DNA bending at adenine · thymine tracts

Koo, Hyeon Sook; Wu, Hen Ming; Crothers, Donald M.

doi:10.1038/320501a0

Cited by 1,080 publications

(956 citation statements)

References 29 publications

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“…One diagnostic feature of bent DNA is its slower mobility at a low temperature during polyacrylamide gel electrophoresis (Diekmann, 1987;Koo et al, 1986). The electrophoretic mobility of TJ1 changes with the temperature of the electrophoresis gel (Figure 3b), a clear indication that TJ1 has bending characteristics characteristic of SARs (Homberger, 1989), which con®rms that TJ1 is an SAR.…”

Section: Resultsmentioning

confidence: 91%

Presence of an SAR‐like sequence in junction regions between an introduced transgene and genomic DNA of cultured tobacco cells: its effect on transformation frequency

et al. 2001

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SummaryA 12.5-kb DNA fragment with junction regions between the transgene and genomic DNA was cloned from a transgenic tobacco cell line obtained by microprojectile bombardment of plasmid pCaMVNEO. Nucleotide sequence analysis of the fragment (DDBJ accession no. D84238 ) showed that it carried a 7.7-kb core sequence (concatemer of a complete pCaMVNEO and a partial pCaMVNEO) and two identical 1.3-kb junction sequences that¯anked both the 5¢ and 3¢ ends of the core sequence and had inverted orientations. These sequences had topoisomerase II (Topo II) cleavage sites and adenine and thimine-rich sequences known to be speci®c to nuclear scaffold-attachment regions (SARs). An in vitro binding assay showed that a 507-bp fragment (designated TJ1 ) from the 1.3-kb sequence had the ability to bind to nuclear scaffold preparations of cultured tobacco cells, con®rmation that the 1.3-kb sequence is an SAR. Insertion of TJ1 at the 5¢ and 3¢ sides of the expression cassette for the npt II gene increased transformant yields 5-to 10-fold and the NPT II enzyme activity per copy of the gene 5-fold. TJ1 enhances the integration or expression of the transgene, or both. Clearly, TJ1 is very useful for producing transgenic plants. This is the ®rst report on an SAR-like sequence that is located in the transgene locus and enhances transformation ef®ciency in eukaryotic cells. The possible role of TJ1-SAR in the molecular evolution of plant genome is discussed.

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Section: Resultsmentioning

confidence: 91%

Presence of an SAR‐like sequence in junction regions between an introduced transgene and genomic DNA of cultured tobacco cells: its effect on transformation frequency

et al. 2001

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“…Because many of the recent users of 3DNA have expressed an interest in illustrations such as those described in our earlier work 8 (reproduced here in Figure 1), we first present the detailed steps needed to generate block images of each of the three types of rigidbody parameters, using propeller as a representative base-pair parameter, rise as a representative local base-pair-step parameter, and inclination as a representative local helical parameter (Fig. 2). (B) Determination of DNA curvature associated with different roll distributions -DNA is not a monotonous, regular straight helix, but rather deforms in response to external stresses in a sequence-dependent manner 9,[52][53][54][55][56] . For example, the catabolic activator protein (CAP) introduces two sharp kinks at pyrimidine-purine (YR) steps in its binding site, bending the DNA at these steps into the major groove via large positive roll 57,58 .…”

Section: Sample Applications Of 3dnamentioning

confidence: 99%

3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures

2008

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We present a set of protocols showing how to use the 3DNA suite of programs to analyze, rebuild, and visualize three-dimensional nucleic-acid structures. The software determines a wide range of conformational parameters, including the identities and rigid-body parameters of interacting bases and base-pair steps, the nucleotides comprising helical fragments, the area of overlap of stacked bases, etc. The reconstruction of three-dimensional structure takes advantage of rigorously defined rigid-body parameters, producing rectangular block representations of the nucleic-acid bases and base pairs and all-atom models with approximate sugar-phosphate backbones. The visualization components create vector-based drawings and scenes that can be rendered as raster-graphics images, allowing for easy generation of publication-quality figures. The utility programs use geometric variables to control the view and scale of an object, for comparison of related structures. The commands run in seconds even for large structures. The software and related information are available at http://3dna.rutgers.edu/.

