Purification, cloning, complementary DNA structure, and predicted amino acid sequence of human estradiol 17 beta-dehydrogenase.
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17-Hydroxysteroid Dehydrogenases↗
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Identification of a DNA structural motif that includes the binding sites for Sp1, p53 and GA-binding protein.
We have analyzed predicted helical twist angles in the 21-bp repeat region of the SV40 genome, using a semi-empirical model previously shown to accurately predict backbone conformations. Unexpectedly, the pattern of twist angles characteristic of the six GC-boxes is repeated an additional five times at positions that are regularly interspersed with the six GC-box sequences. These patterns of helical twist angles are associated with a second, imperfectly-repeated sequence motif, the TR-box 5'-RRNTRGG. Unrelated DNA sequences that interact with trans-acting factors (p53 and GABP) exhibit similar twist angle patterns, due to elements of the general form 5'-RRRYRRR that occur as interspersed arrays with a spacing of 10-11 bp and an offset of 4-6 bp. Arrays of these elements, which we call pyrimidine sandwich elements (PSEs), may play an important role in the interaction of trans-acting factors with DNA control regions. In 13 human proto-oncogenes analyzed, we identified 31 PSE arrays, 11 of which were in the 5'-flanking regions of the genes. The most extensive array was found in the promoter region of the K-ras gene. Extending over 80 bp of DNA, it contained 16 PSEs that showed an average deviation from the SV40 criterion pattern of angles of only 1.2 degrees.
Base Sequence↗
Sequence dependence of DNA structure. The B, Z, and A conformations of polydeoxynucleotides containing repeating units of 6 to 16 base pairs.
In order to study the sequence dependence of the B-Z transition, we have synthesized eight double-stranded polydeoxynucleotides. The polymers have defined alternating purine-pyrimidine sequences with repeating units of 6-16 base pairs, and contain 12.5-33% AT base pairs. A and T nucleotides are in nearest-neighbor positions in the series poly[d[TA(CG)2-7]], but are isolated from each other, with minimum separations of 2 and 6 GC base pairs, in poly[d[TGCA(CG)6]] and poly[T(GC)3A(CG)4)]], respectively. All of the polymers except poly[d[TA(CG)2]] were shown by circular dichroism to undergo a right- to left-hand helical transition at high NaCl concentrations, and all polymers exhibited a B to A transition in the presence of ethanol. Poly[d[TA(CG)7]] was the only polymer to undergo a B to Z to A transition in ethanol. At a constant percentage of AT base pairs, the B-Z transition is sequence-dependent, occurring at lower salt concentrations for polymers containing longer runs of contiguous GC base pairs in the repeating unit.
Chemical Phenomena↗
An eclectic DNA structure adopted by human telomeric sequence under superhelical stress and low pH.
We have found, with the aid of 2-D gel electrophoresis, that double-stranded human telomeric repeat, (T2AG3)12.(C3TA2)12, being cloned within a plasmid, forms a protonated superhelically-induced structure. Experiments on chemical and enzymatic probing also indicate that the human telomeric repeats adopt an unusual structure. We have proposed an eclectic model for this structure in which four different elements coexist: a non-orthodox intramolecular triplex stabilized by the canonical protonated C.G*C+ base-triads and highly enriched by noncanonical base-triads; the intramolecular quadruplex formed by a portion of the G-rich strand; the single-stranded region encompassing a portion of the G-rich strand and, probably, the (C,A)-hairpin formed by a portion of the C-rich strand.
Base Sequence↗
Novel DNA structures resulting from dTam3 excision in tobacco.
A Tam3 two-element system has been designed by combining an immobilized Tam3 element with a non-autonomous dTam3 element inserted into the HPT gene. The phenotypic assay employed, restored hygromycin resistance, indicated that trans-activation of the non-autonomous dTam3 element occurred. Molecular analyses of the excision sites revealed that the ends of the dTam3 element remain in the empty donor sites. The predominant consequence of this type of excision appears to be that excised fragments fail to re-integrate into the tobacco genome. Only one case of dTam3 re-integration could be detected. The ends of this element had been degraded upon integration into the tobacco genome. Either the altered structure of the Tam3 derivatives or tobacco host factors are influencing the trans-activation of a dTam3 element, resulting in aberrant excision.
Base Composition↗
Cytoskeletal and DNA structure abnormalities result from bypass of requirement for the cdc10 start gene in the fission yeast Schizosaccharomyces pombe.
