DNA Topology: Fundamentals

Abstract

Topological characteristics of DNA and specifically DNA supercoiling influence all major DNA transactions in living cells. DNA supercoiling induces the formation of unusual secondary structure by specific DNA repeats which can also affect DNA functioning.

Keywords: supercoiling; knots; catenanes; Z‐DNA; triplexes; cruciforms

Figure 1.

A hypothetical circular DNA molecule in which two DNA strands are linked only once. Untangling of the two strands is impossible, unless one of them is broken.

Figure 2.

Examples of topological domains. (a) Circular DNA, (b) chromosomal DNA loops, (c) linear DNA attached to the membrane, (d) linear DNA attached to protein aggregates.

Figure 3.

Linking number represents an algebraic sum of all the intersections made by one DNA strand across the imaginary surface carved by another DNA strand. The Lk here is +8.

Figure 4.

Local unwinding of relaxed circular DNA leads to positive DNA supercoiling.

Figure 5.

Plectonemic (upper) and solenoidal (lower) DNA supercoils. Arrows illustrate that both molecules here are negatively supercoiled, despite different handedness.

Figure 6.

Elementary knots (upper panel) and catenanes (lower panel) of different signs.

Figure 7.

B‐DNA to cruciform transition. The red and blue strips are complementary halves of an inverted repeat. Black strips are adjacent DNA. Fractalized black strips are unwound regions.

Figure 8.

Transition from the right‐handed B‐DNA into left‐handed Z‐DNA by an alternating purine/pyrimidine sequence. The green/red strips show the region of alternating purines/pyrimidines. Black strips are adjacent DNA. Fractalized black strips are unwound regions.

Figure 9.

H‐DNA is formed by homopurine‐homopyrimidine mirror repeats. A DNA strand from one half of the repeat folds back forming a triplex with the repeat's duplex half, while its complement remains single‐stranded. The black ribbon represents the homopurine strand, the red ribbon is the homopyrimidine strand, and green ribbons are adjacent DNA.

Figure 10.

H‐DNA triads.

Figure 11.

G‐quartet. (a) General overview. The black line is the DNA strand and the purple rectangles are the stacked G‐quartets. (b) Structure of a G‐quartet.

Figure 12.

Formation of slipped‐stranded DNA by direct tandem repeats. Upon strand separation, complementary repeats can mispair, resulting in a combination of double‐helical stretches interspersed with single‐stranded loops. The red and blue strips are complementary strands of a direct tandem repeat; the black strips are adjacent DNA.

Figure 13.

Two‐dimensional electrophoretic analysis of a mixture of DNA topoisomers (a) without local structural transitions and (b) with a local transition into an alternative DNA conformation. Filled brown circles represent relaxed topoisomers, filled red circles are positively supercoiled topoisomers and filled blue circles are negatively supercoiled topoisomers. Empty blue circles in (b) show the expected mobility of topoisomers −15 to −20 if no transition occurred.

Figure 14.

A model of transcriptional DNA supercoiling. RNA polymerase translocates an unwound DNA segment along the transcribed gene. This translocation forces DNA to rotate around DNA polymerase, so that negative and positive DNA supercoiling is generated upstream and downstream of the enzyme, respectively. The grey circle represents RNA polymerase, the brown ribbons are unwound DNA, the red ribbon is a positive supercoiling wave and the blue ribbon is a negative supercoiling wave. Arrow shows the direction of polymerase movement.

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Further Reading

Calladine CR and Drew HR (1997) Understanding DNA: The Molecule and How it Works. 2nd edn. Sandiego, USA: Academic Press.

Frank‐Kamenetskii MD (1997) Unraveling DNA: The Most Important Molecules of Life. Reading, USA: Addison Wesley.

Sinden RR (1994) DNA Structure and Function. San Diego, USA: Academic Press.

Travers A (1993) DNA–Protein Interactions. London, UK: Chapman and Hall.

Vologodskii A (1992) Topology and Physics of Circular DNA. Boca Raton, USA: CRC Press.

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How to Cite close
Mirkin, Sergei M(May 2001) DNA Topology: Fundamentals. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1038/npg.els.0001038]