Poly rA Research Articles

Isolation and characterization of a genomic sequence of maize coding for a zein gene

An EcoRI restriction endonuclease fragment of maize DNA coding for the 19,000 dalton zein protein was cloned in phage λgt WES. The zein gene was identified by the electron microscopic analysis of RNA-DNA hybrids (R-loops) and DNA-DNA hybrids (D-loops). The R-loops were formed with poly(rA)-containing RNA isolated from 18 days post-pollination maize endosperm and showed no intervening non-hybridizing sequences (introns) within their 800 base length. A cDNA clone specific for the 19,000 dalton zein protein formed D-loops in the same position and orientation as the R-loops. The cloned fragment measured 4.4 kilobases (kb), the same size as an EcoRI fragment of maize DNA revealed by “Southern” analysis.

Heterogeneous forms of poly(rA) . oligo(dT)-directed DNA polymerase activity from rat spleen.

Three forms of DNA polymerase, named enzymes A, B, and C, that preferred (rA)n x (dT)12-18 as a template-primer, were partially purified from an extract of rat spleen. Enzymes B and C, both sedimenting at 9S, appeared to correspond to DNA polymerase gamma. However, they differed in their behavior on phosphocellulose and DNA-cellulose column chromatographies, and in their optimum KCl and divalent cation requirements for activity. Enzyme A showed a unique property. Like DNA polymerase beta, it sedimented at 3.8S, was resistant to reagents blocking sulfhydryl groups, and was inhibited by phosphate, but it differed from DNA polymerase beta with respect to elution positions from DEAE-cellulose, phosphocellulose and DNA-cellulose columns, Km value (lower by one order of magnitude for dTTP), and template-primer preference. Enzyme A was found in the mitochondrial fraction, in which DNA polymerase beta was not detectable. Enzymes A and C were isolated from the nuclear fraction, but this fraction did not contain enzyme B. The cytosol contained only enzyme A. The mitochondrial fraction contained enzyme A and enzyme C-like polymerase. Enzyme B was obtained with enzymes A and C only by extraction of the whole cell homogenate. Enzyme B may be labile or may be an artificial form of DNA polymerase gamma formed during the purification procedures.

Fluorescence Decay Studies of 9-Aminoacridine Bound to Polyriboadenylic Acid

Abstract The interaction of the mutagenic dye 9-aminoacridine (9AA) with polyriboadenylic acid (poly rA) was studied by both steady-state and transient fluorescence measurements. It was found that the fluorescence decay of 9AA bound to poly d(A-T) follows a single-exponential decay law but that the decay data of 9AA bound to poly rA can be well described as a sum of two-exponential functions. The fact that nanosecond time-resolved fluorescence spectra are independent of time suggests that the double-exponential decay may be attributed to different microenvironments at the binding sites. The decay parameters, fluorescence emission maxima, and fluorescence quantum yields obtained at acid pH differ from those obtained at neutral pH. The fluorescence behavior of 9AA is discussed in connection with the conformational change of poly rA.

RNA-dependent ATPase from Saccharomyces cerevisiae.

A new RNA-dependent ATPase has been isolated from yeast chromatin extracts and partially characterized. The protein has a sedimentation coefficient of about 7 S. The enzyme hydrolyzes specifically ATP (or dATP) to ADP (or dADP) and Pi in the presence of Mg2+ or Mn2+ ions and requires a single-stranded polynucleotide as cofactor. The order of efficiency of synthetic polymers is poly(rU) > poly(rI) greater than or equal to poly(dU) > poly(rA) greater than or equal to poly(rC). Among natural polymers, single-stranded DNA and poly(rA)-containing mRNA from yeast are also active but less so than poly(rU). The enzyme exhibits a pH optimum of 8 and is fully inhibited by 0.25 M NaCl. The Km for ATP is0.2 mM. The resemblance between this ATPase and DNA-dependent ATPases from other sources, as well as the termination factor rho, is discussed.

Interaction between synthetic analogues of quinoxaline antibiotics and nucleic acids: role of the disulphide cross-bridge and D-amino acid centres in des-N-tetramethyl-triostin A.

