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Biomedical subjects

A Rich

Publications and source records attributed to A Rich.

At least 217 records · Page 12Linked to original sources
PubMed1986

Competitive behavior of multiple, discrete B-Z transitions in supercoiled DNA.

Conformational transitions in topologically constrained duplex DNA necessarily affect and are affected by other transitional processes throughout the entire molecule. This conformational interdependence of discrete sequences within a given superhelical domain arises through a requisite competition for the free energy of supercoiling. Here we present a generalized statistical mechanical analysis of multiple, competing conformational equilibria in superhelical DNA. This model has been applied, using experimentally determined parameters, to the energetic coupling of two independent B-Z transitions. Specifically, we have monitored the extent of B-Z transition, as a function of negative superhelicity, in topoisomers of a plasmid containing two identical d(C-G)n inserts using two-dimensional gel electrophoresis. The theoretical results were found to be in good agreement with the experimental data, and we have used this model to predict the competitive behavior of B-Z transitions within sequences differing in length and sequence composition. This competition is shown to have a profound effect upon the B-Z equilibria of those sequences analyzed, resulting in a complex modulation in the extent of Z-DNA formation as a function of negative superhelicity. These theoretical and experimental results show that DNA sequences separated by large distances are capable of communicating structural information.

DNA↗
PubMed1986

Crystal structure of a Z-DNA fragment containing thymine/2-aminoadenine base pairs.

The Z-DNA structure has been shown to form in two crystals made from self-complementary DNA hexamers d(CGTDCG) and d(CDCGTG) which contain thymine/2-aminoadenine (TD) base pairs. The latter structure has been solved and refined to 1.3 A resolution and it shows only small conformational changes due to the introduction of the TD base pairs in comparison with the structure of d(CG)3. Spectroscopic studies with these compounds demonstrate that DNA molecules containing 2-aminoadenine residues form Z-DNA slightly more easily than do those containing adenine nucleotides, but not as readily as the parent sequence containing only guanine-cytosine base pairs.

2-Aminopurine↗
PubMed1986

Interactions of quinoxaline antibiotic and DNA: the molecular structure of a triostin A-d(GCGTACGC) complex.

The crystal structure of a DNA octamer d(GCGTACGC) complexed to an antitumor antibiotic, triostin A, has been solved and refined to 2.2 A resolution by x-ray diffraction analysis. The antibiotic molecule acts as a true bis intercalator surrounding the d(CpG) sequence at either end of the unwound right-handed DNA double helix. As previously observed in the structure of triostin A-d(CGTACG) complex (A.H.-J. Wang, et. al., Science, 225, 1115-1121 (1984)), the alanine amino acid residues of the drug molecule form sequence-specific hydrogen bonds to guanines in the minor groove. The two central A.T base pairs are in Hoogsteen configuration with adenine in the syn conformation. In addition, the two terminal G.C base pairs flanking the quinoxaline rings are also held together by Hoogsteen base pairing. This is the first observation in an oligonucleotide of. Hoogsteen G.C base pairs where the cytosine is protonated. The principal functional components of a bis-intercalative compound are discussed.

Anti-Bacterial Agents↗
PubMed1985

Anti-Z-DNA antibody binding can stabilize Z-DNA in relaxed and linear plasmids under physiological conditions.

It is shown that anti-Z-DNA antibody binding can stabilize sequences of d(CG/GC)n and d(CA/GT)n in the Z-DNA conformation in a plasmid in the complete absence of supercoiling. This effect is quantitated by using antibody preparations of different affinities and varying concentrations. The d(CG/GC)n sequence can be stabilized under physiological conditions. This is the first demonstration that a region of Z-DNA can be stabilized by protein binding in a completely relaxed plasmid under physiological conditions. The antibody-Z-DNA complex in the relaxed plasmid is shown to be an equilibrium state and not a long-lived kinetic intermediate since specific binding of the antibody to linearized plasmids containing Z-forming sequences is observed.

Antibodies↗
PubMed1985

G.T wobble base-pairing in Z-DNA at 1.0 A atomic resolution: the crystal structure of d(CGCGTG).

