Sedimentation rate as a measure of molecular weight of DNA

The distribution of radioactive recovery in randomly cut and sedimented DNA

Viral DNA is studied by the technique of radioactive labelling and subsequent ultra centrifugation which separates it from reference DNA according to length or density. One hypothesis that frequently is of service is that the strands of DNA being studied are randomly cut along their lengths. Often the average number of cuts, λ, per unit length is either known by the nature of the experiment or is desired as a statistic. If radioactive phosphorous, P32, is used to label the DNA, e.g., 6 P32 atoms per unit length of 200,000 nucleotides (each of which is connected to its neighbor by two phosphorous-containing links) then within two weeks about 3 P32 atoms will have decayed and the DNA obtained, once separated into single stranded form (denatured), will form a predictable distribution of sizes. Of course 3 decays may be obtained more quickly by starting with more than 6 P32 atoms per unit length.

DNA fragment mass distributions following molecular recombination

A mathematical model for the process of recombinational repair of DNA damage is presented. Based on the model, a method is proposed for analyzing fragment mass distributions from experiments designed to detect recombinational repair in cells. The procedures developed can be used to analyze experiments involving sucrose-gradient measurements of mass distributions. The model also provides a framework for discussion of various molecular models of this repair process.

DNA fragment mass distributions following molecular recombination

A mathematical model for the process of recombinational repair of DNA damage is presented. Based on the model, a method is proposed for analyzing fragment mass distributions from experiments designed to detect recombinational repair in cells. The procedures developed can be used to analyze experiments involving sucrose-gradient measurements of mass distributions. The model also provides a framework for discussion of various molecular models of this repair process.

Thymine Starvation and Single-Strand Breaks in Chromosomal Deoxyribonucleic acid of Escherichia coli

Single-strand breaks, as measured by the McGrath and Williams procedure, occur in chromosomal deoxyribonucleic acid of Escherichia coli cells during thymine starvation.

Methods for the determination of deoxyribonucleic Acid homologies in streptomyces

Variations of the membrane filter technique for deoxyribonucleic acid (DNA) hybridizations were studied with respect to Streptomyces species. At the temperatures required for specific hybridization of DNA with the high melting temperature (T(m)) characteristic of Streptomyces, large amounts (up to 97%) of filter-bound DNA became eluted, in all reaction mixtures studied, within 21 hr. In most solutions this leaching was increased by the presence of sheared denatured DNA. Incubation of DNA-loaded filters in a solution of 50% formamide containing 6x standard saline citrate, at 48 C for 40 hr, was judged to be the best set of conditions tested based on relatively good retention of immobilized DNA, very low hybridization with unrelated DNA of a similarly high T(m) (from Sarcina lutea), and the formation of complexes similar in thermal stability to the native DNA. The expression of results as sheared DNA bound in relation to long-chain DNA retained is recommended when a high concentration of sheared DNA relative to immobilized DNA is used.

Heteroduplex mapping of heat-resistant deletion mutants of bacteriophage t5

The bacteriophage T5 is known to spontaneously generate deletion mutants (st mutants) exhibiting enhanced resistance to heat inactivation in citrate buffer. A series of such mutants has been isolated and the deletions visualized by electron microscopy of heteroduplex molecules. The deletions are found to cluster in one region of the chromosome.

DNA FROM BACTERIOPHAGE LAMBDA: MOLECULAR LENGTH AND CONFORMATION

The length of the DNA molecules from wild-type lambda bacteriophage is 17.2 micro, corresponding to a molecular weight of 33 million in the B form. The molecules from a double-deletion mutant of lambda are 23 percent shorter. Both types of molecules join ends at 60 degrees C to form circular molecules or polymers. The point of junction cannot be distinguished by any irregularity in the uniform duplex molecule.

