Granulomatous vasculitis occurring after cutaneous herpes zoster despite absence of viral genome

Granuloma annulare, sarcoidal and other granulomatous dermatitides, pseudolymphoma, lymphoplasmacytoid lymphoma, and Kaposi's sarcoma have been described as sequelae of herpes zoster. We report a new postzoster reaction, granulomatous vasculitis, that caused flat-topped papules restricted to the affected dermatome. Polymerase chain reaction failed to detect varicella-zoster virus in a biopsy specimen. These results suggest that granulomatous vasculitis occurs without persistence of the viral genome and, perhaps, is a reaction to minute amounts of viral proteins.

Ultrastructural, protein composition, and antigenic comparison of psittacine beak and feather disease virus purified from four genera of psittacine birds

Psittacine beak and feather disease (PBFD) virus, was purified from diseased tissues of a lesser sulphur-crested cockatoo (Cacatua sulphurea), a black palm cockatoo (Probosiger aterrimus), a red-lored Amazon parrot (Amazona autumnalis), and a peach-faced lovebird (Agapornis roseicollis). The histopathology of diseased feathers and follicular epithelium from the different species was compared; basophilic intranuclear inclusion bodies were identified in the follicular epithelium and intracytoplasmic globular inclusions were observed within macrophages located in the feather pulp from the four species. Psittacine beak and feather disease virus antigen was specifically detected by colloidal gold immunoelectron microscopy. The different preparations of purified virions displayed an icosahedral symmetry, were non-enveloped, and had a mean diameter that varied from 12 to 15 nm when negatively stained. Two major viral-associated proteins with approximate molecular weights of 26 and 23 kilodaltons (kd) were consistently demonstrated from the four viral preparations. Purified virions from the four genera were antigenically related. These findings suggest that the PBFD virus purified from numerous genera of diseased birds is similar based on ultrastructural characteristics, protein composition and antigenic reactivity.

Mutual exclusion occurs in a Chlorella-like green alga inoculated with two viruses

Progeny viruses resulting from dual inoculations with different and near-isogenic viruses of a Chlorella-like green alga were distinguished by immunoblotting. Plaques arising from single cells inoculated with two viruses usually contained only one of the viruses. Thus the viruses mutually exclude one another. In some combinations the ratio of viruses (as infective centres) recovered differed significantly from the input ratio.

Hepatitis B-DNA replication and histological patterns in liver biopsy specimens of chronic HBsAg positive patients with and without hepatitis delta virus superinfection

The role of active hepatitis B virus (HBV) infection in chronic HBsAg positive hepatitis with and without hepatitis delta virus (HDV) superinfection was analysed in percutaneous liver biopsy specimens from 50 patients. Each specimen was divided into two--one part for histological evaluation and for the detection of HBcAg and delta antigen; the other part was tested for HBV-DNA using Southern blotting. Ten cases were of chronic lobular hepatitis, 10 of chronic persistent hepatitis, and 30 of chronic active hepatitis. Ten cases were delta antigen positive and showed high grade lobular activity but no evidence of HBV-DNA episomal forms or HBcAg reactivity. Twenty one cases showed HBV-DNA replicative intermediate forms; 19 had high grade lobular activity, which occurred in five cases without evidence of free viral DNA. Of the 21 biopsy specimens with HBV-DNA episomal forms, 14 were positive for HBcAg; only one of the 19 cases without detectable viral DNA was positive for such antigen. These data indicate that the presence of HBV or HDV active infection correlates with the histological finding of prominent lobular necrosis. Moreover, intrahepatic HBV-DNA seems to be a more sensitive marker than the presence of viral antigens for indicating HBV replication.

Detection of a human papilloma virus type 5 DNA in a renal allograft patient from Scotland

A renal allograft recipient with small raised red scaly lesions on a forearm is described. The clinical and histological picture was that of similar lesions reported in some epidermodysplasia verruciformis patients. Virological investigations revealed the presence of human papilloma virus type 5; this is the second report of the occurrence of this type in allograft patients. As human papilloma virus type 5 is known to have malignant potential, clinicians should be on the lookout for these banal-looking and distinctly non-warty lesions in renal transplant recipients. Close follow-up is indicated.

