The mapping and ordering of fragments of SV40 DNA produced by restriction endonucleases

Subunit structure of simian-virus-40 minichromosome

Electron microscopic evidence indicates that Simian virus 40 (SV40) minichromosomes extracted from infected cells consist of 20 +/- 2 nucleosomes, each containing 190 -- 200 base pairs of DNA. About 50% of the nucleosomes are not close together, but connected by segments of DNA of irregular lengths which correspond to about 15% of the viral genome, irrespective of the ionic strength. Micrococcal nuclease digestion studies show that there is about 200 base pairs of DNA in the biochemical unit of SV40 chromatin. Therefore, the visible internucleosomal DNA of the SV40 minichromosome does not arise from an unfolding of a fraction of the 190 - 200 base pairs of DNA initially wound in the nucleosome. These results support the chromatin model which proposes that the same DNA length is contained in the nucleosome and the biochemical unit. Results from extensive micrococcal nuclease digestion suggest that an SV40 nucleosome consists of a 'core' containing a DNA segment of about 135 base pairs associated to a DNA fragment more susceptible to nuclease attack. The addition of histone H1 results in a striking condensation of the SV40 minichromosome, which supports the assumption that histone H1 is involved in the folding of chromatin fibers.

Restriction endonucleases

This review provides a comprehensive account of the current status of the biology and biochemistry of restriction endonucleases. Both Class I and Class II restriction endonucleases will be considered. However, emphasis will be placed on the Class II group, which recognizes and cleaves a specific duplex DNA sequence. Their occurrence, purification, and characterization is discussed in detail. The characterization includes physical mapping information and determination of recognition sequences. In addition to detailed discussions of the biochemical properties of the enzymes, considerable attention is paid to the uses of these enzymes as tools for research in molecular biology. These uses include physical mapping of genomes and their transcripts, genetic analysis (marker rescue, etc.), DNA sequence analysis, analysis of complex genomes, and genetic engineering. Specific examples of each use are outlined. Practical aspects of both the isolation and use of the restriction endonucleases form the major theme of this review.

A possible structure for calf satellite DNA I

Calf satellite DNA I (p = 1.715) has been hydrolysed by a number or restriction endonucleases. It consists of a repeating unit of 1460 nucleotide pairs within which the sites of Eco R II Mbo I, Sac I, Alu I, Ava II and Hha I were localised in comparison with those of Eco R I and Hind II. The distribution of the Hpa II, Sac I, Hha I, Hinf I and Mbo II sites within calf satellite DNA I, as well as that of several restriction endonuclease sites within calf satellite DNA III (p = 1.705) allowed me to define subsatellite fractions. Furthermore, some of the sites of the CpG containing restriction enzymes Hpa II and Hha I are lacking. The possible implications of these results are discussed.

DNA of minute virus of mice: self-priming, nonpermuted, single-stranded genome with a 5'-terminal hairpin duplex

The genome of the nondefective parvovirus minute virus of mice (MVM) is a linear DNA molecular weight 1.48 x 10(6), which is single stranded for approximately 94% of its length. In contrast to the genomes from defective parvoviruses MVM DNA does not contain a detectable inverted terminal redundancy. A combination of enzymatic and physical techniques has shown that the molecule contains a stable hairpin duplex of approximately 130 base pairs located at the 5' terminus of the genome. MVM DNA is efficiently utilized as a template-primer by a number of DNA polymerases, including reverse transcriptases. Polymerases lacking 5' to 3' exonuclease activity yield a duplex DNA product with a molecular weight 1.96 times that of the viral genome, in which the newly synthesized complementary strand is covalently attached to the template. This duplex contains an internal "nick" that can be sealed by DNA ligase to produce a self-complementary single-strand circle. The MVM DNA duplex is cleaved twice by EcoR-RI restriction endonuclease to yield three distinct fragments in molar amounts. These results suggest that the initiation of DNA synthesis in vitro occurs at a point within 100 bases of the 3' end of the genome, using the 3' terminus of viral DNA as a primer, and that the sequence of nucleotides in the genome is not permuted.

The initiation region of the SV40 VP1 gene

The sequence of 15 nucleotides located at the 5' terminus of the plus strand of the SV40 Hind K fragment has been determined as (5') A-G-C-T-T-A-T-G-A-A-G-A-T-G-G (3'). The 3' on OH terminal G of this segment is part of the G-C-C codeword for the N terminal alanine of the VP1 protein. This region therefore presumably corresponds to a ribosome binding site on the 16S late mRNA. Complementarily to the 3' OH of eucaryotic 18S ribosomal RNA and homology with the BMV coat ribosome binding site are discussed.

Genomic transcriptional activity and the structure of chromatin

Nucleic acid hybridisation has shown that micrococcal nuclease-derived chromatin subunits from the cells of Xenopus laevis contain fragments of ribosomal 28S, 18S and 5S RNAS within the population of 200 base-pair pieces of DNA. Subunits from cultured embryonic cells actively transcribing ribosomal RNA contain only 70-74% of the cistrons present in undigested wild-type DNA, while subunits from adult erythrocytes not active in RNA transcription contain close to 90% of the ribosomal cistrons in native chromatin.

