DNA looping by FokI: the impact of synapse geometry on loop topology at varied site orientations

David A. Rusling, Niels Laurens, Christian Pernstich, Gijs J. L. Wuite, Stephen E. Halford

Research output: Contribution to journalArticle (Academic Journal)peer-review

10 Citations (Scopus)


Most restriction endonucleases, including FokI, interact with two copies of their recognition sequence before cutting DNA. On DNA with two sites they act in cis looping out the intervening DNA. While many restriction enzymes operate symmetrically at palindromic sites, FokI acts asymmetrically at a non-palindromic site. The directionality of its sequence means that two FokI sites can be bridged in either parallel or anti-parallel alignments. Here we show by biochemical and single-molecule biophysical methods that FokI aligns two recognition sites on separate DNA molecules in parallel and that the parallel arrangement holds for sites in the same DNA regardless of whether they are in inverted or repeated orientations. The parallel arrangement dictates the topology of the loop trapped between sites in cis: the loop from inverted sites has a simple 180 degrees bend, while that with repeated sites has a convoluted 360 degrees turn. The ability of FokI to act at asymmetric sites thus enabled us to identify the synapse geometry for sites in trans and in cis, which in turn revealed the relationship between synapse geometry and loop topology.

Original languageEnglish
Pages (from-to)4977-4987
Number of pages11
JournalNucleic Acids Research
Issue number11
Publication statusPublished - Jun 2012


Dive into the research topics of 'DNA looping by FokI: the impact of synapse geometry on loop topology at varied site orientations'. Together they form a unique fingerprint.

Cite this