Sequence homology between the coat proteins of DNA and RNA plant viruses

The coat proteins of the leafhopper transmitted gemini viruses, viz., maize streak virus and wheat dwarf virus that contain a single circle of DNA in their genomes are shown to bear good amino acid sequence homology with the coat protein of an RNA plant virus, the satellite tobacco necrosis virus. It is suggested that for icosahedral assemblage, the coat protein architecture transcends genomic preferences.

Characterization of the enveloped plasmavirus MVL2 after propagation on three Acholeplasma laidlawii hosts

Plasmavirus MVL2 was propagated on three Acholeplasma laidlawii strains, JA1, S2, or BC1-13. Previously reported host-controlled modification (HCM) of MVL2, as reflected by changes in plating efficiency, was observed. Adsorption rates and one-step growth curves varied according to host used. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis of the three MVL2 populations revealed differences in polypeptide profiles.

Hepatitis viruses: characterization and diagnostic techniques

Two human hypatitis viruses have been identified and characterized, but one or more additional agents exist. Hepatitis B virus (HBV) is a complex 42-nm predominantly double-stranded DNA virus with distinct surface and core antigens and an endogenous DNA polymerase. Hepatitis A virus (HAV) is a 27-nm RNA virus with enterovirus-like properties. Progressively more sensitive and specific immunologic assays have been applied to the study of viral hepatitis and are available for routine diagnostic purposes. As a result we recognize distinct serologic response patterns to infection, new antigenic markers, biochemical-biophysical characteristics of the viruses, and their epidemiologic features. Recombinant DNA technology has permitted the cloning of HBV genetic material and gene products in E. coli, but the virus has not been cultivated in vitro. In contrast, successful in vitro cultivation of HAV has finally been accomplished. Application of sensitive serologic tests for HAV and HBV has revealed that "non-A, non-B" agents account for a substantial proportion of transfusion-associated hepatitis as well as hepatitis occurring in the absence of percutaneous exposure. These agents have been transmitted to chimpanzees, and several putative virus antigen-antibody systems have been described; however, a specific association between these virus antigens and non-A, non-B hepatitis has not been established.

[Nature of the easily melted portions of DNA with a quasi-random base sequence]

The influence of denaturation conditions upon the character of partial denaturation of DNA with random base distribution were thoroughly studied. Maps of partial DNA denaturation were obtained at T less than TAT for phage phiB DNA at pH 10.7 and 5.5; Tg9 DNA at pH 8.8; at T less than TAT for phiB DNA at pH 10.9 and Tg9 DNA at pH 8.8. The map quality was better when obtained at higher pH values; the peaks became sharper and higher against the background. We failed to obtain maps of partial denaturation at pH 5.5, T less than TAT. The improvement of the map quality and existence of the partial denaturation maps at T less than TAT at pH 10.9 were explained by the increase of primary melting probability of AT-rich DNA regions. At high pH the denaturation map quality was temperature independent. This was explained by a very weak temperature dependence of primary melting probability for all maps of equal quality. The map quality became worse, when the quantity of loops was increased.

[Iclusion proteins and viral proteins of the baculovirus of the dipteran Tipula paludosa (Meigen)]

Examination of the polyhedron protein by polyacrylamide gel electrophoresis shows only one polypeptide with a molecular weight of 25,500 +/- 500 daltons, while that of virion proteins reveals 13 polypeptides. No antigenic community could be demonstrated between the polyhedron protein of the Baculovirus of T. paludosa and the polyhedron protein of several other Baculoviruses.

Isolation and properties of the DNA of African swine fever (ASF) virus

African swine fever (ASF) virus was grown either in swine macrophages or in VERO cells and purified free of cell DNA. Virus DNA was isolated from virions as a molecule with a sedimentation coefficient of 60S and a contour of 58 +/- 3 mum. .these two values give a mol. wt. of 102 +/- 5 X 10(6) and 107 +/- 5 X 10(6), respectively, for the genome of ASF virus. Denatured DNA fragments from ASF virus reassociate with a C0t1/2 value of 0-60 +/- 0-05 MS, which compared with the corresponding value for T4 DNA gives for the molecular mass of ASF virus DNA a value of 102 +/- 8 X 10(6) daltons. Only virus DNA is synthesized ASF virus-infected swine macrophages.

