Stabilization of Z DNA in Vivo by Localized Supercoiling

Rahmouni, A. Rachid; Wells, R D

doi:10.1126/science.2678475

Cited by 230 publications

(154 citation statements)

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“…Negative supercoiling is a very powerful factor that enables segments of the DNA double helix to acquire non-B DNA conformations (6,28,29,75). The amount and/or the stabilities of these structures increase with increasing levels of negative supercoiling (Fig.…”

Section: Discussionmentioning

confidence: 99%

Increased Negative Superhelical Density in Vivo Enhances the Genetic Instability of Triplet Repeat Sequences

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Bacolla

Wells

2005

Journal of Biological Chemistry

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The influence of negative superhelical density on the genetic instabilities of long GAA⅐TTC, CGG⅐CCG, and CTG⅐CAG repeat sequences was studied in vivo in topologically constrained plasmids in Escherichia coli. These repeat tracts are involved in the etiologies of Friedreich ataxia, fragile X syndrome, and myotonic dystrophy type 1, respectively. The capacity of these DNA tracts to undergo deletions-expansions was explored with three genetic-biochemical approaches including first, the utilization of topoisomerase I and/or DNA gyrase mutants, second, the specific inhibition of DNA gyrase by novobiocin, and third, the genetic removal of the HU protein, thus lowering the negative supercoil density (؊). All three strategies revealed that higher ؊ in vivo enhanced the formation of deleted repeat sequences. The effects were most pronounced for the Friedreich ataxia and the fragile X triplet repeat sequences. Higher levels of ؊ stabilize non-B DNA conformations (i.e. triplexes, sticky DNA, flexible and writhed DNA, slipped structures) at appropriate repeat tracts; also, numerous prior genetic instability investigations invoke a role for these structures in promoting the slippage of the DNA complementary strands. Thus, we propose that the in vivo modulation of the DNA structure, localized to the repeat tracts, is responsible for these behaviors. Presuming that these interrelationships are also found in humans, dynamic alterations in the chromosomal nuclear matrix may modulate the ؊ of certain DNA regions and, thus, stabilize/destabilize certain non-B conformations which regulate the genetic expansions-deletions responsible for the diseases.Genetic instability of microsatellite sequences have been widely observed throughout genomes of all organisms studied (1-3). In the majority of cases this phenomenon occurs without phenotypical consequences, but in some circumstances instability (mostly expansions of the repeat tracts) results in the development of disease (1, 4, 5). Expansions of tri-, tetra-and pentanucleotide microsatellites are related to the etiology of more than 20 neurological diseases including myotonic dystrophy types I and II, fragile X syndrome, Friedreich ataxia, and spinocerebellar ataxias (1,4,5).Studies on the mechanisms of trinucleotide repeat sequence (TRS) 2 expansions have revealed that replication, recombination, and repair, probably acting in concert, are responsible for the instabilities of the repetitive tracts (1, 4 -7). Several cis elements as well as trans-acting factors influencing genetic instabilities were discovered (8 -11). The sequences of the repeats, their length, and the presence of polymorphisms (interruptions) in the repeating tract are among the most important determinants of the extent of their instability (10,(12)(13)(14)(15). In addition, the orientation of the repeats relative to the origin of replication, their distance from the origin, transcription through the repeats, and DNA methylation status are factors (9, 16 -21).Expansions of the repeats in affected individuals occur ...

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Section: Discussionmentioning

confidence: 99%

Increased Negative Superhelical Density in Vivo Enhances the Genetic Instability of Triplet Repeat Sequences

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Bacolla

Wells

2005

Journal of Biological Chemistry

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“…The technique is very easy and fast. This finding opens the possibility of tailoring experiments in which one can directly monitor local modulations of the supercoiling depending upon local sequences, position of promoters, or vectorial tracking of macromolecular complexes along DNA (2,(22)(23)(24)(25)(26)(27). This technique could also be particularly useful in following conversion from negative to positive supercoiled states which were reported to characterize highly transcribed genes (26).…”

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Chirality of DNA supercoiling assigned by scanning force microscopy.

