Method of operating a measurement system to analyze a polymer
A sequence of polymer units in a polymer ( 3 ), eg. DNA, is estimated from at least one series of measurements related to the polymer, eg. ion current as a function of translocation through a nanopore ( 1 ), wherein the value of each measurement is dependent on a k-mer being a group of k polymer units ( 4 ). A probabilistic model, especially a hidden Markov model (HMM), is provided, comprising, for a set of possible k-mers: transition weightings representing the chances of transitions from origin k-mers to destination k-mers; and emission weightings in respect of each k-mer that represent the chances of observing given values of measurements for that k-mer. The series of measurements is analysed using an analytical technique, eg. Viterbi decoding, that refers to the model and estimates at least one estimated sequence of polymer units in the polymer based on the likelihood predicted by the model of the series of measurements being produced by sequences of polymer units. In a further embodiment, different voltages are applied across the nanopore during translocation in order to improve the resolution of polymer units.
1. A method of operating a measurement system comprising a nanopore to make measurements of a polymer comprising polymer units, the method comprising:
performing a translocation of said polymer in a single direction through the nanopore of the measurement system using a molecular brake that controls a rate at which the polymer moves through the nanopore during said translocation, resulting in the measurement system being in a sequence of states during said translocation, wherein each state of the sequence of states is dependent on a respective k-mer of the polymer being in the nanopore, wherein each k-mer is k polymer units of the polymer, where k is a positive integer;
during said translocation of the polymer through the nanopore, repeatedly applying a continuously varying voltage cycle across the nanopore a plurality of times, wherein applying the voltage cycle comprises applying a plurality of different voltage levels across the nanopore, including a first voltage level and a second voltage level, different from the first voltage level, and wherein the voltage cycle has a cycle period shorter than a duration of a state of the sequence of states; and
measuring, by the measurement system during said translocation of the polymer through the nanopore, ion current flow through the nanopore one or more times at each of the first and second voltage level of each voltage cycle applied across the nanopore, the ion current flow being dependent on an identity of the k-mer in the nanopore at each state of the sequence of states, thereby producing an input signal comprising a plurality of ion current flow measurements each made at one of the first or second voltage levels of the voltage cycle.
2. The method according to claim 1 , wherein each continuously varying voltage cycle has a cycle period of at least 0.5 ms and at most 3 s.
3. The method according to claim 1 , wherein the cycle period of each continuously varying voltage cycle is shorter than the average 90% of durations of states in the sequence of states.
4. The method according to claim 1 , wherein a number of voltage cycles applied during a state of the sequence of states is between 2 and 10.
5. The method according to claim 1 , wherein the different voltage levels are each applied continuously for partial periods of said voltage cycle.
6. The method according to claim 1 , wherein transitions between said different voltage levels in said voltage cycle are shaped to reduce capacitive transients in the ion current flow measurements when changes in said different levels of said voltage occur.
7. The method according to claim 1 , wherein a difference between said different voltage levels is in a range from 10 mV to 1.5V.
8. The method according to claim 1 , wherein the different voltage levels are of the same polarity.
9. The method according to claim 1 , wherein said measurements of ion current flow through the nanopore are measurements of DC ion current flow through the nanopore.
10. The method according to claim 1 , further comprising:
making groups of multiple measurements of the ion current flow at each one of said different voltage levels, wherein the different voltage levels are each applied continuously for a period of time;
deriving one or more summary measurements from each group of multiple measurements at each one of said different levels to constitute separate measurements in respect of an individual k-mer; and
during each respective period of time, making one of the groups of multiple measurements of the ion current flow at one of the said different voltage levels applied during the respective period of time.
11. A method of operating a measurement system comprising a nanopore to analyze a polymer comprising polymer units, the method comprising:
translocating a polymer through the nanopore of the measurement system in a single direction using a polymer binding moiety that controls a rate at which the polymer moves through the nanopore during said translocation, resulting in the measurement system being in a sequence of states during said translocation, wherein each state of the sequence of states is dependent on a respective k-mer of the polymer being in the nanopore, wherein each k-mer is k polymer units of the polymer, where k is a positive integer;
during the translocation of the polymer through the nanopore, repeatedly applying a continuously varying voltage cycle across the nanopore a plurality of times, wherein applying the voltage cycle comprises applying a plurality of different voltage levels across the nanopore, including a first voltage level and a second voltage level, different from the first voltage level, and wherein the voltage cycle has a cycle period shorter than a duration of a state of the sequence of states; and
measuring, by the measurement system during said translocation of the polymer through the nanopore, ion current flow through the nanopore one or more times at each of the first and second voltage level of each voltage cycle applied across the nanopore, the ion current flow being dependent on an identity of the k-mer in the nanopore at each state of the sequence of states, thereby producing an input signal comprising a plurality of ion current flow measurements each made at one of the first or second voltage levels of the voltage cycle applied across the nanopore.
12. The method according to claim 11 , wherein the polymer binding moiety that controls the rate at which the polymer moves through the nanopore throughout said translocation is a molecular motor.
13. The method according to claim 11 , wherein the polymer binding moiety that controls the rate at which the polymer moves through the nanopore throughout said translocation is a molecular brake.