PubMed Health⌕ Search

Biomedical subjects

D M Gray

Publications and source records attributed to D M Gray.

At least 73 records · Page 4Linked to original sources
PubMed1984

Evidence for sequence heterogeneity among the double-stranded RNA segments of Penicillium chrysogenum mycovirus.

We have examined the dsRNA segments of the multipartite virus from Penicillium chrysogenum (ATCC 9480). A fourth RNA segment has been detected recently and, in the present work, we separated the four RNA segments and looked for possible homologies among them by thermal denaturation and electron microscopical heteroduplex studies. Differences were found between the differential melting profiles of the separated RNA segments, and no extensive regions of homology were detected among the various RNA segments by heteroduplex analyses. The results suggest that each RNA segment contains unique sequences. A comparison of the lengths of the RNA segments determined by electron microscopy with those determined by gel electrophoresis suggests that one of the segments has a distinct tertiary structure.

Electrophoresis, Agar Gel↗
PubMed1983

A circular dichroism study of the structure of Penicillium chrysogenum mycovirus.

We have examined the absorption and circular dichroism spectra of intact Penicillium chrysogenum virus, empty capsid particles, and isolated double-stranded RNA. The absorbance at 260 nm of intact virus was less than 4% hypochromic relative to the absorbances of the free double-stranded RNA and free viral protein, indicating very little change in the base stacking interactions of the RNA. Circular dichroism studies of intact virus indicate that the capsid protein consists of 45% alpha-helix. Empty capsids, containing a protein of the same molecular weight as intact virus protein, were found to have 30% alpha-helix, suggesting a conformational change in the capsid upon assembly with RNA. The conformation of double-stranded RNA in the virus was slightly altered from the solution structure of the RNA in 0.01 M Na+ and resembled the conformation of double-stranded RNA partially bound with spermidine. However, the virus does not appear to contain polyamines. Electrophoretic experiments indicate a pH- and salt-titratable RNA binding site on the capsid protein in virus disrupted by urea or non-ionic detergents. The results are consistent with significant ionic interactions between the RNA and the capsid protein in the virus.

Capsid↗
PubMed1982

Neutron scattering data on reconstituted complexes of fd deoxyribonucleic acid and gene 5 protein show that the deoxyribonucleic acid is near the center.

We have performed low-angle neutron scattering studies on reconstituted complexes of fd DNA and the gene 5 protein that is produced during infection of Escherichia coli by filamentous fd phage. Essentially identical helical complexes have been made with normal protonated DNA or DNA in which at least 87% of the nonexchangeable protons are replaced by deuterium. From neutron scattering profiles of both complexes over a range of D2O/H2O solvent mixtures, the DNA deuteration is shown to have a dramatic influence on the measured cross-sectional radius of gyration. Most importantly, data for the complex containing deuterated DNA lead to a more negative slope in a plot of the square of the cross-sectional radius of gyration vs. the inverse of the solute-solvent contrast, compared with the slope of a plot of data for the complex containing protonated DNA. This means that, in a cross-sectional view of the complex, the DNA is near the center of the structure. By our analysis, the DNA has a cross-sectional radius of gyration of 17.6 +/- 3 A, while the protein has a cross-sectional radius of gyration of about 33.5 A. Therefore, the model for the structure of the helical complex that has been proposed from X-ray diffraction studies on gene 5 protein crystallized with oligodeoxynucleotides [McPherson, A., Jurnak, F., Wang, A., Kolpak, F., Rich, A., Molineux, I., & Fitzgerald, P. (1980) Biophys. J. 32, 155-170] is not valid for the complex in solution. From our neutron diffraction data we have also obtained values for the solvent-excluded volume and mass per unit length. The relation of our findings to the solution structure of the complex is discussed.

Bacteriophages↗
PubMed1980

Circular dichroism and fluorescence-detected circular dichroism of deoxyribonucleic acid and poly[d(A-C).d(G-T)] in ethanolic solutions: a new method for estimating circular intensity differential scattering.

