containing 11 (10.90) and 9 (8.85) Gla residues have now been isolated from normal bovine plasma. The isomers were isolated by barium citrate adsorption, elution, and finally by heparin-agarose, DEAE-cellulose, and immuno-affinity chromatographies. Each of the purified isomers showed a single component by agar gel and sodium dodecyl sulfate - polyacrylamide gel electrophoresis. By agar gel electrophoresis, the 11-Gla prothrombin isomer moved the fastest, followed by the 10-, and lastly the 9-Gla isomer, independent of Ca2+. The corresponding 9-, 10-, and 11-Gla prothrombin fragments 1 exhibited similar migration tendencies. By gel electrofocusing, 11- and 9-Gla fragments 1, respectively, focused anodal and cathodal to 10-Gla fragment 1. The Ca2+-induced decrease in the intrinsic fluorescence in 11-, 10-, and 9-Gla fragments 1 was 48, 40, and 45%, respectively. This metal-induced structural change did not correlate with the functional, thrombin-generating property of the isomers, as the 9-Gla variant exhibited 75%, and the 11-Gla 110-115%, of normal coagulant activity.     

A 19F-NMR study of 3-fluoro-4-demethoxydaunomycin intercalation complexes with the hexanucleotide d(CTGCAG)2

Equilibrium systems containing intercalation complexes formed between the novel anthracycline drug, 3-fluoro-4-demethoxydaunomycin (3FD), and the hexanucleotide duplex d(CTGCAG)2 have been studied by 19F-NMR spectroscopy. Solutions containing a 1:1 molar ratio of 3FD/d(CTGCAG)2 gave four 19F signals which have been assigned to each of four possible intercalation isomers for the 1:1 3FD.d(CTGCAG)2 complex, which we denote by [d(CTGCAG)2][3FD]; these were where 3FD bound between the 5'-CT-3', 5'-TG-3', 5'-GC-3' or 5'-CA-3' base sequences, with the drug sugar moiety lying in the minor groove and pointed in the 3' direction in each case. Changes in temperature and NaCl concentration affecting the equilibrium distribution of these isomers were studied and indicated that no overriding binding site preference prevailed under standard biochemical conditions. Formation of some of the 2:1 3FD.d(CTGCAG)2 complex occurred when a solution of [d(CTGCAG)2][3FD] was exposed to excess 3FD; however, this complex was unstable to gel filtration and no co-operative binding of the second 3FD molecule was observed.     

Effect of fluorophore linkage position of n-(9-anthroyloxy) fatty acids on probe distribution between coexisting gel and fluid phospholipid phases

The quenching of probe fluorescence by spin-labeled phospholipid has been used to determine the distribution of a series of n-(9-anthroyloxy) fatty acids between coexisting gel and fluid liquid-crystal phases in multilamellar phospholipid vesicles. The phase distribution ratio in every case is found to favor the fluid lipid phase, but is much greater between fluid and Ca2+-induced gel than between fluid and thermal gel. For a given gel type, n-(9-anthroyloxy)stearic acids with n = 3, 6, 9 or 12 as well as 11-(9-anthroyloxy)undecanoic acid all exhibit similar behavior, favoring the fluid phase by about a factor of 4 over thermally-induced lipid gel phase and by 18 over Ca2+-induced gel phase. 16-(9-Anthroyloxy)palmitic acid, with the bulky probe at the terminus of the 16-carbon chain, favors the fluid phase less strongly, by a factor of 1.5 or 11 over thermally-induced or Ca2+-induced gel phase, respectively, indicating better packing of this probe in phospholipid gel phases.     

Formation of a parallel-stranded DNA homoduplex by d(GGA) repeat oligonucleotides.

