Analysis of simian virus 40 DNA with the restriction enzyme of Haemophilus aegyptius, endonuclease Z

Human cytomegalovirus genome: partial denaturation map and organization of genome sequences

Contour-length measurements of both nondenatured and partially denatured DNA from purified extracellular human cytomegalovirus indicate that more than one size class of viral DNA is encapsidated. In addition to a size class averaging about 100 x 10(6) daltons, a much less abundant class of larger viral DNA molecules, 150 x 10(6) to 155 x 10(6) daltons, was extracted from purified extracellular virus. As predicted by melting-curve analysis, partial denaturation of human cytomegalovirus DNA generates denaturation maps showing distinctive adenine plus thymidine (A+T)-rich and guanine plus cytosine (G+C)-rich localizations. Alignment of partial denaturation maps of both 100 x 10(6)- and 150 x 10(6)- to 155 x 10(6)-dalton molecules from maximum overlap of common A+T- and G+C-rich zones clearly shows six unique zones contained in a length equal to the longest class, 150 x 10(6) to 155 x 10(6) daltons. However, various alignments of the smaller class of the molecules within the confines of the approximately 100 x 10(6)-dalton-length equivalent are nondistinctive. Of the six unique A+T- and G+C-rich zones, five are linked in a specific sequence and maintain the same relative orientation; these features indicate the absence of major inversions within these zones. The sixth unique zone may occur at either end of this five-zone series, but it was never found at both ends of the same molecule. Additionally, this terminal zone appears to undergo complete inversions at least at one end of the alignment, and perhaps at both. These data indicate that 150 x 10(6)- to 155 x 10(6)-dalton molecules comprise human cytomegalovirus-specific genetic information.

Sedimentation of homogeneous double-strand DNA molecules

Sedimentation velocity studies have been carried out with isolated double-strand DNA fragments prepared by digestion of PM2 phage with the restriction endonuclease Hae III. The results show that DNA molecules shorter than about 200 base pairs behave almost exactly as rigid rods with a diameter of 27 A. The behavior of the larger fragments (up to 1735 base pairs) can be described very well by either the theory of Yamakawa and Fujii (Yamakawa, H., and Fujii, M. (1973), Macromolecules 6. 407) using the same diameter and a persistence length of 575 A, or the theory of Hearst and Stockmayer (Hearst, J.E., and Stockmayer, W.H. (1962), J. Chem. Phys. 37, 1425) using a diameter of 20 A and a persistence length of 525 A.

Chromatin and nucleosome structure

Chromatin nucleosomes (mononucleosomes through pentanucleosomes) have been isolated by staphylococcal nuclease digestion of calf thymus nuclei. The peak value ellipticity is the same for all oligomers, 1900 deg cm2, mol-1 at 280-nm, 23 degrees C. The dh280/dT vs T show a progressive increase in Tm of the main thermal band (73.5 degrees C, monomer; 79 degrees C, pentamer). Very small amounts of free DNA can be observed in the melting profiles, and shoulders at 60 degrees C and 93 degrees C appear and increase in magnitude as the particle size increases. The magnitude of the change, delta[theta]280, increases with oligomer size. This pattern could result from an initial unfolding of an asymmetric assembly of nucleosomes (polynucleosome superhelix) in addition to the denaturation of the internal nucleosome structure, and a subsequent or simultaneous denaturation of the double strand DNA. The extent of this unfolding appears to depend upon the size of the oligomer and therefore implies interactions between asymmetrically assembled neighboring nucleosomes.

Analysis of cytomegalovirus genomes with restriction endonucleases Hin D III and EcoR-1

Cleavage of genomes of eleven human, one simian, and one simian-related cytomegalovirus (CMV) isolate by the restriction endonucleases HinD III and EcoR-1 generated reproducible DNA fragments. The size range of CMV DNA fragments as estimated by contour length measurements in comparison with simian virus 40 form II DNA and by coelectrophoresis with EcoR-1 fragments of herpes simplex virus DNA varied between 15 X 10(6) and 0.5 X 10(6) daltons. Comparison of the cleavage products of each isolate in 1% agarose slab gels showed extensive comigration of fragments among the human CMV isolates. In the HinD III digests, three fragment bands comigrated among all human CMV isolates, and six fragments comigrated among most, but not all, human CMV isolates. In the EcoR-1 digests, nine fragment bands comigrated among all human CMV isolates, and five bands comigrated among most, but not all human isolates. Each isolate had a distinctive electrophoretic profile with either HinD III or EcoR-1 digests. No two isolates had identical HinD III or EcoR-1 patterns although some isolates did share more general pattern similarities than others. No clear-cut subgrouping of isolates based on cleavage pattern characteristics could be discerned. Comparison of HinD III and EcoR-1 patterns showed that human isolates differ greatly from nonhuman CMV isolates. HinD III and EcoR-1 digests of each isolate contained both major and minor molar classes of DNA fragments that ranged from about 1 and multiples of 1 M down to about 0.25 M; however, the summed molecular weights for major molar fragments resulting from HinD III or EcoR-1 digests of several isolates closely approximated the molecular weight of 10(8) of the intact genome.

