The Statistics of DNA Capture by a Solid-State Nanopore Mirna

A solid-state nanopore can electrophoretically capture a DNA molecule and pull it through in a folded configuration. The resulting ionic current signal indicates where along its length the DNA was captured. A statistical study using an 8 nm wide nanopore reveals a strong bias favoring the capture of molecules near their ends. A theoretical model shows that bias to be a consequence of configurational entropy, rather than a search by the polymer for an energetically favorable configuration. We also quantified the fluctuations and length-dependence of the speed of simultaneously translocating polymer segments from our study of folded DNA configurations. 1 ar X iv :1 20 9. 32 50 v1 [ ph ys ic s. bi oph ] 1 4 Se p 20 12 A voltage-biased nanopore is a single-molecule detector that registers the disruption of I, the ionic current through the nanopore, caused by the insertion of a linear polyelectrolyte [1–3]. Most previous studies have focused on instances where the nanopore electrophoretically captures DNA at one end and then slides it through in a linear, head-to-tail fashion. However, a ≈ 10 nm-wide solid-state nanopore can also capture DNA some distance from its end and pull it through in a folded configuration [4–6]. Folded DNA translocations entail the simultaneous motion of multiple segments through the nanopore, which may exhibit cooperative behavior that alters the translocation dynamics [7]. The mechanical bending energy associated with folds may influence the capture of DNA [8]. Importantly, the study of folded configurations provides snapshots of molecules at the moment of insertion, which offer clues about how the nanopore captures them from solution. The capture process is relevant to applications of nanopores that seek to extract sequence-related information from unfolded molecules. When DNA encounters a nanopore, the electrophoretic force can initiate translocation by inducing a hairpin fold in the molecule that protrudes into the nanopore. Two segments of DNA extend from the initial fold, a long one of length Ll and a short one of length Ls (Fig. 1(a)). The capture location, x ≡ Ls Ls+Ll , is the fractional contour distance from the initial fold to the nearest end. The time for each segment to translocate is measurable from the time trace of I [4–6] and can be used to estimate x. Storm et al. inferred the distribution of x for λDNA translocations and concluded that folds occur with equal probability everywhere along a molecule’s length, but that the DNA is more likely to be captured at its ends because of the lower energetic cost of threading an unfolded molecule [6]. This implies that molecules test multiple configurations prior to capture, which is a statistical process governed by energetic considerations. By contrast, Chen et al. reported a bias for unfolded translocations that increased with applied voltage [5]. This finding implies that molecules pre-align in the fields outside the pore rather than sample multiple configurations prior to capture. No model for the distribution of x is available to help evaluate these competing pictures. Here, we present a study of DNA translocations of an 8 nm-wide solid-state nanopore which reveals a strongly biased distribution of capture locations, where the probability of capture increases continuously and rapidly towards the DNA’s ends. The equilibrium distribution of polymer configurations outside the nanopore offers a natural explanation for