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Nucleic Acids and Molecular Biology pp 23–54Cite as

Superhelix Density as an Intensive Thermodynamic Variable

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Part of the book series: Nucleic Acids and Molecular Biology ((NUCLEIC,volume 6))

Abstract

If a double-stranded DNA molecule is in the form of a ring, the topology of each of the two complemetary strands cannot evolve independently. The parameter which describes this constraint is the linking number (Lk), the number of times one strand links through the closed circle formed by the other strand (for reviews, see Wang 1980; Benham 1985). Lk is an invariant integer for a permanently closed DNA duplex and the family of molecules differing only in their linking number forms the distribution of topoisomers. The reference state for this distribution is the relaxed state where no topological constraint (other than the winding of the two strands as in the corresponding linear molecule) is imposed on the structure. Its linking number, L°k is equal to N/h°, where h° is the average number of base pairs present per helical turn, and N is the number of base pairs. Great care must be taken in defining L°k because the average number of base pairs per turn, h°, largely depends on internal as well as external parameters (ionic strength, temperature, primary sequence of DNA, presence or absence of atypical structures, like Z-DNA, presence of local perturbations, due for example to the intercalation of a drug or to the binding of a protein). As a result L°k will also depend on these variables. Practically, however, L°k can always be defined as the linking number of the covalently closed DNA relaxed under the appropriate conditions (Wang et al. 1983).

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Authors and Affiliations

  1. Institut Pasteur, Unité de Physicochimie des Macromolécules Biologiques (URA1149 du CNRS), 75724, Paris Cédex, France

    M. Amouyal

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  1. H. Buc
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  2. M. Amouyal
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Editors and Affiliations

  1. Max-Planck-Institut für Experimentelle Medizin, Hermann-Rein-Straße 3, W-3400, Göttingen, Germany

    Fritz Eckstein

  2. Biochemistry Department, University of Dundee, DD1 4HN, Dundee, UK

    David M. J. Lilley

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© 1992 Springer-Verlag Berlin Heidelberg

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Buc, H., Amouyal, M. (1992). Superhelix Density as an Intensive Thermodynamic Variable. In: Eckstein, F., Lilley, D.M.J. (eds) Nucleic Acids and Molecular Biology. Nucleic Acids and Molecular Biology, vol 6. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-77356-3_2

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  • DOI: https://doi.org/10.1007/978-3-642-77356-3_2

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  • Print ISBN: 978-3-642-77358-7

  • Online ISBN: 978-3-642-77356-3

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