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“…1) are located immediately upstream of the Ϫ35 and Ϫ10 hexamers. Koo et al (15) determined that homopolymeric AT tracts at least 4 bp long positioned in phase with the helical screw contribute to overall DNA bending. As shown in Fig.…”

Section: Figmentioning

confidence: 99%

Analysis of Genetic Elements ControllingStaphylococcus aureus lrgABExpression: Potential Role of DNA Topology in SarA Regulation

2000

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Penicillin-induced killing and murein hydrolase activity in Staphylococcus aureus are dependent on a variety of regulatory elements, including the LytSR two-component regulatory system and the virulence factor regulators Agr and Sar. The LytSR effects on these processes can be explained, in part, by the recent finding that a LytSR-regulated operon, designated lrgAB, affects murein hydrolase activity and penicillin tolerance. To examine the regulation of lrgAB expression in greater detail, we performed Northern blot and promoter fusion analyses. Both methods revealed that Agr and Sar, like LytSR, positively regulate lrgAB expression. A mutation in the agr locus reduced lrgAB expression approximately sixfold, while the sar mutation reduced lrgAB expression to undetectable levels. cis-acting regulatory elements involved in lrgAB expression were identified by fusing various fragments of the lrgAB promoter region to the xylE reporter gene and integrating these constructs into the chromosome. Catechol 2,3-dioxygenase assays identified DNA sequences, including an inverted repeat and intrinsic bend sites, that contribute to maximal lrgAB expression. Confirmation of the importance of the inverted repeat was achieved by demonstrating that multiple copies of the inverted repeat reduced lrgAB promoter activity, presumably by titrating out a positive regulatory factor. The results of this study demonstrate that lrgAB expression responds to a variety of positive regulatory factors and suggest that specific DNA topology requirements are important for optimal expression.Peptidoglycan or murein hydrolases are a family of enzymes that catalyze the cleavage of specific structural components of the bacterial cell wall. These enzymes are involved in several important physiological processes, including peptidoglycan turnover and recycling, cell wall expansion during bacterial growth, septation, and daughter cell separation (13, 32). Due to the potential of these enzymes to compromise cell wall integrity, leading to cell lysis (autolysis), murein hydrolase activity must be carefully regulated. This regulation includes transcriptional control, blocked access to the specific substrate, inhibition by choline or teichoic acid, and substrate modification (13, 32).The Staphylococcus aureus lytS and lytR genes, whose products are members of the two-component regulator family of proteins, are involved in the control of murein hydrolase activity (3). A lytS mutant phenotypically displays altered murein hydrolase activity and an increased rate of penicillin-and Triton X-100-induced lysis (3, 11). Immediately downstream of lytS and lytR are two genes, lrgA and lrgB, whose transcription is dependent upon lytS and lytR. LrgA and LrgB show no sequence similarity to known murein hydrolases. Instead, LrgA has structural characteristics in common with the bacteriophage-encoded holin proteins involved in murein hydrolase export (4, 11). Recent data generated in our laboratory indicate that the LrgA and LrgB gene products inhibit extracellular murein hy...

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DNA bending at adenine · thymine tracts

Cited by 1,080 publications

References 29 publications

Presence of an SAR‐like sequence in junction regions between an introduced transgene and genomic DNA of cultured tobacco cells: its effect on transformation frequency

Presence of an SAR‐like sequence in junction regions between an introduced transgene and genomic DNA of cultured tobacco cells: its effect on transformation frequency

3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures

Analysis of Genetic Elements ControllingStaphylococcus aureus lrgABExpression: Potential Role of DNA Topology in SarA Regulation

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