PubMed Health⌕ Search

Biomedical subjects

R D Wells

Publications and source records attributed to R D Wells.

29 records · Page 2Linked to original sources
PubMed1977

Action of single-strand specific nucleases on model DNA heteroduplexes of defined size and sequence.

The sensitivity of the model DNAs containing dA-dG and dtg-dG heteroduplex regions of defined length to S1 and mung bean single-strand specific nucleases was tested by polyacrylamide gel electrophoretic analysis of the distribution of product oligonucleotides. Single-base mismatch heteroduplexes were extremely resistant to these nucleases, although low levels of cleavage at the heteroduplex nucleotide were observed at high nuclease concentrations. The nuclease sensitivity of dA-dtg heteroduplex regions increased gradually as the length of the heteroduplex region increased frome one to six nucleotides. The sensitivity of dG-dG heteroduplexes three to five nucleotides long was considerably greater than that of the single dtg-dG mismatch.

DNA, Single-Stranded↗
PubMed1977

High resolution proton nuclear magnetic resonance investigation of the structural and dynamic properties of d(C15A15)-d(T15G15).

The high resolution proton nuclear magnetic resonance (NMR) spectra of the synthetic DNA block polymer d(C15A15)-d(T15G15) were studied in order to more completely understand telestability in DNA, and to provide fundamental NMR data on DNA helices and random coils. Spectra were measured in the spectral region from 0 to 15 ppm downfield from the usual standard, sodium 4,4-dimethyl-4-silapentane-1-sulfonate(DSS), at various temperatures (24-98 degrees C) in solution containing either moderate or high ionic strength. The effect of actinomycin binding to the block polymer also was studied. The major conclusions derived from this study are as follows: (1) The majority of base pairs in the AT helix of the block polymer have the same conformation as in d(A)n-d(T)25 and d(A)21-d(T)21. (2) The conformation of the GC helix in the block polymer is different from the AT helix and this perturbs the conformation of three or four A-T base pairs at the junction of the AT-GC helix. (3) The conformation of the AT helix is unaffected by salt over the range examined (approximately 0.04 - approximately 2 M), but the conformation of the GC helix changes. (4) There are subtle changes in the conformation of the AT helix as the temperature is increased and resonances characteristic of the random coil and the double-helical state can be simultaneously observed. (5) Binding of actinomycin, which is specific for the GC helix, induces quite large (over 1 ppm) upfield shifts of the resonances from the GC base pairs. This is consistent with an intercalation model in which actinomycin D (Am) is assymetrically sandwiched between two GC base pairs in such a manner that overlap with the guanosine residues is greater than with the neighboring cytidines. (6) The presence of the drug may also perturb A-T base pairs located near the AT-GC junction, but it has no effect on the majority of the AT pairs. However, as expected, Am elevated the Tm of the AT helix, even though it binds to the other end of the DNA.

DNA↗
PubMed1977

RNA polymerase binding sites in lambdaplac5 DNA.

The in vitro binding of the Escherichia coli RNA polymerase (nucleosidetriphosphate:RNA nucleotidyltransferase; EC 2.7.7.6) to fragments of lambdaplac5 DNA generated by restriction endonucleases HindII and HindIII has been studied by a filter binding technique. The results are consistent with RNA polymerase binding at p(R)', the INT promoter (p(I)), several sites in the b2 region, the mis promoter, the oop promoter (or p(O)), and p(rm). Binding was also observed on some fragments that are not known to contain active promoters, including the fragment from the cIII-t(L) region. Some of these binding reactions might also be explained by interaction of RNA polymerase with termination sites. Additional polymerase binding sites have been detected by examining which HindII and HindIII sites were not cleaved when digestion was performed after RNA polymerase had been bound to the DNA. This technique revealed polymerase binding at p(L), at p(R), at a site between R and cos, and at a site at the junction of the gamma and cIII-t(L) fragments. A comparison of the location of polymerase binding fragments with the partial denaturation map of the lambda genome indicates that RNA polymerase binding sites are located within A-T rich regions. It is suggested that RNA polymerase binding is a function both of specific sequences (where recognition occurs) and of the base composition of the surrounding regions (which affects the stability of the helix at the specific site).

Binding Sites↗
PubMed1976

Coumerimycin A1: A preferential inhibitor of replicative DNA synthesis in Escherichia coli. II. In vivo characterization.