The DNA oligomer d(CGCGTG) crystallizes as a Z-DNA double helix containing two guanine-thymine base pair mismatches of the wobble type. The crystal diffracts to 1 A resolution and the structure has been solved and refined. At this resolution, a large amount of information is revealed about the organization of the water molecules in the lattice generally and more specifically around the wobble base pairs. By comparing this structure with the analogous high resolution structure of d(CGCGCG) we can visualize the structural changes as well as the reorganization of the solvent molecules associated with wobble base pairing. There is only a small distortion of the Z-DNA backbone resulting from introduction of the GT mismatched base pairs. The water molecules cluster around the wobble base pair taking up all of the hydrogen bonding capabilities of the bases due to wobble pairing. These bridging water molecules serve to stabilize the base-base interaction and, thus, may be generally important for base mispairing either in DNA or in RNA molecules.

Base Sequence↗
PubMed1985

Z-DNA forms without an alternating purine-pyrimidine sequence in solution.

Nuclear magnetic resonance spectra (proton and phosphorus-31) and ultraviolet absorption spectra of the DNA decamer d(br5CGbr5CGATbr5CGbr5CG), in which the central two adenine-thymine base pairs are out of order with the rest of the purine-pyrimidine alternation sequence, indicate that under appropriate solvent conditions (high salt and methanol) the molecule undergoes a structural transition from a right-handed B-DNA conformation to a left-handed Z-DNA conformation. Measurements of the two-dimensional nuclear Overhauser effect on the decamer indicate that all of the guanines as well as the two equivalent thymines adopt the syn conformation.

Base Sequence↗
PubMed1985

Isolation and characterization of Z-DNA binding proteins from wheat germ.

The preparation of a heterogeneous non-histone protein extract from wheat germ utilizing Br-poly(dG-dC).poly(dG-dC) (Z-DNA) affinity chromatography is described. The binding characteristics of antibodies against Z-DNA are used as a model system to define important criteria that the DNA binding behavior of a Z-DNA binding protein should display. We show that the wheat germ extract contains DNA binding proteins specific for left-handed Z-DNA by these criteria. The affinity of the proteins measured by competition experiments was approximately 10(5) greater for Br-poly(dG-dC).poly(dG-dC) (Z-DNA) than for poly(dG-dC).poly(dG-dC) (B-DNA). The affinity of the proteins for plasmid DNA increases with increasing negative superhelicity which is known to stabilize Z-DNA. The proteins are shown to compete with Z-DNA antibodies for binding to supercoiled plasmids. Finally, the affinity for two plasmids at a given superhelical density is greater for the plasmid containing an insert known to form Z-DNA than for a plasmid without the insert. The proteins exhibit a 2-3-fold greater affinity for stretches of (dC-dA)n.(dT-dG)n over stretches of (dG-dC)n.(dG-dC)n when both sequences are induced to form Z-DNA by supercoiling.

Animals↗
PubMed1985

Thermal regulation of beta-galactosidase synthesis using anti-sense RNA directed against the coding portion of the mRNA.

The in vivo production of RNA that is complementary to the mRNA of a particular target gene (anti-sense RNA) appears to be an effective tool for the regulation of genes in Escherichia coli (Coleman, J., Green, P.J., and Inouye, M. (1984) Cell 37, 429-436). These investigators demonstrated that short anti-sense transcripts which are complementary to the ribosome binding site of the target mRNA are overwhelmingly the most effective in blocking protein synthesis. We have constructed plasmids which produce thermally regulated anti-sense transcripts of three regions of the E. coli lac Z gene coding sequence, and have examined the relative effects of these constructs on the synthesis of the lac Z gene product, beta-galactosidase. We conclude that there is a strong correlation between the length of RNA complementarity and the suppression of beta-galactosidase synthesis. Furthermore, a significant inhibition of translation can be obtained when the anti-sense transcript lacks complementarity to the 5' noncoding region of the mRNA, provided that the extent of complementarity with the coding sequence is considerable.

DNA Restriction Enzymes↗
PubMed1985

A comparison of the structure of echinomycin and triostin A complexed to a DNA fragment.