THE ARRANGEMENTS OF NUCLEOTIDE SEQUENCES IN T2 AND T5 BACTERIOPHAGE DNA MOLECULES

The genetic map of T4 (and T2) bacteriophage is circular but the DNA molecule that is liberated by phenol extraction is a linear duplex of polynucleotide chains. If the genetic map is related to the physical structure of the DNA molecule, the problem arises as to how a linear molecule can give rise to a circular map. An explanation can be made on the basis that the bacteriophage liberate molecules which have nucleotide sequences which are circular permutations of each other. Thus, markers which are most distant on one molecules are closest together on another. To test this hypothesis, the middles of T2 and T5 DNA molecules were mechanically deleted and the absence of certain nucleotide sequences was tested by "renaturation" or "reannealing" experiments using columns containing denatured DNA immobilized in agar beads. The results indicate that when the middles are deleted from the T5 DNA molecule, some special sequences are removed; whereas, when the middles are deleted from the T2 DNA molecule, no special group of sequences is removed. This would indicate that T2 molecules begin at different points in their nucleotide sequence, while T5 molecules all begin at the same point. It is likely that this permutation of sequences of T2(T4) molecules is related to the circularity of their genetic map.

INDUCTION AND PROPERTIES OF A TEMPERATURE BACTERIOPHAGE FROM BACILLUS STEAROTHERMOPHILUS

Welker, N. E. (University of Illinois, Urbana), and L. Leon Campbell. Induction and properties of a temperate bacteriophage from Bacillus stearothermophilus. J. Bacteriol. 89:175-184. 1965.-Bacillus stearothermophilus 1503-4R growing at 55 C was induced to lyse either when 0.05 mug/ml of mitomycin C was added or when it was exposed to ultraviolet light for 30 sec. Lysis of the induced cultures occurred 45 to 60 min after induction. Phage were assayed on B. stearothermophilus 4S giving turbid plaques 0.05 to 0.3 cm in diameter. Noninduced cultures of 1503-4R spontaneously produced one phage per 2.8 x 10(6) bacterial cells. The optimal temperature for phage production and assay was found to be 55 C. B. stearothermophilus 1503-4R was immune to the isolated temperate phage (TP-1) and to a clear-plaque mutant phage (TP-1C), even when tested at phage mutliplicities of 100. TP-1 and TP-1C phage were identical morphologically having a head 65 mmu in diameter and a tail 240 mmu long and 12 mmu wide. TP-1C phage deoxyribonucleic acid (DNA) had an S(20,w) value of 24.1 and a calculated molecular weight of 1.21 x 10(7). DNA base compositions of TP-1 and TP-1C phage were identical (42% guanine + cytosine), but differed significantly from those of the lysogenic or indicator strains of B. stearothermophilus (50% guanine + cytosine). No unusual bases were detected in either the bacterial or phage DNA.

Oligomerization and intracellular protein transport: dimerization of intestinal dipeptidylpeptidase IV occurs in the Golgi apparatus

It was postulated that newly synthesized membrane proteins need to be assembled into oligomers in the endoplasmic reticulum in order to be transported to the Golgi apparatus. By use of the differentiated human adenocarcinoma cell line Caco-2, the general validity of this proposal was studied for small intestinal brush border enzymes which are dimers in most mammalian species. Chemical cross-linking experiments and sucrose gradient rate-zonal centrifugation revealed that dipeptidylpeptidase IV is present as a dimer in the brush border membrane of Caco-2 cells whereas the disaccharidase sucrase-isomaltase appears to be a monomer. Dipeptidylpeptidase IV was found to dimerize immediately after complex glycosylation, an event associated with the Golgi apparatus. Dimerization of this enzyme was inhibited by CCCP but did not depend on complex glycosylation of N-linked carbohydrates as assessed by the use of the trimming inhibitor 1-deoxymannojirimycin. It is concluded that dimerization of dipeptidylpeptidase IV occurs in a late Golgi compartment and therefore cannot be a prerequisite for its export from the endoplasmic reticulum.

Formation and stability of interstrand cross-links induced by cis- and trans-diamminedichloroplatinum (II) in the DNA of Saccharomyces cerevisiae strains differing in repair capacity

Four haploid yeast strains differing in proficiency for DNA repair were treated with cis- or transDDP. The wild type was least sensitive while the excision-deficient mutants rad1, rad2 and snm1 exhibited higher sensitivities to either platinum compound. In all four strains tested cisDDP showed a two- to five-fold higher cytotoxicity than equimolar concentrations of transDDP. DNA interstrand cross-linking was caused by both agents in all strains. However, transDDP introduced more DNA cross-links at exposure times up to 6 h while cisDDP was the more active cross-linking agent at longer times. There was no clear-cut correlation of the number of DNA interstrand cross-links with survival. Formaldehyde-treated cells showed DNA with lower buoyant density due to proteinase K sensitive DNA-protein cross-linking; this effect was not observed after treatment with either platinum compound. Post-treatment incubation of wild-type cells exposed to cisDDP led to degradation of DNA by single and double-strand breaks, parallel with further increase of DNA interstrand cross-linking. DNA from transDDP-treated cells did not show extensive degradation although interstrand cross-links were lost during liquid holding.