Detection of human cytomegalovirus and analysis of strain variation

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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.

Specific cleavage analysis of mammalian mitochondrial DNA

Mitochondrial DNA from several mammalian species has been digested with a site-specific restriction endonuclease (HaeIII) from Haemophilus aegyptius. A quantitative analysis of the resulting specific fragments indicates that the mtDNA of any individual mammal is predominantly a single molecular clone. Gel analysis of specific cleavage products has proven quite sensitive in detecting differences in mtDNA: mtDNAs from the more distantly related mammals studied (e.g., donkey and dog) are found to have few bands in common and very closely related mammals (e.g., donkey and horse) share only about 50% of their bands. This procedure has detected several intraspecies mtDNA differences. Six distinct human patterns have been found, with one pattern usually differing from another in two or three bands. mtDNAs from different organs of single individuals have also been analyzed, and no differences have been found.

Yeast chromatin subunit structure

Micrococcal nuclease digestion of in situ (intranuclear) and in vitro yeast chromatin produces distributions of DNA molecules of discrete sizes. In both cases, these molecules appear to be integral multiples of the smallest size on polyacrylamide gel electrophoresis. This result implies a widespread generic occurrence of the periodic organization of chromatin seen in mammalian systems.

In vitro polyoma DNA synthesis: inhibition by 1-beta-d-arabinofuranosyl CTP

The effects of 1-beta-D-arabinofuranosyl CTP (ara-CTP) on DNA replication were studied in an in vitro system from polyoma-infected BALB/3T3 cells. Ara-CTP concentrations of larger than or equal to 150 muM were found to block in vitro DNA synthesis completely, and concentrations of smaller than or equal to 0.3 muM had no inhibitory effect. Intermediate concentrations resulted in a concentration-dependent reduction of the in vitro synthesis rate. Long-term labeling with [alpha-32-P]ara-CTP demonstrated the incorporation of the analogue into cellular and viral DNA concomitantly with [3-H]TTP. In pulse-labeling experiments, at noninhibitory concentrations of the analogue, ara-CTP was incorporated into short DNA fragments and long growing strands to relatively the same extent as TTP. Partial venom phosphodiesterase digestion liberated the incoporated are-CTP at essentially the same rate as incorporated TTP, excluding a predominantly terminal incorporation, and after total venom phosphodiesterase digestion greater than 80% of the incorporated ara-CTP was recovered as 5'-ara-CMP. Analysis of the long-term in vitro viral DNA product made in the presence of partially inhibiting ara-CTP concentrations demonstrated that none of the steps leading to mature viral DNA were totally inhibited at the ara-CTP concentrations used. Pulse labeling of replicating viral DNA in the presence of ara-CTP revealed two consistent differences in the pattern found in control pulses: (i) predominant labeling of short chains (5S) with reduced amounts of radioactivity in the longer growing viral DNA strands (smaller than or equal to 16S), and (ii) a one-third to one-half reduction in size for short DNA chains labeled in the presence of ara-CTP. Release of the ara-CTP inhibition with excess dCTP resulted in covalent extension of these smaller short chans to approximately the size of regular short chains labeled in the absence of the inhibitor. Isolated short chains synthesized in the presence of ara-CTP exhibited a slightly lower degree of self-complementarity than regular short chains. The predominant labeling of short chains during pulses is, therefore, not a consequence of discontinuous growth on both sides of the replication fork. Similar results were obtained with ara-ATP and N-ethylmaleimide. The experiments indicate that ara-CTP acts primarily on DNA-polymerizing activities, affecting different DNA polymerases to varying degrees. The results are discussed in terms of the possible number and identity of polymerases involved in viral (and cellular) DNA replication.

Physical map of polyoma viral DNA fragments produced by cleavage with a restriction enzyme from Haemophilus aegyptius, endonuclease R-HaeIII

Digestion of polyoma viral DNA with a restriction enzyme from Haemophilus aegyptius generates at least 22 unique fragments. The fragments have been characterized with respect to size and physical order on the polyoma genome, and the 5' to 3' orientation of the (+) and (-) strands has been determined. A method for specific radiolabeling of adjacent fragments was employed to establish the fragment order. This technique may be useful for ordering the fragments produced by digestion of complex DNAs.

