Determination of the nuclear DNA content of Saccharomyces cerevisiae and implications for the organization of DNA in yeast chromosomes.

The DNA content of the nucleus of the yeast Saccharomyces cerevisiae has been determined by both renaturation kinetics and DNA per cell measurements. Renaturation kinetics experiments were performed by following the decrease of optical hyperchromicity at 260 nm and by hydroxyapatite chromatography. DNA per cell measurements were made by the diaminobenzoic acid method and by the ethidium bromide method of Klotz &; Zimm (1972b). The conclusion from the above experiments is that the S. cerevisiae nucleus contains 9 × 10⁹ ± 2 × 10⁹ daltons of DNA. Previously we (Lauer &; Klotz, 1975) had measured the molecular weight of the largest piece of DNA in the yeast nucleus to be 2 × 10⁹ ± 0.2 × 10⁹. Here we extend this work by using a more highly protein-denaturing buffer system and conclude that the largest piece of DNA in the S. cerevisiae nucleus contains 1.5 × 10⁹ to 2.2 × 10⁹ daltons of DNA in both haploid and diploid cell lysates. From genetics, the largest yeast chromosome should contain 13% of the genome, or 0.9 × 10⁹ to 1.5 × 10⁹ daltons of DNA (using our DNA per cell range). Thus, the large DNA we measure contains from one to two times the amount of the DNA predicted from genetics to be in the largest chromosome. In light of these new data, viscoelastic measurements on yeast DNA are now consistent with the idea that each chromosome contains one piece of DNA.     

A newly isolated densonucleosis virus from Pseudoplusia includens (Lepidoptera: Noctuidae)

An icosahedral DNA virus isolated from the soybean looper, Pseudoplusia includens, was characterized. Purified virus had a diameter of 20 ± 1 nm and negatively stained preparations showed a trend to form linear to three-dimensional crystals. The virus had a sedimentation coefficient of 120 ± 3 S and a buoyant density of 1.40 ± 0.01 g/cm³. The DNA content of the virus was 37.8 ± 0.1% and the absorption spectrum showed it to be a typical nucleoprotein. Viral DNA in situ was shown to be single-stranded by staining the virus with acridine orange as well as by reaction to formaldehyde. Evidence of inverted terminal repetition of the DNA was observed by electron microscopy. The terminal repetition comprises ca. 6–7% of the genome. The molecular weight of the ssDNA was 2.0 ± 0.1 × 10⁶ as determined by agarose gel electrophoresis or 2.1 ± 0.1 × 10⁶ as determined by electron microscopy. Four virion proteins with molecular weights of 46.5 ± 0.1, 54.0 ± 0.1, 64.0 ± 0.2, and 87.0 ± 0.1 × 10³ were detected by 9% SDS-polyacrylamide gel electrophoresis. Double-diffusion tests showed the virus to be serologically related but not identical to DNV-1. Ultrathin sections showed that the nucleus of the hemocyte, muscle, hypodermal, and fat body cells contained virus-like particles. The chromatin of an infected nucleus always underwent a margination and the nucleoplasm was often replaced largely by virions.Data indicate that the virus belongs to the Densovirus of the family Parvoviridae.     

Transfection of restrictionless Escherichia coli by bacteriophage T7 DNA: Effect of in vitro erosion of DNA by λ exonuclease

T7 bacteriophage infects with equal efficiency restriction-proficient Escherichia coli K12 cells and the restriction-deficient mutants. To the contrary, the purified phage DNA transfects wild-type cells at a very low efficiency (10^?9 plaques/genome equivalent). Mutations in the recB recC (exonuclease V) and sbcB (exonuclease I) loci increase the transfecting efficiency tenfold. A 1000-fold increase is obtained with cells deficient in restriction. No further increase is observed in hosts carrying both sets of mutations. The transfecting activity of the DNA on restriction-deficient hosts increases another 20-fold (up to 4 × 10^?5 plaques/genome equivalent) by complete erosion of the redundant regions of DNA with λ exonuclease, both in rec⁺ and recB recC sbcB genotypes. Circles and linear oligomers arising from the annealing of eroded DNA show the same transfecting activity as the unannealed monomers. The terminal redundancy of the genome, as measured by the onset of annealability of eroded molecules, was found to comprise 50 to 100 base-pairs.     

