Structures of Supercoiled DNA and their Biological Implications

The double-helical structure of DNA rapidly adapts to changes in the molecule’s degree of supercoiling. The overwound or underwound double-helical axis can assume exotic forms such as plectonemes (the braided forms that appear on twisted phone cords) [1], and supercoiling-induced denaturation of certain DNA sequences can allow the formation of stem-loop structures or cruciforms [2]. In the thirty-odd years since DNA supercoiling was discovered [3], it has been shown that supercoiling is involved in or affected by biological processes such as DNA transcription [4, 5], DNA recombination [6], DNA replication [7] and the packaging of eukaryotic genomes [8]. Until today, it was only possible to control the supercoiling of circular plasmid DNAs using intercalators (such as ethidium bromide) or commercially available topoisomerases. These techniques have several disadvantages; they do not allow for real-time modification and analysis of DNA supercoiling, nor do they allow for precise, controllable and reversible DNA supercoiling. We have established a new technique based on the tools of DNA micromanipulation which gives us the possibility of executing precise, quantitative and reversible supercoiling of an individual linear DNA molecule in real time [9]. Here we will describe our experimental setup and the properties of supercoiled DNA, and then present preliminary experiments concerning the supercoiling-assisted hybridization of homologous DNA sequences and its possible implications for genetic recombination.