Ten proteins required for conversion of phiX174 single-stranded DNA to duplex form in vitro. Resolution and reconstitution

Protein requirements for conversion of phiX174 single-stranded DNA to a double-stranded replicative form with a small gap (RF II) have been determined by resolution and reconstitution of the multienzyme system from extracts of gently lysed Escherichia coli. Assays depended on: (a) complementation of extracts of thermosensitive mutants and (b) fractionation of extracts of wild type cells to divide essential components into groups, each of which was further resolved. These procedures have yielded eight proteins: dnaB protein, dnaC protein, proteins i and n (two novel proteins without a defined genetic locus), dnaG protein, DNA polymerase III holoenzyme (polymerase III and copolymerase III), and DNA unwinding protein; purification procedures for the first four are presented here. (Closure of RF 22 requires as with phage M13, DNA polymerase I and ligase.)

DNA sequence analysis. Terminal sequences of bacteriophage phi80

Sequences of the cohesive ends and the 3'-terminal regions of phi80 DNA have been determined. Sequences of the cohesive ends were obtained through the use of two standard methods. The first method involved the incorporation of all four labeled deoxyribonucleotides into the phi80 cohesive ends using DNA polymerase I. The DNA was then partially digested with micrococcal nuclease or pancreatic DNase. The products were separated by two-dimensional electrophoresis and characterized by composition, 3'-terminal, and nearest neighbor analyses. The second method involved partial incorporation using one, two, or three labeled deoxyribonucleotides followed by similar analyses. Sequences of the double-stranded regions adjacent to the cohesive ends were determined by three new methods. These methods were: (a) the DNA was specifically labeled at the 3' terminus and then partially degraded. Labeled oligonucleotide products were sequenced by their mobilities on various separation systems. (b) The cohesive ends were enlarged by limited degradation with exonuclease III. After this treatment, the DNA was partially repaired with labeled nucleotides, digested, and the products were analyzed. (c) A synthetic ologonucleotide primer was bound to phi80 DNA which had been repaired with DNA polymerase I, and then partially digested with lambda-exonuclease. The primer was extended into the region of interest by partial repair with labeled nucleotides. The extended primer was isolated and analyzed.

Nucleotide sequence determination of bacteriophage T4 species I ribonucleic acid

The nucleotide sequence of T4 species I RNA, one of several stable RNA's specifically coded for by bacteriophage T4, has been determined using 32-P-labeled material from T4-infected cultures of Escherichia coli. The purified RNA species which has been sequenced has been shown to hybridize well to T4 DNA (Wilson J.H., Kim, J.S., and Abelson, J.N. (1972) J. Mol. Biol. 71, 547-556). The sequence is: pCGAUUCGAGGAAAUAUCUUUGCCGUAAGCCGAGUAGCGUUUUUGACGGAACGUUCGGAUAUGGUUGAGAUAUGGCCUUUUAAAAUAUUGAGUAGCGUCAACUACUUAAUAACCGGGUUCGAAUCCCGGCGUUUCGU-CAA-OHACA-OH. Species I RNA which is 140 nucleotides long is also found to occur in shorter versions with 135 to 136 nucleotides which terminate with a 3'-phosphate. The molecule can be arranged in a secondary structure which shows some striking similarities to the classic cloverleaf pattern of a tRNA. The molecule is specifically cleaved by an E. coli nuclease into three segments by cleavage at a double-stranded region in the molecule. The function of species I RNA is unknown, but evidence presented elsewhere (Paddock, G.V., and Abelson, J. (1975) J. Biol. Chem. 250, 4207-4219) indicates that the gene for this RNA molecule has been preserved in evolution. The position of a mutation within species I RNA has been determined. This mutation results in incorrect processing of the RNA and lower relative yields of the RNA are present.