Multiple forms of human dihydrofolate reductase messenger RNA: Cloning and Expression in Escherichia coli of their DNA coding sequence

The programming capacity for the synthesis of human dihydrofolic acid reductase in a rabbit reticulocyte lysate has been found to be greatly enhanced in the polysomal poly(A)-containing RNA from a methotrexate-resistant human cell variant (6A3), as compared to the RNA from its parental line (VA₂-B). A major fraction of this promoting activity is associated with a 3.8 × 10³ base RNA species detectable as a band in the ethidium bromide-stained electrophoretic pattern of the RNA from 6A3 cells, but not in the RNA from VA₂-B cells. Furthermore, sucrose gradient fractionation experiments have indicated that another substantial portion of the messenger activity is associated with RNA components around 10³ bases in size. Double-stranded complementary DNA synthesized from total poly(A)-containing RNA of 6A3 cells has been size fractionated, and both large (1400 to 3800 base-pairs) and small size complementary DNA (600 to 1400 base-pairs) species have been used separately to transform Escherichia coli χ2282 with pBR322 as a vector. Of 76 transformants obtained with the large size complementary DNA, identified by a differential colony hybridization assay, none has expressed the dihydrofolic acid reductase coding sequence in E. coli, as judged by resistance to trimethoprim. By contrast, eight trimethoprim-resistant transformants have been obtained using the small size complementary DNA, and their plasmids have been shown to contain the dihydrofolic acid reductase coding sequence by restriction mapping and DNA sequencing; moreover, immunoautoradiographic experiments have revealed the presence in the extracts of two of these transformants of a protein with the electrophoretic mobility and immunoreactivity of human dihydrofolic acid reductase. Restriction mapping and DNA transfer hybridization experiments have further indicated that the inserts of the chimaeric plasmids conferring trimethoprim resistance upon the host and of those lacking this capacity cover together a complementary DNA region of about 3.35 × 10³ base-pairs, in which the 564 base-pair dihydrofolic acid reductase coding stretch is located near the 5′ end of the sense strand. RNA transfer hybridization experiments using different cloned complementary DNA fragments as probes have shown the presence of three species of dihydrofolic acid reductase-specific messenger RNAs, with sizes of 3.8 × 10³, 1.0 × 10³ and 0.8 × 10³ bases, differing in the length of the 3′ untranslated region, in the poly(A)-containing RNA from two methotrexate-resistant variants, 6A3 and 10B3, and, in greatly reduced amounts, in the RNA from their respective parents, VA₂B and HeLa BU25.     

The ribosomal DNA of Calliphora erythrocephala: The cistron classes of total genomic DNA

The composition of the genome set of ribosomal DNA cistrons in Calliphora erythrocephala (a Dipteran fly) has been analyzed. In contrast to previously cloned fragments of the rDNA (see Beckingham & White, 1980), the great majority of the rDNA cistrons do not contain introns in the 28 S β coding region. In the strain of flies studied, however, most cistrons fall into two discrete length classes that are present in approximately equal amounts in the genome. These results from distinct size variants of the non-transcribed spacer in the cistron population.The major genome class of intron-containing (intron⁺) rDNA cistrons was found to constitute approximately 5% of all cistrons and to contain introns of 6·1 × 10³ base-pairs. Interestingly, the intron⁺ cistrons were shown to be clustered within the rDNA and to contain a different population of non-transcribed spacer/external transcribed spacer (NTS + ETS) regions to that seen amongst the intron^? cistrons. The implications of these findings in relation to the mechanisms that maintain homogeneity within tandemly repeated gene sets are discussed.Some evidence for the existence of intron sequence DNA outside the rDNA is presented.     

The DNA content of sperm and hemocyte nuclei of the silkworm,Bombyx mori L.

To estimate the size of the haploid genome of the silkworm, Bombyx mori (Lepidoptera), amounts of Feulgen-DNA staining in individual nuclei of primary spermatocytes, spermatids, maturing sperm, and larval or pupal hemocytes were determined with an integrating microdensitometer and compared with the Feulgen-DNA levels found for chicken erythrocyte nuclei, or the sperm and erythrocyte nuclei of Xenopus laevis that were included with each Bombyx preparation as empirical reference standards of 2.5, 3.15, and 6.3×10^?12 g DNA per cell, respectively. Under these conditions, the haploid male genome of B. mori was estimated as 0.52±0.01 (S.E.)×10^?12 g DNA, corresponding to a molecular weight of roughly 3.1×10¹¹ daltons. From similar measurements of Feulgen-stained hemocyte nuclei, approximately 1.0±0.05 (S.E.)×10^?12 g DNA was estimated for the diploid or 2C male genome of Bombyx. These values compare favorably with estimates of genome size based upon analysis of the kinetics of reassociation of DNA isolated from B. mori and provide an independent basis for assessing the degree of polyploidy achieved by the giant nuclei in the posterior silk gland prior to its secretion of fibroin at the end of the fifth larval instar.     