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

SV40 DNA is cleaved by the Eco RII and Hae restriction endonucleases to give rise to two different sets of 16 fragments each. These fragments have been ordered by analysis of the products of redigestion of one set of fragments with another restriction enzyme. The cleavage sites have been precisely mapped based on length measurements of the products of each cleavage. This provides a convenient group of small DNA fragments suitable for sequence analysis investigation of the transcripts present in infected cells, or construction of deletion substitution variants of the virus.

Simian virus 40 transcription in productively infected and transformed cells

Several independent cell lines transformed by simian virus 40 carry a species of viral RNA of 900,000 to 1,000,000 daltons. A viral RNA species of similar size is found early in the lytic cycle. Late in the viral lytic cycle, two prominent viral RNA species of about 600,000 and 900,000 daltons are seen. The larger late species shares nucleotide sequences with, and is less stable than, the smaller. These RNA species are located in the cytoplasm of the infected cell. The regions of the viral genome coding for these RNA species are mapped by hybridization of lytic RNA species to fragments of the genome produced by cleavage with Haemophilus aegyptius endonuclease.

Polyoma DNA: a physical map

The action of restriction enzymes on polyoma DNA was studied with uniformly (32)P-labeled viral DNA obtained from either infected 3T6 or secondary mouse-embryo cells. Three restriction enzymes were used to construct a physical map of the polyoma genome. An enzyme from Hemophilus parainfluenzae, Hpa(II), cleaved polyma DNA into eight unique fragments (Hpa(II)-1 to Hpa(II)-8), ranging in size from 27.3 to 1.8% of the genome. An enzyme from Hemophilus influenzae, Hin(III), gave two fragments (56 and 44%); and a third enzyme from Escherichia coli, EcoR(I), cut at a single unique site. The physical map of the polyma genome was constructed from methods involving: (1) further digestion of the fragments produced by enzymes EcoR(I) and Hin(III) with Hpa(II), and (2) analysis of the products of partial digestion with Hpa(II). Analysis by electron microscopy of replicating DNA molecules (less than 50% replicated) cut with the Hin(III) enzyme, in combination with other studies, has indicated that the origin of DNA replication is located at 71 +/- 3 map units from the EcoR(I) cleavage site, probably in Hpa(II)-5.

The nucleotide sequence preceding an RNA polymerase initiation site on SV40 DNA. Part 1. The sequence of the late strand transcript

The nucleotide sequence of the transcript of the "late" strand of the region of SV40 DNA preceding the preferred initiation site for Escherichia coli RNA polymerase has been determined to be U-G-U-A-A-C-C-A-U-U-A-U-A-A-G-C-U-G-C-A-A-U-A-A-A-C-A-A-G-U-U-A-A-C-A-A-C-A-A-C-A-A-U-U-G-Cp. Hemophilus influenza restriction endonuclease cleaves this region 30 nucleotides (base pairs) before the site of initiation of RNA synthesis by RNA polymerase.

Cleavage of circular, superhelical simian virus 40 DNA to a linear duplex by S1 nuclease

S(1) nuclease, the single-strand specific nuclease from Aspergillus oryzae can cleave both strands of circular covalently closed, superhelical simian virus 40 (SV40) DNA to generate unit length linear duplex molecules with intact single strands. But circular, covalently closed, nonsuperhelical DNA, as well as linear duplex molecules, are relatively resistant to attack by the enzyme. These findings indicate that unpaired or weakly hydrogen-bonded regions, sensitive to the single strand-specific nuclease, occur or can be induced in superhelical DNA. Nicked, circular SV40 DNA can be cleaved on the opposite strand at or near the nick to yield linear molecules. S(1) nuclease may be a useful reagent for cleaving DNAs at regions containing single-strand nicks. Unlike the restriction endonucleases, S(1) nuclease probably does not cleave SV40 DNA at a specific nucleotide sequence. Rather, the sites of cleavage occur within regions that are readily denaturable in a topologically constrained superhelical molecule. At moderate salt concentrations (75 mM) SV40 DNA is cleaved once, most often within either one of the two following regions: the segments defined as 0.15 to 0.25 and 0.45 to 0.55 SV40 fractional length, clockwise, from the EcoR(I) restriction endonuclease cleavage site (defined as the zero position on the SV40 DNA map). In higher salt (250 mM) cleavage occurs preferentially within the 0.45 to 0.55 segment of the map.