In vitro and in vivo transcription from a computer predicted promoter.

A fragment (172 bp) of B. subtilis phage phi29 DNA, which does not contain a functional promoter for phage transcription, has been shown to direct transcription in the promoter-probe plasmid pPV33. The promoter candidate found in this fragment by the computer method of acceptability is compared with cryptic promoters selected by this computer method. It is characterized in vitro by electron microscopic visualization of RNA polymerase binding and 'run off' transcription, and in vivo by high resolution S1 mapping.

Avian myeloblastosis virus core-bound 7 S DNA, a collection of minute replicative host-cell DNA structures.

The early replicative nature of avian myeloblastosis virus core-bound 7 S DNA (AMV DNA), indicated by our preceding findings (Ríman et al., 1993), has been confirmed using various experimental approaches. It has been shown by agarose and polyacrylamide gel electrophoresis that this DNA represents actually a collection of molecules the size of which is strongly reminiscent of the minute early replicative structures found in DNA of sea urchin embryos (Baldari et al., 1978). With such a characteristic correspond, the sequence properties of the individual AMV DNA clones, the majority of which were found to be AT-rich with ARS-like motifs and stretches of A-residues carrying conformational requirements for bending. In comparative hybridization experiments, AMV DNA exhibited the highest homology with chicken leukaemic myeloblast scaffold-bound DNA. Compatible with high replicative activity of AMV DNA was also found its specific [methyl-3H]thymidine radioactivity. The constancy of the virus content of this DNA and its virus age-dependent cleavage changes taking place inside the virus core structure open the question of possible significance of this special host DNA for the reaction machinery represented by the retroviral nucleoprotein core complex.

A novel method for promoter search enhanced by function-specific subgrouping of promoters--developed and tested on E.coli system.

A new method for evaluating some complex characteristics of the primary structure of E.coli promoters is proposed. The method, of nonparametric statistical significance, selects important conserved single-base positions in combination with 2-base coupling relations of identity and complementarity. The extended consensus of promoter characteristics thus obtained was used to scan unknown sequences for similarity with E.coli promoters. In terms of this method, a complete set of 244 E.coli promoters was shown to be structurally inconsistent. The set was then broken down into functionally homogeneous subsets of promoters to enhance the selectivity of the search for E.coli-specific promoter sequences, with a high significance level being attained.

Consensus symmetry pattern in E. coli promoter sequences.

A computer method was used to select two subgroups in 172 Escherichia coli promoter nucleotide sequences characterized by "standard" 17 bp and "non-standard" 17 +/- 2 bp spacing between the Pribnow box and -35 region. The conservation of the two-fold rotational (2f) and true palindrome (tp) symmetry relations was determined between nucleotide doublets in both promoter subgroups which represent consensus symmetry patterns. Statistically significant symmetries were primarily distinguished from those established by the nucleotide sequence conservation. The consensus symmetry pattern of standard promoters involves 45 of the 60 promoter nucleotide positions at which less strongly conserved and non-conserved sequences were mostly occupied (per se). They also show a high level of symmetry centre conservation. The conservation of the statistically significant 2f symmetry centres at positions -4.5 and -31.5 suggests partial conservation of the Pribnow box and -35 pentamer in the codogenic strand in an opposite orientation, respectively. The non-standard promoters differ from the standard ones by the consensus symmetry pattern and by the 2f and tp symmetry centre distribution with an overall lower degree of symmetry conservation in the -35 region. It has been suggested that the conserved symmetry relations provide an additional condition necessary for the specific interaction of RNA polymerase with the promoter sequence to initiate transcription.

High mobility group proteins HMG1 and HMG2 do not decrease the melting temperature of DNA.

High mobility group proteins 1 and 2 isolated in non-denaturing conditions cannot decrease the temperature of denaturation of DNA. When they are isolated or treated with tricloroacetic acid a hyperchromic peak below the melting temperature of free DNA appears in agreement with previous data ( Javaherian et al. (1979) Nucl . Acids Res. 6, 3569-3580). We show that this is due to light scattering of aggregated protein at submelting temperatures and not to melting of DNA.

Comparison of Bacillus subtilis phages PZA, phi 29 and phi 15.

Morphologically identical phages PZA, PZE , phi 29, and phi 15 can be distinguished by the neutralization test with rabbit antisera and by host range specificity. Each member of this phage group contains 18 kb double-stranded linear DNA carrying proteins covalently attached to its 5' ends. Physical maps of their DNA constructed with the use of restriction endonucleases EcoRI, HpaI, HindIII, BspRI, and XbaI and DNA-DNA hybridization experiments show a closer relationship between phi 29 and PZE than between phi 29 and phi 15 or phi 29 and PZA. phi 15 is closer to PZA than to phi 29. This conclusion is supported by analysis of differential denaturation profiles of the phage DNAs. Sequencing of selected parts of phi 29 and PZA DNAs reveals 93% homology with a preference for synonymous base replacements (silent mutations) randomly distributed in the coding regions. Using promoter-probe plasmid pPV33 -H the region functioning as a promoter in E. coli was localized on the smallest EcoRI fragment of PZA and phi 29 DNAs. Comparison of the nucleotide sequence of this region with known promoters of B. subtilis shows extensive homologies with at least two types of promoters of different specificities, namely those recognized by factors sigma 28 of B. subtilis and sigma gp28 of phage SPO1 . These promoter-like regions overlap and the whole sequence is conserved in both phages.

A comparative study of G+C-rich satellite components of sheep and goat DNA.

Restriction fragment patterns of G+C-rich satellites of sheep and goat DNA were compared. The 1,712 g/cm3 satellites of both species appear homologous, consisting of repeats 760 base pairs long and showing coincidence of position of primary+ EcoRI, BamHI and most BspRI restriction target sites. The EcoRI and BamHI endonucleases produce mostly monomers of the repeating unit, while oligomers prevail in the A1uI and Bg1II digests. Species-specific differences in the frequency, position and mode of distribution of secondary+ restriction target sites for EcoRI, Bg1II and A1uI were observed. Unlike the 1,712 g/cm3 satellites, the 1,723 g/cm3 component of sheep DNA and the 1,719 g/cm3 material from goat DNA appear species--specific, since no homologous material could ever be detected in the DNA of the other species.

High resolution thermal denaturation of mammalian DNAs.

High resolution melting profiles of different mammalian DNAs are presented. Melting curves of various mammalian DNAs were compared with respect to the degree of asymmetry, first moment, transition breath and Tmi of individual subtransitions. Quantitative comparison of the shape of all melting curves was made. Correlation between phylogenetical relations among mammals and shape of the melting profiles of their DNAs was demonstrated. The difference between multi-component heterogeneity of mammalian DNAs found by optical melting analysis and sedimentation in CsCl-netropsin density gradient is also discussed.

Base composition heterogeneity of mammalian DNAs in CsCl-netropsin density gradient.

DNAs of 15 mammals and some lower organisms were analysed by CsCl-netropsin density gradient centrifugation. Increased resolving power of this method enabled to detect many new components in mammalian DNAs. Distinct components were detected in the density range of the main band. These components found in different mammalian DNAs have probably limited variation in the G+C content. Most of other components seems to be species specific. The DNAs of lower organisms form homogeneous band even in the presence of netropsin. The relation between densities in CsCl-netropsin and CsCl density gradient is nonlinear. This result supports a hypothesis that in high ionic strength netropsin is preferentially bound to (dA.dT) clusters.