A method is presented for determining the circular dichroism (CD) of systems whose CD spectra contain contributions from CD differential scattering. The technique is shown to detect light over 4 pi steradians, and thus, for the first time, a complete correction for scattering is possible. The method is applied to ethanol-condensed DNA and poly[d(A-C).d(G-T)]. From the results obtained, the former are proposed to have an A-type secondary structure. The condensed polynucleotide particles are shown to exhibit behavior similar to that of cholesteric liquid crystals. CD difference spectra, obtained from the scattering corrections and showing the contributions to different sections of the scattering envelope, are displayed. It is asserted that these scattering patterns contain information about the tertiary structure of the condensed DNA particles studied.

1-Naphthylamine↗
PubMed1980

Circular dichroism spectra show that repeating dinucleotide DNAs may form helices in which every other base is looped out.

We have found that the CD spectrum of poly [d(C-T)] undergoes a marked change upon protonation, taking on the unmistakable features of the spectrum of poly[d(C) x d(C+)]. The acid poly[d9C-T)] structure appears to be one in which each of the T residues is individually looped out of a helix formed by stacked C x C+ base pairs. We also present data for poly[d(C-A)] and review data for the other four possible repeating DNA dinucleotide sequences. These data show that self-complexes in which up to 50% of the residues are extrahelical may be unexceptional.

Circular Dichroism↗
PubMed1979

The circular dichroism and X-ray diffraction of DNA condensed from ethanolic solutions.

It is known that DNA in aqueous-ethanol solutions undergoes a B to A conformational change between 60% and 80% (w/w) ethanol. We have found that precipitates formed by adding salt to DNA in 60% and 80% ethanolic solutions can be very different. DNA precipitated from 60% ethanol forms a fine condensate that only slowly settles out of suspension and shows a characteristic differential scattering of circularly polarized light at long wavelengths. DNA precipitated from 80% ethanol forms a flocculent aggregate that exhibits the CD spectral features of the A conformation. Data from circular dichroism spectra of natural and synthetic nucleic acids and from X-ray diffraction patterns of the precipitates show that DNA molecules precipitated from 60% and 80% ethanol are, respectively, in the B and A conformation. Therefore, the different secondary conformations of DNA in ethanolic solutions are maintained during precipitation under these conditions. These results are of general importance for the preparation and study of condensed forms of DNA, since a relatively small change in the extent of dehydration can change the secondary conformation of DNA and markedly affect the character of a subsequent precipitate.

Animals↗
PubMed1978

A comparison of the circular dichroism spectra of synthetic DNA sequences of the homopurine . homopyrimidine and mixed purine- pyrimidine types.

We have obtained the ultraviolet circular dichroism spectra of two repeating trinucleotide DNAs, poly [d(A-G-G).d(C-C-T)] and poly[d(A-A-G).d(C-T-T)], that have all purines on one strand and all pyrimidines on the other. These spectra, together with spectra of other synthetic polymers, can be combined to give 3 first-neighbor calculations of the spectrum of poly[d(A).d(T)] and 2 first-neighbor calculations of the spectrum of poly [d(G).d(C)]. The results show (1) that first-neighbor calculations utilizing only spectra of homopurine.homopyrimidine DNA sequences are no more accurate than are similar calculations that involve spectra of mixed purine-pyrimidine sequences, demonstrating that double-stranded homopurine.homopyrimidine sequences do not obviously belong to a special class of secondary conformations, and (2) that the wavelength region above 250 nm in the CD spectra of synthetic DNAs is least predictable from first-neighbor equations, probably because this region is especially sensitive to sequence-dependent conformational differences.

Base Sequence↗
PubMed1976

Preparation and properties of the repeating sequence polymers d(A-I-C)n-d(I-C-T)n and d(A-G-C)n-d(G-C-T)n.

The repeating sequence polymer d(A-I-C)n-d(I-C-T)n has been prepared using the chemically synthesized oligomers d(A-G-C)4 and d(C-T-G)4 and the DNA polymerase from Micrococcus luteus. The enzymatically synthesized polymer was used as template for preparation of d(A-G-C)n-d(G-C-T)n. Both deoxyribonucleotide polymers were characterized by nearest neighbor analyses, buoyant density measurements in cesium chloride and cesium sulfate, melting temperature, and circular dichroism (CD) spectra. The ribopolymers r(A-I-C)n-r(I-C-U)n and r(A-G-C)n-r(G-C-U)n were transcribed from d(A-I-C)n-d(I-C-T)n, and their CD spectra were compared with those of the respective deoxyribonucleotide polymers.

Base Sequence↗