Preferred breakage points in T5 DNA molecules subjected to shear

Cloning of genes for bacteriophage T5 stable RNAs

One EcoRI-generated fragment (440 basepairs) and two EcoRI/HindIII fragments (220 and 960 basepairs) from the deletion region of T5 phage have been inserted into the phage lambda XIII and the plasmid pBR322 as vectors. Recombinant DNA molecules were studied by hybridization with in vivo 32P-labeled T5 4-5 S RNAs on nitrocellulose filters. Two-dimensional polyacrylamide gel electrophoretic fractionation and fingerprint analysis of the RNAs eluted from the filters were carried out to identify RNAs coded by cloned fragments. For the accurate localization of the genes for these RNAs, RNA-DNA hybrids were treated with T1 and pancreatic RNAases, and the eluted RNA fragments stable against RNAase action were electrophoresed. It was shown that the EcoRI 440 fragment contains the gene for tRNA 10 (tRNAAsp), the EcoRI/HindIII 220 fragment contains the gene for RNA III (107 bases) and parts of the genes for RNA I (107 bases) and tRNA 12 (tRNAHis), and the EcoRI/HindIII 960 fragment contains only a part of the gene for tRNA 9 (tRNAGln). The arrangement of these genes on the physical map of T5 phage was as follows: -tRNAGln-tRNAHis-RNA III-RNA I-...-tRNAAsp.

Unique double-stranded fragments of bacteriophage T5 DNA resulting from preferential shear-induced breakage at nicks

Nicks within one strand of the bacteriophage T5 DNA molecule act as " weak points" for a novel kind mechanical breakage that can be utilized for "dissecting" the genome. The products from sheared T5(+) DNA include five unique double-stranded segments of the molecule and various combinations of adjacent segments. These specific fragments are not obtained after repair of the nicks with DNA ligase (EC 6.5.1.1). The duplex fragments and most of their single-stranded components have been separated, identified, and mapped by means of agarose gel electrophoresis. Even the complementary strands of the unique fragments separate in agarose gels; hence, there are now three useful classes of DNA fragments available from T5: the natural r-strand fragments, their complements from the normally intact l strand, and the corresponding duplex segments. By summing the apparent molecular weights of their single-stranded components, the unique duplex fragments from T5(+) DNA can be assigned molecular weights of approximately 6 x 10(6) (A), 8 x 10(6) (B), 11 x 10(6) (C), 27 x 10(6) (D), and 30 x 10(6) (E) from left to right along the genome. The most abundant overlapping fragments are segments AB (14 x 10(6)) and ABC (26 x 10(6)). Differences in the number and relative positions of nicks within two distinct groups of heatstable deletion mutants [represented by T5st(O) and T5b3] account for the large differences observed in their patterns of breakage products.

Chromatography of transforming deoxyribonucleic acid on methylated albumin and by gel filtration

1. Native DNA from two strains of Bacillus subtilis was chromatographed by stepwise elution from MAK (methylated albumin on kieselguhr). 2. Transforming activity was confined to two out of the three main fractions, activity being distributed between the two peaks differently for DNA from the different strains. 3. Fractionation of DNA from both strains on 2% agarose gel gave two components. Approx. 75% of the material was eluted within the void volume of the column. Approx. 25% of the material consisted of degradation products of lower molecular weight. 4. Chromatography on MAK of the material of high molecular weight eluted from agarose gel gave a number of peaks differing in molecular weight, indicating that degradation of the DNA takes place during chromatography on MAK. 5. The distribution of transforming activity among the fractions from MAK suggests that degradation occurs preferentially in certain regions of the DNA.

Location of single-strand interruptions in the DNA of bacteriophage T5

The positions of three single-strand interruptions in the DNA of phage T5(+) have been located by electron microscopy. All three interruptions were found in the same strand. Uneven base composition along the molecule is indicated by the preferential melting of certain regions. The data suggest a model according to which (1) the first-step-transfer DNA section is separated by a single-strand interruption from the rest of the phage genome, (2) the phage carries only one such section and therefore transfers the asymmetrical DNA molecule always in the same direction into the host cell, and (3) single-strand interruptions are points of preferred breakage.