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P B Moore

Publications and source records attributed to P B Moore.

At least 19 recordsLinked to original sources
PubMed1992

Solution structure of an unusually stable RNA tetraplex containing G- and U-quartet structures.

A model for the solution structure of an RNA tetraplex, (rUGGGGU)4, has been obtained by two-dimensional NMR spectroscopy and molecular dynamics. The molecule is parallel stranded and Hoogsteen base-paired in 50 mM KCl, and it is so stable that three of its six imino protons have exchange half-lives measured in days at 40 degrees C. The tetraplex is stabilized by base stacking and by the hydrogen bonds in four G quartets and at least one U quartet. This is the first indication of the existence of U-quartet structures of which we are aware.

Hydrogen Bonding↗
PubMed1992

NMR analysis of helix I from the 5S RNA of Escherichia coli.

The structure of helix I of the 5S rRNA from Escherichia coli has been determined using a nucleolytic digest fragment of the intact molecule. The fragment analyzed, which corresponds to bases (-1)-11 and 108-120 of intact 5S rRNA, contains a G-U pair and has unpaired bases at its termini. Its proton resonances were assigned by two-dimensional NMR methods, and both NOE distance and coupling constant information have been used to calculate structural models for it using the full relaxation matrix algorithm of the molecular dynamics program XPLOR. Helix I has A-type helical geometry, as expected. Its most striking departure from regular helical geometry occurs at its G-U, which stacks on the base pair to the 5' side of its G but not on the base pair to its 3' side. This stacking pattern maximizes interstrand guanine-guanine interactions and explains why the G-U in question fails to give imino proton NOE's to the base pair to 5' side of its G. These results are consistent with the crystal structures that have been obtained for wobble base pairs in tRNAPhe [Mizuno, H., & Sundaralingam, M. (1978) Nucleic Acids Res. 5, 4451-4461] and A-form DNA [Rabbinovich, D., Haran, T., Eisenstein, M., & Shakked, Z. (1988) J. Mol. Biol. 200, 151-161]. The conformations of the terminal residues of helix I, which corresponds to bases (-1)-11 and 108-120 of native 5S RNA, are less well-determined, and their sugar puckers are intermediate between C2' and C3'-endo, on average.

Base Composition↗
PubMed1991

An NMR characterization of the regA protein-binding site of bacteriophage T4 gene 44 mRNA.

The conformations of two RNA dodecamers that differ markedly in affinity for the regA protein from bacteriophage T4 have been examined by NMR to see if the ability of that protein to discriminate between mRNAs is based on pre-existing differences in their three-dimensional structures. One of the RNAs examined has the same sequence as the site where regA protein binds when it inhibits the expression of gene 44's mRNA. The second RNA differs from the first in having a U instead of a G at position -9; it binds regA protein 100 times less tightly. The NMR data indicate that both RNAs have similar single-stranded conformations and that they each resemble an isolated strand of a double helix. They also show that most, if not all of the ribose rings in both molecules have appreciable 2'-endo puckering. It is unlikely that regA protein distinguishes between these two molecules on the basis of differences in their global conformations in solution.

ADP Ribose Transferases↗
PubMed1991

Tetramerization of an RNA oligonucleotide containing a GGGG sequence.

Poly rG can form four-stranded helices. The Hoogsteen-paired quartets of G residues on which such structures depend are so stable that they will form in 5'-GMP solutions, provided that Na+ or K+ are present (see for example, refs 2-4). Telomeric DNA sequences, which are G-rich, adopt four-stranded antiparallel G-quartet conformations in vitro, and parallel tetramerization of G-rich sequences may be involved in meiosis. Here we show that RNAs containing short runs of Gs can also tetramerize. A 19-base oligonucleotide derived from the 5S RNA of Escherichia coli (strand III), 5'GCCGAUGGUAGUGUGGGGU3', forms a K(+)-stabilized tetrameric aggregate that depends on the G residues at its 3' end. This complex is so stable that it would be surprising if similar structures do not occur in nature.

Base Sequence↗
PubMed1991

Screening rabbit colonies for antibodies to Pasteurella multocida by an ELISA.

