A contribution to immunological specificity of DNA in leukosis.

Active antisera containing antibodies to deproteinized DNA preparations of normal tissue and the spleen of cows suffering from myeloleukosis were obtained. The anti DNA sera to DNA preparations contained complement fixing antibodies related to gamma M globulins. In the study of leukosis and normal anti DNA sera in quantitative CFR with the corresponding test antigens, immunological specificity of DNA preparations isolated from the organs of cows affected with myeloleukosis was established. Immunological specificity of leukosis DNA was confirmed in tests with the absorption of leukosis anti DNA sera by DNA preparations of homologous normal tissues. This specificity is an inherent quality of not only the native but also the heat-denatured DNA molecule.     

Cell response to penetration by informational macromolecules]

A relation is shown between the kinetic for of DNA uptake by the thymocytes (extremal or monotonous), the level of uptake (low or high) and the origin of DNA (hetero-or homologous). Preliminary irradiation of cells promotes a manifestation of a cytopathogenous effect of the heterologous DNA. The association between the cytopathogenous effect of DNA and that of its information characteristics has been confirmed. The demonstration of cytopathogenous effects of native and degraded DNA was studied as a function of time of their storage. The chromatographic analysis of dispersion of the molecular weights of preparations at different time of their starage allowed a conclusion of the important role played by structure defects in manifestation of cytopathogenous properties of DNA.     

Luminescence analysis of the structure of human alpha-1-microglobulin

Absorption, fluorescence, and fluorescence excitation spectra in UV and visible regions are studied for alpha-1-microglobulin preparations isolated from human urine by gel chromatography and immunoaffinity chromatography with charcoal adsorption. The possible nature of low-molecular-weight compounds that impart yellow-brown color to alpha-1-microglobulin preparations and their role in the stabilization of the structure of protein globule is discussed. The effect of urea (1–10 M) and guanidine hydrochloride (0.25–6 M) on the conformational state and fast internal dynamics of alpha-1-microglobulin is studied by tryptophan fluorescence. The unfolding of the protein under the action of denaturants is attended with pronounced activation of its nanosecond internal dynamics. Alpha-1-microglobulin can regain the initial conformation and internal dynamics typical of native protein after denaturation unfolding of the globule with 10 M urea or 6 M guanidine hydrochloride. Alpha-1-microglobulin isolated by gel chromatography can exist in a partially folded thermodynamically stable state in 4–6 M urea.     

Exogenous DNA transcription in cells with their native DNA inhibited. 1. DNA incorporation into homologous and heterologous cells.

The incorporation of mouse S-EAC DNA into homologous normal cells (mouse embryo secondary cultures), and into heterologous cancer cells (TC-SV40 line), with both systems having their native DNA blocked by BrUdR incorporation, was studied. 3H-TdR-DNA was inoculated with DEAE-D to protect it and to potentiate its incorporation, the process being autoradiograohically controlled. The amount of incorporated DNA was radioisotopically determined, and the incorporation process was studied by analysing the fractions obtained after density gradient centrifugation separation of the inoculated cells DNA. Receptivity was greater in those cells inoculated with DEAE-D-protected DNA. The incorporation was slightly greater for cells whose DNA had been blocked by BrUdR incorporation, and for homologous with respect to heterologous cells. In those cells inoculated while the DNA blockade was incomplete, part of the inoculated DNA became incorporated into the cell genome (L-H chains). However, in the completely blocked cells it could not be determined if the incorporation occurred in a lysogenic-like or in an episomic-like form.     

Clustering of transfer RNA genes of Xenopus laevis

The arrangement of the reiterated DNA sequences complementary to transfer RNA has been studied in Xenopus laevis. Prehybridization of denatured DNA with an excess of unfractionated tRNA results in a small but well-defined increase in the buoyant density of fragments which contain sequences homologous to tRNA. The density increase is smaller than that found for 5 S DNA, but is the same or nearly so for all tRNA coding sequences examined. These results indicate that the majority of tRNA genes are clustered together with spacer DNA, the average size of which is estimated to be approximately 0.5 × 10⁶ daltons (native) DNA.In high molecular weight native DNA preparations, the sequences homologous to unfractionated tRNA, tRNA^Val, tRNA₁^Met and tRNA₂^Met band in CsCl at 1.707, 1.702, 1.708 and 1.711 g cm^?3, respectively. The mean buoyant densities are constant at all molecular weights examined but they do not correspond to the base compositions of the complementary tRNA species. These results indicate that isocoding genes are linked to spacer DNA in separate and extensive gene clusters, and that the different clusters contain different spacer DNA sequences. These clusters form well-defined cryptic DNA satellites which are potentially separable from each other as well as from other chromosomal DNA.     