Nucleotide sequence determination of bacteriophage T2 and T6 species I ribonucleic acids

The nucleotide sequences of species I RNA coded for by bacteriophages T2 and T6 have been analyzed using 32-P-labeled material from T2 and T6-infected cultures of Escherichia coli. The T1 and pancreatic ribonuclease digestion products were partially analyzed and the results were compared with nucleotide sequences from T4 species I RNA to obtain a minimum estimate of the number of nucleotide sequence differences among the three species I RNAs. Analysis of fragments obtained by digestion with epsilon-carboxymethyl-lysine-41-pancreatic ribonuclease and with E. coli Q13 S30 crude extract was also performed to provide some additional confirmation for the nucleotide sequences that were derived for the T2 and T6 species I RNAs. T2 species I RNA was found to be different at three positions in the nucleotide sequence, and unlike T4 species I RNA, contained in addition the modified nucleotide, psi, in a region where the proposed secondary structure is identical to the TpsiC-loop of a tRNA. T6 species I RNA was found to contain nucleotide differences from the T4 species I RNA sequence at four positions. The U at position 119 in the sequence appears to be modified to psi only to a small extent. While a biological function for species I RNA is unknown, the fact that there is over 97% homology in the sequences suggests strong evolutionary pressures to retain the nucleotide sequence in the T-even genomes.

New method for isolation and sequence determination of 5'-terminal regions of bacteriophage phiX174 in vitro mRNAs

We have determined the nucleotide sequences of the 5'-terminal oligonucleotides, produced by RNase T1 digestion of bacteriophage phiX174 mRNAs synthesized in vitro. The major sequences are: pppCpGp(Ap), pppApUpCpGp(Cp), pppAp(Ap)2UpCp(Up)2Gp(Gp), and pppAp(Ap)3UpCp(Up)2Gp(Gp). The sequences of several minor 5'-terminal oligonucleotides were also determined. For this research we have devised a simple isolation procedure, for the 5'-terminal oligonucleotides, based upon hydroxylapatite chromatography and two-dimensional thin-layer separation. This method allows for the rapid and quantitative recovery of all oligonucleotides containing 5'-triphosphate end groups and should be generally useful for sequence on 5' termini of mRNAs.

Studies on bacteriophage M13 DNA. 1. A cleavage map of the M13 genome

A physical map of the bacteriophage M13 genome has been constructed on the basis of specific cleavage of M13 replicative form DNA by bacterial restriction endonucleases. The 13 fragments produced by the enzyme from Haemophilus aphirophilus (endonuclease R.Hap II) as well as the 10 fragments produced by the enzyme from Haemophilus aegyptius (endonuclease R.Hae III) have been ordered by analysis of partial digest products and by analysis of overlapping sets of fragments. In addition, the single site in M13 replicative form DNA cleaved by the restriction enzyme from Haemophilus influenzae Rd (endonuclease R.Hin dII) has been located more precisely. With this unique site as a reference point, the H. aphirophilus cleavage sites and the H. aegyptius cleavage sites have been localized on the map.

Studies on bacteriophage M13 DNA. 2. The gene order of the M13 genome

The double-stranded replicative form DNA of bacteriophage M13 was cleaved into 13 specific fragments by the restriction endonuclease from Haemophilus aphirophilus. The individual DNA fragments from wild-type replicative form molecules were then annealed to circular, single-stranded DNAs of phage M13, bearing amber mutations as genetic markers. When such DNA hybrids infected competent Escherichia coli cells, only those duplexes which were genetically heterozygous gave rise to wild-type phages in the progeny. In this way, the genetic markers carried on the individual DNA fragments could be determined. In addition, marker rescue in each gene was obtained with the 10 specific fragments of M13 replicative form DNA, produced by cleavage with the restriction endonuclease from Haemophilus aegyptius. From these results and the enzyme cleavage maps of both types of restriction fragments a distribution of genetic markers along the physical map could be obtained, which allowed an arrangement of M13 genes into a genetic map. Evidence is presented that the gene order of M13 is: IV-(I,VI)-III-VIII-VII-V-II with II and IV being contiguous on the circular map.

Molecular weight of base plates of bacteriophage T4D

Highly purified base plates of bacteriophage T4D were obtained from lysate of gene 19 am mutant of this phage by differential centrifugation and sucrose gradient. Base plates were studied by means of high speed sedimentation equilibrium. The molecular weight determined by this method is (6.7 plus or minus 0.2)-10-6.

