Degradation Of Polynucleotides Research Articles

Polymer monoliths as efficient solid phases for enzymatic polynucleotide degradation followed by fast HPLC analysis

Two ribonuclease A bioreactors based on lab-made macroporous monolithic columns and intended for polynucleotide degradation were prepared using in situ free-radical polymerization. Different methods of enzyme immobilization were applied. In the first case, the biocatalyst molecule was attached to the solid surface via direct covalent binding, while in the second bioreactor the flexible-chain synthetic polymer was used as an intermediate spacer. The effect of temperature, substrate flow rate, and loaded sample volume on the biocatalytic efficiency of the immobilized enzyme was examined. The kinetic parameters of the enzymatic degradation of synthetic polycytidylic acid were calculated and compared to those found for hydrolysis with soluble ribonuclease A. The monitoring of substrate splitting was carried out by means of fast anion-exchange HPLC on an ultra-short monolithic column (disk) using off- and on-line analytical approaches.

Stability of ribonuclease A under hydrothermal conditions in relation to the origin-of-life hypothesis: verification with the hydrothermal micro-flow reactor system

The stability of ribonuclease A (RNase A) was quantitatively investigated with the hydrothermal micro-flow reactor system (HFRS) at temperatures of up to 275 °C from the viewpoint of the hydrothermal origin-of-life hypothesis. The enzymatic activity of RNase A was studied with regard to the catalytic degradation of polynucleotides with anion-exchange high-performance liquid chromatography, while the degradation of RNase A to shorter molecules was analyzed by size exclusion chromatography (SEC) and mass spectrometry (MS). The degradation of RNase A started within 10 s at 200 °C, and the enzymatic activity disappeared almost completely after 25 s. SEC and MS analyses indicated that RNase A was thermally degraded to 2 large fragments, which, along with RNase A, were further decomposed to smaller fragments. This study showed that RNase A is fairly stable under normal conditions, but its enzymatic activity disappears rapidly at extremely high temperatures. The half life of RNase A and its fragments under hydrothermal conditions is comparable to or longer than the enzymatic reaction time scale of modern enzymes. Furthermore, this study demonstrates that HFRS is reliable and useful for verifying the stability of several proteins in fundamental and applied research as well as for studying the origin-of-life problem.

Polynucleotide degradation during early stage response to oxidative stress is specific to mitochondria

Oxidative stress is known to modulate RNA expression in both prokaryotic and eukaryotic cells. We have previously determined that a preferential and calcium-dependent downregulation of mitochondrial RNA occurs in HA-1 hamster fibroblasts in response to hydrogen peroxide, and that this is accompanied by the degradation of mitochondrial genomic DNA. Here we extended these studies to determine whether downregulation is specific to transcripts derived from mitochondrial-encoded genes; to determine whether genomic DNA degradation occurs in the nucleus; and to compare overall polynucleotide stress response with cellular growth arrest and apoptosis. We observed that nuclear genome-encoded mRNAs whose protein products are targeted for the electron transport chain of mitochondria were not degraded. Furthermore, early stage degradation of genomic DNA, assessed within the first 5 h of peroxide exposure, was specific to mitochondria, as nuclear genomic DNA was not degraded under the same treatment conditions. These differential degradations occurred under conditions where extensive growth-arrest and moderate apoptosis were observed, and were accompanied by significant induction of the growth arrest mRNAs gadd45, gadd153, and adapt15/gadd7. Combined, these results indicate that there is a general degradation of mitochondrial- but not nuclear-polynucleotides during early stage response of HA-1 fibroblasts to oxidative stress.

Oxidative stress causes a general, calcium-dependent degradation of mitochondrial polynucleotides

Oxidative stress has many effects on biological cells, including the modulation of gene expression. Reactive oxygen species are known to up-regulate and down-regulate RNA expression in prokaryotic and eukaryotic cells. We have previously reported that a preferential and calcium-dependent down-regulation of mitochondrial RNAs occurs when HA-1 hamster fibroblasts are exposed to hydrogen peroxide. Here we extend these studies to determine whether this down-regulation is specific to mitochondria RNA or involves general polynucleotide degradation. Degradation and associated decreases in the levels of 16S mitochondrial rRNA following exposure of cells to 400 μM hydrogen peroxide were found to be dependent on calcium at 2 and 5 h. Degradation of mitochondrial genomic DNA was also observed following peroxide exposure, and occurred at similar time points as for mitochondrial RNA degradation. As with mitochondrial RNA degradation, this mitochondrial genomic DNA degradation was dependent on calcium. These results indicate that there is a general, calcium-dependent degradation of mitochondrial polynucleotides following exposure of HA-1 fibroblasts to oxidative stress, and suggest that a dramatic shut-down in mitochondrial biosynthesis is an early-stage response to oxidative stress.

Apoptosis.

