Denaturation maps of complete and defective simian virus 40 DNA molecules

Absence of a protein constituent and occurrence of an oversized DNA genome in a high density mutant particle of phage P22

Mutants of P22 phage with abnormal density in CsCl solution (P22ndc phage) were analyzed in detail for this report. Two dimensional polyacrylamide gel electrophoresis revealed that wild-type P22ndc+ phage virions contained a new protein (gpU) in addition to nine already identified proteins, while P22ndc lacked gpU. The molecular weight of gpU was essentially the same as that of gp5 (45,500), and one mature virion of phage P22ndc+ contained as many as 30-50 molecules of gpU. As P22ndc is a plaque-forming phage, gpU cannot be essential for the growth and assembly of P22 phage. Both genetical and biochemical analysis of the phage DNA in the virion revealed that P22ndc phage contained 2%-4% longer DNA than wild type P22ndc+. A model is presented to account for the formation of P22ndc phage.

DNA electron microscopy

In recent years DNA electron microscopy has become a tool of increasing interest in the fields of molecular genetics and molecular and cell biology. Together with the development of in vitro recombination and DNA cloning, new electron microscope techniques have been developed with the aim of studying the structural and functional organization of genetic material. The most important methods are based on nucleic acid hybridizations: DNA-DNA hybridization (heteroduplex, D-loop), RNA-DNA hybridization (R-loop), or combinations of both (R-hybrid). They allow both qualitative and quantitative analysis of gene organization, position and extension of homology regions, and characterization of transcription. The reproducibility and resolution of these methods make it possible to map a specific DNA region within 50 to 100 nucleotides. Therefore they have become a prerequisite for determining regions of interest for subsequent nucleotide sequencing. Special methods have been developed also for the analysis of protein-DNA interaction: e.g., direct visualization of specific protein-DNA complexes (enzymes, regulatory proteins), and analysis of structures with higher complexity (chromatin, transcription complexes).

Electron microscopic observation of new transposable elements inserted into P22 phage genome from R plasmids

By using phage P22spl, a deletion mutant of phage P22, the structures of two new transposons on P22 genomes were studied by the electron microscopic heteroduplex method. One of these was the Cm (chloramphenicol) transposon derived from an R plasmid, NR1, and the other the Km (kanamycin) transposon frin obr502. the heteroduplex between P22 phage DNAs with and without the Cm transposon revealed that the Cm transposon was similar in structure to the Tn9 element, a well-known Cm transposon derived from the R plasmid pMS14. On the other hand, the Km transposon of pNR502 was quite different in structure from other Km transposons reported previously. This transposon consists of a 6.8 kilobase (kb) segment of DNA, in which a short inverted repeat is contained. The heteroduplex experiments showed that a 4.5 kb segment of DNA was deleted from the P22 genome in the P22spl genome. Because of a shorter unit length of the genome, phage P22spl is considered to be useful of assaying various kinds of transposable elements.

Positioning of the A . T-rich regions in rat mitochondrial DNA by electron microscopy and analysis of the hysteresis of denaturation

Intramolecular heterogeneity in the base composition of rat mitochondrial DNA (mtDNA) was shown by a combination of an improved denaturation mapping technique using electron microscopy and analysis of high-resolution optical melting-renaturation profiles. Circular mtDNA starts to melt in one specific region and then forms loops in four other regions in random order. These five early melting regions are all located in one half of the molecule. The arrangement of the early melting regions in rat mtDNA bears a remarkable resemblance not only to those of mtDNAs from several species of Drosophila but also to those of several species of Drosophila but also to those of several plasmid DNAs and phage DNA.