A protein from Ustilago which forms an acid-soluble complex with deoxyribonucleic acid

A protein which can render DNA largely acid-soluble has been purified 1600-fold from high salt extracts of Ustilago maydis. The activity is unusual in that substrate DNA is not made acid-soluble through hydrolysis to small oligomers. Rather, the protein appears to bind to DNA to form a complex which itself is acid-soluble. The activity of conversion of DNA to an acid-soluble form is cold-labile, but the inactivation by cold is reversible by brief heat treatment. Divalent cations stimulate the activity; phosphate is inhibitory. Optimal activity is observed at pH 6.0 and again at pH 9.0. Nucleoside triphosphates and diphosphates stimulate activity at low protein concentrations but are not hydrolyzed during the course of reaction. The protein behaves anomalously on gel filtration columns and is completely excluded by Sephadex or agarose gels. When analyzed by sedimentation velocity, the protein was found to sediment at 5.3 S, the same rate at which a globular protein of 65,000 daltons would sediment. Dependence of activity upon protein concentrations is sigmoidal. K+ and to a lesser degree NH4+ are partially effective in abolishing the lag in the concentration curve. The protein displays a saturation curve when exposed to increasing DNA concentrations. Such a curve could only result from a non-random or cooperative mode of binding of the protein to DNA. A mutant sensitive to gamma and ultraviolet radiation with an abnormally high level of the protein has been found. Haploid populations of the mutant grow slowly and contain a large proportion (10 to 20%) of inviable cells. Diploids are defective in mitotic allelic recombination and fail to complete meiosis. It is speculated that the protein may be important in the regulation of chromosome condensation.

A new method for mapping nucleic acid sequence homology by electron microscopy

We describe here a new method for the electron microscopic mapping of sequence homology in nucleic acids. Specific segments of the T7 chromosome have been isolated following digestion with the restriction endonuclease from Hemophilus aegyptious (Haey). Denatured segments are annealed to the l-strand of T7 DNA; treatment of the hybrid with glyoxal allows only guanosine residues in the single-chain region to the reacted, producing an adduct which will no longer hydrogen bond with its complement on the r-strand. When the segment is displaced and the glyoxalated l-strand allowed to renature with the r-strand, "H" shaped structures are produced in which the duplex region corresponds to the position of sequence homology with the segment. The conditions employed for glyoxalation do not detectably disrupt duplex regions as small as 400 base pairs. This procedure should be generally useful for observing sequence homology in more complex DNA molecules containing duplex regions which can be specifically enriched for and their arrangement determined by electron microscopy.

Endonuclease II of Escherichia coli: degradation of gammairradiated DNA

Irradiation of DNA in a nitrogen atmosphere with 60Co gamma-radiation produces at least two types of damage. The first type leads to single strand breaks in the DNA observed after exposure to alkali. This type of alkali-labile bond will be designated a spontaneous break. The second type of damage to DNA is an alteration which makes the DNA susceptible to phosphodiester bond hydrolysis by a 1600-fold purified preparation of endonuclease II of Escherichia coli and is designated an enzyme-sensitive site. This site is not alkali-labile. After irradiation, preincubation of the DNA either for days at 0 degrees or for 4 hr at 37 degrees increases both the spontaneous breaks and the enzyme sensitive sites. There is a greater increase of spontaneous breaks when the preincubation is in O2 compared to N2. The increase of enzyme sensitive sites due to the preincubation is not altered significantly by O2. The increase of spontaneous breaks during the preincubation is almost completely prevented by addition of either NaBH4 or NH2OH after the irradiation. The treatment can be before or after the preincubation. This effect indicates that these breaks are due to alkali-labile bonds possibly produced by depurination or depyrimidination reactions. That the spontaneous breaks are due primarily to alkali-labile bonds is supported by an experiment in which formamide gradients were used. Neither NaBH4 nor NH2OH has any effect on the enzyme sensitive sites. Addition of beta-mercaptoethanol (0.5 M) at the start of the preincubation prevents in part the appearance of both spontaneous breaks and enzyme-sensitive sites. It has no effect when added at the end of the preincubation. Catalase added before the preincubation has no effect on either type of damage. It is postulated that the spontaneous breaks occur because purine or pyrimidine radicals are formed (possibly hydroxyl radicals) which can then interact with oxygen to produce unstable intermediates. The intermediates then undergo either depurination or depyrimidination. The subsequent alkali catalyzed beta-elimination reaction of depurinated or depyriminidinated DNA is prevented by NaBH4 or NH2OH. An alternative hypothesis would involve damage to the sugar rather than to bases. The enzyme-sensitive sites represent another form of base damage which is not oxygen dependent. The chemical nature of either form of primary damage is not known.

