Direct observation of positive supercoils introduced by reverse gyrase through atomic force microscopy

Li, Dawei; Lv, Bei; Wang, Qiang; Liu, Yun; Zhuge, Qiang

doi:10.1016/j.bmcl.2017.07.044

Cited by 7 publications

(9 citation statements)

References 21 publications

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“…Previous experiments showed that, whereas −SC molecules (minicircles as well as plasmids) expose single strand regions even at room temperature, +SC molecules do not 27 , 28 . We set up a similar experiment with our molecule populations: when incubated with the ssDNA endo-exonuclease Bal31 (which is able to cut single strand DNA in denatured bubbles), −SC DNA was degraded completely after 1 hour at 30 °C (Fig.…”

Section: Resultsmentioning

confidence: 97%

“…Among the time course products, four plasmid populations with defined mean σ (−0.04; +0.01; +0.03; ≥ +0.04) were selected, purified and analysed by AFM in air. Since the only images available so far for positive plasmids were obtained on silanized mica 28 , it is not known whether these molecules are affected by the deposition procedure, prompting us to explore different deposition methods. In order to increase the mica affinity for negatively charged molecules such as DNA, different strategies can be followed.…”

Section: Resultsmentioning

confidence: 99%

“…Although many structural studies have been reported on −SC plasmids, little information is available for +SC plasmids. Only recently two papers reported the first observations at single molecule level of +SC DNA molecules, giving important impulse to the field 27 , 28 . However, further analyses are required to extend these results and fill important gaps.…”

Section: Introductionmentioning

confidence: 99%

“…analyzed by AFM +SC plasmids and measured different lengths between positive and negative topoisomers, whose ΔLk was however undefined. These measurements rely on few molecules only and their conclusions might be of limited relevance because of the reduced ensemble investigated 28 .…”

Section: Introductionmentioning

confidence: 99%

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Structure and Properties of DNA Molecules Over The Full Range of Biologically Relevant Supercoiling States

Bettotti¹,

Visone²,

Lunelli³

et al. 2018

Sci Rep

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Topology affects physical and biological properties of DNA and impacts fundamental cellular processes, such as gene expression, genome replication, chromosome structure and segregation. In all organisms DNA topology is carefully modulated and the supercoiling degree of defined genome regions may change according to physiological and environmental conditions. Elucidation of structural properties of DNA molecules with different topology may thus help to better understand genome functions. Whereas a number of structural studies have been published on highly negatively supercoiled DNA molecules, only preliminary observations of highly positively supercoiled are available, and a description of DNA structural properties over the full range of supercoiling degree is lacking. Atomic Force Microscopy (AFM) is a powerful tool to study DNA structure at single molecule level. We here report a comprehensive analysis by AFM of DNA plasmid molecules with defined supercoiling degree, covering the full spectrum of biologically relevant topologies, under different observation conditions. Our data, supported by statistical and biochemical analyses, revealed striking differences in the behavior of positive and negative plasmid molecules.

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Section: Resultsmentioning

confidence: 97%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Structure and Properties of DNA Molecules Over The Full Range of Biologically Relevant Supercoiling States

Bettotti¹,

Visone²,

Lunelli³

et al. 2018

Sci Rep

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show abstract

“…It has been reported that disintegration of non-B structures and reformation of duplex can increase the the contour lengths of DNA circle [ 38 , 39 ]. The structural parameters (length and height) of topoisomers (DNA C1, DNA 1, and DNA 3) were measured in order to fruther confirm the G-quadruplexes in DNA 1 has been thanformed into double helix in DNA 3.…”

Section: Resultsmentioning

confidence: 99%

Transformation of a Thermostable G-Quadruplex Structure into DNA Duplex Driven by Reverse Gyrase

Wang

Liu

et al. 2017

Molecules

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Reverse gyrase is a topoisomerase that can introduce positive supercoils to its substrate DNA. It is demonstrated in our studies that a highly thermal stable G-quadruplex structure in a mini-plasmid DNA was transformed into its duplex conformation after a treatment with reverse gyrase. The structural difference of the topoisomers were verified and analyzed by gel electrophoresis, atomic force microscopy examination, and endonuclease digestion assays. All evidence suggested that the overwinding structure of positive supercoil could provide a driven force to disintegrate G-quadruplex and reform duplex. The results of our studies could suggest that hyperthermophiles might use reverse gyrase to manipulate the disintegration of non-B DNA structures and safekeep their genomic information.

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Small DNA circles as bacterial topoisomerase I inhibitors

Wang

Zhou

et al. 2019

RSC Adv.

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Direct observation of positive supercoils introduced by reverse gyrase through atomic force microscopy

Cited by 7 publications

References 21 publications

Structure and Properties of DNA Molecules Over The Full Range of Biologically Relevant Supercoiling States

Structure and Properties of DNA Molecules Over The Full Range of Biologically Relevant Supercoiling States

Transformation of a Thermostable G-Quadruplex Structure into DNA Duplex Driven by Reverse Gyrase

Small DNA circles as bacterial topoisomerase I inhibitors

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