The GGA9-H molecules consisting of a double helical stretch followed by a single-stranded 3'-terminal overhang of nine GGA sequence repeats exhibited a gel mobility-shifted band in a concentration-dependent manner, suggestive of the intermolecular complex formation. The position of the shifted band in a gel was almost identical to that of the Y-shaped dimer marker of the same molecular weight that had the two double-helices at one side. This suggests that GGA9-H dimerizes in a parallel orientation without the formation of four-stranded hairpin structure. Since the GGA9-H homoduplex was stably formed at pH 4, 7 and 9, the formation does not require protonation or deprotonation of the N1 position of adenines. Neither does it require the N7 group of guanines responsible for Hoogsteen base pairing from the methylation interference and modification studies. Modification of the N7 group of guanines with dimethyl sulfate (DMS) did not inhibit the association and also the N7 group in the homoduplex was not protected from DMS. On the other hand, the GAA9-H having the G to A base substitution did not show such an association with either GGA9-H or GAA9-H. These results suggest that the homoduplex formation may be due to G.G base pairing through non-Hoogsteen hydrogen bonds.     

Selection for thermodynamically stable DNA tetraloops using temperature gradient gel electrophoresis reveals four motifs: d(cGNNAg), d(cGNABg),d(cCNNGg), and d(gCNNGc)

Hairpins play important roles in the function of DNA, forming cruciforms and affecting processes such as replication and recombination. Temperature gradient gel electrophoresis (TGGE) and in vitro selection have been used to isolate thermodynamically stable DNA hairpins from a six-nucleotide random library. The TGGE-selection process was optimized such that known stable DNA tetraloops were recovered, and the selection appears to be exhaustive. In the selection, four families of exceptionally stable DNA loops were identified: d(cGNNAg), d(cGNABg), d(cCNNGg), and d(gCNNGc). (Lowercase denotes the closing base pair; N = A, C, G, or T; and B = C, G, or T.) It appears that the known stable d(cGNAg) triloop motif can be embedded into a tetraloop, with the extra nucleotide inserted into either the middle of the loop, d(cGNNAg), or at the 3'-end of the loop, d(cGNABg). For d(cGNNAg) and d(cGNABg), a CG closing base pair was strongly preferred over a GC, with DeltaDeltaG degrees (37) approximately 2 kcal/mol. Members of the two families, d(cCNNGg) and d(gCNNGc), are similar in stability. The loop sequences and closing base pairs identified for exceptionally stable DNA tetraloops show many similarities to those known for exceptionally stable RNA tetraloops. These data provide an expanded set of thermodynamic rules for the formation of tetraloops in DNA.     

Biomesogenic matrix systems

The bifunctionally reactive nucleoside and distant nucleoside analogs adenosine (Ado), S-[(adenine-9-yl)methoxyethyl]-L-cysteine (Na-salt) (cysA) and 9-vinyladenine (vA) in aqueous solutions assemble on complementary polyuridylic acid templates to form complex lyomesophases. The systems are investigated by polarizing microscopy, differential scanning calorimetry (DSC) and 1H- and 31P-nmr spectroscopies, assisted by molecular modeling studies. The results indicate the importance of biomesogenic (pre)ordering in nucleic acid native and artificial matrix reactions.     

Application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology

Here, the state of the art of the application of denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE) in microbial ecology will be presented. Furthermore, the potentials and limitations of these techniques will be discussed, and it will be indicated why their use in ecological studies has become so important.     

Normal two-dimensional gel electrophoresis of alpha-2-macroglobulin in cystic fibrosis.

Some studies have suggested that a mutant form of alpha-2-macroglobulin (alpha-2-M) could be the primary defect in cystic fibrosis (CF). To test for the presence of charge change amino acid substitutions, alpha-2-M was examined by two-dimensional gel electrophoresis following complete denaturation of the proteins. The pattern of nine charge isomers observed was the same in homozygous, heterozygous, and normal individuals.     

Time-resolved fluorescence emission and excitation spectroscopy of d(TA) and d(AT) using synchrotron radiation