The ubiquitous nuclear protein, NHP1, binds with high affinity to different sequences of the chicken vitellogenin II gene.

In gel shift assays, affinity chromatography-purified NHP1 forms a stable complex with different sequences of the chicken vitellogenin II gene. The apparent KD of NHP1 with the estrogen response element (ERE) containing 5-methylcytosine is 1 X 10(-11) M. NHP1 does not form a complex with the Xenopus vitellogenin ERE where the GCG bases are replaced by CAG. NHP1 is closely related if not identical to the other ubiquitous proteins NHP2, NHP3 and NHP4 that bind specifically to different sequences. All four proteins behave identically on chromatography and give identical patterns in proteolytic bandshift assays. NHP1, NHP2 and NHP3 have a native molecular weight of 170,000 and are composed of two polypeptides of 85 and 75 kDa. The possible function of NHP1 is discussed.     

Fission yeast Rad50 stimulates sister chromatid recombination and links cohesion with repair.

To study the role of Rad50 in the DNA damage response, we cloned and deleted the Schizosaccharomyces pombe RAD50 homologue. The deletion is sensitive to a range of DNA-damaging agents and shows dynamic epistatic interactions with other recombination-repair genes. We show that Rad50 is necessary for recombinational repair of the DNA lesion at the mating-type locus and that rad50Delta shows slow DNA replication. We also find that Rad50 is not required for slowing down S phase in response to hydroxy urea or methyl methanesulfonate (MMS) treatment. Interestingly, in rad50Delta cells, the recombination frequency between two homologous chromosomes is increased at the expense of sister chromatid recombination. We propose that Rad50, an SMC-like protein, promotes the use of the sister chromatid as the template for homologous recombinational repair. In support of this, we found that Rad50 functions in the same pathway for the repair of MMS-induced damage as Rad21, the homologue of the Saccharomyces cerevisiae Scc1 cohesin protein. We speculate that Rad50 interacts with the cohesin complex during S phase to assist repair and possibly re-initiation of replication after replication fork collapse.     

Competition between replicative and translesion polymerases during homologous recombination repair in Drosophila

In metazoans, the mechanism by which DNA is synthesized during homologous recombination repair of double-strand breaks is poorly understood. Specifically, the identities of the polymerase(s) that carry out repair synthesis and how they are recruited to repair sites are unclear. Here, we have investigated the roles of several different polymerases during homologous recombination repair in Drosophila melanogaster. Using a gap repair assay, we found that homologous recombination is impaired in Drosophila lacking DNA polymerase zeta and, to a lesser extent, polymerase eta. In addition, the Pol32 protein, part of the polymerase delta complex, is needed for repair requiring extensive synthesis. Loss of Rev1, which interacts with multiple translesion polymerases, results in increased synthesis during gap repair. Together, our findings support a model in which translesion polymerases and the polymerase delta complex compete during homologous recombination repair. In addition, they establish Rev1 as a crucial factor that regulates the extent of repair synthesis.     

Comparison between histones FV and F2a2 of chicken erythrocyte. II. Interaction with homologous DNA.

The conformation and stability of artificial complexes between chicken erythrocyte DNA and homologous histones FV and F2a2 was studied by circular dichroism (CD) and thermal denaturation followed by both absorbance and CD measurements. The complexes are made after a stepwise potassium fluoride gradient dialysis without urea and studied at low ionic strength (10-minus 3 M). 1) No structural changes of the DNA can be detected up to r equals 0.2 with FV and r equals 0.6 for F2a2. With FV at higher values of r the CD spectrum is altered, indicating the organization of DNA and histones in some kind of aggregate. 2) The conformation of histone molecules inside the complexes is not related to the ionic strength of the medium but to an effective ionic environment close to 0.1 M. This ionic strength would also correspond to the melting temperature of histone-covered DNA. 3) From the analysis of the absorbance melting profile the length of DNA covered with an histone molecule can be estimated. A good agreement is found between the negative charge of this piece of DNA and the net positive charge of the histone. 4) Since the CD transition at 227 nm occurs before the second absorbance transition at 280 nm, the DNA is stabilized no longer by native histone but partially or fully denatured histones. The helical regions of the histone molecule are not involved in the binding process, which appears to be almost purely coulombian and most likely related to some structural fit between the pattern of negative charges in the DNA helix and that of positive charges along the peptide chain.     