Chemical modifications of functional residues of fd gene 5 DNA-binding protein

The binding of gene 5 protein from bacteriophage fd to poly[d(A-T)], fdDNA, and poly(A) is accompanied by a dramatic reversal in the signs of the large ellipticity bands of the nucleic acid chromophores from 250 to 290 nm. The change in the circular dichroism of the DNA induced by the protein, which reaches a maximum at a protein to nucleotide molar ratio of 1:4, has been used as an assay of the alterations in binding of gene 5 protein to DNA accompanying changes in the ionic environment and subsequent to chemical modification of the protein. Divalent cations completely dissociate the gene 5 protein-fd DNA complex at 0.1 M, while 0.5 M monovalent cations are required. All cations are more effective in dissociating the complex with poly[d(A-T)] commensurate with the accompanying stabilization of the double helix to which gene 5 protein does not bind. Acetylation of all six lysyl residues and three of the five tyrosyl residues of the protein with N-acetylimidazole prevents complex formation. Removal of the three tyrosyl O-acetyl groups with hydroxylamine does not restore the binding of gene 5 protein to DNA. Tetranitromethane nitrates the same three tyrosyl residues (Tyr-26, Tyr-41, and Tyr-56 as determined by peptide mapping) and reduces the binding affinity of the protein for fd DNA by similar to 100-fold. The 19F NMR spectrum of gene 5 protein labeled with m-fluorotyrosine shows three surface and two buried fluorotyrosyl residues. All tyrosyl residues are protected from nitration in the complex with fd DNA, but acetylimidazole acetylates surface lysyl residues in the complex and dissociates it. The intrinsic circular dichroism of the acetylated and nitrated gene 5 proteins is not significantly altered. In contrast maleic anhydride reacts with the seven amino groups of the protein and changes the secondary structure to one similar to that present in 6 M guanidine-HCl. The single SH group of the native protein does not react with Ellman's reagent, but it reacts rapidly with one Hg2+ ion which unfolds the protein; fd DNA prevents reaction with Hg2+. Electrostatic forces may be as important as hydrogen bonding in maintaining the native structure of this protein. The lysyl groups of the protein, exposed in both the free protein and the DNA complex, appear to be of prime importance in DNA binding, probably through electrostatic interactions with the DNA binding, probably through electrostatic interactions with the DNA phosphate groups. Three tyrosyl residues also contribute to binding affinity through hydrogen bonding or intercalation. A model of gene 5 protein structure in relation to interactions with a tetranucleotide is presented.

Subunit arrangement in the extended sheath of pyocin R

An optical diffraction study has been made of electron micrographs of extended sheaths of pyocin R. It has been demonstrated that the extended sheath consists of annuli of six subunits, which are arranged in a helix of 3.57 annuli per one turn. The annulus repeat in the helix direction is 35A. The dimensions and probably the helical parameters of pyocin R sheath are different from those of T4 phage tail, but a structural correlation appears to exist between the extended sheath of pyocin R and that of the phage tail.

Near-ultraviolet light-induced strand breaks in DNA pretreated with the carcinogen, N-acetoxy-2-acetylaminofluorene

Neutral sucrose gradients of supercoiled DNA (phiX-174 RF I) were used to measure the in vitro production of strand breaks by the carcinogen, N-acetoxy-2-acetylaminofluorene (AcO-AAF). Treatment with AcO-AAF in 10% dimethyl sulfoxide did not directly yield strand breaks. Breaks in relatively low yield appeared after alkali treatment (pH 13, 60 min) of the RF I previously reacted with AcO-AAF. The DNA treated with AcO-AAF was sensitive to single-strand breakage by 303 nm near-ultraviolet light under neutral conditions. The greater the prior AcO-AAF treatment, the greater the sensitivity to 303 nm light. Post-irradiation alkali treatment greatly enhanced the light-induced strand breakage.

