Intermediates of chromosomal DNA replication 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.

Energy flow considerations and thermal fluctuational opening of DNA base pairs at a replicating fork: unwinding consistent with observed replication rates

The effect of an open loop of various sizes on the thermal stability of the adjoining intact base pairs in a duplex DNA chain is studied in a lattice model of Poly(dG).Poly(dC). We find that for a Y-shaped fork configuration the thermal fluctuation at the fork is so enhanced that the life time of the adjoining base pair is much smaller than the 1 millisecond time scale associated with helicase separation of a base pair in some systems. Our analysis indicates that thermal fluctuational base pair opening may be of importance in facilitating the enzyme unwinding process during chain elongation of a replicating DNA. It is most likely that the thermal fluctuational opening of the base pair at the junction of a replicating fork is fast enough so that a DNA unwinding enzyme can encounter an unstacked base pair with reasonable probability. This conclusion can explain several experimental observations regarding the temporal relationship between ATP hydrolysis by accessory proteins and primer elongation by a holoenzyme complex in ssDNA. We also discuss a mechanism by which the energy associated with ATP hydrolysis may enhance the thermal driven base opening mechanism.

Illegitimate recombination in an Escherichia coli plasmid: modulation by DNA damage and a new bacterial gene

We studied DNA rearrangements in Escherichia coli by using a plasmid-based system with a transcriptionally silent tet gene and selecting for Tetr isolates. The predominant activating event was a 1.3-kilobase-pair deletion in the plasmid between two sites, with 14 of 19 base pairs being identical. These deletions occurred equally frequently in a recA+ strain and a recA13 mutant. However, the frequency of Tetr occurrence was stimulated 50-fold by treatment of the cells with UV light in a process that was at least partly independent of the SOS response. Bacterial mutants deleted for the xth-pnc region of the chromosome exhibited a strongly elevated spontaneous frequency of Tetr isolates, all with the same 1.3-kilobase-pair deletion. This phenotype of high-frequency deletion could be complemented by an episome covering this region, but not by the cloned xth gene. These studies helped to define the role of different DNA damages in illegitimate recombination and identify a region of the E. coli chromosome that contains a gene whose product normally suppresses illegitimate deletions.