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Chapter 7 : Topological Behavior of Plasmid DNA

Authors: N. Patrick Higgins1, Alexander V. Vologodskii2
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Affiliations: 1: Department of Biochemistry and Molecular Genetics, University of Alabama at Birmingham, Birmingham, AL 35294; 2: Department of Chemistry, New York University, New York, NY 10003
Content Type: Monograph
Publication Year: 2015

Category: Clinical Microbiology

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Abstract:

DNA topology is a critical factor in essentially all chromosomal processes, including DNA replication, RNA transcription, homologous recombination, site-specific recombination, DNA repair, and integration of the abundant and mechanistically distinct forms of transposable elements. Plasmids can be invaluable tools to define the dynamic mechanisms of proteins that shape DNA, organize chromosome structure, and channel chromosome movement inside living cells. The advantages of plasmids include their ease of isolation and the ability to quantitatively measure DNA knots, DNA catenation, hemi-catenation between two DNA molecules, and positive or negative supercoils in purified DNA populations. Under ideal conditions, and results can be compared to define the complex mechanism of enzymes that move along and change DNA chemistry in living cells. Many techniques that can be easily done with plasmids are not feasible for the massive chromosome that carries most of the genetic information in or . Whereas a large fraction of contemporary chromosomal “philosophy” is based on extrapolation of results from small plasmids such as pBR322 to the 4.6-Mb bacterial chromosome, the comparison is not always valid. One aim of this article is to explain how results derived from small plasmids can be misleading for understanding and interpreting the DNA structure of the large bacterial chromosome.

Citation: Higgins N, Vologodskii A. 2015. Topological Behavior of Plasmid DNA, p 105-131. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0036-2014
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Topological Behavior of Plasmid DNA
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Citation: Higgins N, Vologodskii A. 2015. Topological Behavior of Plasmid DNA, p 105-131. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0036-2014
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Figure 1
The simplest knots (a) and catenanes (b). DNA molecules are capable of adopting these and many more complex topological states.
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Figure 1

The simplest knots (a) and catenanes (b). DNA molecules are capable of adopting these and many more complex topological states.

Citation: Higgins N, Vologodskii A. 2015. Topological Behavior of Plasmid DNA, p 105-131. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0036-2014
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Figure 2
Diagram of closed circular DNA. The linking number, of the complementary strands is 18.
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Figure 2

Diagram of closed circular DNA. The linking number, of the complementary strands is 18.

Citation: Higgins N, Vologodskii A. 2015. Topological Behavior of Plasmid DNA, p 105-131. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0036-2014
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Figure 3
Typical simulated conformations of supercoiled DNA 4.4 kb in length. The conformations correspond to a DNA superhelix density of (a) –0.030 and (b) –0.060.
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Figure 3

Typical simulated conformations of supercoiled DNA 4.4 kb in length. The conformations correspond to a DNA superhelix density of (a) –0.030 and (b) –0.060.

Citation: Higgins N, Vologodskii A. 2015. Topological Behavior of Plasmid DNA, p 105-131. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0036-2014
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Figure 4
Electrophoretic separation of topoisomers of pUC19 DNA. The mixture of topoisomers covering the range of Δ from 0 to –8 was electrophoresed from a single well in 1% agarose that was run from top to bottom. The topoisomer with Δ = 0 has the lowest mobility: it moves slightly slower than the open circular form (OC). The value of (–Δ) for each topoisomer is shown.
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Figure 4

Electrophoretic separation of topoisomers of pUC19 DNA. The mixture of topoisomers covering the range of Δ from 0 to –8 was electrophoresed from a single well in 1% agarose that was run from top to bottom. The topoisomer with Δ = 0 has the lowest mobility: it moves slightly slower than the open circular form (OC). The value of (–Δ) for each topoisomer is shown.

Citation: Higgins N, Vologodskii A. 2015. Topological Behavior of Plasmid DNA, p 105-131. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0036-2014
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Figure 5
Separation of pUC19 DNA topoisomers by two-dimensional gel electrophoresis. Topoisomers 1 to 4 are positively supercoiled; the rest have negative supercoiling. After electrophoresis in the first direction, from top to bottom, the gel was saturated with ligand intercalating into the double helix. Upon electrophoresis from left to right in the second direction, the 2nd and 13th topoisomers turned out to migrate near the relaxed position in the second dimension. The spot in the top-left corner corresponds to the open circular form (OC); the spot near the middle of the gel corresponds to linear DNA (L).
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Figure 5

Separation of pUC19 DNA topoisomers by two-dimensional gel electrophoresis. Topoisomers 1 to 4 are positively supercoiled; the rest have negative supercoiling. After electrophoresis in the first direction, from top to bottom, the gel was saturated with ligand intercalating into the double helix. Upon electrophoresis from left to right in the second direction, the 2nd and 13th topoisomers turned out to migrate near the relaxed position in the second dimension. The spot in the top-left corner corresponds to the open circular form (OC); the spot near the middle of the gel corresponds to linear DNA (L).