Rabbit serum samples from eleven different research facilities were evaluated for the presence of immunoglobulin G against Pasteurella multocida by using an enzyme-linked immunosorbent assay (ELISA). Each facility which submitted serum samples also provided a brief history of each rabbit colony tested. Rabbits from colonies reported to have endemic P. multocida or of undetermined status had 83 (58.9%) of 141 rabbits that were positive. Colonies reported to be free from P. multocida had 110 (92.4%) of 119 rabbits that were negative by ELISA. The ELISA test described here showed a high degree of agreement (92-94%) with two other P. multocida ELISAs at different diagnostic facilities. This study confirms that an ELISA testing for serum antibodies against the P. multocida is a reliable diagnostic tool to screen colonies for P. multocida.

Animals↗
PubMed1990

On the use of T7 RNA polymerase transcripts for physical investigation.

A few years ago we made some observations which raised questions about the accuracy with which T7 RNA polymerase transcribes templates in vitro, and the suitability of its in vitro products for biophysical study (1). The experiments described below demonstrate that there is no reason for concern; the products of T7 RNA polymerase transcription in vitro are as suitable for biophysical characterization as RNAs synthesized in vivo. It is likely that aggregation involving the transcribed portions of the T7 RNA polymerase promoter caused our initial observations.

Base Sequence↗
PubMed1989

Physical studies of 5S RNA variants at position 66.

Two variants of the 5S RNA of E. coli have been examined by imino proton NMR spectroscopy, one of them a deletion of A66 (Christiansen, J., Douthwaite, S.R., Christensen, A. and Garrett, R.A. (1985) EMBO J. 4, 1019-1024) and the other a replacement of A66 with a C (Goringer, H.U. and Wagner, R. (1986) Biol. Chem. Hoppe-Seyler 367, 769-780). Both are of interest because the role the bulged A in helix II of 5S RNA is supposed to play in interactions with ribosomal protein L18. The data show that the structural perturbations that result from these mutations are minimal, and assign the resonances of some of the imino protons around position 66. Some mutations at or near position 66 greatly reduce the L18-dependent increase in the circular dichroism of 5S RNA at 267 nm first observed by Bear and coworkers (Bear, D.G., Schleich, T., Noller, H.F. and Garrett, R.A. (1977) Nucl. Acids Res. 4, 2511-2526).

Base Sequence↗
PubMed1989

A study of the conformation of 5S RNA by 31P NMR.

Only a small number of resolved, single phosphorous, phosphodiester resonances are observed in the 31P spectrum of the 5S rRNA from E. coli. Its spectrum is much simpler than that of a tRNA (Gueron, M. and Shulman, R.G. (1975) Proc. Natl. Acad. Sci. 72, 3482-3484), which suggests that 5S RNA does not have a tightly folded, tRNA-like, tertiary structure. The resolved resonances in the 5S spectrum originate in loops D and E, near bases 88 and 76, respectively.

Base Sequence↗
PubMed1989

An NMR study of the helix V-loop E region of the 5S RNA from Escherichia coli.

Experiments are described that complete the assignment of the imino proton NMR spectrum of the fragment 1 domain from the 5S RNA of Escherichia coli. Most of the new assignments fall in the helix V-loop E portion of the molecule (bases 70-78 and 98-106), the region most sensitive to the binding of ribosomal protein L25. The spectroscopic data are incompatible with the standard, phylogenetically derived model for 5S RNA, which makes all the base pairs possible in loop E with the sequences aligned in parallel (C70-G106, C71-G105, etc.) [see Delihas et al. (1984) Prog. Nucleic Acid Res. Mol. Biol. 31, 161-190]. Furthermore, the alternative loop E model proposed for spinach chloroplast 5S RNA by Romby et al. [(1988) Biochemistry 27, 4721-4730] does not apply to the closely homologous 5S RNA from E. coli. The 5S RNAs from E. coli and spinach chloroplasts do not have the same secondary structures in solution despite their strong sequence homologies, and neither appears to conform to the standard model for 5S RNA in the loop E region.

Chloroplasts↗
PubMed1988

Tumor necrosis factor induced DNA fragmentation of HL-60 cells.