Samorı̀

Siligardi

Quagliariello

et al. 1993

Proc. Natl. Acad. Sci. U.S.A.

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Reproducible images of pBR322 plasmid molecules have been recorded by scanning force microscopy under 1-propanol. Most of the plasmids were found in a coiled state. The supercoiled molecules of our samples look like branched or unbranched interwound superhelixes. This is consistent with available electron microscopy data on circular DNA molecules. By applying a stratigraphic analysis which takes advantage of the height information contained in the scanning force microscopy images, it is possible to assign the chirality of the local supercoiling of the individual molecules.

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“…Negative supercoiling induces the Z-DNA conformation even in physiological salt conditions because formation of Z-DNA significantly relieves torsional stress. Z-DNA has also been shown to exist stably in vivo in the presence of physiological negative supercoiling (9,10).…”

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Minute negative superhelicity is sufficient to induce the B-Z transition in the presence of low tension

Lee

Kim

Hong

2010

Proc. Natl. Acad. Sci. U.S.A.

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Left-handed Z-DNA has fascinated biological scientists for decades by its extraordinary structure and potential involvement in biological phenomena. Despite its instability relative to B-DNA, Z-DNA is stabilized in vivo by negative supercoiling. A detailed understanding of Z-DNA formation is, however, still lacking. In this study, we have examined the B-Z transition in a short guanine/cytosine (GC) repeat in the presence of controlled tension and superhelicity via a hybrid technique of single-molecule FRET and magnetic tweezers. The hybrid scheme enabled us to identify the states of the specific GC region under mechanical control and trace conformational changes synchronously at local and global scales. Intriguingly, minute negative superhelicity can facilitate the B-Z transition at low tension, indicating that tension, as well as torsion, plays a pivotal role in the transition. Dynamic interconversions between the states at elevated temperatures yielded thermodynamic and kinetic constants of the transition. Our single-molecule studies shed light on the understanding of Z-DNA formation by highlighting the highly cooperative and dynamic nature of the B-Z transition.NA is capable of adopting various conformations in addition to the conventional right-handed B-DNA double helix (1, 2). One of the most dramatic examples is Z-DNA, which is a lefthanded helical form with a zigzag backbone (3, 4). Since its discovery, Z-DNA has drawn considerable attention from a broad range of research areas, including physical biochemistry, structural biology, and molecular biology, because of its intriguing and unusual structural features (3). The bases in Z-DNA alternate in syn-and anti-conformations while all the bases in B-DNA adopt the anti-conformation. Because the syn conformation is more stable for purines (Pu) than for pyrimidines (Py), alternating Pu and Py sequences readily adopt the Z-DNA conformation. Another striking feature of Z-DNA is the overturning of base pairs, posing a steric dilemma known as the chain sense paradox (3, 5).Although Z-DNA is less stable than B-DNA at physiological ionic conditions, Z-DNA exists stably under certain conditions such as high ionic strength or negative supercoiling (4, 6-8).In the presence of a high-salt solution, the electrostatic repulsion between the phosphate backbones, which are closer in Z-DNA than in B-DNA, is reduced, stabilizing the Z-DNA conformation. Negative supercoiling induces the Z-DNA conformation even in physiological salt conditions because formation of Z-DNA significantly relieves torsional stress. Z-DNA has also been shown to exist stably in vivo in the presence of physiological negative supercoiling (9, 10).Although there were first doubts as to whether Z-DNA plays any biological role, considerable experimental evidence for biological functions of Z-DNA has accumulated over the past two decades (11). In addition to the discovery of antibodies and proteins that bind selectively to Z-DNA (12, 13), Z-DNA formation has been strongly correlated with transcriptional acti...

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Stabilization of Z DNA in Vivo by Localized Supercoiling

Cited by 230 publications

References 50 publications

Increased Negative Superhelical Density in Vivo Enhances the Genetic Instability of Triplet Repeat Sequences

Increased Negative Superhelical Density in Vivo Enhances the Genetic Instability of Triplet Repeat Sequences

Chirality of DNA supercoiling assigned by scanning force microscopy.

Minute negative superhelicity is sufficient to induce the B-Z transition in the presence of low tension

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