Specific cleavage and physical mapping of simian-virus-40 DNA by the restriction endonuclease of Arthrobacter luteus

Simian virus 40 (SV40) DNA (strain 776) is cleaved by the restriction endonuclease from Arthrobacter luteus into 32 specific fragments including 20 large pieces designated Alu-A through T as well as 12 minor products named Alu m1 through m8. These were mapped on the SV40 genome by double digestion experiments. Alu fragments were treated with Hind enzymes and vice versa. Similar reciprocal digestions were also carried out with Hae III enzyme. In this way a detailed cleavage map of the SV40 genome could be constructed.

Cleavage map of the simian-virus-40 genome by the restriction endonuclease III of Haemopholus aegyptius

Enzymic digestion of Simian virus 40 (SV40) DNA with Haemophilus aegyptius restriction endonuclease Hae III results in 10 major and eight minor fragments. These were resolved by electrophoresis on graduated polyacrylamide slab gels. All fragments have been characterized with respect to the size relative to the Haemophilus influenzae Rd fragments (Hind). They were ordered on the SV40 DNA map by means of overlap analysis of the double cleavage products derived from sequential digestion of Hind fragments with Hae III endonuclease and Hae fragments with Hind II + III enzyme, as well as by other reciprocal cleavage experiments, including those involving Haemophilus para-influenzae fragments. In this way the 18 Hae III cleavage sites and the 13 Hind sites have been localized on the circular SV40 DNA map.

Sequences spanning the EcoRI substrate site

Substrate recognition by the EcoRI restriction endonuclease was investigated by analysis of the nucleotide sequences at the sites of enzymatic cleavage in various DNA molecules. 5'-end labeling and homochromatographic fingerprinting led to the determination of a 17-base-pair sequence spanning the EcoRI site of simian virus 40 DNA and a 15-base-pair sequence overlapping the EcoRI site of Col El plasmid DNA. Three other DNAs were similarly tested, although extended sequences were not determined in these cases. The EcoRI site was shown to be symmetric double-stranded equivalent of -N-G-A-A-T-T-C-N-.

Investigation of the repetitive sequences in calf DNA by cleavage with restriction nucleases

Calf thymus DNA was digested with the restriction nucleases from Escherichia coli carrying resistance transfer factor I, Haemophilus influenzae Rd and Bacillus subtilis X5 (EcoRI, Hind II, and Bsu, respectively) and submitted to polyacrylamide gel electrophoresis. About 10% of the DNA migrated as discrete fragments in 8, 16, and 30 bands, respectively, superimposed upon a continuous distribution of various size DNA fragments. The fragments within the bands are repeated 2000 to 160000 times in the haploid genome. Their sizes range from about 10 to a few thousand nucleotide pairs. About 5% of the DNA in EcorRI and Hind II digests migrated in a band at the position of undigested DNA, probably due to the resistance of long stretches of DNA against these nucleases. Calf DNA fragments obtained with EcoRI and Hind II were isolated by preparative gel electrophoresis. DNA from the bands showed the behaviour of repetitive DNA in renaturation experiments. An EcoRI fragment 1300-nucleotide-pairs long, which represents 6% of the calf genome and occurs 130000 times, is tandemly repeated (derived from the satellite of 1.714 g/cm3, see below). Another EcoRI fragment of 970 nucleotide paris, which represents 0.5% of the calf genome and is derived from the DNA of 1.710 g/cm3 seems to be structurally related to the foregoing fragment since it shows a similar Hind II and Bsu cleavage pattern. It alternates with a 1550-nucleotide-pairs-long EcoRI fragment. In another series of experiments total calf DNA was separated into main-band and satellite fractions by density-gradient centrifugation and chromatography in the presence of a base-specific dye. Purified fractions were characterized by analytical ultracentrifugation and by Hind II and EcorRI digestions. From the cleavage patterns of purified fractions an assignment of the bands found with total calf DNA to satellite fractions was possible. Most fragments were derived from the components of density 1.709 and 1.710 g/cm3. The 1.714-g/cm3 satellite was cleaved into a 1300-nucleotide-pairs-ling EcorRI fragment and two Hind II fragments of 1100 and 180 nucleotide pairs. The satellites of 1.723 g/cm3 and 1.705 g/cm3 were not cleaved by either Hind II or EcoRI DNAase. On digestion of main band DNA with Bsu a 160-nucleotide-pairs-long fragment was obtained which was also observed, at a frequency of about 160000, in the Bsu digest of EcoRI fractions from total calf DNA.

The length of the terminal repetition in adenovirus-2 DNA

Adenovirus-2 DNA was end-labeled by partial digestion with Escherichia coli exonuclease III and resynthesis with the DNA polymerase from avian myeloblastosis virus and alpha-(32)P-labeled deoxyribonucleoside triphosphates. This end-labeled DNA was cleaved with several specific endonucleases and the terminal fragments were characterized by gel electrophoresis and pyrimidine tract analysis. Two endonucleases gave identical fragments from both ends, presumably from cleavage within the inverted terminal repetition, while all other endonucleases gave dissimilar fragments from the two ends. From the sizes of these fragments it is estimated that the inverted terminal repetition is between 100 and 140 nucleotide pairs long.