Residual transforming activity of denatured Haemophilus influenzae DNA

Defective Bacteriophage PBSH in Bacillus subtilis: III. Properties of Adenine-16 Marker in Purified Bacteriophage Deoxyribonucleic Acid

The adenine-16 (ade-16) marker (the marker nearest the chromosomal origin of Bacillus subtilis) in purified PBSH deoxyribonucleic acid (DNA) renatured more rapidly and to a greater extent than any other marker in the phage DNA, and more rapidly and to a greater extent than all markers, including ade-16, in bacterial DNA. The renaturation of the phage DNA ade-16 marker followed a first-order reaction, whereas renaturation of bacterial markers was initially a second-order reaction. No cross-linkages were detected in DNA molecules containing the ade-16 marker. Buoyant density measurements and inactivation by heat and micrococcal deoxyribonuclease of the ade-16 marker did not reveal large segments of clusters of the individual bases in these molecules. Alternative mechanisms for the unique renaturation behavior of the ade-16 marker are discussed.

Transformation in Bacillus subtilis with nitrogen mustard crosslinked DNA. Effect on cotransformation and mutation frequencies

Bacillus subtilis DNA was treated in vitro with nitrogen mustard and the crosslinked molecules were purified, after alkali denaturation, by hydroxyapatite chromatography. When tested for the ability to transform the trpC2-hisB2 segment, these molecules exhibited a decrease in the cotransformation index (r) as compared to native or renatured DNA. The decrease in r was not accompanied by an increase in mutagenicity.

Structure of Caulobacter deoxyribonucleic acid

The deoxyribonucleic acid of the dimorphic bacterium Caulobacter crescentus contains a component that renatures with rapid, unimolecular kinetics. This component was present in both swarmer and stalked cells and exhibited the sensitivity to endonuclease S1 expected for hairpin loops. Double-stranded side branches between 100 and 600 nucleotide pairs in length were visible in electron micrographs of rapidly reassociating deoxyribonucleic acid isolated by hydroxyapatite chromatography. No extrachromosomal elements were found in spite of systematic attempts to detect their presence. These results indicate that the rapidly reassociating fraction derives from inverted repeat sequences within the chromosome and not from cross-links or plasmids. We estimate that there are approximately 350 inverted repeat regions per Caulobacter genome. The kinetic complexity of Caulobacter deoxyribonucleic acid, however, is no greater than that of other bacteria.

A study of foldback DNA

Nuclear DNA from eucaryotes contains a significant fraction which forms duplexes very rapidly and also independently of the DNA concentration. This fraction can be isolated by adsorption to hydroxylapatite and has been called foldback DNA (Britten and Smith, 1970). Here we extend previous studies to show that the foldback fraction is due to the existence of a finite number of foldback foci in each genome equivalent of DNA, approximately 10(5) in the case of Xenopus laevis. More significantly, we have isolated the foldback fraction in quantity from DNA of such a size (in one case broken randomly and in another digested with a restriction endonuclease) that only about 10% of the total DNA has foldback properties. If the foldback foci were located in precisely the same positions in all sets of the Xenopus laevis genome, the prediction would be that these foldback fractions would contain sequences representing 20% (random shear) and 10% (restriction endonuclease) of the total genome. In contrast, our results show that in both cases the foldback fraction contains the entire Xenopus laevis DNA sequence. One possible explanation of these observations is that as in procaryotes, eucaryotic DNA is randomly cross-linked. We show that cross-linkage of Xenopus laevis DNA is not sufficient to explain our observations. In consequence, we have adopted the hypothesis that the formation of foldback DNA is mainly an intrastrand phenomenon, but nevertheless occurs at different sites in different sets of the Xenopus laevis genome.

Hydroxyapatite chromatography and formamide denaturation of adenovirus DNA

Denatured adenovirus DNA was retained by hydroxyapatite columns under conditions generally used for selective retention of double-stranded DNA, probably due to several partially complementary sequences within single-stranded DNA. It was found that addition of formamide reduced the fraction of sonically treated, denatured adenovirus DNA bound to hydroxyapatite from about 30% to less than 1%. This led to a study of the effect of formamide on the melting temperature (T(m)) of double-stranded DNA in solution or bound to hydroxyapatite. The T(m) of DNA decreases 0.56 C/1% formamide, a value determined in buffered solutions with purified formamide.

Chromatographically fractionated complementary strands of Bacillus subtilis deoxyribonucleic acid: biological properties

Biological, physical, and chromatographic properties of methylated albuminkieselguhr (MAK)-fractionated complementary strands, designated as light (L) and heavy (H), of Bacillus subtilis deoxyribonucleic acid (DNA) are presented. The pattern of transforming activity along the MAK elution profile of alkilidenatured DNA shows that the residually active molecules selectively fractionated ahead of the L strand fraction, whereas the most active self-annealed molecules fractionated preferentially at the trailing end of the H strand fraction. The restoration rate of transforming activity in the late-eluting H molecules was rapid and independent of concentration during the annealing reaction. The data suggest that the self-annealing activity in the H strand is due in part to the formation of intrastrand secondary structures. Hydroxyapatite chromatography of self-annealed L and H strands yielded a major fraction (I) of highly purified strand preparations devoid of transforming activity and hypochromicity, and a minor "nativelike" fraction (II). Sedimentation velocity measurements show that, in addition to the mutual complementary nature of the L and H fractions, they differ in molecular size and possibly configuration.

Nature of the ethylenediaminetetraacetic acid requirement for transformation of Bacillus subtilis with single-stranded deoxyribonucleic acid

The ethylenediaminetetraacetate (EDTA) requirement for transformation of Bacillus subtilis with single-stranded deoxyribonucleic acid (DNA) was examined. The results indicate that a chelating agent such as EDTA is a stringent requirement for transformation with single DNA strands only at nonsaturating DNA concentrations, and that EDTA, when required, must be present during several steps in the transformation process and appears to insure the survival of single-stranded DNA by rendering a nuclease in competent populations inactive.

Natural occurrence of cross-linked vaccinia virus deoxyribonucleic acid

The molecular weight of native vaccinia deoxyribonucleic acid (DNA) is 1 to 1.17 times that of native T4 DNA. Sedimentation of denatured vaccinia DNA through alkaline sucrose gradients yields an apparent molecular weight greater than twice that of denatured T4 DNA, implying that the complementary strands of vaccinia DNA do not separate upon denaturation. When alkali-denatured vaccinia DNA is neutralized, it has the physical chemical properties of native DNA when tested by sedimentation through neutral sucrose gradients, banding in CsCl, and by hydroxylapatite chromatography. We conclude that almost all mature vaccinia DNA molecules contain a small number of naturally occurring cross-links.

Competent Diplococcus pneumoniae accept both single- and double-stranded deoxyribonucleic acid

The transforming activity of fractionated complementary strands of Diplococcus pneumoniae deoxyribonucleic acid (DNA) bands at the position of fully denatured DNA in CsCl at pH 11.0, and is completely (> 99.8%) destroyed by digestion with exonuclease-I. These results prove that pure single strands transform the normally prepared competent cells of this species. Their efficiency is about 0.5% that of native DNA of comparable size.