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Wartell,
Roger M.
Wartell,
Roger M.
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ItemLocalization of the intrinsically bent DNA region upstream of the E.cofi rrnB P1 promoter(Georgia Institute of Technology, 1994-06-25) Gaal, Tamas ; Rao, Lin ; Estrem, Shawn T. ; Yang, Jin ; Wartell, Roger M. ; Gourse, Richard L. ; University of Wisconsin--Madison. Dept. of Bacteriology ; Georgia Institute of Technology. School of BiologyDNA sequences upstream of the rrnB P1 core promoter (-10, -35 region) increase transcription more than 300-fold in vivo and in vitro. This stimulation results from a cis-acting DNA sequence, the UP element, which interacts directly with the alpha subunit of RNA polymerase, increasing transcription about 30-fold, and from a positively acting transcription factor, FIS, which increases expression another 10-fold. A DNA region exhibiting a high degree of intrinsic curvature has been observed upstream of the rrnB P1 core promoter and has thus been often cited as an example of the effect of bending on transcription. However, the precise position of the curvature has not been determined. We address here whether this bend is in fact related to activation of rRNA transcription. Electrophoretic analyses were used to localize the major bend in the rrnB P1 upstream region to position approximately -100 with respect to the transcription initiation site. Since most of the effect of upstream sequences on transcription results from DNA between the -35 hexamer and position -88, i.e. downstream of the bend center, these studies indicate that the curvature leading to the unusual electrophoretic behavior of the upstream region does not play a major role in activation of rRNA transcription. Minor deviations from normal electrophoretic behavior were associated with the region just upstream of the -35 hexamer and could conceivably influence interactions between the UP element and the alpha subunit of RNA polymerase.
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ItemInteraction of RNA polymerase with DNA sites(Georgia Institute of Technology, 1982) Wartell, Roger M. ; Georgia Institute of Technology. Office of Sponsored Programs ; Georgia Institute of Technology. School of Physics
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ItemInfluence of nearest neighbor sequence on the stability of base pair mismatches in long DNA: determination by temperature-gradient gel electrophoresis(Georgia Institute of Technology, 1993-11-11) Ke, Song-Hua ; Wartell, Roger M. ; Georgia Institute of Technology. School of BiologyTemperature-gradient gel electrophoresis (TGGE) was employed to determine the thermal stabilities of 48 DNA fragments that differ by single base pair mismatches. The approach provides a rapid way for studying how specific base mismatches effect the stability of a long DNA fragment. Homologous 373 bp DNA fragments differing by single base pair substitutions in their first melting domain were employed. Heteroduplexes were formed by melting and reannealing pairs of DNAs, one of which was ³²P-labeled on its 5'-end. Product DNAs were separated based on their thermal stability by parallel and perpendicular temperature-gradient gel electrophoresis. The order of stability was determined for all common base pairs and mismatched bases in four different nearest neighbor environments; d(GXT) d(AYC), d(GXG) d(CYC), d(CXA) d(TYG), and d(TXT) * d(AYA) with X,Y = A,T,C, or G. DNA fragments containing a single mismatch were destabilized by 1 to 5°C with respect to homologous DNAs with complete Watson - Crick base pairing. Both the bases at the mismatch site and neighboring stacking interactions influence the destabilization caused by a mismatch. G - T, G - G and G - A mismatches were always among the most stable mismatches for all nearest neighbor environments examined. Purine- purine mismatches were generally more stable than pyrimidine- pyrimidine mispairs. Our results are in very good agreement with data where available from solution studies of short DNA oligomers.
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ItemInteraction of RNA polymerase with DNA sites(Georgia Institute of Technology, 1980) Wartell, Roger M. ; Georgia Institute of Technology. Office of Sponsored Programs ; Georgia Institute of Technology. School of Physics
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ItemPredicted structure and phyletic distribution of the RNA-binding protein Hfq(Georgia Institute of Technology, 2002) Sun, Xueguang ; Zhulin, Igor ; Wartell, Roger M. ; Georgia Institute of Technology. School of BiologyHfq, 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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ItemThe 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. ; Georgia Institute of Technology. School of Biology ; Georgia Institute of Technology. School of PhysicsThe 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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ItemConformations of ligand-DNA complexes and DNA oligomers(Georgia Institute of Technology, 1979) Wartell, Roger M. ; Georgia Institute of Technology. Office of Sponsored Programs ; Georgia Institute of Technology. School of Physics ; Georgia Institute of Technology. Office of Sponsored Programs
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ItemKinetic study of the binding between the regulatory repressor protein and DNA operator region of the lactose genes(Georgia Institute of Technology, 1974) Wartell, Roger M. ; Georgia Institute of Technology. Office of Sponsored Programs ; Georgia Institute of Technology. School of Physics
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ItemSmall instrumentation grant(Georgia Institute of Technology, 1993-08) Wartell, Roger M. ; Georgia Institute of Technology. Office of Sponsored Programs ; Georgia Institute of Technology. School of Biology
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ItemInteraction of RNA polymerase with DNA sites(Georgia Institute of Technology, 1983) Wartell, Roger M. ; Georgia Institute of Technology. Office of Sponsored Programs ; Georgia Institute of Technology. School of Physics