Wartell, Roger M.

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    Predicted structure and phyletic distribution of the RNA-binding protein Hfq
    (Georgia Institute of Technology, 2002) Sun, Xueguang ; Zhulin, Igor ; Wartell, Roger M. ; College of Sciences ; School of Biological Sciences
    Hfq, a bacterial RNA-binding protein, was recently shown to contain the Sm1 motif, a characteristic of Sm and LSm proteins that function in RNA processing events in archaea and eukaryotes. In this report, comparative structural modeling was used to predict a three-dimensional structure of the Hfq core sequence. The predicted structure aligns with most major features of the Methanobacterium thermoautotrophicum LSm protein structure. Conserved residues in Hfq are positioned at the same structural locations responsible for subunit assembly and RNA interaction in Sm proteins. A highly conserved portion of Hfq assumes a structural fold similar to the Sm2 motif of Sm proteins. The evolution of the Hfq protein was explored by conducting a BLAST search of microbial genomes followed by phylogenetic analysis. Approximately half of the 140 complete or nearly complete genomes examined contain at least one gene coding for Hfq. The presence or absence of Hfq closely followed major bacterial clades. It is absent from high-level clades and present in the ancient Thermotogales-Aquificales clade and all proteobacteria except for those that have undergone major reduction in genome size. Residues at three positions in Hfq form signatures for the beta/gamma proteobacteria, alpha proteobacteria and low GC Gram-positive bacteria groups.
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    DNA conformational change in Gal repressor-operator complex: involvement of central G-C base pair(s) of dyad symmetry
    (Georgia Institute of Technology, 1988-12-23) Wartell, Roger M. ; Adhya, Sankar Lal ; College of Sciences ; School of Biological Sciences
    Gal repressor dimer binds to two gal operator sites, O[subscript E] and O[subscript I], which are 16 bp long similar sequences with hyphenated dyed symmetries (11,12). Repressor occupation hinders the reactivity of the N7 atoms in the major groups of guanines, located at positions 1,3 and 8, and the rotational 1′, 3 and 8′ of the symmetries. We have shown that Gal repressor binding to O[subscript E] or O[subscript I] DNA fragments increases the circular dichroism (CD) spectral peak in the 270 to 300 nm range. The CD change is similar to that observed for Lac repressor binding to its operator site (14). It is consistent with a DNA conformational change during complex formation between Gal repressor and O[subscript E] and O[subscript I] DNA. The CD spectral change was not observed when the central 8,8′ C-C base pairs in the DNA-protein complex were replaced by A-T base pairs, whereas substitution of the 1,1′ G-C base pairs do show the accompanying increase in the spectra during repressor binding. The absence of CD change of the Gal repressor complex with DNA mutated at the 8,8′ base pairs suggest that the central G-C base pairs are required for the repressor induced conformational change.
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    Sequence distributions associated with DNA curvature are found upstream of strong E. coli promoters
    (Georgia Institute of Technology, 1987-01-26) Plaskon, R. Richard ; Wartell, Roger M. ; College of Sciences ; School of Biological Sciences
    The regions upstream from forty-three procaryotic promoters were examined for nucleotide distributions which have been associated with DNA curvature. The analysis procedure assigned a DNA curvature score based on the phasing of the 5' and 3' ends of An and Tn tracts, n greater than or equal to 3. The weighting scheme for the curvature score was based on recent studies which showed that tracts of An and Tn periodically phased with the helix repeat cause DNA curvature. Results show that promoters which have high transcription initiation rates in vivo tend to have high curvature scores in their upstream regions. Regions downstream from the transcription start-point do not have sequences correlated with DNA curvature. Four promoters which have been shown to have upstream activation regions have curvature scores above 1.5 in their -40 to -150 regions. The correlations observed lend support to the hypothesis that DNA curvature is associated with upstream activation of transcription
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    The catabolite activator protein stabilizes its binding site in the E. coli lactose promoter
    (Georgia Institute of Technology, 1985-10-25) DeGrazia, Henry ; Abhiraman, Saraswathy ; Wartell, Roger M. ; College of Sciences ; School of Biological Sciences
    The effect of catabolite activator protein, CAP, on the thermal stability of DNA was examined. Site specific binding was studied with a 62 bp DNA restriction fragment containing the primary CAP site of the E. coli lactose (lac) promoter. A 144 bp DNA containing the lac promoter region and a 234 bp DNA from the pBR322 plasmid provided other DNA sites. Thermal denaturation of protein-DNA complexes was carried out in a low ionic strength solvent with 40% dimethyl sulfoxide, DMSO. In this solvent free DNA denatured below the denaturation temperature of CAP. The temperature stability of CAP for site specific binding was monitored using an acrylamide gel electrophoresis assay. Results show that both specific and non-specific CAP binding stabilize duplex DNA. Site specific binding to the 62 bp DNA produced a 13.3 degrees C increase in the transition under conditions where non-specific binding stabilized this DNA by 2-3 degrees C.