The photophysics of the sequence isomers d(TA) and d(AT) has been investigated at room temperature in 5 x 10(-5) M neutral aqueous solution using pulsed ultraviolet excitation from the ACO synchrotron and detection by time correlation or gated single-photon counting. Decay profiles of the emissions at 350, 400 and 460 have been analyzed both independently and globally by reiterative non-linear least-squares fitting to models of two and three independently emitting species. No evidence has been observed for excited-state reaction. Time-windowed spectra, both emission and excitation, have been collected for three time windows and have been deconvoluted to give time-resolved spectra using the lifetimes resulting from the decay analyses. Spectra are separated into two classes, with picosecond and nanosecond lifetimes, respectively. The picosecond spectra have the emission and excitation spectral characteristics of mixed monomer (A and T) fluorescences and are assigned as originating from the unstacked fractions of d(TA) and d(AT). The nanosecond emission spectra from d(TA) and d(AT) are both two-component, with lambda max approximately 350 and approximately 425 nm and lifetimes of 2.3 and 6.1 ns, respectively. The time-resolved excitation spectra for the nanosecond emissions are quite different from the isotropic absorption spectra of d(TA) and d(AT) but correlate with the anisotropic absorption for out-of-plane transitions between stacked bases of co-crystals of 9-methyladenine and 1-methylthymine reported by Stewart and Davidson. The nanosecond spectra thus represent the direct excitation and emission of stacked pairs of bases. These results provide no evidence for energy transfer and are probably related to sequence-specific photo-adduct formation.     

Vinyldeoxyadenosine in a sarcin-ricin RNA loop and its binding to ricin toxin a-chain

8-Vinyl-2'-deoxyadenosine (8vdA) is a fluorophore with a quantum yield comparable to that of 2-aminopurine nucleoside. 8vdA was incorporated into a 10-mer stem-tetraloop RNA (8vdA-10) structure for characterization of the properties of the base, 8-vinyladenine (8-vA), with respect to adenine as a substrate or inhibitor for ribosome-inactivating proteins. Ricin toxin A-chain (RTA) and pokeweed antiviral protein (PAP) catalyze the release of adenine from a specific adenosine on a stem-tetraloop (GAGA) sequence at the elongation factor (eEF2) binding site of the 28S subunit of eukaryotic ribosomes, thereby arresting translation. RTA does not catalyze the release of 8-vinyladenine from 8vdA-10. Molecular dynamics simulations implicate a role for Arg180 in oxacarbenium ion destabilization and the lack of catalysis. However, 8vdA-10 is an active site analogue and inhibits RTA with a Ki value of 2.4 microM. Adenine is also released from the second adenosine in the modified tetraloop, demonstrating an alternative mode for the binding of this motif in the RTA active site. The 8vdA analogue defines the specificities of RTA for the two adenylate depurination sites in a RNA substrate with a GAGA tetraloop. The rate of nonenzymatic acid-catalyzed solvolysis of 8-vinyladenine from the stem-loop RNA is described. Unlike RTA, PAP catalyzes the slow release of 8-vinyladenine from 8vdA-10. The isolation of 8-vA and its physicochemical characterization is described.     

Application of a single-cell gel electrophoresis (comet) assay to screen the antimutagenic activity in foods

Three cell lines (HL60, U937 and RAW264.7) were studied for their sensitivity against mutagens by using a single-cell gel electrophoresis (comet) assay. RAW264.7, the most sensitive one, was chosen to screen the antimutagenic activity in swine and bovine offal. Aqueous extracts of the swine stomach (0.2 mg/ml) and heart (10 mg/ml) were found to have antimutagenic activity against MeIQx (+ S9mix)-treated cells.     

Chitosan gel beads immobilized Cu (II) for selective adsorption of amino acids

Chitosan (CS) gel beads were prepared by using phase inversion and precipitation technique. The gel beads could bind copper (II), by which Cu (II) ion-immobilized chitosan gel beads (CS-Cu²⁺ gel beads) were prepared, and the amount of the immobilized Cu (II) was about 35 mg/g when the CS gel beads were incubated in 150 ppm cupric sulfate solution. The CS-Cu²⁺ gel beads could selectively adsorb histidine (His) from the mixed solution containing His and tryptophan (Trp); and the selective coefficient which was defined as the adsorbed amount ratio of His to Trp was about 8.0 at the pH value of 7.4. The effect of the pH value on the amino acid adsorption was also studied. In order to investigate the relationship of the amino acid adsorption and protein adsorption, the adsorbed amounts for IgG and albumin were determined; and the results indicated that the CS-Cu²⁺ gel beads could adsorb a larger amount of IgG than albumin due to the larger amount of the exposed residual His. The study provided a sorbent and a method to selectively remove His and IgG.     