Apoptosis is a process of cell suicide, the mechanisms of which are encoded in the genomes of all higher eukaryotes. The mechanisms involved in apoptosis suggest that the process is based on a viral defense originally developed in primitive multicelled eukaryotes and that the fundamental execution platform of the process involves 1) inhibition of protein synthesis at the level of translation initiation, 2) proteolysis specifically involving degradation of DNA repair mechanisms, and 3) polynucleotide degradation. In mammals this execution platform is regulated by a complex molecular signaling system that includes feedback mechanisms tending toward activation of all elements of the execution platform if only one element is initially engaged. Tissue ischemia and reperfusion activate elements of the apoptosis system, which thus represents a therapeutic target for emerging treatment approaches to preserve cellular integrity in critical organs such as the heart and brain.

A new cationic liposome encapsulating genetic material. A potential delivery system for polynucleotides.

The endeavour to enhance gene therapy has led to increased research on the development of simple, efficient and safe delivery systems. This study deals with the use of an artificial cationic lipid on the encapsulation of genetic material in liposomes. The addition of a biologically degradable cationic phospholipid, dipalmitoyl-L-alpha-phosphatidylethanolamine covalently coupled to L-lysine, in a standard liposome formulation allowed us to obtain vesicles with high entrapment of various polynucleotides. Polynucleotide degradation by nucleases is markedly prevented by these liposomes. The preparations were stable in both culture medium and human plasma. This latter finding is consistent with the weak binding of plasma proteins on the liposome surface. The efficiency of this new delivery system was demonstrated in antiviral assays. Finally, these liposomes displayed a relatively low cellular toxicity. All these findings indicate that these cationic vesicles are very suitable for genetic material vehiculation.

Purification and characterization of the 180- and 86-kilodalton subunits of the Saccharomyces cerevisiae DNA primase-DNA polymerase protein complex. The 180-kilodalton subunit has both DNA polymerase and 3‘—-5‘-exonuclease activities.

The yeast Saccharomyces cerevisiae catalytic DNA polymerase I 180-kDa subunit and the tightly associated 86-kDa polypeptide have been purified using immunoaffinity chromatography, permitting further characterization of the DNA polymerase activity of the DNA primase-DNA polymerase protein complex. The subunits were purified to apparent homogeneity from separate overproducing yeast strains using monoclonal antibodies specifically recognizing each subunit. When the individual subunits were recombined in vitro a p86p180 physical complex formed spontaneously, as judged by immunoprecipitation of 180-kDa polypeptide and DNA polymerase activity with the anti-86-kDa monoclonal antibody. The 86-kDa subunit stabilized the DNA polymerase activity of the 180-kDa catalytic subunit at 30 degrees C, the physiological temperature. The apparent DNA polymerase processivity of 50-60 nucleotides on poly(dA).oligo(dT)12 or poly(dT).oligo(A)8-12 template-primer was not affected by the presence of the 86-kDa subunit but was reduced by increased Mg2+ concentration. The Km of the catalytic 180-kDa subunit for dATP or DNA primer terminus was unaffected by the presence of the 86-kDa subunit. The isolated 180-kDa polypeptide was sufficient to catalyze all the DNA synthesis that had been observed previously in the DNA primase-DNA polymerase protein complex. The 180-kDa subunit possessed a 3'----5'-exonuclease activity that catalyzed degradation of polynucleotides, but degradation of oligonucleotide substrates of chain lengths up to 50 was not detected. This exonuclease activity was unaffected by the presence of the 86-kDa subunit. Despite the striking physical similarity of the DNA primase-DNA polymerase protein complex in all eukaryotes examined, the data presented here indicate differences in the enzymatic properties detected in preparations of the DNA polymerase subunits isolated from S. cerevisiae as compared with the properties of preparations from Drosophila cells. In particular, the 3'----5'-exonuclease activity associated with the yeast catalytic DNA polymerase subunit was not masked by the 86-kDa subunit.

Thermodynamic analysis of transfer RNA unfolding

The results of calorimetric studies of specific transfer RNAs (tRNA Val, tRNA Phe, tRNA t Met, tRNA Ile, tRNA Ser, tRNA Asp) are summarized and analyzed thermodynamically. It is shown that the overall melting enthalpies are larger and do not depend significantly on temperature and ionic conditions, as was previously thought. In all cases the melting curves are very complicated and cannot be approximated by a function for the two-state transition. The apparent reason for the discrepancy is the large breadth of transition over the temperature scale in magnesium-free solutions, which complicates the determination of the heat effect. The presence of magnesium ions sharpens the transition, but also induces the degradation of polynucleotides at elevated temperatures, which is observed as a large increase in heat capacity. It is shown that the unfolding process can be represented as a sequence of independent two-state transitions. The steps of unfolding were identified by using the known experimental facts and by comparing the experimentally obtained thermodyriamic characteristics of the steps with the calculated values for the different parts of the structure. According to the received ascription, the first two steps of unfolding correspond to disruption of tertiary structure and the dhU branch, i.e. the disruption of the tRNA core, after which it unfolds into a topologically flat structure with separate branches. This explains the experimentally observed independence of the steps involved in the unfolding and folding of the tRNA native structure. It is suggested that this property is important for the folding of various tRNA polynucleotide chains into a unified three-dimensional structure.

