Recombinant DNA molecules of bacteriophage phi chi174

Inverted repeats in chloroplast DNA from higher plants

The circular chloroplast DNAs from spinach, lettuce, and corn plants have been examined by electron microscopy and shown to contain a large sequence repeated one time in reverse polarity. The inverted sequence in spinach and lettuce chloroplast DNA has been found to be 24,400 base pairs long. The inverted sequence in the corn chloroplast DNA is 22,500 base pairs long. Denaturation mapping studies have shown that the structure of the inverted sequence is highly conserved in these three plants. Pea chloroplast DNA does not contain an inverted repeat. All of the circular dimers of pea chloroplast DNA are found to be in a head-to-tail confirmation. Circular dimers of spinach and lettuce were also found to have head-to-tail conformation. However, approximately 70-80% of the circular dimers in preparations of lettuce and spinach chloroplast DNA were found to be in a head-to-head conformation. We propose that the head-to-head circular dimers are formed by a recombination event between two circular monomers in the inverted sequence.

The search for a human Holliday junction resolvase

Four-way DNA intermediates, known as Holliday junctions, are formed during mitotic and meiotic recombination, and their efficient resolution is essential for proper chromosome segregation. Bacteria, bacteriophages and archaea promote Holliday junction resolution by the introduction of symmetrically related nicks across the junction, in reactions mediated by Holliday junction resolvases. In 2008, after a search that lasted almost 20 years, a Holliday junction resolvase was identified in humans. The protein, GEN1, was identified using MS following the brute-force fractionation of extracts prepared from human cells grown in tissue culture. GEN1 fits the paradigm developed from studies of prokaryotic Holliday junction resolvases, in that it specifically recognizes junctions and resolves them using a mechanism similar to that exhibited by the Escherichia coli RuvC protein.

Synthetic junctions as tools to identify and characterize Holliday junction resolvases

Genetic exchanges between chromosomes can lead to the formation of DNA intermediates known as Holliday junctions. The structure of these intermediates has been determined both biochemically and structurally, and their interactions with Holliday junction processing enzymes have been well characterized. A number of proteins, from both prokaryotic and eukaryotic sources, have been identified that promote the nucleolytic resolution of junctions. To facilitate these studies, synthetic DNA substrates that mimic true Holliday junctions have been developed. These now provide an important resource for both the identification and the characterization of novel Holliday junction resolvase activities. This chapter describes methods detailing the preparation and use of synthetic Holliday junctions and how they are best utilized in the study of proteins that might exhibit resolvase activity. Additionally, a method is described that can be used to rapidly screen a TAP-tagged library of proteins for resolvase activity without a need for conventional purification procedures.

Happy Hollidays: 40th anniversary of the Holliday junction

In 1964, the geneticist Robin Holliday proposed a mechanism of DNA-strand exchange that attempted to explain gene-conversion events that occur during meiosis in fungi. His proposal marked the birthday of the now famous cross-stranded DNA structure, or Holliday junction. To understand the importance of the Holliday model we must look back in the history of science beyond the last 40 years, to a time when theories of heredity were being proposed by Gregor Johann Mendel.

Effect of DNA topology on Holliday junction resolution by Escherichia coli RuvC and bacteriophage T7 endonuclease I

Holliday junctions are key intermediates in homologous genetic recombination. Their resolution requires specialised nucleases that nick pairs of strands at the junction point, leading to the separation of mature recombinants. Resolution occurs in either of two orientations, according to which DNA strands are cut. We show that DNA topology can determine the efficiency and outcome of a recombination reaction. Using two Holliday junction resolvases, Escherichia coli RuvC protein and T7 endonuclease I, we observed that supercoiled figure-8 DNA molecules containing Holliday junctions were resolved with a specific orientation bias, and that this bias was reversed by the presence of a topological tether (catenation). In contrast, when all topological constraints were removed by restriction digestion, the recombination intermediates were resolved equally in the two orientations. These results show that topological constraints affecting Holliday junction structure influence the orientation of resolution by cellular resolvases.