Molecular dosimetry of 8-MOP + UVA-induced DNA photoadducts in Saccharomyces cerevisiae: correlation of lesions number with genotoxic potential

Acid hydrolysis of purified DNA extracted from cells of a haploid repair-proficient (RAD) yeast strain that had been treated with 8-MOP + UVA revealed the existence of two major and one minor thymine photoproduct. At survival levels of the RAD strain between 100% and 1% furanside monoadducts constituted the major DNA lesion, followed by diadducts that, at the lowest survival level, nearly reached 50% of the thymine photoproducts; pyrone-side monoadducts were only detectable at the highest UVA exposure dose applied and clearly constitute a minority photoproduct. The number of induced diadducts was verified by determination of interstrand cross-links via denaturation and renaturation of 8-MOP + UVA-treated DNA from RAD and rad2 yeast strain. 8-MOP + UVA was shown to induce two types of locus-specific mutations: reversion of the lys1-1 ochre allele was between 20- to 50-fold higher than that of the his4-38 frameshift allele. Mutant yield for the lys 1-1 reversion was the same in RAD and excision repair-deficient rad2-20 strains whereas frameshift mutagenesis was about eightfold higher in the rad2-20 background.

Inactivation of human hepatitis B virus DNA polymerase by pyridoxal 5'-phosphate

Human hepatitis B virus (HBV) DNA polymerase activity was inhibited by pyridoxal 5'-phosphate (PLP) specifically and noncompetitively with respect to deoxythymidine triphosphate (DTTP). NaBH4 reduction of PLP-HBV core proteins resulted in the complete inactivation of HBV DNA polymerase, and PLP modification of the enzyme was though to be mediated through Schiff-base formation. HBV DNA polymerase has a Michaelis constant (Km) of 0.31 microM for dTTP and an apparent inhibition constant (Ki) of 0.2 mM for PLP. Its inactivation and modification by PLP may be useful in the study of not only the reaction mechanism of catalysis, but also the physicochemical nature of the enzyme.

Techniques to measure DNA single-strand breaks in cells: a review

Alkaline sucrose sedimentation was for a number of years the standard procedure for the measurement of single-strand breaks. Some years ago a number of new techniques with improved sensitivity were introduced. The following techniques are presented and discussed: alkaline unwinding, alkaline filter elution, nucleoid sedimentation, viscoelastometry, microelectrophoresis of single cells, DNA precipitation, pulse field gel electrophoresis, fluctuation spectroscopy and nick translation.

Effects of excess thymidylate on thymidylate low-requiring strains of Saccharomyces cerevisiae: high mutagenicity and absence of DNA strand breaks

dTMP exposure concentrations of 0.1 mM or higher are genotoxic in exponentially growing cells of thymidylate low-requiring mutants of Saccharomyces cerevisiae. Mutagenicity of excess dTMP is highest in an exposure concentration 10-fold of that needed for external supplementation of endogenously blocked thymidylate synthesis. Still higher dTMP concentrations are primarily cytotoxic. The canavanine forward-mutation system shows excess dTMP to be as potent a mutagen as irradiation by ultraviolet light. Mutagenicity of excess dTMP, however, differs from that of direct DNA-attacking mutagens in that it is highest in the absence of significant toxicity. Alkaline sucrose gradient centrifugation shows that excess dTMP does not induce significant numbers of DNA single- or double-strand breaks, while conditions of thymidylate deprivation lead to DNA-strand breaks and thymineless death.

