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R L Ratliff

Publications and source records attributed to R L Ratliff.

At least 37 records · Page 2Linked to original sources
PubMed1985

Photochemical demonstration of stacked C.C+ base pairs in a novel DNA secondary structure.

The secondary structure of the alternating polydeoxynucleotide sequence poly[d(C-T)] was studied as a function of pH by ultraviolet absorbance and circular dichroism spectroscopy and by the analysis of UV-induced photoproducts. As the pH was lowered, poly[d(C-T)] underwent a conformational transition that was characterized by changes in the long-wavelength region (280-320 nm) of the CD spectrum. These changes have previously been interpreted as evidence for the formation of a core of stacked, protonated C X C+ base pairs in a double-helical complex of poly[d(C-T)], with the thymidyl residues being looped out into the solvent [Gray, D. M., Vaughan, M., Ratliff, R. L., & Hayes, F. N. (1980) Nucleic Acids Res. 8, 3695-3707]. In the present work, poly[d(C-T)] was labeled with [U-14C]cytosine and [methyl-3H]thymine and irradiated at pH values both above and below the conformational transition point (monitored by CD spectroscopy). The distribution of radioactivity in uracil means value of uracil dimers, uracil means value of thymine dimers (the deamination products of cytosine means value of cytosine and cytosine means value of thymine dimers, respectively), and thymine-means value of thymine dimers was then determined. As the pH was decreased, we found an increase in the yield of uracil means value of uracil dimers and a decrease in the yield of uracil means value of thymine dimers, which occurred concomitantly with the change in the CD spectrum.(ABSTRACT TRUNCATED AT 250 WORDS)

Base Composition↗
PubMed1984

Circular dichroism measurements show that C.C+ base pairs can coexist with A.T base pairs between antiparallel strands of an oligodeoxynucleotide double-helix.

We have studied the coil-to-helix transition of the DNA oligomer d(C4A4T4C4), using circular dichroism measurements to monitor the formation of A.T base pairs within the central self-complementary A4T4 region and the formation of protonated C.C+ base pairs at the ends of the oligomer. We found that both A.T and C.C+ base pairs formed in a coordinated fashion as the temperature and pH were lowered. The CD data of the helix form of the oligomer were consistent with the presence of paired oligomers, but not with hairpin loops. The pKa for formation of C.C+ base pairs between the C4 ends of the oligomer was higher than the pKa for formation of C.C+ base pairs in d(C8), indicating that the formation of C.C+ base pairs in the oligomer was influenced by the presence of a paired A4T4 region. We conclude that A.T and C.C+ base pairs coexist in the self-complex of the oligomer and, therefore, that C.C+ base pairs can form between antiparallel DNA strands.

Base Sequence↗
PubMed1984

Structure of a pleiomeric form of poly d(AT):poly d(AT).

A chemically simple polynucleotide duplex, poly d(AT):poly d(AT), has been trapped in a fibrous form with a complex helical secondary structure with a large (7.4 nm) axial repeat 24 nucleotides long. The motif which is repeated by the symmetry elements is a hexanucleotide in which two residues (both TpA) have the less common gauche minus conformation at C3'-O3' and consequently distinctive phosphate orientations. This reinforces earlier conclusions that PypPu nucleotides tend to have different shapes from PupPy nucleotides and that DNA surfaces may signal what base sequences lie beneath them. The morphological differences between this pleiomeric DNA polymer and closely-related, but more symmetrical allomorphs are just as great as those observed in short DNA fragments in crystals.

Base Sequence↗
PubMed1983

Evidence of 2-aminopurine-cytosine base mispairs involving two hydrogen bonds.

It is shown that the mutagen base analogue 2-aminopurine is hydrogen-bonded at its 1-ring position when annealed with cytosine in DNA. The presence of stably hydrogen-bonded regions proximal to the 2-aminopurine-cytosine base mispair is a prerequisite for the occurrence of two hydrogen bonds coupling the bases at their 1-3- and 2-2-positions. We consider the possibility that, in the resulting heteroduplex base mispair, 2-aminopurine or cytosine may be present as a disfavored imino tautomer.

2-Aminopurine↗
PubMed1983

Wrinkled DNA.

The B form of poly d(GC):poly d(GC) in orthorhombic microcrystallites in oriented fibers has a secondary structure in which a dinucleotide is the repeated motif rather than a mononucleotide as in standard, smooth B DNA. One set of nucleotides (probably GpC) has the same conformations as the smooth form but the alternate (CpG) nucleotides have a different conformation at C3'-O3'. This leads to a distinctive change in the orientation of the phosphate groups. Similar perturbations can be detected in other poly d(PuPy):poly d(PuPy) DNAs such as poly d(IC):poly d(IC) and poly d(AT):poly d(AT) in their D forms which have tetragonal crystal environments. This suggests that such perturbations are intrinsic to all stretches of duplex DNA where purines and pyrimidines alternate and may play a role in the detection and exploitation of such sequences by regulatory proteins.

DNA↗
PubMed1981

Reactions induced in vitro between model DNA and benzo[a]pyrene by near-ultraviolet radiation.