Size fractionation of double-stranded DNA by precipitation with polyethylene glycol

We show that DNA molecules of differing molecular mass are separable by selective precipitation with polyethylene glycol (PEG+.. Higher molecular mass DNA precipitates at lower PEG concentrations than lower molecular mass DNA. Double-stranded DNA can be fractionated at least in the range of 3 times 10-7 to 1 times 10-5 daltons. The effects on PEG concentration, sodium chloride concentration, DNA concentration, pH, divalent ions, precipitation time, and centrifugal force have been determined. These studies show PEG precipitation offers a size fractionation method for DNA which is convenient, of high capacity, and applicable over a wide range of conditions. However, resolution is not high and separation of two species approaches 100% only if they differ in molecular mass by at least a factor of two.

Characterization of ribonuclease NU cleavage sites in a bacteriophage phi80-induced ribonucleic acid

Ribonuclease NU, an endoribonuclease isolated from human KB tissue culture cells, can cleave a bacteriophage phi80-induced RNA at four distinct sites. Nucleotide sequence analysis of the eight cleavage products has shown that the enzyme produces oligonucleotides terminating in 3'-phosphate groups, and that the four cleavage sites are in the only nonhydrogen-bonded region of the substrate. Various aspects of the cleavage reaction with this RNA and with other substrates are discussed.

Purification of closed circular lambda deoxyribonucleic acid and its sedimentation properties as a function of Sodium chloride concentration and ethidium binding

The sedimentation of circular lambda DNA suggests that the molecular undergoes significant changes in shape and super-coiling as the NaC1 concentration increases. Closed circular lambda DNA, species I, isolated and purified from superinfected immune bacteria, sediments in sucrose gradients of low ionic strength at a rate 2.0 times faster than linear lambda DNA, species III. The addition of ethidium causes the sedimentation rate of species I DNA to decrease until enough dye is bound to remove 121 supercoils per molecule. At this point, species I co-sediments with nicked and nonsupercoiled species II. Futher additions of ethidium cause the sedimentation rate to increase until the relative rate of species I is again at least twice that of species III. This classical behavior is altered when NaC1 is present in the buffer. In 1.0 M NaC1 the changes in S are complex. Initially, species I sediments 1.55 times faster than species III. Titration with ethidium caused a decrease in S to an early minimum value, than an increase to a first maximum, followed by a decrease to the S of species II. At this point enough dye has intercalated to remove 208 superhelical turns. Further additions of dye introduce supercoils and cause S to increase again. In 0.1 to 0.4 M NaC1 the relative S of species I is 1.69 and 1.59, respectively. If titrated with ethidium, S first increases to a maximum value then decreases to the minimum rate when enough dye is bound to remove 158 and 183 supercoils, respectively. The results indicate an increase in the superhelix density from 0.026 turns per 10 base pairs in buffer alone to 0.045 in the same buffer with 1.0 M NaC1. If this change in superhelix density results from a concomitant change in the average rotation angle between base pairs in the Watson-Crick helix, the addition of 1.0 M NaC1 alters the rotation angle by 0.68 degrees per base pair.

Ethidium binding affinity of circular lambda deoxyribonucleic acid determined fluorometrically

Ethidium-binding isotherms for purified circular lambda DNA, isolated from a superinfected lysogen, and for linear lambda DNA, isolated from the purified phage, were constructed from fluorescence measurements of ethidium-DNA MIXTURES. The measurements were made in 0.01 M Tris-HC1-0.001 M EDTA,pH 7.1, buffer at 20 degrees and in the same buffer containing 0.1, 0.4, or 1.0 M NaC1. When NaC1 was present, differences in the binding affinity for supercoiled and linear DNA could be quantitated. As the ethidium concentration was increased, supercoiled lambda DNA molecules bound the intercalating dye first more and then less avidly than nonsupercoiled ones. The number of potential supercoils in a circular lambda DNA molecular in the absence of dye was calculated from the amount of dye bound when it exhibited the same affinity for dye as its linear counterpart. The point of equivalent affinity shifted from 0.053 mol of dye bound per mol of nucleotide in 0.1 M NaC1 to 0.067 mol in 1.0 M NaC1. This corresponds to the removal of 164 and 206 supercoiling turns per molecule and superhelix densities in the absence of dye equal to 0.036 and 0.045 superhelical turns per 10 base pairs. If this difference in the number of supercoils reflects a salt-dependent change in the average rotation angle between base pairs of the Watson-Crick helix the angle differs by 0.32% in the two ionic environments.