1 [Ala3, Ala7] TANDEM is an analogue of des-N-tetramethyl-triostin A (TANDEM) in which both L-Cys residues of the octapeptide ring are replaced by L-Ala; accordingly it lacks the disulphide cross-bridge which limits the conformational flexibility of TANDEM. 2 In [L-Ser1] TANDEM the configuration of one of the serine residues is inverted, altering the disposition of one of the quinoxaline chromophores with respect to the peptide ring. 3 Both compounds interact weakly but detectably with natural DNAs as judged by spectral shifts and increases in the thermal denaturation ('melting') temperature Tm. They also raise the Tm of poly rA . poly rU. 4 Binding isotherms determined by solvent partition analysis with [Ala3, Ala7] TANDEM yield association constants of about 10(3) M-1 for its interaction with natural DNAs. A Scatchard plot for binding to poly(dA-dT) determined by solvent partition and spectrophotometric methods shows marked evidence of cooperativity with an intrinsic association constant 1.9 x 10(4) M-1, 8.7 nucleotides per binding site, and cooperativity parameter 15. 5 Binding of [Ala3, Ala7] TANDEM to short rod-like fragments of poly(dA-dT) increases their contour length by almost the theoretical amount expected for an ideal process of bifunctional intercalation. 6 No effect of either compound on the winding of the DNA helix could be detected in sedimentation experiments with closed circular duplex PM2 DNA. 7 It is concluded that the cross-bridge of TANDEM greatly stabilizes its binding to DNA, most probably via entropic factors, but is not the only structural feature that influences its AT sequence-selectivity. The consequences of epimerising one of the D-Ser residues appear as disastrous as epimerising both. 8 The experimental details for the synthesis of [Ala3, Ala7] TANDEM and [L-Ser1] TANDEM are given in an appendix to this paper.

PHOTOCHEMICAL REACTIONS BETWEEN TRYPTOPHAN AND POLYNUCLEOTIDES*

Abstract— Anaerobic solutions of 14C labelled tryptophan and single‐stranded synthetic polyribonucleotide form adducts when irradiated with UV light at wavelengths longer than 270 nm. These adducts are stable to cold 10% trichloroacetic acid and are also more resistant to hydrolysis catalyzed by bovine ribonuclease A than non‐irradiated controls. All polyribonucleotides reacted with trp to some extent with reactivities in the order poly rU > poly rC = poly rA > poly rG.

EXCITED STATES OF DNA AND ITS COMPONENTS AT ROOM TEMPERATURE—IV. SPECTRAL, POLARIZATION AND QUANTUM YIELD STUDIES OF EMISSIONS FROM CpC AND POLY rC

Abstract— Corrected normalized emission spectra are reported for poly rC, CpC and CMP in neutral aqueous solution at room temperature. The emissions from CpC and poly rC show progressive and extensive depolarization across the emission band compared with CMP. Self‐consistent analysis of the polarization and spectral data allows the resolution of red‐shifted component emissions from the overall spectra and the evaluation of component polarizations. By comparison with experimental reference spectra three long wavelength components are identified in the poly rC emission and assigned as excimer fluorescence, monomer phosphorescence and excimer phosphorescence, whereas for CpC only two components are observed. The quantum yields are interpreted quantitatively in terms of the known stacking behavior of CpC and poly rC. with excimer emissions originating from the stacked fraction. Quantitative differences between CpC and poly rC are due to their different hypochromism and degree of stacking. Differences of polarization of excimer fluorescence are a consequence of different stacking geometries, and the directional properties of the transition moment suggest the excimer fluorescence is largely charge‐resonance in nature. The behavior of the CpC/poly rC system is compared with ApA/ poly rA.

EXCITED STATES OF DNA AND ITS COMPONENTS AT ROOM TEMPERATURE—III. SPECTRA, POLARISATION AND QUANTUM YIELDS OF EMISSIONS FROM ApA AND poly rA*

Abstract— Corrected normalised emission spectra from 300 to 480 nm and their polarisation are reported for neutral and poly rA at room temperature. Yields are 4 times (ApA) and 6 times (poly rA) greater than the monomer. Comparison of emission spectra and polarisation spectra demonstrates heterogeneity of emission and, following attempts at spectral synthesis, comparison with experimental reference spectra allows the observed total emission spectra to be resolved into four components assigned as I monomer‐like emission, II excimer fluorescence, HI monomer phosphorescence, IV excimer phosphorescence; the polarisation of the excimer fluorescences of ApA and poly rA are deduced. The observations can be understood quantitatively using a simple stacking model with excimer emissions originating in the stacked components. Quantitative differences between ApA and poly rA are due to their different hypochromism and extent of stacking. Differences of polarisation are attributed to different stacking geometries, and the directional properties of the transition moment suggest that the excimer fluorescence is largely charge‐resonance in nature.