The cdc10 gene of the fission yeast S. pombe is required for traverse of the start control in late G1 and commitment to the mitotic cell cycle. To increase our understanding of the events which occur at start, a pseudoreversion analysis was undertaken to identify genes whose products may interact with cdc10 or bypass the requirement for it. A single gene, sct1+ (suppressor of cdc ten), has been identified, mutation of which suppresses all conditional alleles and a null allele of cdc10. Bypass of the requirement for cdc10+ function by sct1-1 mutations leads to pleiotropic defects, including microtubule, microfilament and nuclear structural abnormalities. Our data suggest that sct1 encodes a protein that is dependent upon cdc10+ either for its normal function or expression, or is a component of a checkpoint that monitors execution of p85cdc10 function.
Alleles↗
Lanthanide ion luminescence as a probe of DNA structure. 2. Non- guanine-containing oligomers and nucleotides.
Oligo(dC)8, oligo(dA)8, and oligo(dT)8 as well as d-CMP, d-AMP, and d-TMP, when complexed to Eu(3+), possess two classes of Eu(3+) binding environment. The binding environments consist of two classes, tight sites which coordinate two H2O molecules, and weaker sites which coordinate six or seven, analogous to the previously studied guanine-containing molecules. It is inferred that the tight class of Eu(3+) ion site observed with these oligomers and nucleotides corresponds to dimeric or polymeric structures. Comparison of the results for the guanine and non-guanine containing oligomers suggests that Eu(3+) possibly coordinates base nitrogen atoms in the former and in an outer sphere mode (hydrogen bonding via the H2O molecules coordinated to Eu(3+)) in the species examined here.
Binding Sites↗
DNA structural features responsible for sequence-dependent binding geometries of Hoechst 33258.
The complexes of Hoechst 33258 with poly[d(A-T)2], poly[d(I-C)2], and poly[d(G-C)2], and poly[d(G-m5C)2] were studied using linear dichroism, CD, and fluorescence spectroscopies. The Hoechst-poly[d(I-C)2] complex, in which there is no guanine amino group protruding in the minor groove, exhibits spectroscopic properties that are very similar to those of the Hoechst-poly[d(A-T)2] complex. When bound to both of these polynucleotides, Hoechst exhibits an average orientation angle of near 45 degrees relative to the DNA helix axis for the long-axis polarized low-energy transition, a relatively strong positive induced CD, and a strong increase in fluorescence intensity--leading us to conclude that this molecule also binds in the minor groove of poly[d(I-C)2]. By contrast, when bound to poly[d(G-C)2] and poly[d(G-m5C)2], Hoechst shows a distinctively different behavior. The strongly negative reduced linear dichroism in the ligand absorption region is consistent with a model in which part of the Hoechst chromophore is intercalculated between DNA bases. From the low drug:base ratio onset of excitonic effects in the CD and fluorescence emission spectra, it is inferred that another part of the Hoechst molecule may sit in the major groove of poly[d(G-C)2] and poly[d(G-m5C)2] and preferentially stacks into dimers, though this tendency is strongly reduced for the latter polynucleotide. Based on these results, the importance of the interactions of Hoechst with the exocyclic amino group of guanine and the methyl group of cytosine in determining the binding modes are discussed.
Base Sequence↗
[Lambda H-lambda T 80 hybrid study of the DNA structural gene region in lambda and phi 80 phages].
Hybrids lambda H lambda T80 are formed due to recombination of the phage lambda att80 and phi 80 prophage partially deleted in the region of structural genes. Genetic structure of 22 independently isolated lambda H lambda T80 hybrids was determined by the restriction method and it was shown that recombination took place in the genes A, C, D and H. The frequencies of hybrid formation diminish from 1.10(-3) to 4.10(-5) for this gene order, which suggests that the polar divergence of nucleotide sequencies in the region of structural genes exists. It was found that formation of hybrids with recombination in the region of "weak" homology (gene H) was possible only when the region of "strong" homology was present in the deleted phi 80 prophage to initiate recombination.
Bacteriophage lambda↗
TOL plasmid pWW0 in constructed halobenzoate-degrading Pseudomonas strains: enzyme regulation and DNA structure.