Replication and packaging of choleraphage phi 149 DNA

The intercellular replication of the circularly permuted DNA of choleraphage phi 149 involves a concatemeric DNA structure with a size equivalent to six genome lengths. The synthesis of both monomeric and concatemeric DNAs during replication of phi 149 occurred in the cytoplasm. The concatemers served as the substrate for the synthesis of mature phage DNA, which was eventually packaged by a headful mechanism starting from a unique pac site in the concatemeric DNA. Packaging of DNA into phage heads involved binding of concatemeric DNA to the cell membrane. A scheme involving sequential packaging of five headfuls proceeding in the counterclockwise direction from the pac site is proposed. After infection under high-phosphate conditions, the concatemeric DNA intermediates were not formed, although synthesis of monomeric molecules was unaffected.

A virion-like particle (VLP) released from an Epstein-Barr virus-producing cell sub-line of P3HR-1: identification of a specific cellular DNA contained within VLPs

A virion-like particle (VLP) was isolated from the culture fluid of P3HR-I cells. VLPs were separable from the enveloped Epstein-Barr virus (EBV) through rate-velocity sedimentation by virtue of their greater density. VLPs comprised electron-dense nucleoid material and the surrounding round or oval envelope which ranged from 100 to 150 nm in diameter. The polypeptide constitution of VLPs was very similar to that of enveloped EBV by SDS-polyacrylamide gel electrophoresis. VLPs contained reasonably specific cellular DNA (VLP DNA) with a sedimentation coefficient of 48S, which was cleaved into 5, 8, and at least 30 specific DNA fragments by digestion with BamHI, SalI, and EcoRI, respectively. Blot hybridization data suggested a limited heterogeneous genomic organization of VLP DNA and the presence of a VLP DNA-related molecule(s) in human cord lymphocytes.

Improved simple chromatographic method for the fractionation of major classes of mammalian nucleic acids

CL-Sepharose 4B column chromatography has been used for the separation of four major classes of mammalian nucleic acids in a single chromatographic run. Gel filtration at 2.5 M NaCl separated DNAs (containing RNA hybrids) from tRNAs. The 18 S RNA (containing 3-5 wt% of small 5 S RNA and RNA degradative products) was eluted at 0.7 M NaCl, and 28 S RNA (containing hnRNAs) was eluted at 0.1 M NaCl. Poly(A)+ mRNAs were detected in both 18 and 28 S RNA fractions. The present procedure is suitable for both analytical and preparative work and may serve as an initial step for the further isolation of ultrapure nucleic acid preparations.

Presence of random single-strand gaps in mycobacteriophage I3 DNA

The genomic double-stranded DNA of mycobacteriophage I3, when denatured with alkali, heat, formamide or dimethylsulfoxide, breaks down to heterogeneous-sized single-strand (ss) fragments smaller than the expected intact unit genome length suggesting the presence of random ss interruptions on both the strands. The occurrence of the interruptions at random is also demonstrated by two-dimensional gel electrophoresis of the restriction fragments of I3 DNA. These interruptions have no adverse effect on the phage infectivity or DNA transfectivity. Studies with nuclease BAL 31 and end-labeling analysis confirm the presence of random interruptions. Detailed analysis using T4 DNA ligase, nuclease S1 and DNA polymerase I Klenow fragment revealed that the interruptions are in the form of small gaps rather than single phosphodiester bond breaks. The average length of the gap is about 10 nucleotides long and there are 13 to 14 such gaps per DNA molecule.

The contribution of the nuclear reaction 1H(n, gamma)2D to the yield of DNA single strand breaks in cultured mammalian cells irradiated by thermal neutrons

The yield of single strand breaks (ssb) in DNA of the HeLa S-3 cells after thermal neutron irradiation was examined using the alkaline sucrose gradient method. The contribution of the 1H(n, gamma)2D reaction to the yield of ssb was determined by substituting D2O for H2O in the irradiated medium. Calculation shows that when cells are irradiated in the H2O medium, the per cent contribution of the contaminating gamma-rays, the nuclear reaction 1H(n, gamma)2D and the other nuclear reactions is 31, 44 and 25 per cent respectively assuming additivity of effects. The estimated number of ssb induced by the nuclear reaction 1H(n, gamma)2D was at least 4.4 times greater than that by 60Co gamma-rays at the same absorbed dose. Two possible interpretations are discussed to explain the high efficiency of the 1H(n, gamma)2D reaction for ssb induction.