Apparent gene conversion in an Escherichia coli rec+ strain is explained by multiple rounds of reciprocal crossing-over

Gene conversion, the non-reciprocal transfer of sequence information between homologous DNA sequences, has been reported in lower eukaryotes, mammals and in Escherichia coli. In an E. coli rec+ strain, we established a plasmid carrying two different deleted neo genes (neoDL and neoDR) in an inverted orientation and then selected for homologous recombination events that had reconstructed an intact neo+ gene. We found some plasmids that had apparently experienced intramolecular gene conversion. Further evidence, however, suggests that they are products of multiple rounds of reciprocal crossing-over, apparently involving two plasmid molecules. First, most of the Neo+ clones contained multiple types of Neo+ plasmids, although the frequency of producing the neo+ clones was low. Second, all the neo+ clones also contained, as a minority, one particular form of dimer, which can be formed by reciprocal crossing-over between neoDL of one plasmid molecule and neoDR of another plasmid molecule. Third, in reconstruction experiments, we cloned and purified this dimer and transferred it back into the rec+ cells. The dimer gave rise to clones containing multiple types of neo+ recombinant monomers, including those apparent gene conversion types, and containing only few molecules of this dimer plasmid.

Specific binding of cruciform DNA structures by a protein from human extracts

A gel electrophoresis binding assay has been used to probe extracts from cultured human lymphoblasts for proteins that bind cruciform structures in duplex DNA. Proteins have been detected that form complexes with synthetic X- and Y-junctions. Several lines of evidence suggest that binding is specific for DNA structure rather than sequence: (1) X- and Y-structures were bound whereas linear duplexes containing identical DNA sequences were not, (2) Binding occurred with equal efficiency to two X-junctions that were constructed from DNA strands of different sequence, (3) One X-junction successfully competed with another for binding whereas linear duplex DNA did not; and (4) protein-DNA complexes were observed at probe:non-specific competitor DNA ratios of 1:10,000.

Plasmid recombination intermediates generated in a Saccharomyces cerevisiae cell-free recombination system

We have developed an assay utilizing Saccharomyces cerevisiae cell extracts to catalyze recombination in vitro between homologous plasmids containing different mutant alleles of the tet gene. Electrophoretic analysis of product DNA indicated that a number of novel DNA species were formed during the reaction. These species migrated through agarose gels as distinct bands with decreased electrophoretic mobility compared with the substrate DNA. The DNA from each individual band was purified and shown to be enriched 5- to 100-fold for tetracycline-resistant recombinants by using a transformation assay. The structure of the DNA molecules present in these bands was determined by electron microscopy. Recombination between circular substrates appeared to involve the formation and processing of figure-eight molecules, while recombination between circular and linear substrates involved the formation of molecules in which a circular monomer had a monomer-length linear tail attached at a region of homology.

Partial purification of an enzyme from Saccharomyces cerevisiae that cleaves Holliday junctions

An enzyme from Saccharomyces cerevisiae that cleaves Holliday junctions was partially purified approximately 500- to 1000-fold by DEAE-cellulose chromatography, gel filtration on Sephacryl S300, and chromatography on single-stranded DNA-cellulose. The partially purified enzyme did not have any detectable nuclease activity when tested with single-stranded or double-stranded bacteriophage T7 substrate DNA and did not have detectable endonuclease activity when tested with bacteriophage M13 viral DNA or plasmid pBR322 covalently closed circular DNA. Analysis of the products of the cruciform cleavage reaction by electrophoresis on polyacrylamide gels under denaturing conditions revealed that the cruciform structure was cleaved at either of two sites present in the stem of the cruciform and was not cleaved at the end of the stem. The cruciform cleavage enzyme was able to cleave the Holliday junction present in bacteriophage G4 figure-8 molecules. Eighty percent of these Holliday junctions were cleaved in the proper orientation to generate intact chromosomes during genetic recombination.

Plasmid recombination intermediates generated in a Saccharomyces cerevisiae cell-free recombination system

We have developed an assay utilizing Saccharomyces cerevisiae cell extracts to catalyze recombination in vitro between homologous plasmids containing different mutant alleles of the tet gene. Electrophoretic analysis of product DNA indicated that a number of novel DNA species were formed during the reaction. These species migrated through agarose gels as distinct bands with decreased electrophoretic mobility compared with the substrate DNA. The DNA from each individual band was purified and shown to be enriched 5- to 100-fold for tetracycline-resistant recombinants by using a transformation assay. The structure of the DNA molecules present in these bands was determined by electron microscopy. Recombination between circular substrates appeared to involve the formation and processing of figure-eight molecules, while recombination between circular and linear substrates involved the formation of molecules in which a circular monomer had a monomer-length linear tail attached at a region of homology.