Electron microscopic band-interband pattern of polytene chromosomes in Drosophila nasuta albomicans. 1. Salivary gland chromosome 2R

The band-interband pattern of salivary gland chromosome 2R in Drosophila nasuta albomicans (division 53-83) was studied by light (LM) and electron microscopy (EM) using squash preparations and surface-spread polytene (SSP) chromosome preparations, respectively. LM and EM maps were compiled. Based on the digitized EM patterns of five homologous SSP chromosomes a computerized chromosome map was plotted. The EM pattern analysis showed a total number of 662 chromosome bands with an almost 98% increase compared with the LM analysis of squash preparations. The majority (about 92%) of interband lengths in SSP chromosome 2R ranged between 0.25 and 0.64 microns, which equal about 0.8-2.1 kb of totally extended DNA or 2.5-6.4 kb of DNA, if a DNA packing ratio of 0.1 microns/kb is assumed for the interbands of SSP chromosomes.     

A stimulatory RNA associated with RecBCD enzyme.

RecBCD enzyme acts in the major pathway of homologous recombination of linear DNA in Escherichia coli. The enzyme unwinds DNA and is an ATP-dependent double-strand and single-strand exonuclease and a single-strand endonuclease; it acts at Chi recombination hotspots (5'-GCTGGTGG-3') to produce a recombinogenic single-stranded DNA 3'-end. We found that a small RNA with a unique sequence of approximately 24 nt was tightly bound to RecBCD enzyme and co-purified with it. When added to native enzyme this RNA, but not four others, increased DNA unwinding and Chi nicking activities of the enzyme. In seven similarly active enzyme preparations the molar ratio of RNA molecules to RecBCD enzyme molecules ranged from 0.2 to <0.008. These results suggest that, although this unique RNA is not an essential enzyme subunit, it has a biological role in stimulating RecBCD enzyme activity.     

Deoxyribonucleic acid homology in bacterial taxonomy: effect of incubation temperature on reaction specificity

Parameters affecting deoxyribonucleic acid duplex (DNA-DNA) formation on membrane filters were evaluated. The reference strains used were Cytophaga succinicans strain 8, which has a guanine plus cytosine (GC) content of 38%, and Myxococcus xanthus strain FB, which has a GC content of 70%. Both organisms are gliding bacteria classified among the myxobacteria. Among the parameters evaluated, the incubation temperature used during duplex formation was found to be the most important in terms of the physical nature of the reaction product. When an incubation temperature 25 C below the melting point (T(m)) of the native DNA was used, homologous duplexes exhibited a thermal stability similar to that of native DNA. At 35 C below the T(m), a considerable proportion of the duplexes were of much lower stability; at 40 C below the T(m), most of the duplexes were of much lower stability. Similar duplexes of low stability were also formed between DNA molecules from morphologically and nutritionally diverse organisms, provided the GC percentages of the DNA preparations were similar. Competition between unlabeled and labeled DNA fragments for binding sites on immobilized DNA was also greatly influenced by the incubation temperature. Heterologous DNA-DNA complexes exhibited thermal stabilities which correlated with measurements of DNA homology in experiments involving competition. In addition, the difference in thermal stabilities of heterologous and homologous DNA complexes (DeltaT'(m)) may provide a measure of divergence in nucleotide sequences.     

应用抗体探针对人食管癌组织，Eca－109细胞及其染色体的NHP免疫反应性研究

应用自制的癌非组蛋白（ＮＨＰ）抗体探针,探讨了人食管癌Ｅｃａ－１０９细胞及其染色体和人食管癌组织的ＮＨＰ免疫反应性。结果表明：①以０．４ｍｏｌ／Ｌ及０．３５ｍｏｌ／ＬＮａＣｌ提取的ＮＨＰ均含１．１４万－４万道尔顿分子量的高速泳动族蛋白（Ｈｉｇｈｍｏｂｉｌｉｔｙｇｒｏｕｐｐｒｏｔｅｉｎ,ＨＭＧＰ）。②在人食管癌切片标本上癌细胞核、胞质、胞核均呈免疫反应阳性,且胞膜、胞质反应强于胞核。并见到癌巢周缘细胞比癌巢中心的细胞反应较强。③人食管瘤Ｅｃａ－１０９细胞的胞膜、胞质、胞核均呈ＮＨＰ免疫反应阳性,多见胞膜、胞质强于胞核。④人食管癌Ｅｃａ－１０９细胞的分裂中期染色体上,免疫反应呈阳性。这提示０．４ｍｏｌ／ＬＮａＣｌ提取的ＮＨＰ含有ＤＮＡ特异结合的ＮＨＰ组分。     

