Calibration of molecular weight scales for DNA

Repair of double-strand breaks and lethal damage in DNA of Ustilago maydis

The size of nuclear DNA from wild-typeUstilago maydiswas determined to be approximately 6·09 ± 0·3 × 108daltons from neutral sucrose gradient sedimentation analysis. Following exposure to ionizing radiation the nuclear DNA size was reduced due to the production of double-strand breaks in the DNA. These breaks were repaired when the irradiated cells were incubated in medium for at least one hour after irradiation. The repair was seen as a shift in the DNA profile from a low molecular weight region where the control DNA sedimented. Inhibition of protein synthesis by cycloheximide prevented this type of repair. Blocking protein synthesis also decreased the survival of irradiated wild-type cells but not radiation-sensitive mutants. Protein synthesis was necessary within the first one and a half hours after irradiation for the survival of wild-type cells to be unaffected. The results provide additional evidence for an inducible repair process inU. maydis.

Recombination in bacteriophage P2: recA dependent enhancement by ultraviolet irradiation and by transfection with mixed DNA dimers

Bacteriophage P2 is known for its exceptionally low rate of spontaneous (non-integrative) recombination, which however may be stimulated by ultraviolet irradiation of the phage. We show here that ligated dimers, made in vitro from mixtures of DNAs of two P2 mutants, upon transfection of lysozyme-spheroplasts give origin to recombinants at high frequency. While spontaneous P2 recombination occurs independently of the main recombination pathway of the bacteria, P2 recombinant formation following either ultraviolet irradiation or transfection with DNA dimers requires at least some element of such a pathway, since it is absent or greatly reduced in recA- bacteria or spheroplasts. It would seen that, in the course of its lytic development, P2 deploys a mechanism that inhibits the main recombination pathway of the host cell, or assumes DNA configurations refractory to it.

High-molecular-weight DNA and the sedimentation coefficient: a new perspective based on DNA from T7 bacteriophage and two novel forms of T4 bacteriophage

The DNA molecules from T7 bacteriophage and a recently obtained mutant form of T4D were studied. The DNA of this T4 mutant contains cytosine in place of all of the glucosylated hydroxymethylcytosines normally present in T4. Molecular weights were measured with an electron microscope technique, and sedimentation coefficients were determined in isokinetic sucrose gradients. T7 DNA was found to have an Mr of 26.5 x 10(6). The T4 mutant, which we have termed T4c, produces two distinct phage head and DNA size clases. DNA from the standard heads (T4c DNA) has an Mr of 114.9 x 10(6), and DNA from the petite heads (T4cp DNA) has an Mr of 82.9 x 10(6). This enabled the derivation of an equation of sedimentation coefficient at zero concentration corrected to water at 20 degrees C versus Mr for the molecular weight range of 25 x 10(6) to 115 x 10(6) that is based solely on cytosine-containing DNA standards, thereby avoiding possible anomalies introduced by the glucosylation and hydroxymethylation of cytosine. The theory of Gray et al. provided the best description of the sedimentation coefficient versus Mr relationship, based on the sedimentation coefficients and the molecular weights of the three DNA standards and other evidence.

Biochemical analysis of damage induced in yeast by formaldehyde. I. Induction of single-strand breaks in DNA and their repair

Analysis of sedimentation profiles in alkaline sucrose gradients showed that, through a metabolic process, formaldehyde (FA) produced single-strand breaks in DNA of exponential phase cells of haploid wild-type Saccharomyces cerevisiae. The production of this type of lesion was dose-dependent. Strains defective in excision-repair of pyrimidine dimers induced by ultraviolet (UV) irradiation showed a reduced capacity to undergo single-stand breaks after treatment with FA. This indicates that the repair pathways of damage induced by UV and FA share a common step. Post-treatment incubation of wild-type cells in growth medium indicate a lag in cell division during which a slow recovery of DNA with a normal size was observed.

