Kinetics of DNA-dependent RNA synthesis: couple synthesis of di-, tri- and tetranucleotides in the presence of a limited set of substrates

The qualitative and quantitative characteristics of the short oligonucleotides synthesis by Escherichia coli RNA polymerase on A1 promoter of the bacteriophage T7 in the presence if incomplete set of nucleoside triphosphates were studied. The binding of the fourth substrate with enzyme-template complex was shown to occur after binding of the third substrate only. The curves of di-, tri- and tetranucleotide synthesis as the function of CTP and GTP concentration were constructed. The empiric formulas for the rates of the coupled synthesis if tri- and tetranucleotides were derived from these curves. A kinetic scheme describing the experimental data was proposed.     

RNA synthesis in the presence of transfer RNa by DNA-dependent RNA polymerase II from mouse ascites sarcoma cells

RNA polymerase II from mouse sarcoma cells catalyzed the incorporation of UMP into an acid-insoluble fraction in the presence of tRNA. This reaction was not affected by DNase or actinomycin D but was inhibited by α-amanitin. This reaction was dependent on nucleoside triphosphate and manganese ions. RNA synthesized in the presence of tRNA could be digested with RNase A. These results suggest that the RNA synthesis by RNA polymerase II from mouse sarcoma is dependent on the presence of tRNA.     

Kinetics of inhibition by 8-oxy-ATP of the dinucleotide pppApU synthesis catalyzed by Escherichia coli RNA-polymerase on the promoter A1 of phage T7 delta D111 DNA during coupled synthesis of di- and trinucleotides and a limited set of substrates

A kinetic analysis of inhibition of synthesis of dinucleotide pppApU catalyzed by Escherichia coli RNA-polymerase on A1 promoter of the DNA from T7 delta DIII phage mutant by 8-oxy-ATP under the conditions of the coupled synthesis of pppApU and pppApUpC and in the presence of an incomplete set of substrates, namely ATP, UTP, CTP, has been performed. It was found that 8-oxy-ATP is an unproductive analog of both ATP and CTP. A comparative analysis of the dissociation constants shows that 8-oxy-ATP binds at ATP center 3.3. times and at CTP center 540 times weaker than natural substrates. At the UTP center 8-oxy-ATP does not bind at all.     

Synthesis and characterization of fluorescent dinucleotide substrate for the DNA-dependent RNA polymerase from Escherichia coli

New fluorescent derivatives of dinucleoside monophosphates, (5'-AmNS)UpA/ApU/GpU/CpA, with a fluorophore, 1-aminonaphthalene-5-sulfonic acid (AmNS), attached to the first nucleotide of the dinucleoside monophosphates via a 5'-secondary amine linkage were synthesized in good yield. The chemical structure of (5'-AmNS)ApU was proved by the phosphodiesterase digestion followed by Whatman No. 3MM paper chromatographic and spectroscopic analysis of the digested products. The ability of these analogs to be incorporated into the 5' terminus of RNA chain forming fluorescent oligonucleotides by Escherichia coli RNA polymerase was studied in the presence of a synthetic DNA template. The enzymatic reaction of (5'-AmNS)UpA and [3H]UTP in the presence of poly(dA-dT) yielded (5'-AmNS)UpAp[3H]U in greater than 30% yield with the Km values of 5 and 2.5 microM and Vmax values of 17 and 25 nmol/min/mg of enzyme for (5'-AmNS)UpA and UpA, respectively. The structure of this fluorescent trinucleotide was identified by RNase A digestion and paper chromatographic analysis of the digested products. (5'-AmNS)UpA or (5'-AmNS)ApU exhibits two absorption maxima around 270 and 340-350 nm and a fluorescent emission maximum at 445 nm when excited at 340 nm. These spectral characteristics permit their use as energy donors for the transfer of energy to the intrinsic cobalt of the cobalt-substituted RNA polymerases. Upon hydrolysis of the phosphodiester bond of these analogs by venom phosphodiesterase, the absorption at 340 and 270 nm increased by 5 and 20%, respectively, while their fluorescence at 445 nm was enhanced by 25%. Thus, these analogs can be used for studying the dynamics of initiation and elongation reactions catalyzed by DNA-dependent RNA polymerases by absorption and fluorescence spectroscopies.     

Viral RNA synthesis and levels of DNA-dependent RNA polymerases during replication of adenovirus 2.

