Determination of RNA orientation during translocation through a biological nanopore

Abstract

We investigate single-molecule electrophoretic translocation of A(50), C(50), A(25)C(50), and C(50)A(25) RNA molecules through the alpha-hemolysin transmembrane protein pore. We observe pronounced bilevel current blockages during translocation of A(25)C(50) and C(50)A(25) molecules. The two current levels observed during these bilevel blockages are very similar to the characteristic current levels observed during A(50) and C(50) translocation. From the temporal ordering of the two levels within the bilevel current blockages, we infer whether individual A(25)C(50) and C(50)A(25) molecules pass through the pore in a 3'-->5' or 5'-->3' orientation. Correlation between the level of current obstruction and the inferred A(25)C(50) or C(50)A(25) orientation indicates that 3'-->5' translocation of a poly C segment causes a significantly deeper current obstruction than 5'-->3' translocation. Our analysis also suggests that the 3' ends of C(50) and A(25)C(50) RNA molecules are more likely to initiate translocation than the 5' ends. Orientation dependent differences in a smaller current blockage that immediately precedes many translocation events suggest that this blockage also contains information about RNA orientation during translocation. These findings emphasize that the directionality of polynucleotide molecules is an important factor in translocation and demonstrate how structure within ionic current signals can give new insights into the translocation process.

FIGURE 1

Translocation of RNA through α-HL can be divided into four phases shown schematically in the upper portion of the figure. The lower portion of the figure shows an ionic current signal recorded during translocation of a single A₅₀ RNA molecule through an α-HL pore. Passage of the RNA through the pore results in a brief blockage of the ionic current through the pore. In the MS, the ionic current is reduced to ∼35–85% of the OS value. The MS occurs with varying likelihood for all polynucleotides. It is thought to be related to a polymer that has entered the vestibule portion of the pore but that has not yet threaded into the narrowest part of the pore. During the TS, the ionic current is reduced to ∼0–20% of the OS value. The TS is indicative of a segment of RNA present in the narrowest section of the pore.

FIGURE 2

Translocation event classification scheme. An algorithm was used to classify each event as one of these six “types”. The six types arise from the presence or absence of an MS combined with three possible TS signatures. For example, a MidLoHi event begins with a ∼35–85% mid-state current level. It then transitions to a very low ∼0–10% “Lo” TS level and finally to a moderately low ∼10–20% “Hi” TS level before returning to the initial open-state level.

FIGURE 3

Example fit to a C₅₀A₂₅ translocation event. The dark line shows the best fit to the data. The functional form of this fit is given in Eq. 1 and the event is classified as MidHiLo. Comparison of this fit to the MidNoStep fit with the F-test yielded a p-value of ∼10⁻¹⁴.

FIGURE 4

Distribution of TS durations and current levels for A₅₀, C₅₀, C₅₀A₂₅, and A₂₅C₅₀ RNA. Each point represents one translocation event. The coordinates of the point correspond to the duration and average current of the TS of the event. TS current is expressed as a fraction of the OS current level. (a) Data for A₅₀ RNA. (b) Data for C₅₀ RNA. A₅₀ events fall into one main group, whereas C₅₀ events fall into two well-resolved groups. In c and d, the duration and current characteristics of the main groups of C₅₀A₂₅ and A₂₅C₅₀ events are approximately intermediate between C₅₀ and A₅₀ current blockage and translocation duration characteristics. Events falling outside of the dotted rectangles may arise from incomplete translocation of full-length RNA molecules, from translocation of RNA fragments produced by degradation, or from very rapid translocation of full-length molecules. Lacking a clear interpretation of these events, we chose exclude them from our analysis. The number of events indicated in each panel correspond to the number of points falling within the dashed rectangles. These four data sets were obtained under identical experimental conditions with 120 mV (cis side negative) applied across the bilayer. All results presented in this manuscript are derived from these four data sets. The trends seen in these data sets were consistently observed in data from many repeated experiments.

