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Biomedical subjects

M E Hogan

Publications and source records attributed to M E Hogan.

70 records · Page 4Linked to original sources

Site-specific oligonucleotide binding represses transcription of the human c-myc gene in vitro.

A 27-base-long DNA oligonucleotide was designed that binds to duplex DNA at a single site within the 5' end of the human c-myc gene, 115 base pairs upstream from the transcription origin P1. On the basis of the physical properties of its bound complex, it was concluded that the oligonucleotide forms a colinear triplex with the duplex binding site. By means of an in vitro assay system, it was possible to show a correlation between triplex formation at -115 base pairs and repression of c-myc transcription. The possibility is discussed that triplex formation (site-specific RNA binding to a DNA duplex) could serve as the basis for an alternative program of gene control in vivo.

Electrophoresis↗

DNA structure equilibria in the human c-myc gene.

We have employed analytical S1 nuclease analysis to identify sites with altered DNA secondary structure in the human c-myc gene. We have mapped several sites of that kind in vitro at one-base resolution but have focused our attention on one particularly stable conformational isomer which occurs approximately 270 base pairs upstream from the preferred transcription origin. We have analyzed the kinetics of that conformational equilibrium as a function of supercoil density and enzyme concentration and find that DNA structure in this region is adequately modeled as a two-state equilibrium between an undistorted (S1 nuclease insensitive) and a distorted (S1-sensitive) state. We find that at fixed supercoil density, S1 nuclease cleavage at this DNA segment can be altered in vitro by a DNA sequence change as far away as 1500 bases. We also find that the S1 nuclease cleavage at this site can be dramatically enhanced by the binding of small RNA molecules. On the basis of an analysis of S1 cutting kinetics and an analysis of DNA sequence at the S1 cleavage site, we conclude that RNA may bind directly to DNA, thereby shifting the underlying conformational equilibrium. Together, these data suggest that as a class, short RNA molecules could serve as site-specific regulatory elements in the myc gene and elsewhere.

Base Sequence↗

Ion-induced DNA structure change in nucleosomes.

Physical methods have been used to study calcium binding to the nucleosome core particle. Equilibrium dialysis of Ca2+ and spectroscopic analysis of a Ca2+ analogue show that the ion binds tightly to the particles, resulting in a significant change of DNA circular dichroism. This suggests that base stacking may be altered as a result of Ca2+ binding. In the presence of Ca2+, the absorbance and fluorescence properties of methylene blue (MB), a DNA-specific intercalator, confirm that the dye binds tightly to nucleosomes by intercalation. However, secondary changes occur which suggest that the MB binding site is altered as a result of Ca2+ binding. Triplet state anisotropy decay and triplet lifetime quenching both show that in the Ca2+-nucleosome complex, methylene blue is capable of wobbling over a substantial angular range at its binding site. To explain these data, it is proposed that Ca2+ binding to nucleosomes causes DNA to fold by means of a series of sharp bends (kinks). The properties of bound MB are best explained if it is presumed that the intercalator binds tightly to such kinked sites in the nucleosome. On the basis of these observations, we discuss the possibility that multivalent ion concentration in the nucleus is high enough that the smooth to kinked helix equilibrium may be near to its midpoint. Near such a midpoint, the secondary structure of DNA in the nucleosome might prove to be sensitive to effector molecule binding and to site-specific variation of DNA or histone composition within genes.

Animals↗

High-resolution mapping of carcinogen binding sites on DNA.

We have used a photochemical method to map covalent binding sites of the carcinogen benzo[a]pyrenediol epoxide (BPDE) within DNA from the transcriptional control region of the chicken adult beta-globin gene. Our preliminary low-resolution mapping has demonstrated that this region contains highly preferred BPDE binding sites [Boles, T.C., & Hogan, M.E. (1984) Proc. Natl. Acad. Sci. U.S.A. 81, 5623-5627]. Here, we find that BPDE binding at individual G residues in this region is influenced by nearest-neighbor interactions and also by longer range interactions that may be attributable to sequence-specific variation of DNA secondary structure. Our findings suggest that long poly(dG) sequences should be preferred sites for BPDE action in other genes.

7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide↗

Labeling of fructans in winter wheat stems.

Fructans synthesized from newly formed assimilates accumulate in wheat stems as nonstructural carbohydrates. Experiments performed tested the hypothesis that the fructose moiety from translocated sucrose is used preferentially in biosynthesis of these fructans. Results indicated: (a) a large percentage of labeled sucrose was translocated and unloaded in an unaltered state; and (b) sucrose contributed its fructose moiety to fructan synthesis in stems.