WR211 and WR216 are derivatives of halobenzoate-degrading Pseudomonas sp. strain B13 into which the 117-kilobase TOL degradative plasmid pWW0 has been transferred from Pseudomonas putida mt-2. WR211 has lost the ability to grow on the TOL-specific substrate m-xylene but retains the ability to grow on its metabolite, m-toluate. An analysis of the induction of enzymes was consistent with WR211 carrying a nonfunctional regulatory gene, xy1R, WR216 is a spontaneous derivative of WR211 which grows on one of the TOL substrates and yet expresses the nonspecific toluate oxidase, which enables it to grow on the novel substrate 4-chlorobenzoate. In addition to the xy1R lesion inherited from WR211, WR216 appears to carry a mutation in the structural gene for catechol 2,3-oxygenase, xy1E. The plasmids in both strains were analyzed by restriction endonuclease digestion. pWW0-1211 in WR211 has a large deletion (39 kilobases) compared with pWW0 and appears to be identical to a previously described plasmid (pWW0-8) which encodes none of the TOL degradative functions. pWW0-1216 in WR216 has undergone a major structural reorganization relative to its parent, pWW0-1211. This plasmid has a smaller deletion (19 kilobases), which is staggered relative to the deletion in pWW0-1211, and in addition it has two 3-kilobase insertions of unknown origin, one of which appears to cause the xylE mutation.
Base Sequence↗
Lanthanide ion luminescence as a probe of DNA structure. 1. Guanine-containing oligomers and nucleotides.
Laser-induced Eu(3+) luminescence spectroscopy is used to probe the interaction of Eu(3+) ion with guanine-containing nucleotides and single-stranded oligomers. By using time-resolved and non-time-resolved Eu(3+) luminescence techniques, two classes of Eu(3+) binding site are observed in oligo(dG)10, oligo(dG)8, oligo(dG)6, oligo(dG)4, and d-GMP. One class of site binds Eu(3+) ions more strongly than the other. Since the "tight" class of bound Eu(3+) ions have two coordinated water molecules, it is inferred that six or seven atoms from the oligomers are coordinating the Eu(3+). The "weaker" class of Eu(3+) ion sites involve the coordination of six or seven water molecules and therefore, are coordinated by one or two atoms from the oligomer. The tight class of Eu(3+) binding site is attributed to an interstrand association of Eu(3+) with the oligomers forming dimeric or polymeric structures. The dissociation constants (Kd) for the 1:1 complexes Eu(d-GMP)+ and Eu(d-GTP)- have been determined as well as the Kd for the dimerization reaction of Eu(d-GMP)+. The Tb(3+) luminescence enhancement properties of these molecules are also examined in relation to their EU(3+) binding characteristics.
Binding Sites↗
The stereostructure of knots and catenanes produced by phage lambda integrative recombination: implications for mechanism and DNA structure.
We studied the mechanism of recombination by determining the structure of the products of the phage lambda Int system. Electron microscopy of RecA-coated products revealed only knots and catenanes containing a regular right-handed spiral structure. The structure and distribution of products establish that the recombination sites pair by essentially random collision, rather than by tracking. However, the distribution also indicates that the binding of the enzyme must introduce nonrandom components into the reaction and stabilize at least two additional supercoils that become links in the product. Moreover, the regularity of the structures indicates that the strand exchange is accomplished in a very simple way, introducing only a single link into the product. All other links result from the direct conversion of substrate supercoils into knot and catenane links. These supercoils must be in a right-handed, braided form, rather than solenoidally wound as in nucleosomes.
Bacteriophage lambda↗
Arabidopsis thaliana centromere regions: genetic map positions and repetitive DNA structure.
The genetic positions of the five Arabidopsis thaliana centromere regions have been identified by mapping size polymorphisms in the centromeric 180-bp repeat arrays. Structural and genetic analysis indicates that 180-bp repeat arrays of up to 1000 kb are found in the centromere region of each chromosome. The genetic behavior of the centromeric arrays suggests that recombination within the arrays is suppressed. These results indicate that the centromere regions of A. thaliana resemble human centromeres in size and genomic organization.
Alleles↗
[Initiation of defects in the secondary structure of DNA by laser radiation].
Kinetic formaldehyde study was carried out of the secondary DNA structure of calf goiter gland after in vitro irradiation with gelium-neon, gelium-cadmium, nitrogen and eximeric (on galogenides of inert gases) lasers. It has been shown that the number of defects in the secondary DNA structure depends on physical parameters of the lasers (first of all on generation wave length), and on the medium composition as well.
Animals↗
The ability of polyamine analogues to induce Z-DNA structure in synthetic polynucleotides in vitro inversely correlates with their effects on cytotoxicity of cis-diaminedichloroplatinum (II) (CDDP) in human brain tumor cell lines.