Two members of the quinoxaline antibiotic family, echinomycin and triostin A, form crystals complexed to a DNA fragment with the sequence d(CpGpTpApCpG). The crystal structure of both complexes was solved by X-ray diffraction to near-atomic resolution. The two structures are similar to each other with differences in some details due to the shorter cross bridge of echinomycin. Both molecules act as bis intercalators surrounding the d(CpG) sequence at either end of the double helix. Alanine forms sequence-specific hydrogen bonds to guanines in the minor groove. The two central AT base pairs are held together by Hoogsteen base pairing with adenine in the syn conformation in both complexes. An octahedrally hydrated magnesium ion is found in the crystal lattice that plays an important role in organizing the lattice as well as stabilizing the complex by hydrogen bonding both to base pairs of DNA and to the quinoxaline ring nitrogen atoms in the major groove side of the DNA double helix. A functional description of the various amino acids in quinoxaline antibiotics is given, together with possible modifications that might affect biological activity.

Base Sequence↗
PubMed1985

Inhibition of deoxyhemoglobin S polymerization by biaromatic peptides found to associate with the hemoglobin molecule at a preferred site.

Association of three succinylated biaromatic peptides with deoxyhemoglobin has been measured. These peptides composed of indolyl or phenyl rings were found to have delta G values for their binding to deoxyhemoglobin between -2.9 and -3.4 kcal/mol at 23 degrees C. Binding experiments among these peptides demonstrate one preferred site, one of strongest binding of the peptide to the Hb molecule, as well as the existence of one or more weaker binding sites. Both aromatic side chains and at least one of the terminal carboxyl groups of the succinylated peptides are involved in the interactions with the hemoglobin (Hb) side chains at the preferred binding site. The latter also was found to be capable of binding monocyclic moieties of sufficient hydrophobicity, i.e., indolyl ring compounds. Increases in deoxyhemoglobin S (deoxy-HbS) solubilities in the presence of these three biaromatic peptides show a strong correlation between the values of their dissociation constants and their ability to destabilize deoxy-HbS aggregation. The symmetric site to which the peptides bind must be located at or near a contact site needed to stabilize the deoxy-HbS polymer.

Binding, Competitive↗
PubMed1985

New estimates of asymmetric decomposition of racemic mixtures by natural beta-radiation sources.

The Vester-Ulbricht hypothesis suggests that the chirality of biological molecules originates from the beta-radiolysis of prebiotic racemic mixtures. Despite the inconclusiveness of past investigations, recent calculations have shown that beta particles, because of their helicity, radiolyse L- and D-enantiomers at slightly different rates, the asymmetry, AR, being predicted to be 10(-11) (new experimental tests, give /AR/ < 2 x 10(-9)). Before this, the size of the radiolysis-induced chiral polarization, eta R (eta triple bond (nL - nD)/(nL + nD) where nL and nD are the numbers of L and D molecules present), was estimated for different values of AR; according to Keszthelyi et al., if /AR/ approximately 10(-11), /eta R/ can never exceed the chiral polarization, /eta F/, produced by statistical fluctuations, thus invalidating the V-U hypothesis. Here we re-examine the major assumptions on which these calculations were based and find that several overly restrictive conditions were imposed, which, when relaxed, allow the condition /eta R/ > /eta F/, in accordance with the V-U hypothesis.

Amino Acids↗
PubMed1985

Structural basis for stabilization of Z-DNA by cobalt hexaammine and magnesium cations.

In the equilibrium between B-DNA and Z-DNA in poly(dC-dG), the [Co(NH3)6]3+ ion stabilizes the Z form 4 orders of magnitude more effectively than the Mg2+ ion. The structural basis of this difference is revealed in Z-DNA crystal structures of d(CpGpCpGpCpG) stabilized by either Na+/Mg2+ or Na+/Mg2+ plus [Co(NH3)6]3+. The crystals diffract X-rays to high resolution, and the structures were refined at 1.25 A. The [Co(NH3)6]3+ ion forms five hydrogen bonds onto the surface of Z-DNA, bonding to a guanine O6 and N7 as well as to a phosphate group in the ZII conformation. The Mg2+ ion binds through its hydration shell with up to three hydrogen bonds to guanine N7 and O6. Higher charge, specific fitting of more hydrogen bonds, and a more stable complex all contribute to the great effectiveness of [Co(NH3)6]3+ in stabilizing Z-DNA.

Cobalt↗
PubMed1985

Receptor-mediated entry of peroxidases into the parasitophorous vacuoles of macrophages infected with Leishmania Mexicana amazonensis.