Use of ethidium bromide fluorescence enhancement to detect duplex DNA and DNA bacteriophages during zone sedimentation in sucrose gradients: molecular weight of DNA as a function of sedimentation rate

Duplex DNA molecules and DNA bacteriophages have been sedimented through 5--25% sucrose gradients containing ethidium bromide. The location of DNA within the gradients has been determined by illuminating gradients with ultraviolet light and observing the ethidium bromide fluorescence enhancement induced by the DNA. The relative sedimentation rates of linear, duplex DNAs from bacteriophages T4, T5, T7 and an 8.3% T7 deletion mutant have been determined. The distances sedimented by DNA have been corrected, when necessary, for a progressive decrease in sedimentation rate that occurs after the DNA has traversed 40% of the sucrose gradient. The corrected distances sedimented by two DNA molecules, r1' and r2', are related to the DNA molecular weights, m1 and m2, by the equation: r1'/r2' = (m1/m2)0.38 when 0.025--0.70 microgram of each type of DNA is sedimented. Intact bacteriophages were also sedimented in ethidium bromide--sucrose gradients and detected by fluorescence enhancement.

Molecular weight of T2 NaDNA from viscoelasticity

The viscoelastic properties of T2 DNA solutions are used to determine the NaDNA molecular weight in four independent ways from the theory of the beads-springs model. The four molecular weights are 131.9, 132.7, 130.5, and 127.6 X 10(6). The average of these values, adjusted for the probable errors in viscoelasticity and concentration measurements, is (126 +/- 5) X 10(6). The four molecular weights are termed Mtaugamma11, Mtaueta, Mtaugamma, and MtauA; each is different in its sensitivity to molecular weight distribution. Their agreement suggests (1) that the theoretical equations relating each M to the corresponding measured properties are valid, (2) that T2 DNA behaves as a partially free-draining polymer chain, and (3) that our solutions were nearly homogeneous in DNA size. We show that serious errors can result if the viscoelastic properties are not extrapolated to their limits at zero shear rate, as well as at zero DNA concentration, before calculating molecular weight.

Electron microscopy of DNA: determination of absolute molecular weights and linear density

The molecular lengths of several phage DNA's and one plasmid DNA have been measured and the molecular linear density of double stranded DNA under standard conditions has been determined. This determination was possible since the absolute molecular weight for phi X 174 DNA has become known from sequence work. RF DNA of phi X 174 phage consists of 5375 +/- 20 basepairs equivalent to a molecular weight of (3.558 +/- 0.013) x 10(6) dalton and since the length of this DNA has been determined to be 1.71 +/- 0.02 micrometer the molecular linear density of double stranded DNA prepared for electron microscopy under the conditions described is (2.08 +/- 0.03) x 10(6) dalton micrometer-1. These data have been used to determine the molecular weights of several phage DNA's and of the plasmid DNA PML 21. The latter DNA exhibits a remarkable heterogeneity with respect to its size.

A counting method for determining the burst size of defective phages from Bacillus subtilis

The defective phages of Bacillus subtilis cannot be counted by plating as they do not form plaques. In addition, counting under the electron microscope with latex spheres as an internal standard is not possible. The reliability of a method using Escherichia coli phage T4 as a substitute for the latex spheres has been tested and the results compared with those of other methods. Using this method, we determined the burst sizes of the defective phages PBS X, PBS Y and PBS Z under various conditions.

The sucrose gradient and native DNA S20,W, an examination of measurement problems

Sedimentation coefficients of T7, T2H AND T4 DNA were determined with isokinetic sucrose gradients in both 0.1 M and 1 M NaCl. The s values were completely equivalent to those measured by analytical ultracentrifuge and no reduction of s20,w was observed due to the presence of sucrose (anomalous sedimentation). s20,w values are calculated on the basis of both partial specific volume (v) and apparent specific volume (0). Using the latter value s20,w molecular weight relations are derived for 0.1 M and 1 M NaCl solvents. The glucosylation of T2H and T4 DNA appears to influence s20,w in a manner disproportionate to the molecular weight added by glucose.

