Specificity of the S1 nuclease from Aspergillus oryzae

Rabbit beta-globin mRNA production in mouse L cells transformed with cloned rabbit beta-globin chromosomal DNA

Mouse thymidine kinase-negative L cells were transformed with a cloned rabbit chromosomal beta-globin gene linked to the clone thymidine kinase gene of herpes simplex virus type 1. Most thymidine kinase-positive cell lines contained one or more copies of rabbit beta-globin DNA and produced up to 2,000 copies of rabbit beta-globin RNA per cell indistinguishable from its authentic counterpart. No mouse beta-globin mRNA was detected.

Differential excision from DNA of the C-8 deoxyguanosine reaction products of N-hydroxy-2-aminofluorene and N-acetoxy-N-acetyl-2-aminofluorene by endonuclease S1 from Aspergillus oryzae

Calf thymus DNA was modified in vitro with [G-3H]N-hydroxy-2-aminofluorene and [G-3H]N-acetoxy-N-acetyl-2-aminofluorene and the nuclease S1 digestion was studied under identical conditions. The ratios of the maximum reaction rate (V) and the Michaelis constant (Km), V/Km, indicate that 2-aminofluorene(AF)-modified DNA is hydrolyzed 3 times more slowly than N-acetyl-2-aminofluorene(AAF)-modified DNA under similar reaction conditions. The AF-modified DNA was slightly more susceptible to partial digestion by nuclease S1 than unmodified control DNA. These results suggest that the local regions of denaturation induced by AF substitution are smaller than those associated with AAF modification.

Yeast chromosomal DNA molecules have strands which are cross-linked at their termini

The microbial eukaryote Saccharomyces cerevisiae has 18 chromosomes, each consisting of a DNA molecule of 1 x 15 x 10(8) daltons (150 to 2,300 kilobase pairs). Interstand cross-links have now been found in molecules of all sizes by examining the ability of high molecular weight DNA to snap back, i.e., to rapidly renature after denaturation. Experiments in which snap back was assessed for molecules broken by shearing indicate that there are probably two cross-links in each chromosome. Evidence that the cross-links occur at specific sites in the genome was obtained by treating total chromosomal DNA with the endonuclease EcoRI which cleaves the yeast genome into approximately 2,000 discrete fragments. Cross-link containing fragments were separated from fragments without cross-links. This purification resulted in enrichment for about 18 specific fragments. To determine whether the cross-links are terminal or at internal sites in chromosomal DNA, large shear-produced fragments were examined by electron microsopy. With complete denaturation few fragments exhibit the X-shaped single strand configuration expected for internal cross-links. When partially denatured fragments were examined some ends had single strand loops as expected for (AT-rich) cross-linked termini. We propose that a duplex chromosomal DNA molecules have cross-linked termini. We propose that a duplex chromosomal DNA molecule in this eukaryote consists of a continuous, single, self-complementary strand of DNA. This structure has implications for the mechanism of chromosome replication and may be the basis of telomere behavior.

S1 nuclease as a probe of yeast ribosomal 5 S RNA conformation

5 S RNA was isolated from Saccharomyces cerevisiae grown in the presence of 32P-phosphate and digested with nuclease S1, a single-strand specific nuclease. Two different procedures were employed to determine the sites of attack on the RNA. First, 5 S RNA was isolated from nuclease S1 digests, digested to completion with ribonuclease T1, and then 'fingerprinted' by two-dimensional electrophoresis. Quantitation of each of the characteristic RNAase T1-derived oligonucleotides was employed to determine the relative susceptibility of various regions of the molecule to nuclease S1. A second procedure to define nuclease S1-susceptible sites in the molecule employed polyacrylamide gel electrophoretic fractionation of nuclease S1 digests followed by identification of the nucleotide sequences of the released RNA fragments. Both procedures showed that the region of the molecule between residues 9 and 60 was most susceptible to nuclease S1, with preferential cleavage occurring between residues 12-25 and 50-60. These results are discussed in relation to a proposed model for the secondary structure of yeast 5 S RNA.

Association of the folded chromosome with the cell envelope of Escherichia coli: nature of the membrane-associated DNA

Membrane-associated folded chromosomes isolated from Escherichia coli in the presence of spermidine sedimented at about 5,800S. The folded chromosome and the membrane fragment were each stable in the absence of the other; a 1,700S folded chromosome was obtained after removal of the membrane by a Sarkosyl treatment, and a 4,000S membrane fragment remained after digestion of the chromosomal DNA with deoxyribonuclease I. The interaction between the folded chromosome and the membrane fragment was stable, and, even when the DNA was unfolded, both components remained associated and cosedimented. The large frictional effect of the unfolded DNA reduced the sedimentation rate of the complex to about 2,000S. Partial removal of this unfolded DNA with restriction endonucleases caused the membrane fragments and the remaining associated DNA to sediment faster, at about 3,500S. The DNA remaining associated with the membrane fragments after restriction endonuclease treatment, about 4.5% of the total DNA when EcoRI was used, was indistinguishable from the DNA released from the membranes by three criteria: (i) DNA size distribution in agarose gels after electrophoresis, (ii) reassociation kinetics, and (iii) thermal elution from hydroxylapatite. This finding, that random DNA sequences rather than specific ones were responsible for the majority of the DNA-membrane interactions, argues against the folded chromosome's being a static structure with specific DNA sequences interacting with the cell envelope.