Restriction endonuclease map of the chloroplast DNA of Chlamydomonas reinhardii

The chloroplast DNA of Chlamydomonas reinhardii has been examined by restriction endonuclease analysis. EcoRI, BamHI and BglII produce 30, 17 and 12 fragments, respectively, whose sites have been determined by electron microscopy and by comparative gel electrophoresis. These fragments have been ordered into a circular map which corresponds to a genome size of M_r = 126 × 10⁶. The map was established by comparing the double digests of individual restriction fragments and by hybridizing purified labelled fragments to restriction enzyme digests of chloroplast DNA. The restriction fragments were isolated by molecular cloning or by preparative agarose gel electrophoresis.The two sets of chloroplast ribosomal RNA genes are contained within two inverted repeats of 13 × 10⁶ molecular weight, which are located nearly at opposite sides of the map. In addition, the mapping studies have revealed the presence of short repeated base sequences which are interspersed throughout the chloroplast genome.     

Pea (Pisum sativum) cells arrested in G2 have nascent DNA with breaks between replicons and replication clusters

DNA fiber autoradiography and alkaline sucrose sedimentation of DNA of cultured pea-root cells (Pisum sativum) arrested in G2 by carbohydrate starvation demonstrated that nascent DNA molecules of replicon (16–27 × 10⁶ D) and apparent cluster (~330 × 10⁶ D) size were not joined. That the arrested cells were in G2 was confirmed by single-cell autoradiography and cytophotometry. In pea there are about 18 replicons per average cluster, 4.2 × 10³ clusters, and 7.7 × 10⁴ replicons per genome.     

Conformation change of cytochrome c. II. Ferricytochrome c refinement at 1.8 A and comparison with the ferrocytochrome structure

The X chromosomal nucleolus organizer of Drosophila hydei contains about 500 ribosomal RNA genes. The 28 S rRNA coding region of about 50% of these genes is interrupted by an intervening sequence of 6.0 × 10³ base-pairs. Restriction enzyme analysis revealed that more than 90% of the rRNA genes with intervening sequences are present as one or a few clusters within the X chromosomal nucleolus organizer. Furthermore, even though X chromosomal rRNA genes show several distinct size classes of non-transcribed spacers, the cluster of repeating units containing an intervening sequence has major spacer lengths of 4.4 × 10³ and 4.6 × 10³ base-pairs; spacers 5.1 × 10³ base-pairs in length are mainly linked with genes lacking the intervening sequence.     

The genetic behaviour of a cloned mouse ribosomal DNA segment mimics mouse ribosomal gene evolution.

A 1.7 × 10³ base-pair SalI fragment of mouse ribosomal gene spacer undergoes recA-independent deletions of DNA in units of approximately 126 base-pairs when cloned in λ or bacterial plasmids. When we examined the structure of the 1.7 × 10³ base-pair piece with PvuII we found it to be composed of about equal numbers of copies of each of two subrepeating units, 120 and 130 base-pairs in size. The correlation between the size of the structural subunits and the functional genetic unit of this fragment as expressed in Escherichia coli led us to study the organization of these sequences in mice. SalI (or HindII) digests of DNA samples from wild and inbred strains revealed extensive heterogeneity in the size of fragments homologous to this 1.7 × 10³ base-pair piece. A total of 15 different size classes were detected in our samples. We found that these fragments were also organized in PvuII repeating units about equal in size to the PvuII repeats in the cloned 1.7 × 10³ base-pair piece. Using an objective analytical procedure (see the Appendix) we determined that the 15 different fragments found in our mouse DNA samples probably originated as a result of genetic events based on a 135 base-pair structural unit.We consider the similarity between the size of the PvuII structural unit and the unit of genetic behavior in both the cloned and uncloned DNA samples to be significant. We suspect that there are aspects of the nucleotide structure or organization of the PvuII repeating units that play a dominant role in its genetic behavior, regardless of whether these sequences are present in E. coli or mice. We believe that the clones containing this mouse sequence may provide an experimental system for studying the nature of the genetic events that are involved in multigene evolution.     