Near-ultraviolet (300--480 nm wavelength) irradiation of the single-strand polydeoxynucleotide poly[d(A,C,G,T)] and carbon-14 labeled benzo[alpha]-pyrene (B[alpha] P) in aqueous dimethylsulfoxide (DMSO) solution led to appreciable binding of labeled hydrocarbon to the polynucleotide. Nuclease digests of polydeoxynucleotide-B[alpha]P complexes were examined by chromatography on Sephadex LH-20; at high fluences of near-ultraviolet light deoxyguanosine (dG) residues of the polymer were largely destroyed when the hydrocarbon was present. Approximately 85% of the B[alpha] P of the digests were recovered as hydrophilic derivatives not adsorbed by Sephadex LH-20. Elution of the columns with an aqueous-methanol gradient indicated that substances similar to the covalent deoxynucleoside-B[alpha] P adducts formed between microsomally-oxidized B[alpha] P and DNA were likewise present in the digests. When the deoxyadenosine (dA), deoxycytidine (dC) or dG moieties of the polymer were tritium-labeled, substances doubly-labeled with tritium and carbon-14 were found; ratios of the two radioactivities indicated that equimolar amounts of deoxynucleoside and hydrocarbon were present.

Benzo(a)pyrene↗
PubMed1980

Left-handed DNA helices.

The synthetic DNA polymerpoly d(GC) . poly d(GC) has been studied by X-ray diffraction of orientated fibres in which it has either the well known (A or B) randed conformations have been observed with poly d(AC) . poly d(GT) and with poly d(As4T) . poly d(As4T), demonstrating that the novel structure is accessible to any DNA segment with an alternating purine-pyrimidine base sequence.

Base Sequence↗
PubMed1979

Cadmium-induced alterations in RNA metabolism in cultures of Chinese hamster cells sensitive to and resistant to the cytotoxic effects of cadmium.

A variant population (CdR) of cultured Chinese hamster cells (line CHO) was derived that is more than 100 times as resistant to the cytotoxic effects of Cd2+ than is the parent population. The effects on RNA metabolism of exposure to sublethal concentrations of Cd2+ were studied in CHO and CdR. Exposure to 2 X 10(-7) M CdCl2 for 24 h resulted in increased polysome content (1.2 times) and increased uridine or adenosine incorporation into heterogeneous nuclear RNA (1.2-1.4 times) and messenger RNA ((1.5-1.7 times) in both populations. Measurement of ATP pool specific activity following exposure to radiolabeled adenosine showed that increased incorporation reflects increased synthesis. The equivalence of CHO and CdR in dose-response in terms of stimulated RNA synthesis and their disparity in dose-response in terms of cytotoxic effects indicate that the systems involved in conferring protection against the lethal effects of Cd2+ are not similarly involved in attenuating the effects on RNA metabolism.

Adenosine↗
PubMed1978

Terminal deoxynucleotidyl transferase in the diagnosis of leukemia and malignant lymphoma.

Neoplastic cells from 253 patients with leukemia and 46 patients with malignant lymphoma were studied for the presence of terminal deoxynucleotidyl transferase (TdT) by biochemical and fluorescent antibody technics. TdT was detected in circulating blast cells from 73 of 77 patients with acute lymphoblastic leukemia, 24 of 72 patients with chronic myelogenous leukemia examined during the blastic phase of the disorder and in cell suspensions of lymph nodes from nine of nine patients with diffuse lymphoblastic lymphoma. Blast cells from six of 10 patients with acute undifferentiated leukemia were TdT positive, but the enzyme was found in only two of 55 patients with acute myeloblastic leukemia. TdT was not detected in other lymphocytic or granulocytic leukemias or in other types of malignant lymphomas. The fluorescent antibody assay for TdT permits rapid and specific identification of the enzyme in single cells. The TdT assay is clinically useful in confirming the diagnosis of acute lymphoblastic leukemia, evaluating patients with blastic chronic myelogenous leukemia, and distinguishing patients with lymphoblastic lymphoma, whose natural history includes rapid extranodal dissemination, from patients with other poorly differentiated malignant lymphomas.

Adolescent↗
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↗
PubMed1975

Lack of specific correlation of the deoxycytidine triphosphate pool level with rate of DNA synthesis.

The levels of the four deoxyribonucleoside triphosphate pools and the distribution of cells in the various phases of the cell cycle have been examined in Chinese hamster cells as thymidine, present as a regular constituent in the growth medium, was removed in stages. The results indicate that: 1. Duration of the DNA synthetic phase was lengthened when thymidine was removed from the growth medium. 2. Temporally correlated with lengthening of the DNA synthetic phase upon thymidine removal was a 7-fold increase in level of the dCTP pool, reduction in the dGTP pools, and little or no change in dATP pool. 3. Radioactive labeling procedures indicated that expansion of the dCTP pool could be completely accounted for by increased ribonucleotide reductase activity and that the dTTP pool switched from a largely exogenous thymidine source to endogenous dTTP synthesis as the extracellular thymidine concentration was reduced. 4. Deoxyuridine and thymidine were apparently transported by the same system in Chinese hamster cells, while deoxycytidine was transported by a different system. Although deoxycytidine transport was unaffected by thymidine, phosphorylation of intracellular deoxycytidine compounds to the triphosphate level was stimulated by thymidine. Cytidine transport was not significantly affected by thymidine.

Cell Line↗