Time dependence of triplet-singlet excitation transfer from compact poly rA to bound dye at 77 K

The nonexponential phosphorescence decay of a highly folded form of poly-riboadenylic acid (poly rA) with noncovalently bound dye is explained by a novel application of a well-known theory of electronic excitation transfer based on the Förster mechanism. This theory, originally used to describe singlet-singlet energy transfer from donor molecules to an acceptor in a solution, is here applied to the transfer of triplet excitation from the adenine (in poly rA) to the singlet manifold of either of the bound dyes, ethidium bromide or proflavine. New experimental data are presented that allow straight-forward theoretical interpretation. These data fit the form predicted by the theory, U(t) exp(-Bt1/2), where U(t) is the decay of the poly rA phosphorescence in the absence of dye, for a range of relative concentrations of either dye. The self-consistency of these theoretical fits is demonstrated by the proportionality of B to the square root of the Förster triplet-singlet overlap integrals for transfer from poly rA to each of the dyes, as demanded by the theory. From these self-consistent values of B, the theory enables one to deduce the mean packing density of nucleotides in this folded poly rA, which we estimate to be approximately 1 nm-3. We conclude that some variations of the method described here may be useful for deducing packing densities of nucleotides in other compact nucleic acid structures.

The mode of inhibitory action by pyridoxal 5-phosphate on DNA polymerase-alpha and -beta.

The kinetics of the inhibition of DNA polymerases-alpha and -beta from sea urchin embryos by pyridoxal 5-phosphate were studied. The inhibition of DNA polymerase-alpha activity by pyridoxal 5-phosphate was competitive with activated DNA but noncompetitive with each deoxynucleoside triphosphate. With poly(dC)-oligo(dG)12-18 as a template-primer, however, the inhibition of DNA polymerase-alpha was competitive with dGTP but noncompetitive with the template-primer. These results suggest that DNA polymerase-alpha interacts with activated DNA and poly(dC)-oligo(dG)12-18 in different ways. The inhibition of DNA polymerase-beta by pyridoxal 5-phosphate was competitive with deoxynucleoside triphosphate using activated DNA as a template-primer and noncompetitive with activated DNA. Using poly(rA)-oligo(dT)12-18 as a template-primer, DNA polymerase-beta activity yielded sigmoid curves against both dTTP and the template-primer concentrations and was inhibited by pyridoxal 5-phosphate noncompetitively with respect to both dTTP and the template-primer. These results indicate that the inhibitory mode of DNA polymerase-alpha by pyridoxal 5-phosphate is different from that of DNA polymerase-beta.

Electrophoretic fractionation and translation in vitro of poly(rA)-containing RNA from maize endosperm. Evidence of two mRNAs coding for zein protein.

In the search for individual mRNAs coding for particular zein proteins, polysomal RNA was isolated from the endosperm of 22-days post-pollination maize kernels. This RNA was enriched for poly(rA)-containing RNAs and then submitted to preparative polyacrylamide gel electrophoresis under denaturing conditions. After electrophoresis, RNA fractions were eluted from the polyacrylamide gel and analyzed for zein mRNA activity by translation in vitro in the wheat germ system. The wheat germ system had previously been optimized for accurate translation of zein mRNAs. By a gel-electrophoretic analysis of immunoprecipitated products from the translation reactions in vitro, it could conclusively be shown that the endosperm of developing maize kernels contains two separable mRNAs for zein, one coding for the 22000-Mr protein and one coding for the 19000-Mr protein.

A low molecular weight DNA polymerase beta in the sea urchin Strongylocentrotus purpurantus. Partial purification, properties, and changes in development.

A low molecular weight DNA polymerase which sediments at 3.3 S on sucrose gradients has been purified from total cell homogenates of rapidly dividing embryos of the sea urchin Strongylocentrotus purpuratus. In the presence of 2 mM N-ethylmaleimide, it is the major polymerase activity in whole cell homogenates when assayed with an oligo(dT)10.poly(dA)200 template; a template which it uses about 200 times more efficiently than activated DNA. The requirement for N-ethylmaleimide exists only in crude cell fractions where it acts to inhibit a template digesting nuclease activity. The polymerase is highly stable if maintained in the presence of 20% glycerol, is completely dependent on added template, and shows no end addition activity. The physical and enzymatic properties of this enzyme clearly distinguish it from the DNA polymerase previously described by Loeb (Loeb, L. A. (1969) J. Biol. Chem. 244, 1672-1681) which sediments as a high moeluclar weight (5.6 to 6.6 S) enzyme and prefers the activated DNA template. In addition, these two DNA polymerase enzymes show distinctive chromatographic properties using DEAE-cellulose and phosphocellulose columns as well as their sensitivity to N-ethylmaleimide. The properties of the low molecular weight polymerase indicate close similarity to the beta-polymerase isolated from mammalian cells. These low molecular weight enzymes are both sensitive to phosphate salt and able to utilize the artificial ribohomopolymer template oligo(dT)10.poly(rA)200. A quantitative analysis of the low molecular weight DNA polymerase during early embryonic development indicates that the activity of this enzyme increases at least 2-fold immediately following fertilization and again during early blastula stage (hatching). Such quantitative changes in a beta enzyme activity are in contrast to findings with the alpha-polymerase which remains constant during early development.