Resolution of synthetic att-site Holliday structures by the integrase protein of bacteriophage lambda

Site-specific recombination of the bacteriophage lambda genome into and out of the host bacterial genome is postulated to involve the formation of Holliday structure intermediates by reciprocal single-strand exchanges. Synthetic analogues of the predicted recombination intermediates are resolved in vitro by the protein product of the lambda int gene. Some of the structural features and reaction conditions for this genetic recombination can now be defined.

Double Holliday structure: a possible in vivo intermediate form of general recombination in Escherichia coli

From Escherichia coli cells we purified '8'-shaped dimeric molecules in which two circular DNA molecules of bacteriophage lambda were joined at a homologous site. Some of them had a complex junction which we interpreted as being two closely spaced Holliday structures because of (i) superhelicity of the molecule, (ii) the sedimentation rate of the molecule in sucrose gradients, and (iii) the appearance in the electron microscope. Other 'figure-eights's' had two separate homologous junctions, presumably two Holliday bridges. A possible role for these 'double Holliday structures' in UV-stimulated recA-dependent recombination in vivo is discussed.

Genetic recombination of bacterial plasmid DNA. Physical and genetic analysis of the products of plasmid recombination in Escherichia coli

Derivatives of plasmid pBR322 DNA containing tet mutations were constructed by inserting XhoI linkers at various sites in the tetracycline resistance gene. Monomer plasmids containing either the tet-10 allele located at nucleotide position 23 or the tet-14 allele located at nucleotide position 1267 were used to construct a circular dimer containing one copy of each allele and a circular trimer containing one copy of the tet-10 allele and two copies of the tet-14 allele. Genetic recombination of these plasmid DNAs to produce a functional tetracycline resistance gene could be detected as the production of tetracycline-resistant progeny during the growth of transformants or using a restriction mapping assay which detected the rearrangement of the mutant alleles. The structure of individual tetracycline-resistant recombination products was determined by restriction mapping. This analysis suggested that as many as 70% of the plasmid recombination events in Escherichia coli AB1157 could have involved gene conversion events. The formation of these recombination products was most easily predicted by a model involving figure 8 recombination intermediates and the formation of symmetric regions of heteroduplex. Recombination in JC10287 delta(srlR-recA)304 occurred at 5% of the wild-type frequency and appeared to occur by a similar mechanism. Recombination in JC9604 recA56 recB21 recC22 sbcA23 occurred at 20 times the wild-type frequency and appeared to involve multiple independent recombination events.

Genetic recombination in avian retroviruses

The avian retroviruses--and probably other retroviruses as well--undergo a variety of recombinational events with relatively high efficiency. An understanding of the molecular basis of these events should provide insight into the important biological properties these agents exhibit when they become integrated into somatic or germ-line host cells, when they exchange genetic information among themselves, or when they transduce host cell genes. In this article we review molecular models for homologous recombination, against a background of the other types of recombination events that are typical of these viruses. It seems probable that the retroviruses will provide useful models for analysis of a variety of DNA rearrangements known to occur in eukaryotic cells.

Genetic recombination of bacterial plasmid DNA: electron microscopic analysis of in vitro intramolecular recombination

a tetramer of pMB9 DNA containing a single EcoRI site per tetramer was used to investigate intramolecular recombination in Escherichia coli. When transformed into wild-type E. coli strains, the tetramer was converted into dimers and a small proportion of trimers and monomers. The conversion was blocked in recA strains and rec B recC recF strains but not in recB recC strains or recF strains. Extracts of E. coli converted the tetramer into dimers, trimers, and monomers. Figure of 8 molecules and catenanes were minor products. The proportion of recombinant molecules ranged from 7% to 14%. Intramolecular recombination in vitro was blocked in extracts of recA strains and recB recC recF strains but not significantly blocked in extracts of recB recC strains and recF strains. recA protein restored activity to recA extracts; activity in recB recC recF extracts was restored by purified exonuclease V (recBC nuclease) or a recF protein donor extract. Novobiocin and oxolinic acid inhibited the reaction by 70-80%.

DNA synaptase: an enzyme that fuses DNA molecules at a region of homology

This paper describes an enzyme from Escherichia coli, and its purification to apparent homogeneity. The protein, which we call "DNA synaptase" and which may be representative of a class of enzymes, fuses double-stranded DNA molecules at a region of homology. In addition, the purified enzyme is able to catalyze the association of single-stranded DNA with homologous duplex DNA. The genome fusion reaction catalyzed by the purified enzyme occurs in the presence of Mg2+, spermidine, and 2-mercaptoethanol and does not require a high-energy cofactor. By bringing two genomes together at a region of homology, DNA synaptase has a property expected for an enzyme that participates in an early step in genetic recombination. However, the synaptase can be recovered from Rec A- cells, and thus it is not yet possible to determine whether this enzyme plays a role in physiological recombination or in another cellular process that involves genome fusion, such as the recombinational repair of damaged DNA.

