= Solution
<RNA polymerase> first recognizes and binds a <gene promoter> to form a closed complex with the local <DNA> duplex still paired. Local strand separation then produces a <transcription bubble> in an <open promoter complex>, making the template available for <RNA> synthesis. Recognition, binding, and opening are distinct events; observing binding alone does not demonstrate strand opening.
In <magnetic tweezers>, a <DNA> tether joins a fixed surface to a magnetic bead, with attachments that prevent free swivelling. The magnets pull upward and can impose turns; the bead height reports tether extension. For a torsionally constrained tether, <linking number> is partitioned into twist and writhe, $Lk=Tw+Wr$. If opening the <transcription bubble> removes helical twist while $Lk$ is fixed, compensating twist or writhe appears elsewhere. In a supercoiled regime, changes in writhe change the extension, making an opening event visible as a bead-height step.
The sign provides an important control. On a positively supercoiled tether, local unwinding requires more positive compensating writhe and generally shortens the tether. On a negatively supercoiled tether, the same unwinding removes some negative writhe and generally lengthens it. A bending or compaction contribution can have the same sign in both cases, whereas the torsional contribution reverses. Comparing signs, together with an extension-versus-turns response measured for the tether, distinguishes local unwinding from mere binding-induced bending. These claims assume the tether remains torsionally constrained and lies in the calibrated supercoiled regime, rather than an arbitrary stretched-DNA regime.
\Image[/past-exam-of-the-biological-physics-course-of-the-university-of-oxford/2015-dna-search-and-tweezers.png]
{title=Original <magnetic tweezers> schematic and the competing time contributions in <facilitated target search>}
Back to article page