Homologous-pairing activity of the Bacillus subtilis bacteriophage SPP1 replication protein G35P

Genetic evidence suggests that the SPP1-encoded gene 35 product (G35P) is essential for phage DNA replication. Purified G35P binds single-strand DNA (ssDNA) and double-strand (dsDNA) and specifically interacts with SPP1-encoded replicative DNA helicase G40P and SSB protein G36P. G35P promotes joint molecule formation between a circular ssDNA and a homologous linear dsDNA with an ssDNA tail. Joint molecule formation requires a metal ion but is independent of a nucleotide cofactor. Joint molecules formed during these reactions contain a displaced linear ssDNA strand. Electron microscopic analysis shows that G35P forms a multimeric ring structure in ssDNA tails of dsDNA molecules and left-handed filaments on ssDNA. G35P promotes strand annealing at the AT-rich region of SPP1 oriL on a supercoiled template. These results altogether are consistent with the hypothesis that the homologous pairing catalyzed by G35P is an integral part of SPP1 DNA replication. The loading of G40P at a d-loop (ori DNA or at any stalled replication fork) by G35P could lead to replication fork reactivation.     

Xeroderma pigmentosum group A correcting protein from calf thymus.

A proteinous factor was purified from calf thymus and HeLa cells, which specifically corrects the excision repair defect of xeroderma pigmentosum complementation group A (XP-A) cells. Recovery of UV-induced unscheduled DNA synthesis after microinjection of XP-A cells was used as a quantitative assay for the correcting activity of protein preparations. XP-A correcting protein appears to be very stable as it withstands heating to 100 degrees C and treatment with SDS or 6 M urea. A molecular weight of 40-45 kD was found both under native (gel filtration) and denaturing (SDS-PAGE) conditions. Calf XP-A protein binds to single-stranded DNA more strongly than to double-stranded DNA, but shows no clear preference for UV-irradiated DNA. Polyclonal antibodies raised against human recombinant XP-A protein, which strongly inhibit UV-induced unscheduled DNA synthesis of normal human cells, completely abolished XP-A correcting activity when mixed with calf thymus preparations. This indicates a close relationship between human gene product and the calf protein. In the final preparation two main protein bands were present. Only one band at approx. 41 kD showed both DNA binding activity in Southwestern blots and immune reaction with human XP-A antibody, suggesting that this is the active calf XP-A correcting factor.     

Physical mapping of Streptomyces coelicolor A3(2). V. Structural modifications of actinophage phiC43 DNA molecules

As shown by genetical and physical methods, the total preparation of phiC43 phage obtained after spontaneous induction of the prophage from S. lividans 803 strain is a heterogenous population. The wild-type phage (phi C43 wt) is only represented in 5--10% of the population. The majority of phage variants are not able to establish the lysogenic state. The structure of DNA molecules of some phages from the total preparations was characterized by electron microscopy of DNA heteroduplexes. Molecules of phiC43 wt DNA appeared to be completely homologous to those of recently studied phiC62 phage, except for two small regions of approximately 0.3 kb in the central part. Phage variants defective in establishment of the lysogenic state were distributed to two groups. One of them consists of deletion variants, the other--deletion/insertion variants. Deletions in DNA molecule of all nonlysogenizing phage overlap. The region of overlapping seems to be responsible for establishment of the lysogenic state. In the same region, deletion of DNA molecules of mutant phiC311 yg2 has been located. Three deletion/insertion variants contain homologous foreign sequences of various length. It is likely that these insertions are fragments of the host chromosomal DNA.     

Urea-induced transformation of native estrogen receptor and evidence for separate DNA-and ATP-binding sites

We have investigated the involvement of hydrophobic receptor domains during transformation of the native estrogen receptor to a form(s) with high affinity for immobilized DNA and ATP. In the presence of 6 M urea the intact estrogen-receptor complex was completely (greater than 90%, n = 12) transformed into a DNA-binding configuration but only partially (35-45%, n = 8) transformed into an ATP-binding state. Similar experiments performed with unliganded receptor preparations further distinguished the receptor's DNA and ATP binding properties. While the urea-induced increase in receptor affinity for DNA-agarose was estrogen-dependent, the urea-induced increase in affinity for ATP-agarose was steroid-independent. This is the first direct evidence that hydrophobic receptor domains may be involved in the steroid-dependent exposure of the DNA binding site. This event is partially reversible and suggests that electrostatic interactions alone may not be sufficient to accurately describe receptor recognition of specific DNA acceptor sites.