Leishmania amastigotes, obligatory parasites of macrophages, lodge and multiply within long-lived phagolysosomelike "parasitophorous vacuoles" (PV). The glycoprotein horseradish peroxidase (HRP) was shown, by light and electron microscopic cytochemistry, to enter the PVs of rat in vitro-derived bone marrow macrophages infected with Leishmania mexicana amazonensis. Uptake was obtained both in preinfected macrophages incubated with HRP and in macrophages pulsed with HRP, infected, and further incubated in ligand-free medium. Peroxidase positive and negative PVs could coexist in the same macrophages. Infected macrophages commonly displayed fewer labeled secondary lysosomes than noninfected cells. Lactoperoxidase (LP) was also shown, by light microscopy, to enter the PVs of rat macrophages. Uptake of HRP and of LP was blocked by mannan, supporting the mannose receptor mediated recognition of these ligands. Transfer of HRP to PVs was much less efficient in resident mouse peritoneal macrophages, even at 50 X higher ligand concentrations. Such macrophages expressed negligible mannose receptor function. The efficient mannan-inhibitable uptake of HRP by rat marrow macrophages was confirmed biochemically. Bulk HRP uptake in infected and noninfected cultures was found to be similar. Peroxidases should be useful in further studies of endocytosis by Leishmania-infected macrophages and in the development of lysosomotropic macrophage-targeted drug carriers.

Animals↗
PubMed1985

Limits on asymmetric orthopositronium formation in high Z optically active molecules.

The proposed connection between the parity violating handedness of beta particles in radioactive decay and the sign (L) of biological chirality (the Vester-Ulbricht [V-U] hypothesis) is experimentally tested. The theoretically predicted asymmetry in triplet positronium formation (Aps) is measured in several high Z optically active molecules using low energy positrons with a net helicity. We find Aps less than 3 X 10(-4) in selenocystine (Z = 34) and thyroxine (Z = 53), excluding part of the theoretically predicted range of 4 X 10(-3) greater than Aps greater than 2 X 10(-6) in these molecules. The connection between these limits and limits on asymmetric radiolysis (AR) is made, with a new limit of AR greater than 10(-9) being placed. This limit on AR, which is thirty times lower than a previous measurement in the amino acid leucine (Z = 6), is still not small enough to rule out the V-U hypothesis. rule out the V-U hypothesis.

Cystine↗
PubMed1985

Chemical probes of DNA conformation: detection of Z-DNA at nucleotide resolution.

Chemical probes sensitive to alterations in DNA conformation, especially Z-DNA, have been identified. These permit cleavage of DNA at sites of unusual structure, the results of which can be displayed on a sequencing gel. Using supercoiled plasmids containing inserts of d(C-G)16 and d(C-A)31 X d(T-G)31, it was found that hydroxylamine and osmium tetraoxide react preferentially with cytosines and thymines, respectively, near B-DNA-Z-DNA junctions; diethylpyrocarbonate reacts more strongly with purines within Z-DNA regions; and dimethylsulfate and diethylsulfate react more strongly with guanines in Z-DNA that are out of phase with the usual pattern of purine-pyrimidine alternation. Our results show that B-Z boundaries are mobile and that with increasing torsional strain, the Z-DNA regions can expand to include nonalternating nucleotide sequences.

Base Sequence↗
PubMed1985

Isolation of Z-DNA binding proteins from SV40 minichromosomes: evidence for binding to the viral control region.

Proteins dissociated from SV40 minichromosomes by increasing NaCl concentration were tested for their binding to Z-DNA [Br-poly(dG-dC)] and B-DNA [poly (dG-dC)]. Z-DNA binding proteins are largely released in 0.2 M NaCl whereas most B-DNA binding proteins are not released until 0.6 M NaCl. Incubation of SV40 minichromosomes with Z-DNA-Sephadex in low salt solution results in proteins with Z-DNA binding activity (PZ proteins). These proteins bind to negatively supercoiled DNAs containing left-handed Z-DNA but not to relaxed DNAs. They compete with anti-Z-DNA antibodies in binding to negatively supercoiled DNAs. The binding is tighter to negatively supercoiled SV40 DNA than to other plasmids, suggesting sequence-specific Z-DNA binding. PZ proteins binding to negatively supercoiled SV40 DNA interfere with cleavage at the Sph I sites, within the 72 bp repeat sequences of the viral control region, but not with cleavage at the Bgl I site, at the origin of replication. Removal of PZ proteins also exposes the Sph I sites in the SV40 minichromosomes while addition of PZ proteins makes the sites inaccessible.

Base Sequence↗