Alignment of partial denaturation maps of circularly permuted DNA by computer

Determination of the patterns of hexanucleotide distribution along DNA by electron microscopy

Hexanucleotides containing modified bases (5-methylcytosine and 2-aminoadenine instead of cytosine and adenine) with increased capacities to bind complementary DNA sequences were used to map the distribution of their complementary sequences in a DNA target using electron microscopy. The method used hexamers to initiate DNA polymerase directed DNA synthesis at complementary sequences along a template. DNA synthesis was limited to about 200 residues by using a low concentration of deoxynucleotide precursors. During DNA synthesis a biotin ligand was incorporated to facilitate the subsequent binding of an electron-dense label (streptavidin-labeled colloidal gold particles) into newly synthesized DNA chains. The method can be implemented with commercially available products. The results demonstrate that the approach can be used to compare primary structural features of DNA fragments. The principles of the method can be adapted to a variety of single molecule detection methods such as electron, scanning tunneling, or atomic force microscopies.

Testing the quality of electron microscope mapping data for DNA molecules with sequence-specific ligands

A procedure for the testing of Electron Microscope (EM) mapping data for DNA molecules with site-specific bound ligands is suggested. The difficulty of distinguishing DNA molecule ends on electron micrographs indicates that their true orientations are not known. This in turn presents problems in obtaining correct maps relating to their alignment, and complicates checking the maps' validity. For these reasons a computer simulation of the EM study of double-stranded DNA molecules with site-specific bound ligands was carried out. The knowledge of the true orientations of the simulated DNA molecules allowed us to examine their final orientations after alignment. We used the number of improper-oriented molecules as the quantitative measure of the map quality. Detailed investigation based on this parameter permitted us to invent the criterion for the map validity, and to suggest the procedure for the testing of alignment of real DNA molecules. This procedure implies multiple randomization of initial orientations of the DNA molecules and minute analysis of the final maps. Most of the molecular, statistical and experimental parameters inherent to EM investigation of site-specific binding, such as the number of specific binding sites (N), the mean number of bound ligands (A), the length of the DNA molecules (L), the specific/non-specific ratio of binding (K), together with the standard deviation of DNA molecule lengths (HL) were tested for their influence upon the quality of EM mapping data. An empirical equation for the ultimate values of these parameters has been found, allowing us to predict the success of EM mapping.

The genome of B. subtilis phage SSP1: the topology of DNA molecules

DNA molecules of B. subtilis phage SPP1 exhibit terminal redundancy and are partially circularly permuted. This was established by the hybridization of selected EcoRI restriction fragments to single strands of SPP1 DNA and by an analysis of the distribution of denaturation loops in partially denatured SPP1 DNA molecules. Deletions in SSP1 DNA are not compensated by an increase in terminally repetitious DNA. This finding, which is unique to SPP1, is discussed in terms of a modification of the Streisinger/Botstein model of phage maturation.

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.

Electron microscopic studies of bacteriophage M13 DNA replication

Intracellular forms of M13 phage DNA isolated after infection of Escherichia coli with wild-type phage have been studied by electron microscopy and ultracentrifugation. The data indicate the involvement of rolling-circle intermediates in single-stranded DNA synthesis. In addition to single-stranded circular DNA, we observed covalently closed and nicked replicative-form (RF) DNAs, dimer RF DNAs, concatenated RF DNAs, RF DNAs with single-stranded tails (theta, rolling circles), and, occasionally, RF DNAs with theta structures. The tails in theta molecules are always single stranded and are never longer than the DNA from mature phage; the proportion of theta to other RF molecules does not change significantly with time after infection. The origin of single-stranded DNA synthesis has been mapped by electron microscopy at a unique location on RF DNA by use of partial denaturation mapping and restriction endonuclease digestion. This location is between gene IV and gene II, and synthesis proceeds in a counterclockwise direction on the conventional genetic map.

On the character of the thermodynamic properties distribution in DNA molecules inside the melting interval

The variances of the distributions of DNA molecules over the degree of helicity and over the number of unwound regions inside the melting interval are calculated. The variance over the degree of helicity is expessed in terms of the values directly available from the experimental data. For the variance over the number of unwound regions a simple interpolation formula based on the machine calculations is proposed. Possible applications of the results obtained to interpolaation of the electron microscopic denaturation maps of DNA are discussed.

Evolution of Drosophila mitochondrial DNAs. Comparison of denaturation maps

In an approach to the functional anatomy of the mitochondrial genome and its evolution, we have compared buoyant densities, contour lengths, and denaturation maps in circular mitochondrial DNAs of the genus Drosophila. Mitochondrial DNAs from three representatives of the subgenus Drosophila (D. virilis, D. hydei, D. funebris) are similar in size (approx. 5 mum or 1 - 10(7) daltons) and buoyant density (approx. 1.685 g/ml), while in two members of the subgenus Sophophora (D. melanogaster, D. simulans), mitochondrial DNAs are longer (approx. 6 mum or 12.4 - 10(6) daltons) and have a lower buoyant density (approx. 1.681 g/ml). The latter mitochondrial DNAs also share one distinctly large early melting region, which in D. melanogaster is equivalent to 1.54 mum of native DNA. The corresponding (A + T)-rich region in D. virilis or D. hydei mitochondrial DNA is 1 mum shorter. Except for this region, denaturation maps of D. melanogaster and D. virilis mitochondrial DNAs are indistinguishable. The addition or deletion of a single block of (A + T)-rich sequences can fully account for the differences in buoyant density and size between the mitochondrial DNAs we have examined. In an appendix, we show that there is an equivalent discrepancy between the extent of strand separation determined by electron by electron microscopy and the actual extent of DNA denaturation, whether this is determined from absorbance changes or inferred from the reduction in contour lengths of individual circular molecules. The reduction in contour length appears to result exclusively from the uniform foreshortening of single-stranded DNA, not only in regions of visible strand separation but also in denatured regions hidden within putatively native segments of molecules. For molecules showing 15--45% strand separation, we estimate that putatively native segments are approximately 50% denatured.

Comparison of the fine structure of mitochondrial DNA from Saccharomyces cerevisiae and S. carlsbergensis: electron microscopy of partially denatured molecules

Denaturation-maps of mitochondrial DNA from Saccharomyces cerevisiae and S. carlsbergensis have been derived from electron microscopic observations of partially denatured complete circular molecules and large fragments of these circles. The mitochondrial DNA from the two species differ by 6% in total length, but seems from the maps to contain some regions of apparent close homology. The cleavage pattern of the two DNAs by the restriction endonuclease EcoRI is compared by gel electrophoresis.