Kinetic studies on the phosphorolysis of polynucleotides by polynucleotide phosphorylase

The kinetics of the phosphorolysis of polynucleotide (as differentiated from oligonucleotide) by polynucleotide phosphorylase of Micrococcus luteus has been investigated. Double reciprocal plots of initial velocity against either inorganic phosphate or polynucleotide concentration are linear, and furthermore, the affinity of the enzyme for either substrate is unaffected by the presence of the other. dADP, an analogue of ADP product, is a competitive inhibitor with respect to Pi and polynucleotidy. (Ap)tA-cyclic-p is a competitive inhibitor with respect to Pi. The results are almost identical with both primer-independent (Form-I) and primer-dependent (Form-T) enzymes, although the various kinetic constants differ. On the vasis of these data a rapid equilibrium random Bi Bi mechanism is proposed. The demonstration of two different inhibitor constants for dADP and the difference between the Michaelis and the inhibitor constant for polyadenylic acid in polynucleotide phosphorolysis indicate at least two binding sites for polyadenylic acid and dADP on M. luteus polynucleotide phosphorylase. Its is suggested that in the phosphorolysis of long chain polymers the second binding site permits the polynucleotide to snap right back into position after removal of I mononucleotide unit and thus leads to the observed processive degradation. A general discussion of oligonucleotide and polynucleotide phosphorolysis and the differences between Form-I and Form-T enzymes in de novo synthesis and degradation of polynucleotides is presented.

Hydrogen Fluoride as an Agent in Organic Reactions. I. Degradation of Polynucleotides with Liquid Hydrogen Fluoride

Hydrogen Fluoride as an Agent in Organic Reactions. I. Degradation of Polynucleotides with Liquid Hydrogen Fluoride

Interaction of metal ions with polynucleotides and related compounds. X. Studies on the reaction of silver (I) with the nucleosides and polynucleotides, and the effect of silver(I) on the zinc(II) degradation of polynucleotides.

AbstractPotentiometric titration curves of the silver(I) complexes of cytidine, adenosine, and uridine show little uptake of base below pH 7, unlike the curve for silver(I)‐guanosine, which shows extensive base uptake at neutral pH. This observation is correlated with spectrophotometric data showing little difference between the silver complex spectra of adenosine, cytidine, and uridine and the spectra of uncomplexed nucleosides, except at high pH, but showing a great difference between the silver complex spectra of guanosine and inosine and the corresponding uncomplexed nucleosides even at pH 6. Similar comparisons of the silver complexes of poly A, poly C, poly I, and poly U, both by potentiometric titration and by spectrophotometry, show that poly I behaves like guanosine and inosine as expected, differing from poly A and poly C. However, poly U behaves like poly I and thus does not resemble uridine in its complexing behavior. There is thus a dichotomy between poly A and poly C on the one hand in silver complexing phenomena, compared with poly U and poly I on the other. When silver(I) is added to systems containing zinc(II) and various polynucleotides, the same dichotomy is noted. Silver(I) inhibits the degradation by zinc(II) of all four polynucleotides, but the degradation of poly I and poly U is prevented virtually completely. Silver(I) alone has no degradative effect on RNA and inhibits, the zinc(II) degradation of RNA. Polynucleotide complexes in which silver(I) and zinc(II) are simultaneously bound to different positions on the macromolecules are postulated as intermediates in the inhibited degradation reactions.

Molecular mechanisms of genetic recombination in bacteriophage: IV. Absence of polynucleotide interruption in DNA of T4 and λ phage particles, with special reference to heterozygosis

A method of band centrifugation in alkaline caesium chloride solution of DNA has been developed and the DNA of T4 and λ phage particles has been analysed. It was found that the structure of the majority of the chromosomes of mature phage T4, including heterozygous ones, and that of λ chromosomes, can be represented by a duplex DNA molecule without an interruption in the strands. In high-frequency transducing λdg DNA, the host gal region and the phage genome are associated by covalent bonds. Alkaline and also thermal degradation of polynucleotides of T4 DNA has been studied by the band centrifugation method.

Interactions of metal ions with polynucleotides and related compounds. IV. Degradation of polyribonucleotides by zinc and other divalent metal ions.

AbstractPolyadenylic acid is degraded into mononucleotides and low molecular weight oligonucleotides in a 20 hr. period at 64°C. by the action of Mn (II), Co (II), Ni (II), and Cu (II) ions, and in a 2 hr. period by Zn (II) ions. The latter also degrade poly C, poly U, and RNA at approximately the same rate, but poly I is degraded very much more slowly. No such difference in reaction rates can be observed in the alkaline degradation of polynucleotides. The sluggishness of the reaction with poly I is not due to any highly ordered structure of the zinc–poly I complex, but probably to the weakening of the zinc–phosphate bond through simultaneous binding of the zinc to the inosine base. Evidence for such a hypothesis is derived from the inhibition of the zinc degradation of poly A by inosinic acid or poly I. No drastic difference in the nucleotide composition of the undegraded residue can be observed in the degradation of RNA by zinc and by alkali.

212. Nucleotides. Part XLVII. The catalytic oxidation of nucleosides and nucleotides: a projected stepwise degradation of polynucleotides

212. Nucleotides. Part XLVII. The catalytic oxidation of nucleosides and nucleotides: a projected stepwise degradation of polynucleotides