Characterization and physical map of choleraphage phi 149 DNA

Choleraphage phi 149 DNA is a linear double-stranded molecule 69 X 10(6) Da or 104 kilobase pairs (kbp). From restriction enzyme analysis, it has been concluded that the DNA is circularly permuted. There are at least three S1 nuclease-sensitive sites along the length of the molecule. These sites represent single-strand interruptions repairable by T4 DNA ligase. A physical map of the DNA has been constructed using the restriction endonucleases BamH1 and BglII.

DNA of Chinese hamster V79 cells newly synthesized after ultraviolet irradiation contains alkali-labile sites

Pulse-labeled daughter DNA of UV-irradiated Chinese hamster V79 cells was denatured in alkaline or neutral conditions and analysed by sucrose gradient centrifugation. A comparison of the sedimentation profiles of DNA treated in alkaline or neutral conditions has shown that in UV-irradiated cells some alkali-labile sites are produced during replication of damaged templates.

The spacing of Escherichia coli DNA gyrase sites cleaved in vivo by treatment with oxolinic acid and sodium dodecyl sulfate

In an attempt to locate gyrase binding sites in a specific region of the chromosome of E. coli, we have reinvestigated gyrase-promoted cleavage of chromosomal DNA by oxolinic acid and sodium dodecyl sulfate. Contrary to a previous report suggesting the presence of one site every 100 kb of DNA (Snyder and Drlica, J. Mol. Biol. 131, 287-302), we found frequencies of one cleavage every 25 or 12 kb depending on the growth medium. A search for cleavage sites by Southern blot hybridization failed to reveal any binding site cleaved at a high frequency. These results suggest that the actual spacing of sites is much closer than that determined from the frequency of cleavage. Measurement of the average size of fragments containing defined DNA sequences indicated that the frequency of sites varies along the chromosome. The region located opposite to oriC carries relatively few sites.

The structure of replicating bacteriophage T1 DNA: comparison between wild type and DNA-arrest mutant infections

Analysis of the structure of replicating phage T1 DNA has identified three major forms of T1+ intracellular DNA; (i) concatemeric molecules with single-stranded interruptions, (ii) monomer-length DNA with single-strand interruptions, and (iii) monomer-length molecules with completely intact single strands. The interruptions in concatemeric DNA are spaced at intervals, with a mean distance equivalent to one monomer length but with a broad distribution and many are in the form of gaps. Type (iii) molecules are probably derived from mature progeny phage particles disrupted during cell lysis. Under nonpermissive conditions, cells infected with amber mutants in T1 genes 3.5 and 4 show the premature arrest of phage DNA synthesis, failure to make concatemeric DNA, and reduced genetic recombination. Intracellular DNA from gene 3.5- and gene 4- infections consist of a uniform population of molecules approximately 10-12% shorter than mature monomers. They are stable throughout infection, contain single-stranded interruptions but not gaps, and are missing terminal sequences. These results are interpreted in terms of concatemer formation by end-to-end recombination between newly synthesised molecules whose terminal sequences are degraded in recombination-defective infections.

Evidence for secondary structure within the virion RNA of echovirus 22

Phenol-extracted echovirus 22 virion RNA is infectious, but unlike poliovirus virion RNA, it resists digestion with pancreatic RNase and nuclease P-1, a 3' exonuclease selective for single-stranded RNA. These data indicate the presence of an enzyme-resistant portion somewhere in the RNA molecule and suggest that it is a double-stranded or base-paired region distant from the unblocked 3' terminus. Equilibrium density gradient centrifugation of native echovirus 22 virion RNA results in a single peak with a density of 1.63 g/cm3. When sheared before centrifugation, the molecule is resolved into two RNA species: one with an approximate density of 1.70 to 1.71 g/cm3, as is observed also for single-stranded poliovirus virion RNA, and the other with a density of 1.58 to 1.59 g/cm3. Data obtained from rate zonal centrifugation may be used to calculate an approximate sedimentation coefficient corrected to water at 20 degrees C of 34 and a molecular weight of 2.4 X 10(6) for the virion RNA. We propose a model for echovirus 22 RNA composed of a linear RNA molecule with a 5' hairpin.