The flexibility of low molecular weight double-stranded DNA as a function of length. I. Isolation andphysical characterization of seven fractions

Sonicated calf thymus DNA was fractionated by rate zonal centrifugation into seven fractions with weight average molecular weights ranging from 0.28 to 1.3 X 10(6) daltons, as determined by sedimentation equilibrium and light scattering measurements (the latter are described in the accompanying paper). Electron microscopy and sedimentation equilibrium analysis revealed these fractions to be narrowly disperse with Mw/Mn ratios averaging about 1.06. Intrinsic viscosities and sedimentation rates were measured and found to vary linearly with molecular weight in double-logarithmic plots in fair agreement with previously published functions relating these parameters for low molecular weight DNA. Thso agreeing with reported estimates of this parameter for short DNA. These data will be used in the second paper of this series to calculate the persistence length of the DNA fragments in each of the seven fractions by light scattering and hydrodynamic theories for the Kratky-Porod worm-like coil.

The structure of kinetoplast DNA. 2. Characterization of a novel component of high complexity present in the kinetoplast DNA network of Crithidia luciliae

1. Degradation of highly purified kinetoplast DNA (kDNA) networks with restriction endonucleases yields "extra" bands in agarose gels that are absent from digests of mini-circles. Each of the five endonucleases tested, i.e. AluI, HapII, EcoRI, Hsu and HindII + III, yields a unique set of "extra" bands. The "extra" bands consist of linear DNA; they are not mini-circle oligomers and their added molecular weight, calculated from mobility in gels, are around 2 X 10(7). Double digests with two restriction endonucleases yield a new set of "extra" bands, showing that the "extra" bands obtained with different enzymes are all derived from the same complex component of kDNA. In digests of 32P-labelled kDNA an average of 2.3% of the radioactivity is recovered in the "extra" bands. 2. Treatment of kDNA networks with the single-strand-specific S1 nuclease of Aspergillus oryzae preferentially releases a linear DNA with a molecular weight of 26 X 10(6), calculated from mobility in gels. We present evidence that the 'extra' bands obtained with restriction endonucleases are derived from this component. 3. DNA-DNA renaturation analysis of fragmented kDNA shows the presence of a minor complex component with a complexity of about 3 X 10(7), making up less than 10% of the total kDNA. 4. From these results we conclude that 3--5% of the kDNA consists of a homogeneous class of maxi-circles catenated in the mini-circle network. The molecular weight of these maxi-circles is about 26 X 10(6) and they contain a unique, non-repetitive, non-mini-circle nucleotide sequence. This component is a prime candidate for the true mitochondrial DNA of trypanosomes.

Isolation and characterization of Caulobacter crecentus bacteriophage phi Cd1

A DNA-containing bacteriophage, phiCd1, was isolated from sewage and shown to infect both stalked and swarmer cells of Caulobacter crescentus strain CB13B1a. phiCd1 is a small, icosohedral bacteriophage, 60 nm in diameter, which possesses a short, noncontractile tail, 10 to 12 nm in length. The bacteriophage particle is composed of at least eight structural proteins. phiCd1 nucleic acid exists as a linear duplex of DNA as judged by: (i) thermal denaturation (Tm), (ii) CsCl density gradient centrifugation, and (iii) chemical analysis of its base composition. The DNA is 61% guanosine plus cytosine, has a buoyant density in CsCl of 1.721 +/- 0.001 g/cm3, and denatures sharply at 78.5 C in 0.1 SSC (standard saline citrate) buffer. The S20, w value for the DNA is 34.3 +/- 0.1S as compared with T7 DNA, indicating a molecular weight of about 29 x 10(6).

The repair of double-strand breaks in the nuclear DNA of Saccharomyces cerevisiae and its genetic control

With the use of neutral sucrose sedimentation techniques, the size of unirradiated nuclear DNA and the repair of double-strand breaks induced in it by ionizing radiation have been determined in both wild-type and homozygous rad52 diploids of the yeast Saccharomyces cerevisiae. The number average molecular weight of unirradiated DNA in these experiments is 3.0 X 10(8)+/-0.3 Daltons. Double-strand breaks are induced with a frequency of 0.58 X 10(-10) per Daltonkrad in the range of 25 to 100 krad. Since repair at low doses is observed in wild-type but not homozygous rad52 strains, the corresponding rad52 gene product is concluded to have a role in the repair process. Cycloheximide was also observed to inhibit repair to a limited extent indicating a requirement for protein synthesis. Based on the sensitivity of various mutants and the induction frequency of double-strand breaks, it is concluded that there are 1 to 2 double-strand breaks per lethal event in diploid cells incapable of repairing these breaks.