Citation: Higgins N, Vologodskii A. 2015. Topological Behavior of Plasmid DNA, p 105-131. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0036-2014
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Figure 6
High-resolution gel electrophoresis of knotted forms of plasmid DNA that was run from left to right. Knot types are described in Fig. 1 (see reference ). Reproduced from the with permission from Elsevier.
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Figure 6

High-resolution gel electrophoresis of knotted forms of plasmid DNA that was run from left to right. Knot types are described in Fig. 1 (see reference ). Reproduced from the with permission from Elsevier.

Citation: Higgins N, Vologodskii A. 2015. Topological Behavior of Plasmid DNA, p 105-131. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0036-2014
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Figure 7
Alternative DNA structures that are stabilized by negative supercoiling.
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Figure 7

Alternative DNA structures that are stabilized by negative supercoiling.

Citation: Higgins N, Vologodskii A. 2015. Topological Behavior of Plasmid DNA, p 105-131. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0036-2014
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Figure 8
Two-dimensional gel showing the transition from B- to left-handed Z-DNA in plasmid DNA. This research was originally published in Kang DS, Wells RD. 1985. B-Z DNA junctions contain few, if any, nonpaired bases at physiological superhelical densities. 7783–7790. © the American Society for Biochemistry and Molecular Biology.
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Figure 8

Two-dimensional gel showing the transition from B- to left-handed Z-DNA in plasmid DNA. This research was originally published in Kang DS, Wells RD. 1985. B-Z DNA junctions contain few, if any, nonpaired bases at physiological superhelical densities. 7783–7790. © the American Society for Biochemistry and Molecular Biology.

Citation: Higgins N, Vologodskii A. 2015. Topological Behavior of Plasmid DNA, p 105-131. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0036-2014
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Figure 9
Conversion of interwound negative supercoils into catenanes linked by site-specific recombination. EM reprinted from Spergler SJ, Stasiak A, Cozzarelli NR. 1985. The stereostructure of knots and catenanes produced by phage lambda integrative recombination: implications for mechanism and DNA structure. 325–334 with permission from Elsevier.
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Figure 9

Conversion of interwound negative supercoils into catenanes linked by site-specific recombination. EM reprinted from Spergler SJ, Stasiak A, Cozzarelli NR. 1985. The stereostructure of knots and catenanes produced by phage lambda integrative recombination: implications for mechanism and DNA structure. 325–334 with permission from Elsevier.

Citation: Higgins N, Vologodskii A. 2015. Topological Behavior of Plasmid DNA, p 105-131. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0036-2014
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Figure 10
Alternative RNA-DNA structures that contribute to constrained supercoiling in a plasmid containing a fragment of the chicken IgA immunoglobulin switch region during transcription. The R-loop structure shown in (A) results in a displaced strand of DNA that constrains a Δ of about +1 for every 10 bp of RNA/DNA hybrid. (B) shows the structure of an intermolecular triplex in which Hoogsteen base pairing occurs in the major groove of the DNA strand (see reference ).
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Figure 10

Alternative RNA-DNA structures that contribute to constrained supercoiling in a plasmid containing a fragment of the chicken IgA immunoglobulin switch region during transcription. The R-loop structure shown in (A) results in a displaced strand of DNA that constrains a Δ of about +1 for every 10 bp of RNA/DNA hybrid. (B) shows the structure of an intermolecular triplex in which Hoogsteen base pairing occurs in the major groove of the DNA strand (see reference ).

Citation: Higgins N, Vologodskii A. 2015. Topological Behavior of Plasmid DNA, p 105-131. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0036-2014
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Figure 11
Proposed mechanism for stable RNA-DNA hybrids that can stimulate repeat instability. Transcription of DNA regions containing CG-rich trinucleotide repeats (red) favors formation of stable RNA-DNA hybrids. The displaced nontemplate DNA strand can adopt non-B DNA structures, such as CTG or CAG hairpins. The unpaired regions of the nontemplate strand are reactive to bisulfite modification. Reprinted from reference with permission from the National Academy of Sciences.
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Figure 11

Proposed mechanism for stable RNA-DNA hybrids that can stimulate repeat instability. Transcription of DNA regions containing CG-rich trinucleotide repeats (red) favors formation of stable RNA-DNA hybrids. The displaced nontemplate DNA strand can adopt non-B DNA structures, such as CTG or CAG hairpins. The unpaired regions of the nontemplate strand are reactive to bisulfite modification. Reprinted from reference with permission from the National Academy of Sciences.

Citation: Higgins N, Vologodskii A. 2015. Topological Behavior of Plasmid DNA, p 105-131. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0036-2014
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Figure 12
Replication intermediates identified in plasmid replication systems. (A) Replication initiated at a unique position leads to dual forms that move toward the terminus of replication. (B) Introduction of positive supercoils leads to replication fork reversal and formation of a four-way junction. (C) Negative supercoiling, which is generated by gyrase ahead of the fork, can be converted into precatenanes (D), which become catenanes (E) upon completion of DNA synthesis. (F, G) Topoisomerase activity in the replicated region can lead to complex knots.
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Figure 12

Replication intermediates identified in plasmid replication systems. (A) Replication initiated at a unique position leads to dual forms that move toward the terminus of replication. (B) Introduction of positive supercoils leads to replication fork reversal and formation of a four-way junction. (C) Negative supercoiling, which is generated by gyrase ahead of the fork, can be converted into precatenanes (D), which become catenanes (E) upon completion of DNA synthesis. (F, G) Topoisomerase activity in the replicated region can lead to complex knots.

