Science2 publishers2 min readPublished
High-speed microscopy films DNA-cutting enzymes returning to bends and loose ends before a break
Kanazawa University researchers filmed single DNase I enzymes going back again and again to exposed DNA ends and bends before the molecule broke apart. The microscope cannot see the cutting chemistry, so the team reports the link between DNA shape and breakage as a correlation.
The Scientist · Science desk
What happened
- Contacts lasted longer at curved stretches of DNA, and those curves were where the molecule was more likely to be cut.
- DNA packed by protamine into rods and ring-shaped toroids stayed intact as DNase I gathered around it, and the enzyme rarely got into a toroid's center.
- Micrococcal nuclease, a different DNA-cutting enzyme, showed similar patterns of sampling, repeated binding, disruption and fragment scattering.
- The work, led by Richard Wong at Kanazawa's Nano Life Science Institute, is published in Nature Communications.
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Why it matters
- capability Labs can now measure how long a single nuclease sits at a site and how often it returns before DNA breaks, behavior that DNase I's well-studied chemistry left out of view.
- constraint Proving that a bend causes a break will need a second method that sees the reaction at the active site, since this imaging places the enzyme and infers the cut.
- precedent Because DNase I and micrococcal nuclease behaved alike, other nucleases are the obvious next test of whether STORM-like behavior is general.
DNase I helps clear DNA released from damaged or dying cells. Problems with that clearance have been associated with inflammatory and autoimmune diseases [12]. The enzyme's chemistry is well studied, but it has been hard to see how a single enzyme molecule approaches DNA and what it does in the moments around a cut [4]. High-speed atomic force microscopy records nanoscale changes in molecules in liquid, with no need to fix or stain them [3]. "Our high-speed AFM imaging allows us to follow the interaction between individual nuclease enzymes and DNA as it happens," said Jingge Yang, a student on Richard Wong's team at Kanazawa University [13][2].
The thing this doesn't tell you is which way the cause runs. A bend that draws DNase I in and an enzyme that bends the DNA it sits on could look much the same on film. In both cases the long contacts would sit at the curves where fragments later appear [6].
Neither published account says how many enzyme molecules or cuts were tracked, or describes a comparison across DNA sequences. On the evidence reported, DNA shape predicts where DNase I spends its time. Finding out whether shape matters more than sequence in choosing the break point would take a separate experiment.
The protamine result needs less inference, because the outcome is on film: intact structures with the enzyme beside them [11]. Protamine is the protein that packs the paternal genome into a very compact form in sperm [10]. "We can see that DNA is not simply a passive target. Its local shape and higher-order organization strongly influence where enzymes interact and whether degradation can proceed," Wong said [14]. In my view the images support "whether degradation can proceed" more directly than "where enzymes interact". An intact toroid is an outcome. A long stay at a bend is a correlation.
From the patterns that kept recurring, the team built a framework it calls STORM, short for Scan, Target, Occupy, Rupture and Mobilize. The authors stress that it describes what the films showed and is not a fixed path every molecule must follow [8]. Their suggestion that it reflects broader physical rules rests on two nucleases, DNase I and micrococcal nuclease [1].
What to watch
- A readout of the cut chemistry at the sites where DNase I lingers, to test whether dwell time predicts the actual break.
- Runs on DNA of one sequence bent into different shapes, or different sequences held in the same shape, to separate shape from sequence.
- Imaging of DNA released from dying cells, where failures of DNase I clearance have been tied to autoimmune disease.