In vitro inhibitions by coumermycin A1 of DNA and RNA synthesis in toluenized cells were studied. In a sensitive strain, 50% inhibitions of replication and transcription were observed at 0.035 and 0.600 mug/ml, respectively. DNA synthesis in a toluenized-resistant mutant was 50% inhibited at 0.140 mug/ml of coumermycin A1, whereas RNA synthesis was unaffected at all concentrations tested. Studies with a mixture of toluenized-sensitive and -resistant bacteria ruled out the presence of a diffusable activator or inhibitor of coumermycin A1 action. Density label studies with toluenized pol A+ and pol A- strains indicated that replicative DNA synthesis was specifically inhibited, in agreement with the in vivo studies in the preceding paper of this issue (Ryan, M. J. (1976), Biochemistry 15). Highly purified Escherichia coli DNA polymerase III and RNA polymerase both were inhibited by this antibiotic. However, the high concentrations necessary for these inhibitions suggest that they are not biologically relevant. No interaction between DNA and coumermycin A1 was observed with the following analytical procedures: ultraviolet difference spectra, DNA absorbance-temperature transitions, equilibrium buoyant density centrifugation, and DNA cross-linking determinations.

Anti-Bacterial Agents↗
PubMed1976

All intact subunit RNAs from Rous sarcoma virus contain poly (A).

The capacity of RNA subunits of Schmidt-Ruppin Rous sarcoma virus to bind (dT)n was studied by cesium sulfate density gradient centrifugation, sucrose gradient centrifugation, or polyacrylamide gel electrophoresis. Two classes of subunits were observed. In agreement with previous reports, 60 to 70% of the purified subunits were capable of binding (dT)n. The remaining, nonbinding RNAs, although indistinguishable in size from whole subunits, were shown to be fragments that had lost the (rA)n terminus by random nucleolytic cleavage. This was deduced from the molecular weight distribution of the nonbinding RNAs from high molecular weight RNA. In addition, virtually all subunit RNA from early harvest virus, which contains a greater proportion of intact subunit, binds (dT)n.

Avian Sarcoma Viruses↗
PubMed1975

Further studies on telestability in DNA. The synthesis and characterization of the duplex block polymers d(C20A10) - d(T10G20) and d(C20A15) - d(T15G20).

The synthesis and characterization of the duplex block polymers d(C20A10) - d(T10G20) and d(C20A15) - d(T15G20) are described. Thermal denaturation studies on these DNAs in the absence and presence of actinomycin, which binds only to the GC portions of these molecules, have confirmed and extended our previous observation that the properties of one region of a DNA can be influenced (telestabilized) by a remote region. In addition, the large scale synthesis of d(C15A15) - d(T15G15) is described.

Animals↗
PubMed1975

Transmission of stability (telestability) in deoxyribonucleic acid. Physical and enzymatic studies on the duplex block polymer d(C15A15) - d(T15G15).

The properties of the duplex block polymer d(C15A15) - d(T15G15) were examined by thermal denaturation and nuclease susceptibility studies in the absence and presence of drugs (actinomycin and netropsin) which bind specifically to only one end of the block polymer. The nucleotide composition of one region of this synthetic double-helical DNA affected the properties of a contiguous but remote region. Furthermore, the binding of actinomycin influenced the properties of both the binding and nonbinding regions. These findings suggest a mechanism for gene regulation at a distance.

Adenosine Monophosphate↗
PubMed1975

The compatibility of netropsin and actinomycin binding to natural deoxyribonucleic acid.

The simultaneous binding of netropsin and actinomycin to four natural DNAs was studied to determine the influence of one ligand on the binding of the other. Actinomycin binds specifically to GC sites, whereas netropsin binds specifically to AT sites. Spectral titrations, thermal denaturation, and analytical buoyant density centrifugation were employed to measure the binding interference of these drugs. The binding of actinomycin to DNA was decreased by the presence of netropsin. Increasing the GC content of the DNA resulted in a decreased effect of netropsin on actinomycin binding. Quantitative analysis of the binding parameters indicated that netropsin and actinomycin can bind in close proximity along the DNA chain. Supercoiled DNA gave the same result as linear DNA. These results imply that DNA can absorb alterations in conformation within a short distance.

Anti-Bacterial Agents↗