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.

Occurrence of crossed strand-exchange forms in yeast DNA during meiosis

The crossed strand-exchange form (Holliday structure, half chiasma) has been predicted as an intermediate in the genetic recombination of eukaryotes. We report here the detection of this form in the yeast plasmid, 2-micron DNA, isolated during meiosis. Physical mapping has previously suggested that two forms of 2-micron DNA arise because of recombination between inverted repeat regions. After appropriate digestion with restriction endonuclease, a crossed strand-exchange form intermediate in this recombination would yield an X-shaped form resistant to loss by branch migration because of nonhomology in sequences flanking the region of homology. We first generated this X-shaped form artificially by reannealing melted restriction fragments of 2-micron DNA. This enabled us to develop a procedure for the physical separation of the X-shaped form by agarose gel electrophoresis. We then used this electrophoretic procedure to isolate a naturally occurring form of identical structure from the 2-micron DNA of meiotic cells. Electron microscopy demonstrated that the exchange junction had the expected configuration of strands and indicated that the junction occurred within the region of homology.

Biochemical assay designed to detect formation of recombination intermediates in vitro

A biochemical assay that is designed to detect recombination intermediates formed in vitro is described. The assay measures the fusion of two essentially homologous plasmids, one of which is radioactively labeled and the other of which carries several copies of the lac operator. The fusion product is radioactive and can be bound to a nitrocellulose filter by lac repressor. This assay for genome fusion is rapid and readily applicable to the many fractions that result during enzyme purification. The fused product is not destroyed in the assay and may be recovered from the filter for further analysis by electron microscopy. The product is then seen to consist of figure 8 structures that can be cleaved by the restriction enzyme EcoRI to give chi forms, structures similar to those recovered from recombination-proficient cells. It is expected that this assay will be useful in the purification of the "recombinase-type" activity detected in crude cell lysates. To demonstrate this point, the assay was applied to the protein fractions recovered from a molecular sieve column. The results indicate that the fusion activity has an apparent molecular weight of 50,000--100,000.

Recombination of bacteriophage phi X174 by the red function of bacteriophage lambda

Recombination of bacteriophage phi X174 was effectively promoted when the Red function of lambda was supplied by either co-infection with lambda or induction of lambda lysogens. Mutations in red alpha and red beta genes of lambda abolished recombination nearly completely, whereas a mutation in gam gene reduced it only slightly. The Red-promoted recombination of phi X174 occurred in recA, recB, and polA mutants as well as in wild-type strains of Escherichia coli. It was further stimulated when phi X174 mutants were irradiated with UV light before infection.

ATP-dependent renaturation of DNA catalyzed by the recA protein of Escherichia coli

The product of the recA gene of Escherichia coli has been purified to near-homogeneity by a simple three-step procedure. Incubation of the recA protein with complementary single strands of DNA, Mg2+, and ATP results in the rapid formation of large DNA aggregates containing many branched structures. As judged by resistance to S1 nuclease and by electron microscopy, these aggregates contain both duplex and single-stranded regions. The renaturation and aggregation of DNA catalyzed by the recA protein is coupled to the hydrolysis of ATP. The recA protein purified from a cold-sensitive recA mutant does not catalyze DNA renaturation or aggregation at 28 degrees C, but does so at 37 degrees C, a finding which correlates with the recombination defect observed in vivo and indicates that this activity is an intrinsic function of the recA protein. These results suggest that the recA protein plays a specific role in strand transfer during recombination and possibly in postreplication repair of damaged DNA.

In vitro system from Escherichia coli that catalyzes generalized genetic recombination

This paper reports an in vitro system for studying generalized genetic recombination. The system uses extracts from Escherichia coli as a source of enzymes and plasmid DNA molecules as substrates. Unit-size plasmid DNA rings are converted into genomes fused at a region of DNA homology at a frequency of about 5-10% over a period of hours. That the fused structures are the result of recombination is supported by two lines of evidence. When two partially homologous plasmids of different sizes are used as substrates for the in vitro system, intermediates containing one plasmid of each size are obtained. Furthermore, fused structures are not formed with high efficiency in extracts from recombination-deficient (Rec A(-)) cells.DNA synthesis does not appear to be required for the formation of the recombination intermediates; it is possible to omit DNA precursors from the reaction mixture and, furthermore, to develop the fused structures even in the presence of chaintermininating dideoxynucleoside triphosphates. The structures formed in vitro have the basic properties of recombination intermediates previously recovered from intact cells. That is, two genomes are demonstrably fused at a region of homology. However, in one way the molecules formed in vitro have a property less frequently observed in vivo-the fused genomes often appear to be connected over an extended region of homology ranging up to several hundred base pairs in length. This extended region of pairing may indicate the presence of two crossover connections very close together and, as will be discussed, may provide an insight into the mechanism by which the recombination intermediate is formed.