The DNA of bacteriophage 643: isolation and properties of the DNA of a bacteriophage infecting lactic Streptococci

The DNA extracted from bacteriophage 643, which infects group N strains of Streptococci, could be separated into four components by electrophoresis on agarose gels. Electron microscopy established the predominant form of the DNA to be a relaxed, circular molecule of molecular weight 14.9 X 10(6). The four species observed on electrophoresis are believed to be a circular monomeric form, a linear form derived from it, a circular dimeric form, and the corresponding linear dimer. Two DNA components were demonstrated by sedimentation velocity in the analytical ultracentrifuge and by zone sedimentation in sucrose gradients. These corresponded to a circular monomeric form and a circular dimeric form; no evidence for supercoiled forms was found by sedimentation in either neutral or denaturing solvents. Bacteriophage 643 DNA was sensitive to cleavage by single-strand-specific nuclease S1 and could be labeled in vitro by the PolI-catalyzed incorporation of [alpha-32P]dATP into the molecule under conditions that did not permit nick translation, suggesting that the circular duplex molecule is interrupted by a single-stranded gap.

DNA polymerase in nuclei isolated from herpes simplex virus type-2-infected cells. Characterization of the reaction product and inhibition by substrate analogs

Nuclei isolated from herpes simplex virus (HSV) type 2-infected KB cells were examined for their capacity to serve as an in situ source of herpes DNA polymerase. In contrast to purified enzymes with added template, approx. 80% of the DNA synthesized in isolated nuclei was viral. The average size of DNA fragments labeled in vitro was 3.2 X 10(6) Da. Based on an increase in DNA density when nuclei were incubated in the presence of BrdUTP rather than dTTP, 16% of the nucleotides were added during the in vitro reaction. Sucrose gradient analysis of DNA polymerase activity in extracts of isolated nuclei demonstrated the nearly exclusive presence of herpes DNA polymerase. Km concentrations for the four dNTPs were from 0.14 to 0.55 microM. DNA synthesis was inhibited competitively by the 5'-triphosphates of ara-A and ara-C (Ki = 0.03 and 0.22 microM, respectively) but not by the 5'-triphosphate of dideoxythymidine. aATP also served as a substrate (Km = 0.014 microM) for the reaction. We conclude that nuclei from HSV-infected cells have significant advantages for the detailed study of inhibitors of herpesvirus replication.

Formation and possible functions of alpha-putrescinylthymine in bacteriophage phi W-14 DNA: analysis of bacteriophage mutants with decreased levels of alpha-putrescinylthymine in their DNAs

The DNA synthesized in the nonpermissive host by the noncomplementing mutants am36 and am42 of bacteriophage phi W-14 contains about half the wild-type level of alpha-putrescinylthymine (putThy) and a correspondingly greater level of thymine. The mechanisms whereby thymine nucleotides are excluded from replicating DNA are functional in both mutants because neither of them incorporates exogenous thymidine into DNA. It is proposed that (i) in wild-type phi W-14, the conversion of hydroxymethyluracil to putThy at the polynucleotide level is sequence specific, but that to thymine is nonspecific; and (ii) in the mutants, the sequence-specific recognition is impaired so that more thymine and less putThy are formed. The thymine-rich DNA can be packaged into phage particles. In the case of am42, the phage particles are morphologically indistinguishable from and have essentially the same polypeptide composition as wild-type particles. However, the DNA molecules they contain are about 11% shorter than those in wild-type phage, am42rev4, a revertant of am42, contains DNA with about 70% of the normal level of putThy; these molecules are about 3% shorter than wild-type DNA. The properties of am42 and am42rev4 are consistent with the suggestion that putThy facilitates the very tight packing of phi W-14 DNA (Scraba et al., Virology 124:152-160, 1983). It also appears that the putThy content of phi W-14 DNA can be reduced by no more than 30% without adversely affecting the production of viable progeny; for example, the burst size of am42rev4 is about 25% of that of the wild type.

Structural features of very fast sedimenting DNA formed by gene 49 defective T4

Very fast sedimenting DNA (VFS DNA) of T4 phage, which is formed by infection with a mutant in gene 49, was examined by electron microscopy after mild treatment with DNase I. It showed Y-shaped, branched strands in addition to linear strands. Each branch contained a single-stranded interruption about 60 nucleotides long at its proximal end. The average number of branches per T4 DNA unit was close to the average number of sites susceptible to gene 49 nuclease. Both numbers were consistently changed by the addition of a secondary mutation in a gene involving recombination.