Verification of a decrease in the rigidity of the phage λ DNA polymeric chain in low ionic strength aqueous solutions by testing the polymer-polymer interlink interactions

Changes in the rigidity of the polymeric chain of phage λ double-strand DNA have been studied by laser correlation spectroscopy. It was shown that, as the ionic strength increases, the effect of the screening of the hydrodynamic interaction of the links of the polymeric chain specific for polymeric coils arises in a DNA solution. It is assumed that the screening occurs when the threshold of the overlapping of DNA coils is achieved. The overlapping of coils is the result of a previously observed significant rise of DNA coil size from abnormally small DNA coils in low ionic strength buffers (about 10⁻² M Na⁺ or less) to maximum possible large coils in the 5SSC and 5SSC-like buffers. Further analysis of the far interlink interactions in linear lambda phage DNA coils in similar buffers at pH 7 and 4 confirms the earlier proposal about the role of H+ ions in the appearance of abnormally small DNA coils. The abnormal decrease in the DNA coil size in low ionic strength buffers is not a specific feature of λ phage DNA only.     

Salt effects on the bacteriophage T7-II structure and activity changes

Optically detected thermal stability and biological activity of phage T7 has been compared as the function of the ionic composition and strength of the buffers. The ionic strength range was studied between 20-140 mmol/1. In Tris buffer containing only monovalent ions the biological activity of the phages decreases abruptly below 50 mmol/1 ionic strength. Structural studies show a logarithmic dependence between the ionic strength and the intraphage DNA stability and no significant change in the thermal stability of the whole phage. Mg2+ and Ca2+ ions at low concentration (1 mmol/1) given into a Tris buffer of 20 mmol/1 original ionic strength highly stabilize the biological activity, which stabilization is also to be seen in the intraphage DNA and also in the whole phage thermal denaturation process.     

Changes in rigidity of the polymeric chain of the lambda-phage DNA in aqueous solutions with low ionic strength over the pH range 4-9.5

It was shown that the decrease in the rigidity (persistent length) of phage lambda DNA, revealed previously by laser correlation spectroscopy, occurs in an aqueous solution at concentrations of sodium salts less than 10(-2) M in the pH range 4-9.5. DNA coils of anomalously small size (approximately twofold less than the size reported by other authors) are formed. The formation of these coils is likely to be due to the separation of "normal", i.e., rigid DNA coils into two phases, which occurs as the concentration of sodium salts decreases to 1.5 x 10(-3) M and pH of the solution decreases to 4. The phase of small-size (nonrigid) coils makes the major contribution to the scattering spectra. The phase of large-size coils disappears at pH 9.5. As pH increases, the size of small coils increases. The occurrence of coils of anomalously small size was registered by another method, quick precipitation. It is assumed that the phase separation of coils is related to the structural features of water.     

A new host-vector system allowing selection for foreign DNA inserts in bacteriophage lambda gtWES.

An improved vector (lambda gtWES.T5-622) for EcoRI fragments has been derived from EK2 vector lambda gtWES.lambdaB' by replacing the lambda B fragment with two identical 1.1 Md fragments from the pre-early region of bacteriophage T5. The new vector has two advantages which facilitate elimination of parental-type recombinants in an in vitro recombination experiment. Firstly, the 1.1 Md insert is too small to be re-inserted into lambda gtWES in a single copy. Secondly the 1.1 Md T5 fragment carries T5 gene A3 which prevents growth of phage retaining this fragment when the Excherichia coli host carries plasmid ColIb. Thus, essentially all plaques are due to phage with donor DNA inserts and are free of T5 DNA fragments. The size usually given as the theoretical minimum size for insertion into the lambda gt series of vectors is 0.66 Md. We have shown that this size is an underestimate and that the lower limit is about 1.6 Md. A precise estimate is difficult since there is strong selection, among phage having small inserts, for those which have acquired additional genetic material by duplication of the lambda DNA.     

Loosening of the phage structure in a low ionic strength environment

Structural parameters of phage T7 were compared in two frequently use Tris buffers of high and low ionic strength, in order to explain the different biological activity and drug-binding characteristics.Characteristics of the whole phage geometry were obtained by viscosimetry, static and quasi-elastic light-scattering and small-angle X-ray scattering. The latter method revealed dissimilarities in the intraphage DNA compactness, consistent with the findings of the optical absorption melting studies.Alterations in the particle dimensions determined in the same sample by different methods are discussed, and a model is constructed to explain the structural modifications that occur on lowering the ionic strength.     