FIGURE 5

Event classification results. The bars in each panel correspond to the percentage of occurrence of the three TS classes: HiLo, NoStep, and LoHi. Panel a shows that the large majority of C₅₀ translocation events do not exhibit strong step signals within the TS ionic current record. Panel c shows that a significant majority of A₂₅C₅₀ events exhibit a strong LoHi step signal. We observe moderate differences in the event-type distributions of A₅₀ and C₅₀A₂₅. Analysis of the current blockage levels of the Lo and Hi substates indicates that most step events observed in A₂₅C₅₀ and C₅₀A₂₅ translocation are produced by the transition between poly A and poly C segments, whereas the step events observed in A₅₀ translocation are produced by fluctuations in ionic current blockage levels that are intrinsic to poly A translocation.

FIGURE 6

Distributions of translocation state current blockage levels. Panels a and b show the distribution of TS current levels for all NoStep events observed in the A₅₀ and C₅₀ data, respectively. The two peaks in the C₅₀ distribution correspond to the two C₅₀ groups shown in Fig. 4. The dashed vertical lines correspond to mean current levels determined by Gaussian fits to the A₅₀ distribution and to the lower and upper C₅₀ distributions. Panels c–f show the distributions of the Hi and Lo TS substate current levels observed in the indicated event classes. From the time ordering of the step signal, we inferred the order in which the segments moved through the pore. Thus, we interpret HiLo events as A₂₅→C₅₀ and LoHi events as C₅₀→A₂₅. Comparing this information with the RNA sequence gives the orientation, 3′→5′ or 5′→3′, of the molecule during translocation. The inferred translocation orientations for each group of copolymer events are indicated in the corresponding panel.

FIGURE 7

Diagram of the relationships between RNA orientation during translocation and observed TS signals for A₂₅C₅₀ and C₅₀A₂₅ copolymers. These relationships are inferred from the time ordering and current obstruction levels of the TS step signals shown in Fig. 6. We infer that poly A translocation results in I/I_OS ≈ 0.13, regardless of orientation. However, poly C translocation results in I/I_OS ≈ 0.03 for 3′→5′ translocation and I/I_OS ≈ 0.08 for 5′→3′ translocation.

FIGURE 8

Distributions of MS durations. Error bars on the data points represent the statistical uncertainty in binning the data. The solid lines show exponential fits to the data. The exponential time constant and 95% confidence intervals derived from the fit are given for each distribution. Panels a and e show that mid-states produced by A₅₀ tend to be significantly longer than mid-states produced by C₅₀. The distributions shown in panels b and c arise from events where we inferred that the molecules entered the pore with the poly A segment first, whereas the distributions in panels f and g correspond to C-first entry. The tendency of an A₅₀ molecule to produce a longer mid-state than a C₅₀ molecule appears to be reflected in copolymer translocation as a tendency for the A₂₅ segment to produce a longer mid-state than the C₅₀ segment. Comparison of the distribution in panel (d) with the distributions in panels b and c suggests that most A₂₅C₅₀ MidNoStep events correspond to A-first entry, whereas comparison of the distribution in panel h with the distributions in panels f and g suggests that most C₅₀A₂₅ MidNoStep events correspond to C-first entry. These observations provide qualitative support for our conjecture that most NoStep copolymer events are a result of the small size of the step signal produced during 5′→3′ translocation.

FIGURE 9

We observed frequent step signals in A₅₀ translocation. Distributions of Hi-state and Lo-state current blockage levels for A₅₀ LoHi and A₅₀ HiLo step events are shown in a and b, respectively. As a comparison, the solid black lines show the corresponding C₅₀A₂₅ current level distributions. The dashed vertical lines correspond to mean current levels determined by Gaussian fits to the A₅₀ distribution and to the lower and upper C₅₀ distributions in Fig. 6. The Lo level in A₅₀ step events causes a smaller ionic current obstruction than either poly C related Lo level. This provides evidence that step events observed in C₅₀A₂₅ and A₂₅C₅₀ translocation are caused by differences between poly A and poly C ionic current obstruction, and not by fluctuations in poly A current obstruction levels.