Synthesis and biological activity of 2-aminopurine methylenecyclopropane analogues of nucleosides

Synthesis and biological activity of racemic 2-aminopurine methylenecyclopropane analogues of nucleosides 4, 5, 10 and 11 is described. One-pot alkylation-elimination of 2-aminopurine (6) with dibromide 7 gave a mixture of four isomeric methylenecyclopropanes. The (E, Z)-N9 and (E, Z)-N7 isomers 8 and 9 were resolved by chromatography on silica gel. Deacetylation of 8 afforded the respective (Z)-N9 and (E)-N9 isomers 4 and 10 which were separated by chromatography on silica gel. In a similar fashion, (E, Z)-N7 mixture 9 furnished (Z)-N7 and (E)-N7 isomers 5 and 11. The S-(+)-enantiomer 4 was obtained by desulfurization of (S)-(+)-6-thiosynguanol (13) with Raney Ni. Compound 13 was obtained from (S)-(+)-2-amino-6-chloro derivative 12 and NaSH in methanol. Racemic analogues 4, 5, 10 and 11 were inactive against HCMV, HSV-1, HSV-2, EBV and VZV. Enantiomer (S)-(+)-4 inhibited replication of HSV-1 in BSC-1 cells (ELISA) with EC50 35 microM and it was non-cytotoxic in KB cells (CC50 > 100 microM). Compound (S)-(+)-4 was also moderately effective against VZV in HFF culture with EC50/CC50 (microM) 60/>460 and it was a substrate for xanthine oxidase.     

Biomesogenic Matrix Systems

Abstract

The bifunctionally reactive nucleoside and distant nucleoside analogs adenosine (Ado), S-[(adenine-9-yl)methoxyethyl]-L-cysteine (Na-salt) (cysA) and 9-vinyladenine (vA) in aqueous solutions assemble on complementary polyuridylic acid templates to form complex lyomesophases. The systems are investigated by polarizing microscopy, differential scanning calorimetry (DSC) and ¹H- and ³¹P-nmr spectroscopies, assisted by molecular modeling studies. The results indicate the importance of biomesogenic (pre)ordering in nucleic acid native and artificial matrix reactions.     

Interaction of double-stranded T4 DNA with cationic gel of poly(diallyldimethylammonium chloride)

Interaction between duplex T4 DNA and a slightly cross-linked cationic gel of poly(diallyldimethylammonium chloride) in aqueous media was studied by fluorescent microscopy. While short DNA chains such as plasmid DNAs penetrate into the gel and form a phase of polyelectrolyte complex with the cationic network, the genomic giant DNA chains of T4 phages form complexes only on local areas of the gel surface. The DNA/gel complex exhibited different characteristic morphologies depending on the conditions for preparing the complex, such as the DNA concentration, flux of the solution, and surface geometry of the gel: (1) In the interaction with the flat surface of film-type gel, compact round objects, which reflected a condensed state of single DNA chains, were observed. (2) In the interaction with partly dried gel, a characteristic pattern similar to propagating waves was formed on the gel surface. (3) When flux is generated for a concentrated DNA solution, long oriented fiberlike structures were formed, which consisted of ensembles of chains. The interaction with small pieces of mechanically decomposed gel leads to complete covering of their surface by the DNA.     

Electronic structure of DNA by DV-X alpha cluster calculations: II. d(GG).d(CC), d(CG)2, d(GC)2 A and B conformations. (Part 2) Sugars and bases

The electronic structure of d(GG).d(CC), d(CG)2, d(GC)2 which are stacked base pairs in the DNA double helix, are elucidated for both A and B conformations in detail by DV-X alpha cluster calculations. These three DNA double helix fragments are contracted from the same bases, G and C, but the electronic structures of the fragments for both A and B conformations are different from each other characteristically. There are some delicate differences in the admixture of the orbital components and the overlap populations of intra- and inter- strand stacked bases among the stacking isomers. On the other hand, the electronic states of sugars differ in the 5'-3' direction, but are not almost dependent on stacked base pairs.