Progress towards understanding the nature of chromatid breakage

The wide range of sensitivities of stimulated T-cells from different individuals to radiation-induced chromatid breakage indicates the involvement of several low penetrance genes that appear to link elevated chromatid breakage to cancer susceptibility. The mechanisms of chromatid breakage are not yet fully understood. However, evidence is accumulating that suggests chromatid breaks are not simply expanded DNA double-strand breaks (DSB). Three models of chromatid breakage are considered. The classical breakage-first and the Revell "exchange" models do not accord with current evidence. Therefore a derivative of Revell's model has been proposed whereby both spontaneous and radiation-induced chromatid breaks result from DSB signaling and rearrangement processes from within large looped chromatin domains. Examples of such rearrangements can be observed by harlequin staining whereby an exchange of strands occurs immediately adjacent to the break site. However, these interchromatid rearrangements comprise less than 20% of the total breaks. The rest are thought to result from intrachromatid rearrangements, including a very small proportion involving complete excision of a looped domain. Work is in progress with the aim of revealing these rearrangements, which may involve the formation of inversions adjacent to the break sites. It is postulated that the disappearance of chromatid breaks with time results from the completion of such rearrangements, rather than from the rejoining of DSB. Elevated frequencies of chromatid breaks occur in irradiated cells with defects in both nonhomologous end-joining (NHEJ) and homologous recombination (HR) pathways, however there is little evidence of a correlation between reduced DSB rejoining and disappearance of chromatid breaks. Moreover, at least one treatment which abrogates the disappearance of chromatid breaks with time leaves DSB rejoining unaffected. The I-SceI DSB system holds considerable promise for the elucidation of these mechanisms, although the break frequency is relatively low in the cell lines so far derived. Techniques to study and improve such systems are under way in different cell lines. Clearly, much remains to be done to clarify the mechanisms involved in chromatid breakage, but the experimental models are becoming available with which we can begin to answer some of the key questions.

Electron microscopy and biological properties of pBR322 DNA condensed with the trivalent cations spermidine and hexammine cobalt (III)

Electron microscopy and the biological properties of susceptibility to DNase I, genetic transcription, and transformation of pBR322 DNA compacted with spermidine or hexammine cobalt (III), were analyzed in order to characterize the association of DNA in its compacted form with these two different trivalent cations. Spermidine and hexammine cobalt (III) produced an average 4-fold reduction of the DNA perimeter in compact DNA forms, which were doughnut-shaped toroids and cylinders. Both compacted DNAs were resistant to the hydrolytic activity of DNase I. However, spermidine-condensed pBR322 DNA was 10-fold and 4 to 6-fold more active in transcription and transformation, respectively, than naked pBR322. I. Hexammine cobalt (III)-condensed pBR322 was inactive in both biological properties. An inhibitory effect of hexammine cobalt (III) on RNA polymerase and genetic transformation activities was discarded because at higher ionic strength, in which DNA is not compacted by hexammine cobalt (III), transcription and transformation were similar to those observed with naked DNA. This information showed that the interaction of hexammine cobalt (III) with the DNA converted the pBR322 DNA into an inert molecule. In contrast, pBR322 did not loose its biological properties after its interaction with the polyamine spermidine; i.e., experimental condensation of pBR322 DNA by spermidine produced compacted DNA that is more similar to compact native genomes than relaxed DNA. These experiments led us to conclude that spermidine-condensed DNA can be used to study the roll of the native supercoiling of DNA in the regulation of genetic replication and transcription, as well as to study the mechanisms that allow the accessibility of the supercoiled or condensed DNA substrate for enzymes.

Exon mapping by fiber-FISH or LR-PCR

In this study we systematically assessed the sensitivity limits of fiber-FISH in model experiments. Exonic fragments and cDNAs with exon sizes of >/=200 bp could be mapped on their cognate cosmid. This positional fiber-FISH mapping was validated by long-range PCR. It is expected that these two independent mapping approaches will help to refine current available gene maps and show their applicability in fine mapping of sequence-tagged sites or expressed sequence tags. Also, they will be useful in resolving gene structures by mapping exon and intron locations.

Optical mapping: a novel, single-molecule approach to genomic analysis

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On the role of ATP hydrolysis in RecA protein-mediated DNA strand exchange. III. Unidirectional branch migration and extensive hybrid DNA formation

We have identified two functions for RecA-mediated ATP hydrolysis during DNA strand exchange. First, ATP hydrolysis renders RecA protein-mediated DNA strand exchange unidirectional (5' to 3' with respect to the single-stranded DNA). In the presence of a nonhydrolyzable analog adenosine 5'-O-(3-thiotriphosphate) (ATP gamma S), DNA strand exchange is bidirectional. Second, ATP hydrolysis is required for extensive formation of hybrid DNA. In the presence of ATP hydrolysis, the length of the exchanged region is limited only by the available homology, whereas in the absence of ATP hydrolysis, only 2 kilobase pairs or less of hybrid DNA are formed before branch migration is blocked in the majority of paired intermediates. Both of these functions of RecA protein-mediated ATP hydrolysis are crucial in ensuring the effectiveness of recombinational DNA repair, especially when the lesion to be repaired is distant from the initial crossover point.