Accelerated screening of cDNA libraries using the polymerase chain reaction and Southern blotting

cDNA libraries are normally constructed in either phage or plasmid vectors and screened for sequences of interest using antibodies or, more commonly, nucleic acid probes. To clone a sequence of interest from a library generally involves at least three rounds of hybridization with ³²P-labeled probes. This approach is highly labor intensive, and no information about the size of the hybridizing insert is obtained until the clones have been purified and the insert DNA analyzed by restriction enzyme digestion. We report on a rapid screening protocol for libraries constructed in bacteriophage lambda vectors involving polymerase chain reaction amplification of the insert from hybridizing phage plaques and on its analysis by agarose gel electrophoresis and Southern blotting. This can take place after only one round of conventional screening, and phage from a large number of positively hybridizing plaques can be analyzed by a “one-tube” reaction.     

Construction and study of a new type of phage lambda DNA vector molecule]

A group of lambda mutants (mutants lambda 0) harbouring lesser number of EcoRI restriction sites on DNA molecules was selected. lambda3-1 recombinant (genotype lambdab221amgamma210Sr1lambda3+c-Px) was created by crosses of lambda02 phage with other lambda mutants. This phage DNA may be used as a vector molecule which makes it possible to select easily phages harbouring insertions of EcoRI DNA fragments. The maximal size of DNA fragment, the insertion of which would not decrease lambda3-1 viability, is 7.7 megadaltone. Lambda3-1 DNA has three regions heterological to lambda DNA, two of which probably include sites SRIlambda4 and SRIlambda5 and some juxtaposed genes. For example, Ptgene of lambda phage in juxtaposition with site SRIlambda4 is substituted by Px gene on the lambda3-1 DNA molecule.     

Irreversible changes in phage DNA after its protonation in solution and inside the virion detected by the transfection method

The dependence of irreversible structural changes in phage lambda DNA on the degree of its protonation in a solution and inside the virion has been found by measuring the transfection activity of bacteriophage. The different effect of ionic strength on pH-dependence of the irreversible changes in the structure of DNA upon its protonation in a solution or in situ has been registered and explained. The insignificant shift of pH from neutral region value in 0.1 M NaCl has resulted in a damaging effect of H+ ions on compact DNA in situ as compared to the DNA in a solution. The effect of H+ ions on compact DNA in situ is mainly based on the formation of noncovalent intermolecular DNA-protein and DNA-DNA linkages.     

Chromatin structure. Further evidence against the existence of a beaded subunit for the 30-nm fiber

The size distribution of chromatin fragments released by micrococcal nuclease digestion of liver chromatin at various ionic strengths was examined. Below 20 mM ionic strength, gradient profiles with a peak centered at 6 nucleosomes are generated, whereas between 20 and 50 mM the peak is always centered on 12 nucleosomes, and above 50 mM ionic strength the 30-nm fiber becomes less accessible to the nuclease and there is a corresponding increase in the size distribution of fragments in the gradients. However, extensive digestions always give profiles with a peak of 12 nucleosomes as nuclease-resistant dodecamers accumulate. All of these observations are consistent with the winding of the 10-nm polynucleosome chain into a helical coil commencing at about 20 mM ionic strength. The helical turns are stabilized by histone H1 interactions between 20 and 50 mM ionic strength producing stable dodecamers. Above 50 mM ionic strength the coil condenses longitudinally and the profiles are consistent with a random attack of this fiber by the nuclease. Consequently it is not necessary to invoke the existence of a subunit bead to explain the profiles. We further define the conditions at which specific structural transitions take place and provide methodology for the preparation of chromatin at various levels of condensation.     

A simple technique for the isolation of deletion mutants of phage lambda.

We describe a simple technique for isolating deletion mutants of phage lambda and use it to dissect a cloned fragment of foreign DNA. The technique is based on our previous finding that the normally essential product of lambda head gene D is dispensible for phage growth if the DNA content of the phage is less than 82% that of lambda wild-type (Sternberg and Weisberg, 1977). A significant fraction of the few phage that form plaques when a D amber mutant is plated on a nonsuppressing host contains deletions that reduce the phage chromosome size to less than 82% that of wild-type. It is possible to isolate deletions ranging in size from less than 1.5 kb to 14 kb (3 to 27% of wild-type lambda), and the size range can be restricted by an appropriate choice of the DNA content of the starting phage. This method, unlike the older EDTA or heat resistance methods, permits the scoring of deletions because of the absence of phenotypic variants. We investigated the effect of several host and phage mutations on deletion frequency and type and have determined that a host polA mutation increases the frequency of deletions about 30-50-fold without changing the type of deletions. A host mutD mutation or thymine deprivation increases deletion frequency about 10-fold. In contrast, a host ligts mutation has no effect on the frequency of deletions. We have also determined that the size of the smallest lambda chromosome packageable in a plaque-forming phage particle is 72-73% that of lambda wild-type.     

Formation of oligomeric structures from plasmid DNA carrying cos lambda that is packaged into bacteriophage lambda heads.