Isolation and characterization of the oligo(dA-dT) clusters and their flanking DNA segments in the rabbit genome

Duplex DNA containing (dA-dT) clusters² can be bound specifically to poly(U)-Sephadex in high-salt solutions by the formation of a (dA-dT)rU triple helix. By decreasing the salt concentration the DNA is fractionated predominantly on the basis of the length of the (dA-dT) cluster it contains, long clusters being bound tighter than short ones. A stepwise elution protocol was used to obtain three fractions containing (dA-dT) clusters of which the average length is approximately 12, 16 and 23 base-pairs, respectively. Each given fraction probably also contains impure (dA-dT) clusters of greater length than these but which have additional bases inserted in the (dA-dT) sequence. When bound to poly(U) these clusters should give triplexes of equivalent stability to those formed with shorter pure (dA-dT) tracts.Measurement of the distribution of rabbit DNA in these poly(U)-Sephadex fractions as a function of DNA size shows that the three (dA-dT) cluster length-classes are interspersed with one another in the rabbit genome. The short, intermediate and long clusters are spaced approximately once every 6000, 12,000 and 18,000 base-pairs throughout at least 80% of the rabbit genome. There is an average of one (dA-dT) cluster every 3300 base-pairs in rabbit DNA.When rabbit DNA is sheared to 400 base-pairs, 50% of the molecules containing a (dA-dT) cluster contain a sequence reiterated approximately 2 × 10⁵-fold in the rabbit genome although only 20% of unfractionated DNA of this size contains such repeated DNA. The remaining 50% of the clusters are linked to DNA sequences occurring one to five times per haploid genome.     

Characterization of repetitive DNA in rye (Secale cereale)

Nuclear DNA of rye (Secale cereale), a plant species with a relatively large genome (i.e., 18 pg diploid), has been characterized by determination of its content in repetitive sequences, buoyant density, and thermal denaturation properties. The reassociation kinetics of rye DNA reveals the presence of 70 to 75% repeated nucleotide sequences which are grouped into highly (Cot 1) and intermediately repetitive (Cot 1–100) fractions. On sedimentation in neutral CsCl gradients, native, high molecular weight DNA forms an almost symmetrical band of density 1.702 g/cm³. The highly repetitive DNA (Cot 1), on the other hand, is separated into two distinct peaks; the minor component has a density of 1.703 g/cm³ corresponding to that of a very rapidly reassociating fraction (Cot 0.01) which comprises 10 to 12% of the rye genome. The latter DNA contains segments which are repeated 6×10⁵ to 6×10⁶ times. The major peak of the Cot 1 fraction shows a density of 1.707 g/cm³ and consists of fragments repeated about 3.7×10⁴ times. The intermediately repetitive DNA is much more heterogeneous than the Cot 1 fraction and has a low degree of repetition of the order of 8.5×10². The melting behavior of the Cot 1 fraction reveals the presence of a high degree of base pairing (i.e., 7% mismatching). When native rye DNA is resolved into fractions differing in GC content by hydroxyapatite thermal column chromatography and these fractions are analyzed for the presence of repetitive sequences, it is observed that the highly redundant DNA (Cot 1) is mostly located in the fraction denaturing between 80° and 90°C. This result suggests that highly repetitive rye DNA occurs in a portion of the genome which is neither very rich in AT nor in GC.     

The free solution mobility of DNA

The free solution mobility of DNA has been measured by capillary electrophoresis in the two buffers most commonly used for DNA gel electrophoresis, Tris-borate-EDTA (TBE) and Tris-acetate-EDTA (TAE). The capillaries were coated with polymers of either of two novel acrylamide monomers, N-acryloylaminoethoxyethanol or N-acryloylaminopropanol, both of which are stable at basic pH and effectively eliminate the electroendosmotic mobility due to the capillary walls. The free solution mobility of DNA in TAE buffer was found to be (3.75 ± 0.04) × 10⁻⁴ cm² V⁻¹ s⁻¹ at 25°C, independent of DNA concentration, sample size, electric field strength, and capillary coating, and in good agreement with other values in the literature. The free solution mobility was independent of DNA molecular weight from ∼ 400 base pairs to 48.5 kilobase pairs, but decreased monotonically with decreasing molecular weight for smaller fragments. Surprisingly, the free solution mobility of DNA in TBE buffer was found to be (4.5 ± 0.1) × 10⁻⁴ cm² V⁻¹ s⁻¹, about 20% larger than observed in TAE buffer, presumably because of the formation of nonspecific borate-deoxyribose complexes. © 1997 John Wiley & Sons, Inc. Biopoly 42: 687–703, 1997     

Specific Origin in SV40 DNA Replication

THE oncogenic virus SV40 contains a covalently closed circular DNA molecule of 3 × 10⁶ molecular weight¹. In infected permissive cells, SV40 DNA replicates through a Cairns type intermediate² with the parental strands forming a partially twisted, covalently closed molecule³. We have used a specific bacterial restriction endonuclease⁴ to analyse SV40 DNA replication. The restriction endonuclease of H. influenzae makes double-strand breaks in DNA at specific hexanucleotide sequences^{5, 6} and splits SV40 DNA into eleven fragments, separable by Polyacrylamide gel electrophoresis, ranging in molecular weight from 6.5 × 10⁵ (about 20% of the molecule) to 7.4 × 10⁴ (about 2.5% of the molecule). The largest eight fragments are present in the digest in amounts equimolar with the starting DNA⁴. Therefore, by digesting labelled replicating SV40 DNA and newly completed DNA and measuring the relative yield of each fragment, we could determine whether a particular region of the DNA is synthesized first or last and also estimate the time needed to replicate one molecule completely.     