The recognition of mismatched base pairs in DNA by DNase I from Ustilago maydis

The activity of Ustilago maydis DNase I, an enzyme implicated in genetic recombination, on DNA substrates containing unpaired or mismatched bases, was examined. The enzyme nicked supercoiled PM-2 molecules, converting these to relaxed circular and linear molecules. Discrete double stranded linear fragments smaller than unit length were also observed after digestion at high enzyme concentration. Heteroduplex molecules were constructed using phi80 bacteriophage derivatives which contained single base substitutions within the E. coli tRNA1tyr gene. Single and double stranded nicking at or near the single mismatched site was observed with three out of the five pairs of heteroduplexes.

Conformation of methylated sequences in HeLa cell 18-S ribosomal RNA: nuclease S1 as a probe

18-S rRNA from HeLa cells was digested with nuclease S1. Under the conditions employed 15% of the total nucleotides and some 50% of the methylated nucleotides were released as low-molecular-weight products. The material which was precipitable by 70% ethanol after nuclease S1 digestion was subjected to further digestion by combined T1 plus pancreatic ribonucleases or by T1 ribonuclease alone, and fingerprints were prepared. It was found that the four sites which are modified late during ribosome maturation, and which contain base modifications, were all accessible to nuclease S1. By contrast fewer than one-half of the sites which are modified early during ribosome maturation, and which contain 2'-O-methyl groups, were accessible to nuclease S1; the remainder were protected, presumably by secondary or tertiary interactions within 18-S rRNA.

Evidence of a repetitive sequence in vaccinia virus DNA

Analysis of vaccinia DNA by reassociation kinetics revealed that 7% of the genome contains a sequence repeated 10 times. This sequence does not contain any host cell DNA, is viral specific, and is found in virions passed at either high or low multiplicities of infection.

Biochemical analysis of genetic recombination in eukaryotes

Recent studies concerning molecular mechanisms of genetic recombination in eukaryotes are reviewed. Since many of these studies have focused on the testable predictions arising from the hybrid DNA theory of genetic recombination, this theory is summarised. Experiments to determine the time of meiotic crossing-over and the structure of the synaptonemal complex which facilitates meiotic crossing-over are described. Investigations of DNA nicking and repair events implicated in recombination are discussed. Properties of proteins which may facilitate hybrid DNA formation, and biochemical evidence for hybrid DNA formation are presented. Finally, a nuclease which has been implicated in gene conversion is described.

Degradation of nucleic acids in cell lysates by S1 nuclease in the presence of 9 M urea and sodium dodecylsulfate

Single-strand-specific nuclease S1 from Aspergillus oryzae is shown to degrade DNA and RNA in lysates of HeLa cells in the presence of 9 M urea and sodium dodecylsulfate. Free dodecylsulfate inhibits S1 nuclease. However, if the detergent is complexed with proteins prior to the addition of the enzyme, S1 nuclease can degrade nucleic acids at dodecylsulfate concentrations which would inhibit the enzyme completely if no other proteins were present. In lysates prepared from HeLa cells by treatment with dodecylsulfate and urea, the detergent is complexed by cellular proteins and therefore S1 nuclease can be used to digest DNA and RNA. DNA can be completely degraded but, even after heat-denaturation, only 60% of the cellular RNA is converted into acid-soluble material. Analysis of the acid-insoluble RNA fragments by gel filtration reveals that the majority of the degradation products is approximately of tRNA size.

Evolutionary divergence and length of repetitive sequences in sea urchin DNA

The organization of repetitive and single copy DNA sequences in sea urchin DNA has been examined with the single strand specific nuclease S1 from Aspergillus. Conditions and levels of enzyme were established so that single strand DNA was effectively digested while reassociated divergent repetitive duplexes remained enzyme resistant. About 25% of sea urchin DNA reassociates with repetitive kinetics to form S1 resistant duplexes of two distinct size classes derived from long and short repetitive sequences in the sea urchin genome. Fragments 2,000 nucleotides long were reassociated to Cot 20 and subjected to controlled digestion with S1 nuclease. About half of the resistant duplexes (13% of the DNA) are short, with a mode size of about 300 nucleotide pairs. This class exhibits significant sequence divergence, and principally consists of repetitive sequences which were interspersed with single copy sequences. About one-third of the long duplexes (4% of the DNA) are reduced in size after extensive S1 nuclease digestion to about 300 nucleotide pairs. About two-thirds of the long resistant duplexes (8% of the DNA) remains long after extensive SI nuclease digestion. These long reassociated duplexes are precisely base paired. The short duplexes are imprecisely paired with a melting temperature about 9 degrees C below that of precisely paired duplexes of the same length. The relationship between length of repetitive duplex and precision of repetition is confirmed by an independent method and has been observed in the DNA of a number of species over a wide phylogenetic area.

Specific excision of the inserted DNA segment from hybrid plasmids constructed by the poly(dA). poly (dT) method

The hybrid plasmid PBETAG, consisting of plasmid PMB9 DNA with an insert of rabbit globin DNA (about 600 base pairs) flanked by poly(dA) poly(dT) regions (Maniatis, T., Kee, S.G., Efstratiadis, A. and Kafatos, F.C. (1976) Cell 8, 163-182), was cleaved into two fragments by endonuclease S1 under conditions of partial denaturation. Only the smaller fragment (575 base pairs) contained globin-specific sequences, showing that excision had occurred in the A-T-rich regions. This method of cleavage provides a useful procedure for assessing the length of inserts in hybrid plasmids prepared by the poly(dA)-POLY(DT) tail method, and allows the preparative recovery of the insert.