Plasmids that carry cos lambda, the region necessary for lambda phage packaging and that are as small as four kilobases in size can be packaged into lambda phage heads in head-to-tail tandem oligomeric structures. Multimeric oligomers as large as undecamers have been detected. Oligomer formation depends upon the products of red and gam of lambda, and the general recombination occurs between different plasmids that share homologous DNA regions. The packaging efficiency of plasmids depends on its copy number in cells and its genome size. Upon injection into a cell, the DNA establishes itself as a plasmid in a tandem structure. When such a plasmid in a high oligomeric structure is used as the source of packaging DNA, the packaging efficiency of the plasmids is elevated. The oligomers are stable in recA cells, whereas they drift toward lower oligomers in recA+ cells.     

A lambda library of Herpes simplex virus type 1 (KOS) DNA fragments obtained by partial digestion with Sau3A

Large fragments of Herpes simplex virus type 1 (HSV-1, strain KOS) DNA were produced by partial cleavage with Sau3A and inserted into a phage lambda BamHI vector. Recombinant phage (lambda KOS) DNA molecules were isolated and characterised. The final collection of phage recombinants contains partially overlapping inserts, which represent most of the HSV-1 genome. Restriction enzyme analysis of many independent clones containing Us sequences revealed sequence polymorphism in two specific regions.     

Comparative study of the iron-binding properties of human transferrins: I. Complete and sequential iron saturation and desaturation of the lactotransferrin

Human lactotransferrin binds 2 Fe³⁺ tightly at two specific sites. In order to demonstrate differences between the stability of the two iron-binding sites, the removal of iron was studied in buffers in the pH range 8-3 varying the ionic strength and with or without metal chelators such as phosphate ions and EDTA.The results show that in the presence of formate and acetate buffers of ionic strength 0.1–0.4 and in a pH range of 5–3, the two Fe³⁺ from human lactotransferrin are removed stimultaneously.Addition of 4 mM EDTA to buffers of ionic strength 0.1 and in the pH range 8–3 shows that between pH 5–4.3 the iron from only one of the binding sites, called the ‘acid labile’ site, is removed.Addition of 0.2 M phosphate ions to buffers of ionic strength 0.2 and in pH range 8–3 containing 4 mM EDTA shows that Fe³⁺ from the ‘acid labile’ site may be completely removed at pH 6. Removal of Fe³⁺ from the ‘acid stable’ site is obtained at pH 4.The differential behavior of the two iron binding sites was also shown by saturation experiments in the presence of citrate/bicarbonate buffers at different pH values. In a pH range 6.2–4.8, 50% saturation was obtained, but at pH 6.35 complete saturation was achieved. When saturation of partially saturated samples of human lactotransferrin was performed with ⁵⁹Fe it was demonstrated that in the pH range 6.2–4.8 iron is bound only to the ‘acid labile’ site.     

A role for recombination in the production of "free-loader" lambda bacteriophage particles

Density-labeled crosses were performed with bacteriophage lambda under conditions which diminish DNA duplication. The production of viable phage containing fully conserved parental DNA was found to be dependent upon the action of the genetic recombination systems. The production of phage containing DNA with one newly synthesized chain was less dependent upon recombination. The production of phage with chromosomes both of whose chains were synthesized following infection show little, if any, dependence on recombination. One can speculate that some step in the maturation process of bacteriophage lambda is inseparable from the reduction of lambda DNA to the monomeric rods characteristic of lambda virions.     

Deoxyribonucleic acid-cytosine methylation by host- and plasmid-controlled enzymes.

Deoxyribonucleic acid (DNA)-cytosine methylation specified by the wild-type Escherichia coli K 12 mec+ gene and by the N-3 drug resistance (R) factor was studied in vivo and in vitro. Phage lambda and fd were propagated in the presence of L-[methyl-3H]methionine in various host bacteria. The in vivo labeled DNA was isolated from purified phage and depurinated by formic acid-diphenylamine treatment. The resulting pyrimidine oligonucleotide tracts were separated according to size and base composition by chromatography on diethylaminoethyl-cellulose in 7 M urea at pH 5.5 and 3.5, respectively. The distribution of labeled 5-methylcytosine in DNA pyrimidine tracts was identical for phage grown in mec+ and mec minus (N-3) cells. For phage lambda the major 5-methylcytosine containing tract was the tripyrimidine, C2T; for both fd-mec minus (N-3) DNA and fd-mec+DNA, C2T was the sole 5-methylcytosine-containing tract. When various lambda DNAs were methylated to saturation in vitro by crude extracts from mec+ and mec minus (N-3) cells, the extent of cytosine methylation was the same. This is in contrast to in vivo methylation where lambda-mec minus (N-3) DNA contains twice as many 5-methylcytosines per genome as lambda-mec+ DNA. Therefore, we suggest that the K12 met+ cytosine methylase and the N-3 plasmid modification methylase are capable of recognizing the same nucleotide sequences, but that the in vivo methylation rate is lower in mec+ cells.     