We studied the effects of 72 h pretreatment with five polyamine analogues on the cytotoxicity of cis-diaminedichloroplatinum (II) (CDDP) in U-251 MG and SF-188 human brain tumor cells. A colony forming efficiency assay showed that the pretreatment with clinically important analogues 1,11-bis(ethylamino)-4, 8-diazaundecane (BE-3-3-3), 1,14-bis(ethylamino)-5,10-diazatetradecane (BE-4-4-4), and 1,l9-bis(ethylamino)-5,10,15-triazanonadecane (BE-4-4-4-4) increased the cytotoxicity of CDDP by 1.3 to 2.3-fold; 1,19-diamino-5,10, 15-triazanonadecane (4-4-4-4) did not affect CDDP cytotoxicity, and 1,11-diamino-4,8-diazaundecane (3-3-3) protected cells from the cytotoxic effects of CDDP. An alkaline elution assay detected a small increase in DNA interstrand crosslinks accompanying the enhancement of CDDP cytotoxicity only in cells pretreated with BE-3-3-3. This study is the first to show that the Z-DNA inducing abilities of the polyamine analogues in synthetic polynucleotides in vitro correlates inversely with their effects on CDDP cytotoxicity in human tumor cells in culture.
Antineoplastic Agents↗
Effect of DNA structure and nucleotide sequence on Holliday junction resolution by a Saccharomyces cerevisiae endonuclease.
Previous studies have demonstrated that mitotic Saccharomyces cerevisiae cells contain an endonuclease that cleaves Holliday junctions. In this paper, the cleavage of a number of model branched substrates has been characterized in detail. Three-armed Y-branched molecules were not substrates for the enzyme. Holliday junction substrates constructed from wild-type lambda att sites were resolved in a concerted reaction by paired single-strand breaks that contained 5'-phosphate and 3'-hydroxyl groups and were often symmetrically related. Holliday junctions were also constructed using DNAs derived from lambda safG and safT mutants to alter the nucleotide sequence immediately flanking the cross-strand exchange. These one to six base-pair changes in nucleotide sequence were observed to have dramatic effects on both the directionality and rate of resolution. More than 90% of wild-type junctions were cleaved in only one direction, while Holliday junctions composed of safT DNA were cleaved equally in both possible directions. Hybrid junctions composed of half wild-type DNA and half safG DNA were cleaved in the same orientation as the wild-type junction but at one-seventh of the rate, while junctions constructed completely from safG DNA were not cleaved at all. The cleavage sites were mapped at the nucleotide level and the locations of the paired nicks made by the endonuclease were also found to be affected by the sequence of the substrates and in such a way as to account for the directionality of cleavage. These results have important consequences for the interpretation of genetic experiments, since they provide biochemical evidence that some of the non-random nature of genetic recombination might be due to non-randomly distributed resolution processes.
Attachment Sites, Microbiological↗
Sequence-dependent differences in DNA structure influence the affinity of P22 operator for P22 repressor.
Although the central bases of the P22 operator are not contacted by P22 repressor, the affinity of repressor for operator varies with the sequence of these bases. The KMnO4 and .OH radical susceptibilities of the central bases of the operator vary with their sequence, whether or not the operator is complexed with protein or free in solution. These data show that the minor groove of a lower affinity operator which bears central C-G bases (9C) is more open than that of the higher affinity 9T operator, which bears central T-A bases. This difference in minor groove width is seen both in the absence and presence of repressor. Results of ring closure studies show that, in the absence of repressor, an operator bearing central C.G base pairs operator is overtwisted relative to an operator which contains central T.A base pairs. The binding of P22 repressor unwinds the two operators to similar extents, thereby preserving the relative differences in twists of these DNAs. Although repressor alters the twist of the operator DNA, our results show that differences in DNA torsional flexibility have no role in determining the affinity of operator for protein. Instead, the results indicate that central sequences affect operator affinity for protein by limiting the degree to which the operator can be deformed in the protein-DNA complex. The stability of the complex is apparently modulated, in a central sequence-dependent manner, by alterations in the number and/or geometry of protein-DNA contacts.
Bacteriophage P22↗
How does cisplatin alter DNA structure? A molecular mechanics study on double-stranded oligonucleotides.
Molecular models for two double-stranded decanucleotides, d(GCCG*G*ATCGC)-d(GCGATCCGGC) (1) and d(GCTG*G*ATCGC)-d(GCGATCCAGC) (2), with the G* guanines cross-linked by a cis-Pt(NH3)2 moiety, were calculated using molecular mechanics. Nine models for 1 and eight models for 2 are reported; in all of them, the double helix is kinked by approx. 60 degrees towards the major groove and slightly unwound. The model building has been guided by comparison with the NMR data available for duplex 1. The influence of the base at the 5'-side of the coordinated G*G* dinucleotide is discussed.
Base Sequence↗