Function of the GrpE heat shock protein in bidirectional unwinding and replication from the origin of phage lambda

The initiation of DNA replication by phage lambda depends on a specialized nucleoprotein structure that provides for the precise localization and activity of the Escherichia coli DnaB helicase at the lambda replication origin. Previous work has shown that the DnaJ and DnaK heat shock proteins function in the initiation pathway by releasing the DnaB helicase from the initiation complex to carry out localized unwinding of origin DNA. This DnaJ.DnaK pathway results in mainly unidirectional DNA unwinding and replication, whereas replication in vivo is mainly bidirectional. Based on recent replication work indicating an important role for the GrpE heat shock protein, we have used electron microscopy to study the action of GrpE in the DNA unwinding and replication reactions. We have found that GrpE acts with DnaJ and DnaK to facilitate the unwinding reaction at low concentrations of DnaK. In the presence of GrpE, bidirectional unwinding occurs in approximately half of the unwound DNA molecules. In addition, GrpE significantly increases the frequency of replication proceeding leftward from the origin. We suggest that reactions including GrpE result in more complete disassembly of the preinitiation nucleoprotein structure, thus allowing replication to proceed in both directions from the origin.

Replicatively active complexes of DnaA protein and the Escherichia coli chromosomal origin observed in the electron microscope

DnaA protein and the Escherichia coli chromosomal origin (oriC) form an initial complex at an early stage in the initiation of DNA replication. We have used electron microscopy to determine which structure among the several formed in the reconstitution of this multicomponent system is the replicatively active complex. One distinctive structure could be correlated with activity and localized to oriC, whilst several others could not. Formation of an open complex in the next stage of initiation was accompanied by the presence of a structure similar in size and shape to that of the functional initial complex. Whereas the initial complex was observed with either ATP or the ADP-forms of DnaA protein, only the ATP-form was effective in producing the open complex. Mutagenesis of several DNA sequence elements in oriC, known to be important for replication, was employed to determine the effects of these alterations on formation of the initial complex. As judged by electron microscopy and by functional assays, the region containing the four 9-mer dnaA boxes proved to be essential for the formation of the initial complex, while the three contiguous AT-rich 13-mers, known sites for opening of oriC, were not.

Microdissection and microcloning of human chromosome 7q22-32 region

Genetic information contributing to cystic fibrosis in addition to the CF gene is suggested to reside on the long arm of the human chromosome 7. In our attempt to analyze this genomic region in detail, we generated a region-specific DNA probe library by microdissection and microcloning of the midpiece of the chromosome 7q arm. Microdissection was performed in unstained metaphase spreads from a human x mouse hybrid cell line containing chromosome 7 as the only human chromosome. We obtained 593 clones from 75 dissected chromosomal fragments. At least 88% of the microclones were true recombinants; 40% of the clones contained repetitive sequences as determined by plaque hybridization with genomic DNA as probe. The overall mean fragment size of insert fragments was 3.2 kb, the median size was 3.5 kb. Regional mapping of 30 DNA fragments was performed by the aid of hybrid cell lines containing different segments of human chromosome 7; 50% of the microcloned inserts were found to map to 7q22-32.

Cytosine methylation as an effector of right-handed to left-handed DNA structural transitions

Cytosine methylation has energetic and structural influences on left-handed Z-DNA formation in supercoiled plasmids. The restriction and modification enzymes from Haemophilus haemolyticus (HhaI and M.HhaI) provide a system to locate and analyze small segments of Z-DNA in large supercoiled plasmids. An approach is outlined that uses M.HhaI as an in vivo conformational probe for the detection of unusual DNA structures in a living cell. Also, characteristic features of the M.HhaI gene and protein are discussed.

Low- and intermediate-copy-number cloning vectors based on the Pseudomonas plasmid pVS1

The cloning vector pME290 (6.8 kb), which is derived from the Pseudomonas plasmid pVS1 and has about 7 copies, was mutagenized in vitro to provide derivatives with altered copy numbers. Thus, pME292 (about 1-3 copies) and pME294 (about 15-20 copies) were isolated. These vectors were used in the characterization of the P. aeruginosa argF gene encoding ornithine carbamoyltransferase.

Curvature of mouse satellite DNA and condensation of heterochromatin

Cloned, sequenced mouse satellite DNA exhibits properties characteristic of molecules that possess a stable curvature. Circularly permuted fragments containing the region predicted to bend were used to map the curvature relative to DNA sequence. The altered mobility of these fragments in polyacrylamide gels is reversed when gels are run in the presence of distamycin A, a drug that binds preferentially to AT-rich DNA. Treatment of living mouse cells with this drug dramatically reduces the condensation of centromeric heterochromatin, the exclusive location of satellite sequences. In situ hybridization of satellite probes to extended chromosomes at the electron microscope level shows that satellite does not comprise a single block but is distributed throughout the centromere region. Based on these experiments, we hypothesize that the structure of mouse satellite DNA is an important feature of centromeric heterochromatin condensation.

Molecular analysis of elements inserted into mouse gamma-actin processed pseudogenes

DNA from ten mouse genomic clones, each containing distinct gamma-actin processed pseudogenes, was subjected to electron microscopic heteroduplex analysis, and in three cases (lambda mA36, lambda mA118 and lambda mA119) the heteroduplex formed with the DNA of a reference clone was found to be interrupted by a single-stranded loop. The genomic regions corresponding to these loops were subjected to structural analysis and they were found to represent different elements (IEs) inserted into the pseudogenes in a manner that gave rise to short target-site direct repeats. IE 36 (500 base-pairs in length) was found to be an intercisternal A-particle solo long terminal repeat (LTR), a 46 nucleotide region of which had undergone five-fold tandem amplification and subsequent mutation. IE 119 (501 base-pairs in length) was also a solo LTR, bearing similarity to the recently-described GLN-3 class of murine retroviral-like elements. IE 118 (865 base-pairs in length) is repeated 1000-2000 times in the mouse genome. It is not related to any known class of mobile elements, but does possess some sequence motifs that suggest it may be an LTR of a hitherto unrecognized family of retroviral-like elements. It also possesses a 26 out of 27 nucleotide identity to a region of the flanking pseudogene, suggesting that it may have suffered gene conversion.