Citation: Higgins N, Vologodskii A. 2015. Topological Behavior of Plasmid DNA, p 105-131. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0036-2014
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Figure 13
Model of replication repair. Strand displacement and branch migration create an alternative replication template allowing replication to bypass a lesion (X). Reproduced from reference with permission from Elsevier.
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Figure 13

Model of replication repair. Strand displacement and branch migration create an alternative replication template allowing replication to bypass a lesion (X). Reproduced from reference with permission from Elsevier.

Citation: Higgins N, Vologodskii A. 2015. Topological Behavior of Plasmid DNA, p 105-131. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0036-2014
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Figure 14
Replication fork reversal (see Fig. 12 ). Reprinted from reference with permission from the American Association for the Advancement of Science.
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Figure 14

Replication fork reversal (see Fig. 12 ). Reprinted from reference with permission from the American Association for the Advancement of Science.

Citation: Higgins N, Vologodskii A. 2015. Topological Behavior of Plasmid DNA, p 105-131. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0036-2014
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Figure 15
Resolution of catenane (CATS) and precatenane links (RI) in plasmid DNA (see Fig. 12 ). Reprinted from reference with permission from Elsevier.
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Figure 15

Resolution of catenane (CATS) and precatenane links (RI) in plasmid DNA (see Fig. 12 ). Reprinted from reference with permission from Elsevier.

Citation: Higgins N, Vologodskii A. 2015. Topological Behavior of Plasmid DNA, p 105-131. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0036-2014
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Figure 16
Schematic models for generating hemicatenanes during DNA replication. Three pathways to yield hemicatenane structures are shown. (Left) Lagging strand synthesis encounters a damage site, and the pairing of the lagging strand with the complementary leading strand can produce a pseudo-double Holliday structure. Dissolution of the pseudo-double Holliday structure leads to hemicatenanes and allows replication to bypass the damage site. (Center) Convergence of two replication forks at the final stage of replication can lead to either a single-strand catenane or hemicatenane conjoining two replicated duplexes. Both single-strand catenanes and hemicatenanes can be resolved by a type IA topoisomerase, allowing the segregation of the daughter chromosomes. (Right). Convergent branch migration of a double Holliday junction can generate a hemicatenane. Reproduced from reference with permission from the National Academy of Sciences.
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Figure 16

Schematic models for generating hemicatenanes during DNA replication. Three pathways to yield hemicatenane structures are shown. (Left) Lagging strand synthesis encounters a damage site, and the pairing of the lagging strand with the complementary leading strand can produce a pseudo-double Holliday structure. Dissolution of the pseudo-double Holliday structure leads to hemicatenanes and allows replication to bypass the damage site. (Center) Convergence of two replication forks at the final stage of replication can lead to either a single-strand catenane or hemicatenane conjoining two replicated duplexes. Both single-strand catenanes and hemicatenanes can be resolved by a type IA topoisomerase, allowing the segregation of the daughter chromosomes. (Right). Convergent branch migration of a double Holliday junction can generate a hemicatenane. Reproduced from reference with permission from the National Academy of Sciences.

Citation: Higgins N, Vologodskii A. 2015. Topological Behavior of Plasmid DNA, p 105-131. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0036-2014
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Figure 17
Knotting of replication bubbles . Reprinted from reference with permission from Wiley.
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Figure 17

Knotting of replication bubbles . Reprinted from reference with permission from Wiley.

Citation: Higgins N, Vologodskii A. 2015. Topological Behavior of Plasmid DNA, p 105-131. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0036-2014
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Tables

Topological Behavior of Plasmid DNA
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Citation: Higgins N, Vologodskii A. 2015. Topological Behavior of Plasmid DNA, p 105-131. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0036-2014
/content/10.1128/9781555818982.chap7.tab7-1
Table 1
Constrained and unconstrained supercoiling in K12-derived strains
Generic image for table
Table 1

Constrained and unconstrained supercoiling in K12-derived strains

Citation: Higgins N, Vologodskii A. 2015. Topological Behavior of Plasmid DNA, p 105-131. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0036-2014
/content/10.1128/9781555818982.chap7.tab7-2
Table 2
Nucleoid-associated proteins
Generic image for table
Table 2

Nucleoid-associated proteins

Citation: Higgins N, Vologodskii A. 2015. Topological Behavior of Plasmid DNA, p 105-131. In Tolmasky M, Alonso J (ed), Plasmids: Biology and Impact in Biotechnology and Discovery. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PLAS-0036-2014

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