Demonstration of infectious DNA in transformed cells. II. Characterization of uptake of SV40-transformed mouse cell DNA by simian cells

The initial steps in the DNA-transfer, or transfection, method of virus rescue were characterized using primary green monkey (GMK) cells exposed to SV40-transformed mouse (SV-3T3) cell DNA in the presence of 1 mg/ml DEAE-dextran. When large amounts (10-50mug) of high molecular weight DNA (greater than 10(7) daltons) were inoculated onto 10(6) GMK cells, usually less than 1 mug became cell-associated. DNA fragmented to a size of 1-3 X 10(6) daltons was bound more efficiently by the recipient cells, but generally only 5-10 per cent of the inoculum (representing 1-4 mug) was taken up. Approximately 50 per cent of the cell-associated DNA had penetrated to a DNase-resistant state by the end of the 30-minute incubation period. The effect of the size of thr transformed cell DNA molecule on the recovery of SV40 in transfection experiments was investigated. The trend appeared to be that rescue was more efficient with the larger molecular weight samples.

In vitro modification and restriction of phage phi-105c DNA with Bacillus subtilis N cell-free extract

The enzymes involved in host-controlled modification and restriction by Bacillus subtilis strain N were detected in cell free extracts. In the presenct of Mg2+ the N-specific endonucleases cleaved unmodified DNA but did not attack phi-105C. N DNA carrying N-specific modification. The restriction endonuclease required neither SAM nor ATP for its activity. The N-specific modification enzyme was active only in the presence of SAM, indicating that modification in this syteem is a methylation of DNA.

Size of the chromosome of Pseudomonas aeruginosa PAO

Electron microscope examination and velocity sedimentation analysis of the deoxyribonucleic acid released from Pseudomonas aeruginosa spheroplasts indicate that this organism carries the bulk of its genetic determinants in a single duplex deoxyribonucleic acid molecule having a molecular mass of 2.1 x 10(9) daltons.

Determination of the sedimentation coefficient of vaccinia virus DNA by analytical ultracentrifugation

By releasing intact molecules of vaccinia virus DNA, it has been possible to determine the sedimentation coefficient by analytical ultracentrifugation. The value found was 92S, which corresponds to a molecular weight of 161x10(6).

Round of replication mutant of a drug resistance factor

A derivative of the R factor NR1 (called R12) has been isolated which undergoes an increased number of rounds of replication each division cycle in Proteus mirabilis, Escherichia coli, and Salmonella typhimurium. The alteration resulting in the increased number of copies (round of replication mutation) is associated with the transfer factor component of the R factor. R12 has the same drug resistance pattern as NR1, is the same size as shown by sedimentation in a sucrose gradient and electron microscopy (63 x 10(6) daltons), and has the same partial denaturation map. The level of the R factor gene product chloramphenicol acetyltransferase has been examined in P. mirabilis and was found to be consistent with gene dosage effects. The plasmid to chromosomal deoxyribonucleic acid ratio of NR1 increases several fold after entry into stationary phase, whereas this ratio for R12 remains approximately constant. Individual copies of R12 are selected at random for replication from a multicopy plasmid pool. A smaller percentage of R12 copies replicate during amino acid starvation than has previously been found for NR1 in similar experiments.

Evidence for heterogeneity in populations of T5 bacteriophage

Each T5 stock contains a population of particular phages that, just after adsorption onto the host bacteria. release their entire chromosome outside the bacterial membrane in a place where it is sensitive to bacterial enzymes. This release takes place before the sensitization step to deprivation of calcium and before the transfer of the first-step DNA fragment. Secondarily, this released DNA is degraded by bacterial enzymes, mainly by the endonuclease I; the products of degradation are spontaneously released in the surrounding medium. Thus, in each T5 phage stock it seems that there is a minor population that is deficient for the mechanism of controlled DNA injection into the bacteria.