The rates of RNA synthesis in cultured human KB cells infected by adenovirus 2 were estimated by measuring the endogenous RNA polymerase activities in isolated nuclei. The fungal toxin alpha-amanitin was used to determine the relative and absolute levels of RNA polymerases I, II, and III in nuclei isolated during the course of infection. Whereas the level of endogenous RNA polymerase I activity in nuclei from infected cells remained constant relative to the level in nuclei from mock-infected cells, the endogenous RNA polymerase II and III activities each increased about 10-fold. These increases in endogenous RNA polymerase activities were accompanied by concomitant increases in the rates of synthesis in isolated nuclei of viral mRNA precursor, which was quantitated by electrophoretic analysis on polyacrylamide gels. The cellular RNA polymerase levels were measured with exogenous templates after solubilization and chromatographic resolution of the enzymes on DEAE-Sephadex, using procedures in which no losses of activity were apparent. In contrast to the endogenous RNA polymerase activities in isolated nuclei, the cellular levels of the solubilized class I, II, and III RNA polymerases remained constant throughout the course of the infection. Furthermore, no differences were detected in the chromatographic properties of the RNA polymerases obtained from infected or control mock-infected cells. These observations suggest that the increases in endogenous RNA polymerase activities in isolated nuclei are not due to variations in the cellular concentrations of the enzymes. Instead, it is likely that the increased endogenous enzyme activities result from either the large amounts of viral DNA template available as a consequence of viral replication of from replication or from functional modifications of the RNA polymerases or from a combination of these effects.     

Template specificities of Aclacinomycin B on the inhibition of DNA-dependent RNA synthesis in vitro

Summary The effect of Aclacinomycin B (ACM-B), an anthracycline antitumor antibiotic, on the DNA-dependent RNA synthesis using single- and double-stranded DNAs of known base content and sequence is studied. The data show that ACM-B effectively inhibits the double-stranded DNA-directed RNA synthesis with a preference of poly[d(A-T)] > poly[d(G-C)] > poly[d(I-C)]. In contrast, it has no inhibitory effect on the template function of single-stranded DNA (e.g. poly dA, poly dT, and poly dC). These results suggest that the mechanism of ACM-13 inhibition, like other anthracycline antibiotics, is by intercalation. In addition to the base specificity, there are also dramatic differences in inhibition depending on the base sequence in the DNA template. Thus, ACM-13 preferentially inhibits the alternating double-stranded copolymers over the double-stranded homopolymers; e.g. poly [d(A-T)] is inhibited to a greater extent than poly dA · poly dT and poly [d(G-C)] is inhibited more than poly dG · poly dC. Since the inhibition by ACM-13 can be totally abolished when assayed in excess amount of DNA, this result suggests that ACM-B inhibition of RNA synthesis is solely on the DNA template (which is in support of the intercalation model), and has ruled out the possibility that ACM-B may also exert an inhibitory effect on the activity of RNA polymerase per se.     

Ribohomopolymer formation as a source of error in the radioactive precursor incorporation studies of nuclear DNA-dependent RNA synthesis

Isolated rat liver nuclei contain ribohomopolymer polymerases with relative activities in the following order: Poly (A) (100%) > Poly (C) (62%) > Poly (U) (34%) > Poly (G) (13%). Because these enzymes share the same substrates with the nuclear DNA-dependent RNA polymerases in nuclei, labelled precursor is therefore concurrently incorporated into both RNA and ribohomopolymer. Thus, experiments designed to study DNA-dependent RNA synthesis are subjected to error. It is estimated when [¹⁴C]ATP is used as the labelled precursor, the error is as high as 35%; [¹⁴C]CTP, 20%; [¹⁴C]UTP or [¹⁴C]GTP, 10%.     

Kinetics of an autocatalytic zymogen reaction in the presence of an inhibitor coupled to a monitoring reaction

A global kinetic analysis of a model consisting of an autocatalytic zymogen-activation process, in which an irreversible inhibitor competes with the zymogen for the active site of the proteinase, and a monitoring coupled reaction, in which the enzyme acts upon one of its substrates, is presented. This analysis is based on the progress curves of any of the two products released in the monitoring reaction. The general solution is applied to an important particular case in which rapid equilibrium conditions prevail. Finally, we suggest a procedure to predict whether the inhibition or activation route dominates in the steady state of the system. These results generalize our previous analysis of simpler mechanisms.     

DNA-dependent RNA synthesis in nuclear chromatin of fixed cells: relationship between dye-binding properties, nuclear protein content and RNA polymerase activity

Fixed mouse kidney epithelial cells have been examined for their capacity to synthesize RNA with their own RNA polymerases when supplied with ribonucleoside triphosphates. The endogenous polymerase activity of chromatin in fixed cells is clearly related to changes in the size and protein content of the nucleus. Cells with small nuclei which do not incorporate ³H-uridine in vivo show very little RNA polymerase activity at the ionic strength of the standard assay procedure. This activity can be enhanced by increasing the ionic strength of the assay medium. Changes in RNA polymerase activity also appear to be related to changes in the ability of chromatin to bind acridine orange (AO).