Tumor necrosis factor (TNF) induces differentiation of HL-60 cells, with only slight effects upon proliferation and little or no cytotoxicity. TNF induced cytotoxicity of other target cell lines has been associated with DNA fragmentation. To assess whether TNF-induced DNA fragmentation might also contribute to HL-60 differentiation, studies were performed using a [3H]-dThd release assay. Between 1 and 2 hours of culture, significant [3H]-dThd release was induced by TNF at concentrations of 10 U/ml and greater. This response was blocked by inhibiting energy metabolism, but not by several inhibitors of cell surface signal transduction, protein or RNA synthesis, or free radical scavengers. DNA electrophoresis of the released DNA disclosed a wide range of low molecular weight fragments. It is possible that TNF-induced DNA fragmentation contributes to HL-60 differentiation.

Cell Differentiation↗
PubMed1988

Exploration of the L18 binding site on 5S RNA by deletion mutagenesis.

Several deletion variants of E. coli 5S RNA have been constructed and produced either in vivo or in vitro using T7 RNA Polymerase. Their structures and ribosomal protein L18 binding properties have been examined. All of them are similar to wild-type 5S RNA in their helix II-III regions, where L18 binds [Huber, P.W. and Wool, I.G. (1984) Proc. Natl. Acad. Sci. (USA) 81, 322-326; Douthwaite, S., Christensen, A., and Garrett, R.A. (1982) Biochemistry 21, 2313-2320.], by NMR criteria. However, none of the molecules examined that lack the helix IV-helix V stem bind L18 efficiently, even though that portion of 5S RNA is outside the L18 footprint. The L18 binding site is clearly more than a simple hairpin loop.

Base Sequence↗
PubMed1988

Calcimedin, calelectrin: correlation of relatedness.

A statistical method has been used to compare the amino acid compositions of several calelectrin proteins and the 67k calcimedin protein. The validity of the method for determining protein relatedness and ancestry has been established with many different proteins. Torpedo calelectrin, p68 brain calelectrin, 67,000 dalton brain calelectrin, 67,000 bovine aorta protein, 32k lipocortin (and probably 67R lung protein) share considerable homology with each other and with calpactin I or lipocortin II, the pp60src tyrosine kinase substrate. The 67k calcimedin appears to be unrelated to these several proteins, in agreement with biochemical evidence, although limited homology may still be present. The lung 67E protein, calregulin and calmodulin, are unrelated to any of the other proteins.

Amino Acids↗
PubMed1988

Cellular immunofluorescence: quantification of low abundance proteins.

Aminofluorescein can be extracted with alkaline carbonate buffer (0.5% Na2CO3 in 0.1 M NaOH) from fixed cells stained in indirect immunofluorescence by fluorescein-conjugated antibody. Fluorescence is then quantified by spectrofluorometry. A standard curve obtained by dilution of known fluorochrome allows for subsequent spectrofluorometric analysis of the extracted aminofluorescein. A saturating quantity of primary antibody should be used to determine the level of staining associated with a cellular antigen. This simple method makes it possible to quantify samples used for immunofluorescence microscopy. It can be adapted for determining the DNA content in the same samples, allowing the quantity of antigen to be equated either to DNA content or to cells plated.

Annexins↗
PubMed1988

67 k calcimedin (67 kDa) is distinct from p67 calelectrin and lymphocyte 68 kDa Ca2+-binding protein.

The 67 k calcimedin is a Ca2+-binding protein present in both muscle cells and peritoneal macrophages. Many tissues, including lymphoid tissues, liver and lymphocytes, have been shown to contain Ca2+-binding proteins of similar molecular size, such as the p67(67 kDa) calelectrin or the 68 kDa lymphocyte protein. We have tested affinity-purified antibodies raised to the smooth-muscle 67 k calcimedin in these several tissues and here report that the 67 k calcimedin is not detectable in liver, thymus, spleen or thymic lymphocytes. These findings support recent biochemical evidence, discussed here, suggesting that the 67 k calcimedin is a protein different from calelectrin and the 68 kDa lymphocyte protein. The more limited tissue distribution of the 67 k calcimedin, which includes muscle and macrophages, suggests that the 67 k calcimedin may function in Ca2+-mediated events special to these cell types. The affinity-purified antibodies to the 67 k calcimedin will be useful in obtaining information concerning the special roles of this Ca2+-binding protein in these cells.

Animals↗