Transfection of Enterobacteriaceae and its applications

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Analysis of the phiX DNA replication cycle by electron microscopy

We have monitored the development of intracellular phiX DNA forms during the course of a virus life cycle that duplicates as closely as possible the normal infection of individual cells by single virions. The viral DNA was isolated in a one-step purification procedure, and quantitative electron microscopy was performed on the samples, resulting in the following conclusions: (i) Early in the life cycle, when the cells accumulate duplex rings, two types of DNA replication intermediates are observed: a rolling circle with a single-stranded tail; and a novel form, a single-stranded circle that is partially duplex. Thus, duplex ring synthesis appears to occur in two asymmetric steps, with positive strand DNA first being processed from the tail of the rolling circle and circularized, before it acts as a template for negative strand synthesis. (ii) Late in the life cycle, as single-stranded circles are synthesized and virus particles are assembled, only one replicating intermediate is observed--the rolling circle with a single-stranded tail. At this stage, the number of rolling circles reaches a level of about 35 per cell. (iii) The net rate of polymerization in the rolling circle intermediates is about 200 nucleotides per sec.

Homology-dependent cutting in trans of DNA in extracts of Escherichia coli: an approach to the enzymology of genetic recombination

An in vitro system is described in which the cutting of crosslinked phiX replicative form (RF) I DNA molecules by the uvr system of Escherichia coli induces the cutting of homologous undamaged DNA during incubation with crude extracts of thermally induced E. coli (lambda precA+) lysogens. This reaction, which has also been observed in intact E. coli lysogens infected with lambda phages, is dependent on the presence of functional recA+ and uvrB+ gene products. Extracts from thermally induced lambda precA+ lysogens of E. coli proved to be substantially more active than extracts from nonlysogenic cells of the same strain. The results provide preliminary evidence for an endonuclease activity that cuts intact superhelical DNA in response to interaction with homologus damaged DNA. In the present paper, we describe an in vitro system in which both the endonucleolytic cutting of DNA containing crosslinks and the induced cutting of undamaged DNA can be studied without purification of the participating enzymes. Although the information obtained is fragmentary and often puzzling, we feel that this system can contribute to an understanding of the complex mechanisms involved in repair and recombination.

Biochemical analysis of genetic recombination in eukaryotes

Recent studies concerning molecular mechanisms of genetic recombination in eukaryotes are reviewed. Since many of these studies have focused on the testable predictions arising from the hybrid DNA theory of genetic recombination, this theory is summarised. Experiments to determine the time of meiotic crossing-over and the structure of the synaptonemal complex which facilitates meiotic crossing-over are described. Investigations of DNA nicking and repair events implicated in recombination are discussed. Properties of proteins which may facilitate hybrid DNA formation, and biochemical evidence for hybrid DNA formation are presented. Finally, a nuclease which has been implicated in gene conversion is described.

Recombination of bacteriophage T7 in vivo

Most recombination following infection with T7 was found to coincide with the time of most repid DNA synthesis, at about 20 min after infection at 30 degrees in minimal medium. Recombining DNA was investigated electron microscopically. Multiply branched DNA structures were observed after infection with T7 wild type, gene 3-, gene 6- and genes 3-, 6- phage, but not after infection with T7 gene 5- phage. Evidence is presented indicating that these structures are T7 DNA molecules in the process of recombining. The detailed structures of these recombinational intermediates suggest mechanisms by which T7 DNA initiates recombination.

