4
Dynamics of DNA Supercoiling
A. Gabibov, E. Yakubovskaya, M. Lukin, P. Favorov, A. Reshetnyak,
and M. Monastyrsky
Summary.A catalytic turnover of supercoiled DNA (scDNA) transformation me-
diated by topoisomerases leads to the changes of the linking number (Lk) of the
polymeric substrate by 1 or 2. While a substrate of the topoisomerisation reaction is
chemically identical to its product, even single catalytic event results in the quantum
leap in the scDNA topology. A continuous non-disturbing assay for measurement of
kinetics of the scDNA topoisomerisation was lacking. The intrinsic connections of
DNA topology, its hydrodynamics and optical anisotropy, studied in this chapter
allowed the use of flow linear dichroism technique (FLD) for continuous monitoring
of scDNA topoisomerisation reaction. This approach permits studying the kinetics
of DNA transformation catalysed by eukaryotic topoisomerases I and II, mechanistic
properties of these enzymes and their interactions with anti-cancer drugs.
Keywords:scDNA transformations, DNA hydrodynamics, linking number
(Lk), topoisomerases, flow linear dichroism, anti-cancer drugs
4.1 Introduction
The dynamics of scDNA transformations is a key point for understanding the
numerous processes that take place in the living cell [1]. Changes of DNA
topology are vital during replication, transcription, recombination, chromo-
some condensation and segregation. From the topological point of view DNA
can be represented by a closed ribbon [2, 3]. Studies of the dynamical aspects
of DNA topology are closely connected with the design of the adequate math-
ematical description of DNA polymeric molecule as well as the methods of
monitoring of its properties [4, 5]. The main topological changes of scDNA in
the cells are catalysed by DNA-specific enzymes, topoisomerases, types I and
II, which induce single and double nicks in DNA strains. This leads to changes
of the linking number (Lk) of the polymer substrate by 1 or 2. The edges of
“closed ribbon” cannot be regarded as “intact” during the catalytic reaction
and DNA molecule can be preferably represented by a “ladder” instead of