Journal Article↗

Differentiation of organics from functional psychiatric patients across various IQ ranges using the Bender-Gestalt and Hutt Scoring System.

This study investigated the effectiveness of the Hutt Scoring System (Hutt, 1977) in differentiating organic from functional psychiatric patients, the relationship of IQ to Bender-Gestalt errors as measured by this scoring system, and examined the discriminative power of this scoring system for various IQ ranges. One hundred eighty patients were utilized, 90 of whom had been classified as organics and matched with the remaining 90 subjects on the basis of age, education, and IQ range. In addition, the organic subjects' secondary diagnosis was matched with the primary diagnosis of the nonorganic patients. Results between WAIS IQ and Hutt error scores for organic subjects yielded an r = -.34 (p less than .01); between WAIS IQ and Hutt error scores for the nonorganic subjects, r = -.61 (p less than .001). No significant results were obtained for organics and nonorganics simultaneously within the same IQ cells.

Bender-Gestalt Test↗

Site-specific carcinogen binding to DNA.

Benzo[alpha]pyrene diol epoxide (BPDE) is a well-studied environmental carcinogen that binds covalently to DNA. Here we describe a photochemical technique that allows us to map BPDE-binding sites within cloned gene sequences. The technique is based upon our observation that, when irradiated with laser light at 355 nm, one single-strand DNA cut is produced at each BPDE binding site. In initial experiments we have studied the distribution of such cuts in cloned DNA from the chicken adult beta-globin gene. We find that BPDE binding in this gene sequence is distinctly nonrandom. While several prominent BPDE-binding sites are evident, a 300-base-pair sequence immediately 5' to the RNA cap site is most strongly attacked by the carcinogen. This region is believed to contain important transcriptional control sequences. We discuss the possibility that sequence-specific binding to such regulatory elements may be an important feature of the mechanism of the carcinogen.

7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide↗

Activity in vivo and redox States in vitro of nitro- and chlorodiphenyl ether herbicide analogs.

Excised cucumber (Cucumis sativus L. cv 447 Wisconsin SMR 18) cotyledons were sensitive to acifluorfen-methyl (methyl 5-[2-chloro-4-(trifluoromethyl)phenoxy]-2-nitrobenzoate) and MC-15608 (methyl 5-[2-chloro-4-(trifluoromethyl)phenoxy]-2-chlorobenzoate). Injury was detected by monitoring efflux of 3-O-methyl-d-[U-(14)C]glucose from herbicide-treated tissue after exposure to light. Efflux kinetics of 3-O-methyl-[(14)C]glucose from cotyledons treated with either acifluorfen-methyl (AFM) or MC-15608 were similar. Neither herbicide was active in darkness.Cyclic voltammetry was used to study redox behavior of AFM and MC-15608 in protolytic and aprotic solvents. In protic media reduction of AFM was chemically irreversible. Reduction of MC-15608 in protolytic solvent was not observed. In aprotic solvent, the electrode reaction of AFM was quasireversible. The voltammogram of MC-15608 in aprotic solvent was indicative of a multielectron, completely irreversible electrode reaction.Although the physiological data indicate that AFM and MC-15608 have similar effects in vivo, the redox behavior of the two compounds is quite different. These results suggest that mechanisms involving direct reduction and reoxidation of the diphenyl ether molecule are probably not the basis for the action of these herbicides.

Journal Article↗

Carcinogen-induced alteration of DNA structure.

We have prepared covalent complexes between defined length DNA fragments and a diol epoxide derivative of the carcinogenic polycyclic aromatic hydrocarbon, benzo(a)pyrene. We have studied the structure of these complexes, using transient electric dichroism, circular dichroism, fluorescence quenching, thermal denaturation, polyacrylamide gel electrophoresis, and nuclease digestion. Our observations suggest that th covalently bound carcinogen is intercalated within the helix, forming a wedge-shaped complex. Binding of the carcinogen distorts the structure of the DNA over a region extending beyond the immediate binding site. The most striking aspect of this distortion is that it produces a bend in the helix.

7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide↗

Internal motions in deoxyribonucleic acid II.

We have measured the 1H, 31P, and 13C NMR parameters of monodisperse deoxyribonucleic acid (DMA) fragments 260 and 140 base pairs long as a function of temperature and solvent viscosity. On the basis of these measurements, we calculate that within a rodlike DNA helix, the base planes, the deoxyribose sugar, and the sugar-phosphate backbone all experience large fast internal motions. The best fit of the data to a two-state model for internal motion specifies for the internal motions the following amplitudes A and correlation times tau: for the base planes, A = +/-20 degrees and tau = 1 X 10(-9) s; for position 2' of the deoxyribose sugar, A = +/-20 to +/-33 degrees and tau = 1 X 10(-9) s; for the P-H vectors of the sugar-phosphate backbone, A = +/-27 degrees and tau = 2.2 X 10(-9) s.