Determination of the molecular weight of Saccharomyces cerevisiae nuclear DNA

Viscoelastic retardation-time experiments on the DNA released from spheroplasts of the yeast Saccharomyces cerevisiae yield a molecular weight of 2 × 10⁹ for the largest DNA, assuming linear unbranched DNA, and of 4.3 × 10⁹ assuming circular unbranched DNA. Both log and stationary-phase cells give the same results. Comparison of these results with the nuclear DNA content of S. cerevisiae determined by renaturation kinetics suggests that the largest piece of DNA in the yeast nucleus may, at least during part of the cell cycle, consist of from one-fourth to all of the yeast genome.     

Characterization of the DNA of Hyalophora cecropia

DNA was isolated from the pupae and various tissues of pharate adults of the silkmoth Hyalophora cecropia. CsCl equilibrium density analysis showed the presence of one major band at 1.693 and two minor satellites, 1.705 and 1.709, comprising 3 and 6% respectively of the total DNA. We could detect no difference in the renaturation kinetics of DNA prepared from pupal or pharate adult tissues. The genome appears to be composed of 30% redundant and 70% unique sequences. The haploid information content of the unique sequences is 11.4 × 10¹⁰ daltons.     

Characterization of cytoplasmic and nuclear genomes in the colorless alga Polytoma

DNA isolated from purified nuclei of Polytoma obtusum has a buoyant density of 1.711 g/ml in CsCl, a Tm of 91.3° C in SSC, and a G + C content of 52.5% as determined by base composition analysis. Thermal dissociation and reassociation studies indicated that this nuclear DNA contains a considerable amount of heterogeneity. Under appropriate reannealing conditions for denatured DNA, about 15% of the DNA reannealed to form a satellite peak at a density of 1.711 g/ml within one hour. Native DNA fractions of different average buoyant densities, ranging from 1.723 to 1.708 g/ml were also obtained in a preparative CsCl gradient, indicating the presence of intermolecular heterogeneity at a molecular size of 8.5×10⁶ daltons. The nuclear DNA reassociated as three distinct classes. The very fast species constituted about 20 % of the total hyperchromicity, the class of intermediate rate comprised roughly 10% of the nuclear DNA, while the remaining 70% consisted of unique sequences. The haploid genome set was estimated by renaturation kinetics studies to contain 5.0×10¹⁰ daltons of DNA or 7.5×10⁷ nucleotide pairs. The analytical complexity of the total nuclear genome was found to be 9.35×10¹⁰ daltons, thus indicating that vegetative cells of P. obtusum are diploid.     

Organization of African green monkey DNA at junctions between alpha-satellite and other DNA sequences

Segments of African green monkey DNA containing sequences of the highly reiterated cryptic satellite DNA called α-satellite were selected from a library in λ bacteriophage. This λ library was constructed to enrich for monkey segments that contain (1) irregular regions of α-satellite and (2) α-satellite linked to other monkey sequences. At least 11 of 15 cloned monkey segments between 13 × 10³ and 16 × 10³ base-pairs in length, selected by hybridization to α-satellite, also include other monkey sequences.In general, α-satellite sequences close to the junctions with non-α-satellite DNA contain an abundance of divergent forms compared to the average frequency of such forms within total α-satellite. Many of the cloned segments are missing some of the HinIII sites that occur once in most monomer units of α-satellite, and likewise several of the cloned segments contain restriction sites that rarely occur in α-satellite as a whole. In some segments HinIII sites occur that are spaced at distances other than the basic multiple of 172 base-pairs. At least one of the cloned segments, however, is composed mainly of typical 172 base-pair long α-satellite monomer units.Several of these cloned DNAs have been mapped by restriction endonuclease digestion and Southern blot analysis and the arrangements of α-satellite and non-α-satellite sequences have been determined. In addition to segments that contain a boundary where satellite meets other types of sequence, some contain two such boundaries and thus satellite flanks a non-α-satellite segment. Further, two different types of non-α-satellite sequence appear to be common to more than one phage, perhaps indicating some recurring organization at boundaries.