Curved helix segments can uniquely orient the topology of supertwisted DNA

Laundon, Caroline H.; Griffith, Jack D.

doi:10.1016/0092-8674(88)90467-9

Cited by 151 publications

(99 citation statements)

References 8 publications

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“…As seen in Figure 2, the X-type cruciforms tend to be localized at the loops of the plectonemic superhelix. As shown earlier, intrinsically bent DNA regions prefer an apical localization in supercoiled DNA (Laundon & Grif®th, 1988). Our data suggest that cruciforms, like bent DNA sequences, are elements that can dictate a spatial geometry to a DNA superhelix.…”

Section: The Dynamics Of Supercoilstabilized Cruciformsmentioning

confidence: 51%

Structure and dynamics of supercoil-stabilized DNA cruciforms

Shlyakhtenko

Potaman

Sinden

et al. 1998

Journal of Molecular Biology

144

104

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Understanding DNA function requires knowledge of the structure of local, sequence-dependent conformations that can be dramatically different from the B-form helix. One alternative DNA conformation is the cruciform, which has been shown to have a critical role in the initiation of DNA replication and the regulation of transcription in certain systems. In addition, cruciforms provide a model system for structural studies of Holliday junctions, intermediates in homologous DNA recombination. Cruciforms are not thermodynamically stable in linear DNA due to branch point migration, which makes their study using many biophysical techniques problematic. Atomic Force Microscopy (AFM) was applied to visualize cruciforms in negatively supercoiled plasmid DNA. Cruciforms are seen as clear-cut extrusions on the DNA ®lament with the lengths of the arms consistent with the size of the hairpins expected from a 106 bp inverted repeat. The cruciform exists in two different conformations, an extended one with the angle of ca. 180 between the hairpin arms and a compact, X-type conformation, with acute angles between the hairpin arms and the main DNA strands. The ratio of molecules with the different conformations of cruciforms depends on ionic conditions. In the presence of high salt or Mg cations, a compact, X-type conformation is highly preferable. Remarkably, the X-conformation was highly mobile allowing the cruciform arms to adopt a parallel orientation. The structure observed is consistent with a model of the Holliday junction with a parallel orientation of the exchanging strands.

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Section: The Dynamics Of Supercoilstabilized Cruciformsmentioning

confidence: 51%

Structure and dynamics of supercoil-stabilized DNA cruciforms

Shlyakhtenko

Potaman

Sinden

et al. 1998

Journal of Molecular Biology

144

104

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“…An example illustrating the strong effect of a bound protein on the concentration of sites in a supercoiled DNA is one proposed for the binding of E. coli RNA polymerase to the sharply bent ends of loops in a supercoiled DNA (Heggeler-Bordellier et al 1992): the concentration of DNA sites in the neighbourhood of the tip of a supercoiled loop is likely to be much lower than that around a DNA site when the DNA is allowed to access all its spatial configurations. The presence of segments with stable bends may similarly reduce greatly the number of configurational states of a supercoiled DNA (Laundon & Griffith 1988).…”

Section: Discussionmentioning

confidence: 99%

The probabilities of supercoil removal and decatenation by yeast DNA topoisomerase II

Roca

Wang

1996

Genes to Cells

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Background: In yeast a single type II DNA topoisomerase is involved in both the removal of DNA supercoils and the unlinking of intertwined pairs of newly replicated chromosomes or plasmids; in bacteria, two type II enzymes, DNA gyrase and DNA topoisomerase IV, function separately in the passage of DNA segments in cis and in trans. To deduce the molecular characteristics of these enzyme-mediated reactions, the efficiencies of supercoil removal and decatenation by the yeast enzyme upon the addition of a nonhydrolysable ATP analogue were determined.

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“…s 2 is favored instead, except for pBR nucleosomes in Mg 2þ -minus buffer ( Table 2). The reason lies in the contributions to G n (i) in equation (11), which were again not taken into account in the theory. In addition to the abovementioned electrostatic repulsion which favors the sO state, two more contributions can be identified.…”

Section: Loop End Conditions and Nucleosome Ability For Positive Crosmentioning

confidence: 99%