Animals↗

Effect of ethidium bromide on deoxyribonucleic acid internal motions.

We have used 31P and 1H NMR to show that DNA internal motions are stopped or greatly hindered when ethidium bromide intercalates into DNA. We show that the effect is localized to a 2 base pair long DNA region at the binding site and that internal motions outside the binding site are nearly unaffected. Based upon the nearly independent behavior of bound and free DNA regions, we conclude that in B-DNA individual base pairs experience internal motion which is independent of the motion of their neighbors.

Animals↗

Internal motions in DNA.

We have measured the 31P and 1H NMR parameters of fractionated double-stranded DNA fragments 600, 300, and 150 base pairs long. The results indicate that, inside an intact double helix, both the deoxyribose and the sugar-phosphate backbone of the helix fluctuate substantially from their equilibrium geometry. The time constant for those coupled motions is of the order of 1 nsec.

DNA↗

Gold labeling of cell monolayers grown on dextran beads.

Gold labeling of antigenic sites has become an increasingly useful tool in the study of cultured cell monolayers. If these monolayers are grown on flat substrates, major difficulties in both scanning (SEM) and transmission electron microscopy (TEM) specimen preparation and imaging may result. An alternate surface, that of dextran microcarrier beads, eliminates a majority of these difficulties and facilitates correlative TEM and SEM. The SEM procedure for using backscattered electron imaging requires the use of carbon planchets as the cell growth matrix to eliminate background signals. These planchets are expensive and are not an optimal cell-attachment matrix in that they result in loose and abnormally shaped cells. In contrast, the dextran beads were produced specifically for cell culture and, therefore, provide an excellent surface for growth. The beads have an average diameter of 100 microns, allowing attachment directly to aluminum stubs without signal generation from the aluminum to interfere with the gold signal. With TEM preparation, the monolayer poses the major disadvantage. Specimen preparation for thin sectioning is often preceded by extensive manipulation. In the microcarrier bead system, the beads are directly sectionable, and it is possible to cut five to eight full beads per thin section. This increase in cell surface makes quantification of gold labeling easier and also provides a more representative sampling of the monolayer. The ease of preparation, the decrease in reagents used (via cell pooling), and the ability to use one cell preparation for TEM and SEM make this procedure an ideal technique for gold labeling.

Animals↗

Evidence for kinks in DNA folding in the nucleosome.

The nucleosome subunit of chromatin consists of DNA folded around a histone core as a 1.8-turn left-handed solenoid. The crystal structure of the nucleosome core particle revealed that it has a dyad symmetry axis and that the minor helix groove faces outwards from the protein core. Richmond et al. noticed that the path traversed by the helix has severe bends at sites approximately one and four helix turns from the dyad axis. We have developed two photochemical methods to study the structure of DNA, and in particular that wrapped around the nucleosome core. One method depends on the sensitization of singlet oxygen production by an eosin analogue. We have monitored the rate at which excited state oxygen diffuses into contact with DNA base planes, and find that it attacks the nucleosome with high specificity. We have also mapped the DNA binding of the intercalating dye methylene blue, and conclude that it binds to the same sites accessible to oxygen by diffusion. On the basis of these results we suggest that the DNA in the nucleosome is bent or kinked at two sites, 1.5 helix turns from the dyad axis.

Animals↗

Importance of DNA stiffness in protein-DNA binding specificity.

From the first high-resolution structure of a repressor bound specifically to its DNA recognition sequence it has been shown that the phage 434 repressor protein binds as a dimer to the helix. Tight, local interactions are made at the ends of the binding site, causing the central four base pairs (bp) to become bent and overtwisted. The centre of the operator is not in contact with protein but repressor binding affinity can be reduced at least 50-fold in response to a sequence change there. This observation might be explained should the structure of the intervening DNA segment vary with its sequence, or if DNA at the centre of the operator resists the torsional and bending deformation necessary for complex formation in a sequence dependent fashion. We have considered the second hypothesis by demonstrating that DNA stiffness is sequence dependent. A method is formulated for calculating the stiffness of any particular DNA sequence, and we show that this predicted relationship between sequence and stiffness can explain the repressor binding data in a quantitative manner. We propose that the elastic properties of DNA may be of general importance to an understanding of protein-DNA binding specificity.

Base Sequence↗