Initiation and release of RNA by DNA-dependent RNA polymerase

Ribonucleic acid (RNA) biosynthesis in human cancer

In many respects, the most remarkable chemical substances within the genome of eukaryotic cells are remarkable proteins which are the critical structural and functional units of living cells. The specifications for everything that goes in the cell are natural digital-to-digital decoding process in an archive sequence by deoxyribonucleic acid (DNA) and an articulate construction by ribonucleic acid (RNA). The products of DNA transcription are long polymers of ribonucleotides rather than deoxyribonucleotides and are termed ribonucleic acids. Certain deoxyribonucleotide sequences, or genes, give rise to transfer RNA (tRNA) and other ribosomal RNA (rRNA) when transcribed. The ribonucleotide sequences fold extensively and rRNA is associated with specific proteins to yield the essential cell components, ribosomes. Transcription of other special sequences yields messenger RNAs (mRNAs) that contain ribonucleotide sequences that will be ultimately translated into new types of amino acid sequences of functional cellular protein molecules. This switch to a different variety of cellular molecular sequences is complex, but each sequence of the three ribonucleotides specifies the insertion of one particular amino acid into the polypeptide chain under production. Whilst mRNA is considered the vehicle by which genetic information is transmitted from the genome and allocated in the appropriate cytoplasmic sites for translation into protein via cap-dependent mechanism, the actual translation depends also on the presence of other so-called household and luxury protein molecules. Recent evidence suggests RNA species are required at initiation, because treatment of cells with antibiotics or drugs that inhibit RNA synthesis cause a decrease in protein synthesis. The rRNA is necessary as a structural constituent of the ribosomes upon which translation takes place, whereas tRNA is necessary as an adaptor in amino acid activation and elongation protein chains to ribosomes. In this article, we review malignant tumor, with stem like properties, and recent technical advances into the phenomenon of micro-particles and micro-vesicles containing cell-free nucleic acids that circulate plasma. New areas of research have been opened into screening tumor telomerase progression, prognosis of aptamers targeting cell surface, monitoring the efficacy of anticancer therapies, oncogenic transformation of host cell, and RNA polymerases role in the cell cycle progression and differentiation.

Short RNA chains synthesized at low pH are initiated at promoter sites

Under non optimal conditions- either with limiting substrate concentrations (1) or at low pH (2)- RNA polymerase of Escherichia coli synthesizes very short RNA chains. By sequencing one RNA species synthesized at pH 5.8 upon T7 DNA we were able to demonstrate that under these conditions transcription is initiated at a normal promoter site (here A1) but however is terminated soon afterwards at specific artificial sites not used in vivo.

End group of naturally terminated and UV lesion terminated T7 in vitro RNA

The 3' terminal nucleosides of RNA transcribed in vitro by E. coli RNA polymerase from T7 DNA and UV irradiated TN DNA were determined. The 3' terminal nucleoside of naturally terminated (t1 termination site) RNA cytidine. In the case of RNA terminated at UV lesions, it is cytidine in 0 per cent of the molecules and adenosine in the remaining 30 per cent. Cytidine trialcohols are labile in high concentrations of KOH and at high temperature and appear to convert to uridine.

Activation of chromatin by acetylation of histone side chains

The ability of calf thymus chromatin to support DNA-dependent RNA synthesis is markedly increased by modification of the histones with acetic anhydride. The extent of chemical acetylation of histones H2a, H2b, H3, and H4 required for the increase of template activity of the chromatin is within that which can be achieved enzymatically in the cell. The evidence suggests that the acetylation of histone side chains stimulates the rate of chain elongation during transcription of chromatin.

The effect of polyamines on the synthesis of ribonucleic acid by Drosophila melanogaster larvae

1. To elucidate further the possible role of polyamines in the synthesis of nuclei acids, a study of the effect of exogenously administered amines on the synthesis of RNA by Drosophila melanogaster larvae was undertaken. This system was chosen because of the previous investigations [Dion, A.S. & Herbst, E.J. (1967) Proc. Natl. Acad. Sci. U.S.A. 58, 2367-2371; Herbst, E.J. & Dion, A.S. (1970) Fed. Proc. Fed. Am. Soc. Exp. Biol. 29, 1563-1567] relating putrescine and spermidine to growth and development of Drosophila.

The effect of modification of T7 DNA by the carcinogen N-1-acetylaminofluorene: termination of transcription in vitro

To study the effects of N-2-acetylaminofluorene (AAF) modification of DNA on transcription, purified DNA from bacteriophage T7 was modified in vitro to varying extent with AAF and transcribed by DNA-dependent RNA polymerase from Escherichia coli. The main effects of AAF modification on transcription are a marked inhibition of the rate and extent of trna synthesis with relatively little effect on initiation except at very high AAF doses. Calibration of the percent modification with [14-C]AAF and analysis of the size of the RNA product by double isotope labeling and polyacrylamide gel electrophoresis support the following mechanism of transcription inhibition: most of the AAF residues bound to the coding strand of the DNA cause premature termination of transcription, at or near the site of modification, with release of RNA polymerase. This results in the production of shorter RNA chains with increasing amounts of bound carcinogen. The data are consistent with there being no reinitiation and/or synthesis of RNA distal to the AAF-modification site.

Transfer RNA synthesis in vitro

During infection of Escherichia coli, bacteriophage T4 directs the synthesis of at least eight transfer RNAs and of two stable RNA species of low molecular weight, of unknown function. When T4 DNA is incubated with purified RNA polymerase and the appropriate substrates, a high molecular weight RNA is produced. This RNA, on further incubation with a supernatant fraction prepared from E. coli, is cleaved to several species of RNA. These cleaved RNAs were analyzed by gel electrophoresis and fingerprint techniques, and were found to be similar or identical to those made in vivo. The fingerprint analysis of one of these, a tRNA(Gly), is presented. The molecule made in vitro, except for the absence of modified bases, appears to be identical to the RNA made by T4-infected cells. Therefore, in this system the tRNA genes are transcribed with fidelity, the transcript is cleaved correctly, and the tRNAs are made in good yield.

Initiation of Bacillus subtilis ribonucleic acid polymerase on deoxyribonucleic acid from bacteriophages 2C, phi 29, T4, and lambda

Ribonucleic acid (RNA) synthesis primed by bacteriophage T4 or lambda deoxyribonucleic acid (DNA) with Bacillus subtilis RNA polymerase is severely inhibited by high ionic strength. In contrast, RNA synthesis on B. subtilis bacteriophage 2C, SPO1, or phi29 DNA is only moderately affected under similar conditions. The basis of this inhibition lies in the inability of the enzyme to initiate RNA chains with adenosine triphosphate or guanosine triphosphate (ATP, GTP). Binding to templates and the rate of catalysis in high salt after initiation do not seem to be affected. Incorporation of gamma-(32)P-ATP and GTP under a variety of conditions suggests that the specificity of B. subtilis RNA polymerase is different from that of the Escherichia coli enzyme and that it recognizes few promoters on T4 and lambda DNA. Although B. subtilis RNA polymerase initiates RNA chains primarily with ATP or GTP, initiations with pyrimidines can occur on DNA molecules in which hydroxymethyluracil replaces thymine. RNA synthesis on denatured DNA does not seem to be inhibited by high ionic strength, and on native T4 or lambda DNA the inhibition of initiation at constant ionic strength is inversely but not linearly proportional to the ionic radii of cations used to stabilize bihelical DNA to denaturation.