PHOSPHORESCENCE QUENCHING OF POLY rA IN GLUCOSE‐SODIUM ACETATE SOLUTION AT 77 K*

Abstract. The phosphorescence of poly rA at 77 K in an aqueous medium containing glucose is half‐quenched by bound ethidium bromide at a fractional concentration, r1/2, of 0.005, and by bound proflavine at r1/2= 0.002: r1/2= 0.024 for Co2+ and r1/2= 0.039 for Mn2+. The decay of the dye‐quenched poly rA phosphorescence is markedly nonexponential and decays more rapidly with increasing dye concentration, while the decay of the metal‐ion quenched poly rA phosphorescence parallels that of the unquenched poly rA, independent of metal‐ion concentration. Förster overlap integrals and critical distances for transfer of both poly rA singlet and triplet excitation to dye singlet states are calculated, and used to explain a consistent interpretation of the experimental results in terms of one‐step direct excitation transfer from base to dye or metal ion in a highly folded polymer conformation.

Replication of poly dA and poly rA by a drosophila DNA polymerase.

The activity of a 7.3S-8.3S Drosophila DNA polymerase was characterized in detail using poly dA.p(dT)[unk] and poly rA.p(dT)[unk]. With poly dA.p(dT)[unk], Mg(2+) ion was the preferred divalent cation, and enzyme activity was inhibited by K(+) ion and by spermidine. With poly rA.p(dT)[unk], Mn(2+) ion was the preferred divalent cation and enzyme activity was stimulated by K(+) ion and by spermidine. The dependence of enzyme activity on the concentration of primer-template and on the ratio of primer to template was the same in both reactions. The two enzyme activities were identically inhibited by N-ethylmaleimide. Poly dA was replicated extensively and poly rA was replicated partially. The activation energy for poly dA replication was twice that for poly rA replication. Enzyme activity with poly dA.p(dT)[unk] was more stable to thermal inactivation than was enzyme activity with poly rA.p(dT)[unk]. These studies suggest that the same enzyme responds to both the deoxy- and the ribohomopolymer template but that the mechanisms of replication may be different.

Effect of isonicotinic acid hydrazide-copper complex on Rous sarcoma virus and its genome RNA

The copper complex of the antituberculous drug, isonicotinic acid hydrazide (INH), inhibits the RNA-dependent DNA polymerase of Rous sarcoma virus and inactivates its ability to malignantly transform chick embryo cells. The INH-copper complex binds to the 70S genome RNA of Rous sarcoma virus (RSV), which may account for its ability to inhibit the RNA-dependent DNA polymerase. The complex binds RNA more effectively than DNA in contrast to M-IBT-copper complexes, which bind both types of nucleic acids equally. The homopolymers, poly rA and poly rU, are bound by the INH-copper complex to a greater extent than poly rC. Isonicotinic acid hydrazide alone and CuSO 4 alone bind neither DNA, RNA, poly (rA), poly (rU), nor poly (rC). However, CuSO 4 alone binds poly (rI); INH alone does not. In addition to viral DNA synthesis, chick-embryo cell DNA synthesis is inhibited by the INH-copper complex. The extent of inhibition of cellular DNA synthesis is greater than that of cellular RNA and protein synthesis. No selective inhibition of transformation in cells previously infected with Rous sarcoma virus is observed.

Studies on spin labeled ribonucleic acids encapsulated by viral proteins

Spin labeled poly rA (sl-poly rA) was encapsulated by the coat proteins of two plant viruses having different morphologies: TMV, a rigid rod and CCMV, an icosahedral sphere. Electron microscopy showed that the resultant particles were morphologically similar to the parent virus from which the coat protein was obtained. Encapsulation produced progressive immobilization of the spin label. The motion of the spin label attached to TMV-sl-poly rA appears anisotropic with a correlation time about the long axis of approximately 5 x 10(-6) sec. Exogenous nuclease had no effect on the epr spectrum of this nucleo-protein complex. The epr spectrum of CCMV-sl-poly rA was isotropic with a correlation time less than 5 x 10(-7). CCMV-sl-poly rA was partially degraded by T2 ribonuclease. Theoretical calculations of correlation times for the motion of the nucleo-protein particles were similar to the experimentally derived values suggesting that the nucleo-protein particles are tightly packed with little potential for internal motion.

