DNA synapsis through transient tetramerization triggers cleavage by Ecl18kI restriction enzyme

Mindaugas Zaremba, Amelia Owsicka, Gintautas Tamulaitis, Giedrius Sasnauskas, Luda S. Shlyakhtenko, Alexander Y. Lushnikov, Yuri L Lyubchenko, Niels Laurens, Bram Van Den Broek, Gijs J L Wuite, Virginijus Siksnys

Research output: Contribution to journalArticle

22 Citations (Scopus)

Abstract

To cut DNA at their target sites, restriction enzymes assemble into different oligomeric structures. The Ecl18kI endonuclease in the crystal is arranged as a tetramer made of two dimers each bound to a DNA copy. However, free in solution Ecl18kI is a dimer. To find out whether the Ecl18kI dimer or tetramer represents the functionally important assembly, we generated mutants aimed at disrupting the putative dimer-dimer interface and analysed the functional properties of Ecl18kI and mutant variants. We show by atomic force microscopy that on two-site DNA, Ecl18kI loops out an intervening DNA fragment and forms a tetramer. Using the tethered particle motion technique, we demonstrate that in solution DNA looping is highly dynamic and involves a transient interaction between the two DNA-bound dimers. Furthermore, we show that Ecl18kI cleaves DNA in the synaptic complex much faster than when acting on a single recognition site. Contrary to Ecl18kI, the tetramerization interface mutant R174A binds DNA as a dimer, shows no DNA looping and is virtually inactive. We conclude that Ecl18kI follows the association model for the synaptic complex assembly in which it binds to the target site as a dimer and then associates into a transient tetrameric form to accomplish the cleavage reaction.

Original languageEnglish (US)
Pages (from-to)7142-7154
Number of pages13
JournalNucleic acids research
Volume38
Issue number20
DOIs
StatePublished - Nov 1 2010

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Chromosome Pairing
DNA
Enzymes
Atomic Force Microscopy

ASJC Scopus subject areas

  • Genetics

Cite this

Zaremba, M., Owsicka, A., Tamulaitis, G., Sasnauskas, G., Shlyakhtenko, L. S., Lushnikov, A. Y., ... Siksnys, V. (2010). DNA synapsis through transient tetramerization triggers cleavage by Ecl18kI restriction enzyme. Nucleic acids research, 38(20), 7142-7154. https://doi.org/10.1093/nar/gkq560

DNA synapsis through transient tetramerization triggers cleavage by Ecl18kI restriction enzyme. / Zaremba, Mindaugas; Owsicka, Amelia; Tamulaitis, Gintautas; Sasnauskas, Giedrius; Shlyakhtenko, Luda S.; Lushnikov, Alexander Y.; Lyubchenko, Yuri L; Laurens, Niels; Van Den Broek, Bram; Wuite, Gijs J L; Siksnys, Virginijus.

In: Nucleic acids research, Vol. 38, No. 20, 01.11.2010, p. 7142-7154.

Research output: Contribution to journalArticle

Zaremba, M, Owsicka, A, Tamulaitis, G, Sasnauskas, G, Shlyakhtenko, LS, Lushnikov, AY, Lyubchenko, YL, Laurens, N, Van Den Broek, B, Wuite, GJL & Siksnys, V 2010, 'DNA synapsis through transient tetramerization triggers cleavage by Ecl18kI restriction enzyme', Nucleic acids research, vol. 38, no. 20, pp. 7142-7154. https://doi.org/10.1093/nar/gkq560
Zaremba M, Owsicka A, Tamulaitis G, Sasnauskas G, Shlyakhtenko LS, Lushnikov AY et al. DNA synapsis through transient tetramerization triggers cleavage by Ecl18kI restriction enzyme. Nucleic acids research. 2010 Nov 1;38(20):7142-7154. https://doi.org/10.1093/nar/gkq560
Zaremba, Mindaugas ; Owsicka, Amelia ; Tamulaitis, Gintautas ; Sasnauskas, Giedrius ; Shlyakhtenko, Luda S. ; Lushnikov, Alexander Y. ; Lyubchenko, Yuri L ; Laurens, Niels ; Van Den Broek, Bram ; Wuite, Gijs J L ; Siksnys, Virginijus. / DNA synapsis through transient tetramerization triggers cleavage by Ecl18kI restriction enzyme. In: Nucleic acids research. 2010 ; Vol. 38, No. 20. pp. 7142-7154.
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