Characteristics of the nascent and non-nascent small DNA molecules found in Escherichia coli

Triplet repeats, over-expanded in neuromuscular diseases, are under-represented in mammalian DNA: a survey of models

Simple tandem repeats represent more than 1% of the human genome: occasionally they exhibit intergenerational expansibility and are associated with neuromuscular diseases. In transgenic mice the same sequences elicit similar symptoms, but do not expand. We have searched for di-, tri-, and tetra-repeats in the published DNA sequences of chromosomes 21 and 22 of Homo sapiens, as well as in more than five megabases of Mus musculus DNA. Human and murine DNA sequences show a shortage in frequency and base coverage of tri-repeats as compared to di- and tetra-repeats. In murine sequences the cumulative frequency of di-, tri-, and tetra-repeats and their overall base coverage are about threefold higher than in human. Models for both the shortage of tri-repeats found in man and mouse and for their dynamic expansions are discussed. We propose that some of the 10 possible tri-repeats may be more prone than others to assume unusual structures capable of interfering with DNA synthesis: hence the shortage of tri-repeats. If such repeats are located at the 3'end of a chain growing and thus approaching another chain annealed to the same template, as Okazaki fragments do during discontinuous and encumbered replication, a combination of strand displacement, template switch, and branch migration may produce structures resistant to removal, hence the expansion of tri-repeats.

DNA synthesis in vivo and in vitro in Escherichia coli irradiated with ultraviolet light

DNA synthesis was followed in vivo and in permeable Escherichia coli after ultraviolet light irradiation, irradiation and incubation in a growth medium containing chloramphenicol and in unirradiated cells. In vitro, replicative type DNA synthesis was partially restored after incubation of cells in medium containing chloramphenicol, but not in vivo. The DNA was pulse-labeled in permeable cells in the presence of deoxyribonucleoside triphosphates and ribonucleoside triphosphates. dCTP was replaced by 5-Hg-dCTP as a substrate for DNA synthesis. Hg-DNA was separated from cellular nucleic acids on thiol-agarose affinity columns. The 5' termini of newly synthesized DNA were analyzed after treatment with alkaline phosphatase and rephosphorylation with polynucleotide kinase and [gamma-32P]ATP. DNA synthesis in unirradiated permeable E. coli represents a replicative process dependent on ATP and inhibited by novobiocin. About 70% of the nascent DNA carried terminally labeled RNA moiety at its 5' end. In vitro DNA synthesis in irradiated cells was suppressed and hardly influenced by the presence of ATP or novobiocin. The 5'-RNA content of this cell population was less than 5%.

Origin and degradation of the RNA primers at the 5' termini of nascent DNA chains in Bacillus subtilis

We had earlier characterized the nascent DNA synthesized in permeable cells of Bacillus subtilis in the presence of 5-mercurideoxycytidine triphosphate and 2',3'-dideoxyATP as being substituted at its 5' end with a ribonucleotide moiety of the sequence pApG(pC)1-2 DNA. In this paper, we examine the origin and turnover of the DNA-linked ribonucleotide and its relationship to DNA replication. At least 50% of the RNA-linked nascent DNA chains served as guanylate acceptors when incubated with GTP and the eukaryotic capping enzyme, indicating the presence of 5'-terminal di- or triphosphate groups and suggesting that the RNA moiety is synthesized de novo and is not a degradation product. In nascent DNA produced without limitation of chain growth by dideoxyATP, the degree of terminal ribonucleotide substitution was reduced by 50%, consistent with a linkage between RNA primer removal and DNA chain growth. Such a relationship was demonstrated directly by examining the RNA primer content of nascent DNA synthesized in the absence of dideoxyATP as a function of DNA chain length. As the DNA size increased from 40 to 200 nucleotide residues, the extent of RNA substitution declined from 80% to nearly 0%. Endgroup analysis showed that the loss of RNA was accompanied by a gradual shift from predominantly adenylate residues to 5'-terminal guanylate, consistent with a stepwise removal of ribonucleotides from the 5' end. Evidence that the nascent mercurated DNA synthesized under our experimental conditions was indeed a replicative intermediate came from the study of the time course of DNA chain growth and pulse-chase experiments. In the presence of the DNA ligase inhibitor NMN, mercurated DNA accumulated in two size classes with average length of approximately 750 and 8000 nucleotide residues, presumably representing the mature size of intermediates in discontinuous DNA synthesis. Comparison with the DNA size range at which the loss of the 5'-terminal RNA moiety occurred (40 to 200 residues) indicated that the processing of RNA primers occurred at an early stage during DNA chain elongation, and that moderate size intermediates in discontinuous DNA replication (greater than 200 nucleotides) have already lost their RNA primers.

Analysis of 5'-ends of short DNA fragments excreted by phytohemagglutinin stimulated lymphocytes

Human peripheral blood lymphocytes were stimulated with phytohemagglutinin and the excreted DNA was isolated from the medium after four days of incubation of cells. The excreted DNA was labeled at the 5'-end with [gamma-32P]ATP and polynucleotide kinase. Analysis of the end-labeled material revealed a size distribution with a chain length of 6 - 60 nucleotides. These short DNA fragments did not contain ribo-nucleotides at their 5'-termini. P1 nuclease digestion did not release specific deoxyribonucleoside monophosphates from the 5'-end of the excreted DNA fragments. These results point to the non-specific degradation of DNA excreted by stimulated lymphocytes.