DNA polymerase-beta from the nuclear fraction of sea urchin embryos: characterization of the purified enzyme.

Approximately 2,500-fold purifications of DNA polymerase-beta from the nuclear fraction of blastulae of the sea urchin, Hemicentrotus pulcherrimus, was performed. The enzyme preparation, which was devoid of DNase and terminal deoxynucleotidyl transferase as contaminants, showed a sedimentation constant of 3.0 S in a sucrose density gradient, a molecular weight of 50,000 by gel filtration, and an isoelectric point of pH 8.1. The enzyme activity was resistant to sulfhydryl group inhibitors. Its optimal pH was 9.0-9.5 in Tris-maleate buffer and 10.0 in glycine buffer. The optimal NaCl concentration for the activity was 30-60 mM and about half of the activity remained at 0.4 M NaCl. As a template-primer, the enzyme preferred synthetic homopolymers to activated DNA. The order of this preference was as follows; poly (dA)-oligo (dT)12-18 greater than poly (rA)-oligo (dT)12-18 greater than activated DNA. The above results indicate that the enzyme corresponds to DNA polymerase-beta from vertebrate cells.

Lymphocytes Binding Polyriboadenylic Acid and Synthesizing Antibodies to Nucleic Acids in Autoimmune and Normal Mice

Splenic lymphocytes from both normal and autoimmune mice bind significant quantities of polyriboadenylic acid (poly rA) when incubated with radiolabeled poly rA for 40 min at 37 degrees C. This poly rA binding is specifically inhibited by an excess of nonradioactive poly rA and by anti-mouse immunoglobulin. Poly rA binding is decreased by exposing spleen cells to Pronase and is restored by subsequent culture for 18 to 72 hr. Poly rA-binding activity is associated more with bone marrow-derived than with thymus-derived lymphocytes. These results suggest the presence of autoantigen-binding lymphocytes in normal as well as autoimmune mice. Furthermore, spleen cells from normal and autoimmune mice cultured for 72 hr synthesize and secrete antibodies to poly rA and DNA. These antibodies can be recovered from the culture supernatants by a solid immunoadsorbent technique and antibody immunoprecipitation. The synthesis of antibodies to nucleic acids by normal spleen cells suggests that autoreactive lymphocytes may be released from normal immunoregulatory control during in vitro culture conditions.

THE INHIBITION OF RAUSCHER LEUKEMIA VIRUS AND AVIAN MYELOBLASTOSIS VIRUS DNA POLYMERASES BY ANTHRACYCLINE COMPOUNDS

Studies by other investigators have shown that adriamycin and daunorubicin exhibit antitumor and antiviral activity. A possible antiviral mechanism for the anthracycline compounds is the potent inhibition of viral DNA polymerases. Five anthracycline compounds were tested against purified Rauscher leukemia virus and avian myeloblastosis virus DNA polymerases. All compounds were found to be potent inhibitors of viral DNA polymerase activity. Inhibition was found to be primarily due to the planar ring structure (daunomycinone) common to all of these compounds. The degree of inhibition was dependent on the templates used: activated DNA, synthetic hybrids, poly(rA).dT12-18 and poly(rC).dG12-18, and the synthetic copolymer, poly(DA-dT). Alteration of the group substituent on the planar ring affected the degree of viral DNA polymerase inhibition. The inhibitory effects by anthracycline compounds appear to be relatively specific for viral polymerases.

A particulate DNA polymerase activity in adult rat brain

A particulate fraction of adult rat brain (sucrose buoyant density 1.24 gm/ml) catalyzed the incorporation of [ 3H]dTTP into an acid-insoluble product in an endogenously templated reaction sensitive to ribonuclease pretreatment. Upon fractionation, this activity was identified in the cerebellum, pons, frontal lobes and base. The DNA polymerase present in these brain fractions exhibited a strong preference for the synthetic template dT 12–18·poly rA rather than dT 12–18·poly dA; dT 10 was completely inactive. Purification and equilibrium Cs 2SO 4 gradient centrifugation of the [ 3H]DNA product-endogenous template complex suggested that RNA was serving as primer for endogenous DNA synthesis.