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    Repression of TAT activated HIV-LTR directed gene expression
    (Georgia Institute of Technology, 1994-06) Wartell, Roger M. ; Georgia Institute of Technology. Office of Sponsored Programs ; Georgia Institute of Technology. School of Biology
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    American scientists survey-phase II
    (Georgia Institute of Technology, 2011-03-15) Walsh, John P. ; Huang, Hsin-I ; No, Yeonji ; Wartell, Roger M. ; Bayer, Charlene W. ; Tornabene, Thomas G. ; School of Public Policy ; Office of Sponsored Programs ; Ivan Allen College of Liberal Arts ; College of Sciences ; School of Biological Sciences
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    The formation of adjacent triplex-duplex domains in DNA
    (Georgia Institute of Technology, 1999-02) Nam, Kang Hoon ; Abhiraman, Saraswathy ; Wartell, Roger M. ; College of Sciences ; School of Biological Sciences
    The ability of single-stranded DNA oligomers to form adjacent triplex and duplex domains with two DNA structural motifs was examined. Helix–coil transition curves and a gel mobility shift assay were used to characterize the interaction of single-stranded oligomers 12–20 nt in length with a DNA hairpin and with a DNA duplex that has a dangling end. The 12 nt on the 5'-ends of the oligomers could form a triplex structure with the 12 bp stem of the hairpin or the duplex portion of the DNA with a dangling end. The 3'-ends of the 17–20 nt strands could form Watson–Crick pairs to the five base loop of the hairpin or the dangling end of the duplex. Complexes of the hairpin DNA with the singlestranded oligomers showed two step transitions consistent with unwinding of the triplex strand followed by hairpin denaturation. Melting curve and gel competition results indicated that the complex of the hairpin and the 12 nt oligomer was more stable than the complexes involving the extended single strands. In contrast, results indicated that the extended single-stranded oligomers formed Watson–Crick base pairs with the dangling end of the duplex DNA and enhanced the stability of the adjacent triplex region.
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    Detecting base pair substitutions in DNA fragments by temperature-gradient gel electrophoresis
    (Georgia Institute of Technology, 1990-05-11) Wartell, Roger M. ; Hosseini, Seyed Homayoun ; Moran, Charles P., Jr. ; College of Sciences ; School of Biological Sciences ; Emory University. School of Medicine
    A vertical gel electrophoresis apparatus is described which can distinguish DNA fragments differing by single base pair substitutions. The system employs a homogenous polyacrylamide gel containing ureaformamide and a temperature gradient which runs either perpendicular or parallel to the direction of electrophoresis. The temperature-gradient system simplifies several features of the denaturant-gradient system (1) and is relatively inexpensive to construct. Eight homologous 373 bp DNAs differing by one, two, or nine base pair substitutions were examined. DNA electrophoretic mobility changed abruptly with the temperature induced unwinding of DNA domains. GC to AT substitutions at different locations within the first melting domain, as well as an AT to TA transversion were separated with temperature gradients parallel to the electrophoretic direction. The relative stabilities of the DNAs observed in the gels were compared to predictions of DNA melting theory. General agreement was observed however complete correspondence was not obtained.
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    Interaction of RNA polymerase with DNA sites
    (Georgia Institute of Technology, 1980) Wartell, Roger M. ; College of Sciences ; School of Physics ; Office of Sponsored Programs
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    Interaction of RNA polymerase with DNA sites
    (Georgia Institute of Technology, 1983) Wartell, Roger M. ; College of Sciences ; School of Physics ; Office of Sponsored Programs