Deionization of formamide with Biorad AG501-X(D)

Near-continuously synthesized leading strands in Escherichia coli are broken by ribonucleotide excision

In vitro, purified replisomes drive model replication forks to synthesize continuous leading strands, even without ligase, supporting the semidiscontinuous model of DNA replication. However, nascent replication intermediates isolated from ligase-deficient Escherichia coli comprise only short (on average 1.2-kb) Okazaki fragments. It was long suspected that cells replicate their chromosomal DNA by the semidiscontinuous mode observed in vitro but that, in vivo, the nascent leading strand was artifactually fragmented postsynthesis by excision repair. Here, using high-resolution separation of pulse-labeled replication intermediates coupled with strand-specific hybridization, we show that excision-proficient E. coli generates leading-strand intermediates >10-fold longer than lagging-strand Okazaki fragments. Inactivation of DNA-repair activities, including ribonucleotide excision, further increased nascent leading-strand size to ∼80 kb, while lagging-strand Okazaki fragments remained unaffected. We conclude that in vivo, repriming occurs ∼70× less frequently on the leading versus lagging strands, and that DNA replication in E. coli is effectively semidiscontinuous.

S1 nuclease analysis of alternatively spliced mRNA

The characterization of alternatively spliced RNA is a frequently performed task in the molecular biology laboratory. Several methods have been established to characterize specific transcripts, of which microarrays, northern analysis, RT-PCR and nuclease protection assays are the most frequently performed methods in the laboratory. Here, we describe the analysis of alternatively spliced RNA by using 5(')-end labelled DNA oligonucleotide probes and S1 nuclease. The method is sensitive, allowing detection of as little as a few hundred femtograms of a specific RNA, and useful for the quantitation of alternatively spliced mRNA isoforms. Because of its insensitivity towards RNA secondary structures and partially degraded RNA, it may perform better in the quantitation of RNA than northern analysis or RT-PCR, especially when long transcripts are studied.

Expression of hepatitis B virus surface antigen containing the pre-S region in mammalian cell culture system

The surface antigen of hepatitis B virus (HBV) has been expressed in a mouse cell line using metallothionein-bovine papilloma virus vectors. Four different recombinant plasmids were used and it was found that the expression level varies significantly from one plasmid to another. Removing the HBV polyadenylation signal from the plasmid drastically reduced the expression level. Providing even a heterologous polyadenylation signal improved the expression level from the reduced one by at least tenfold. The steady-state level of cytoplasmic HBV-specific RNA was much higher when the polyadenylation signal was present. One of the constructs gave a very high expression level and has been characterized further. It was possible to detect any plasmid in the episomal form in the producing clones and all the HBV DNA was found to be integrated in the mouse chromosome at more than one site. The copy number of the plasmid varied greatly between different clones and in the best one it is approximately 150 copies per haploid genome. Cells can be grown continuously in the presence of cadmium chloride without splitting for more than two months and the excreted surface antigen can be harvested during this period. Western blot analysis showed that the antigen contains the pre-S region.