Influence of ionic strength on the stability of phage t2r to osmotic shock

The authors assume that an increase in the ionic strength of the medium results in dissociation of the DNA-polyamine complex in the phage head. The released polyamines and internal protein molecules are unable to permeate into the external environment. Their thermal movement causes constant pressure within the phage; this contributes to rupture of the head by osmotic shock and probably plays a decisive role in injection of the phage DNA into the bacterium. Study of osmotic shock by glycerol in media of different ionic strengths showed that, as the ionic strength increases, the bacteriophage is at first destabihized by the action of the released polyamines and that only when the ionic strength is raised still further, it is restabilized by the influence of the ionic strength on the resistance of the membrane. The osmotic prossures required to rupture the phage head are practically the same for NaCl and KCl solutions, while for shock by glycerol solutions, considerably lower values were measured in media of low ionic strengths. The authors attribute these differences to differences in the rate of permeation of the shocking substance across the phage membrane. The equilibrium for NaCl and KCl is established in less than one minute and for glycerol in 5–10 min.     

Micelles of cerebroside sulphate

The critical micelle concentration of cerebroside sulphate in water is 0-01 mM: it increases with increasing concentrations of buffer to 0-07 mM in 0-1 M sodium acetate and formate buffers, pH 5-6 and 4-5 respectively. The partial specific volume of the micelles is about 0-94. The behaviour of the micelles in the ultracentrifuge and on Sephadex G-200 shows them to be grossly heterogeneous with respect to size. In 0-1 M buffer s20,w is about 26 S; in water or 0-01 M buffer smaller micelles with an s20,w of about 6 S are also present. In 0-01 M formate, pH 4-5, the smallest species detectable by equilibrium ultracentrifugation had a micellar weight of about 180,000 corresponding to an aggregation number of about 180. Much larger aggregates were also present. It is suggested that the smallest micelles are the substrate for sulphatase A when this is acting as a cerebroside sulphatase in buffers of low ionic strength.     

Ar+ plasma-induced damage to DNA in bacteriophage lambda: implications for the arrangement of DNA in the phage head.

Bacteriophage lambda was bombarded with low-energy Ar+ ions with the goal of determining whether particular regions of the DNA genome are found preferentially in the outer portion of the packaged DNA mass. The strategy was to fragment the DNA selectively near the surface of the virus by exposing intact phage to Ar+ ions energetic enough to break covalent chemical bonds in DNA but not energetic enough to penetrate deeply beneath the viral capsid shell. Broken DNA was then isolated, and its genomic origin was identified by Southern hybridization to mapped restriction fragments of lambda DNA. Analysis of such Southern blots revealed that all regions of the lambda genome were represented among the small DNA fragments generated during all times of Ar+ bombardment examined. Depending on the duration of exposure, however, particular regions of the genome were found to be enriched in the small-fragment population. After short periods of exposure, sequences from the leftmost 10% and from the right half of the standard genetic map were enriched in the broken-DNA fraction. Among sequences in the right half of the genome, the enrichment was progressively more pronounced beginning in the middle of the genetic map and proceeding toward the right end. In phage bombarded for longer periods of time, rightward sequences were preferentially depleted in the small-fragment population. In contrast, when Ar+ bombardment was carried out with free lambda DNA rather than intact phage, small DNA fragments arose uniformly from all regions of the genome at all times of exposure examined. The results indicate that in the intact phage, DNA sequences from the right half and from the very leftmost regions of the genome have a tendency to lie closer to the capsid than does the remainder of the genome. Since DNA is packaged into the prohead beginning at the left end, our results suggest that packaging occurs in such a way that newly entering DNA tends to be disposed externally to that packaged at earlier times.     

The DNA between Rz and cosR in bacteriophage lambda is nonessential

Near the right end of phage lambda DNA, between gene Rz and the cos site, are 2050 bp of apparently non-coding DNA. We have cloned a lambda DNA fragment containing this DNA into a plasmid and constructed a deletion, omega l, extending from a site within the Rz gene to a site about 560 bp from cos. This deletion could be recombined into viable lambda phage at a frequency equal to that observed for the undeleted sequence. Recombinant phage lambda carrying the omega l deletion were demonstrated to have the same burst size and kinetics of phage production as undeleted lambda. The omega l deletion can be used to extend the capacity of lambda cloning vectors and to provide a region for the insertion of heterologous DNA which should exhibit controllable high level expression from the lambda late promoter, p'R.