Recombination promoted by superhelical DNA and the recA gene of Escherichia coli

When a mixture of superhelical DNA (RFI) of phage phiX174 am3 and fragments of single-stranded DNA from wild-type phiX174 was added to spheroplasts of E. coli carrying an amber suppressor, several percent of the progeny phage were recombinant. The yield of wild-type progeny was 10(3) to 10(4) times lower when the fragments came from phiX174 am3 or phage G4 am+, or when fragments were absent. Fewer recombinants were produced in proportion to the decrease in the fraction of RFI in samples treated with S1 nuclease, whereas the total yield of phage did not decrease. Transfection by fragments and superhelical DNA produced 20 to 100 times more recombinants than transfection by fragments and either nicked circular DNA or relaxed closed circular DNA. Transfection of a recA- strain by RFI DNA and fragments yielded 5-10% as many recombinants as transfection of a rec+ strain. This partial requirement for recA was bypassed by transfection with complexes of RFI AM3 DNA and am+ fragments made in vitro.

On the mechanism of genetic recombination: electron microscopic observation of recombination intermediates

This paper deals with the nature of recombination intermediates. Using the electron microscope to study the DNA of the plasmid colicin E1, we have observed more than 800 molecules that appear to represent intermediates in the process of recombination. Specifically, after isolating colicin DNA and linearizing it with the restriction enzyme EcoRI, we find crossed molecules with twice the normal colicin DNA content. These forms consist of two genome-length elements held together at a region of DNA homology. The molecules can be recovered from wild type and Rec B-C host cells but are not present among the colicin DNA forms isolated from recombination-deficient Rec A cells. We have termed the experimentally observed molecules "chi forms" and believe that they represent the recombination intermediate of the Holliday model.

Replication of kinetoplast DNA of Crithidia acanthocephali. I. Density shift experiments using deuterium oxide

The protozoan Crithidia acanthocephali contains, within a modified region of a mitochondrion, a mass of DNA known as kinetoplast DNA (kDNA). This DNA consists mainly of an association of approximately 27,000 covalently closed 0.8-mum circular molecules which are apparently held together in a definite ordered manner by topological interlocking. After culturing of C. acanthocephali cells for 25 generations in medium containing 75% deuterium oxide, both nuclear DNA (rhonative, nondeuterated=1.717 g/cm3) and kDNA (rhonative, nondeuterated=1.702 g/cm3) increased in buoyant density by 0.012 g/cm3. The replication of the two DNAs was studied by cesium chloride buoyant density analysis of DNAs from exponentially growing cells taken at 1.0, 1.4, 2.0, 3.0, and 4.0 cell doublings after transfer of cells from D2O-containing medium into medium containing only normal water. The results obtained from analysis of both native and denatured nuclear DNAs indicate that this DNA replicates semiconservatively. From an analysis of intact associations of kDNA, it appears that this DNA doubles once per generation and that the newly synthesized DNA does not segregate from parental DNA. Fractions of covalently closed single circular molecules and of open circular and unit length linear molecules were obtained from associations of kDNA by sonication, sucrose sedimentation, and cesium chloride-ethidium bromide equilibrium gradient centrifugation. Buoyant density profiles obtained from these fractions indicate that: (a) doubling of the kDNA results from the replication of each circular molecule rather than from repeated replication of a small fraction of the circular molecules; (b) replication of kDNA is semiconservative rather than conservative, but there is recombination between the circles at an undefined time during the cell cycle.

Uptake of homologous single-stranded fragments by superhelical DNA: a possible mechanism for initiation of genetic recombination

Superhelical [3-H]DNA (replicative form I, RFI) of bacteriophage phiX174 slowly but spontaneously took up 32-P-labeled homologous single-stranded fragments at 4 degrees. Uptake was accelerated by heating to 75 degrees. RFI did not take up single-stranded fragments derived from DNA of Escherichia coli or from separated strands of phage lambda. Uptake was inhibited by low concentrations of ethidium bromide. Relaxed circular phiX174 DNA did not take up homologous fragments. Per molecule of RFI, the complexes contained as much as 90 nucleotide residues of homologous fragment. The 32-P-lebeled fragments were largely resistant to digestion by exonuclease I, and were not displaced by heating complexes at 60 degrees for 1 min in 16 mM or 100 mM NaCl. Under comparable conditions of temperature and salt all of the fragments were displaced from complexes in which at least one phosphodiester bond was cleaved by pancreatic DNase, but a significant fraction of the fragments was retained in complexes that were relaxed by digestion with S1 nuclease. These observations are interpreted to mean that S1 nuclease digested the plus (viral) strand of the recipient RF at the site of uptake in some instances. Transfection of E. coli by heterozygous complexes produced recombinant progeny, thereby showing that genetic information can be transferred from the fragment of plus strand to progeny plus strands. We propose that both uptake of a third strand by superhelical DNA and the action of nucleases on the resulting complex may simulate early steps in genetic recombination.