Analyte sequencing with nanopores
Provided herein are methods and systems pertaining to sequencing units of analytes using nanopores. In general, arresting constructs are used to modify an analyte such that the modified analyte pauses in the opening of a nanopore. During such a pause, an ion current level is obtained that corresponds to a unit of the analyte. After altering the modified analyte such that the modified analyte advances through the opening, another arresting construct again pauses the analyte, allowing for a second ion current level to be obtained that represents a second unit of the analyte. This process may be repeated until each unit of the analyte is sequenced. Systems for performing such methods are also disclosed.
1 . A method of slowing or stepping the rate that a modified analyte translocates through an opening of a nanopore, the method comprising:
(a) providing a nanopore positioned between a cis side comprising a first conductive liquid medium and a modified analyte and a trans side comprising a second conductive liquid medium, wherein the modified analyte comprises a first arresting construct;
(b) causing the first arresting construct of the modified analyte to cause a first pause of the modified analyte upon entering the opening of the nanopore;
(c) detecting a first ion current level produced by the first pause to associate the detected first ion current level with at least one unit or a set of units of the modified analyte adjacent to the first arresting construct;
(d) altering the first arresting construct of the modified analyte, the alteration allowing the modified analyte to advance toward the trans side;
(e) causing a second arresting construct of the modified analyte to cause a second pause of the modified analyte upon entering the opening of the nanopore;
(f) detecting a second ion current level produced by the second pause to associate the detected second ion current level with a second unit or a set of units of the modified analyte adjacent to the second arresting construct;
(g) altering the second arresting construct of the modified analyte, the alteration allowing the modified analyte to advance toward the trans side; and
(h) comparing the first ion current level and the second ion current level with a known ion current level of a known unit to sequence two or more units of the analyte,
wherein the modified analyte has an average translocation velocity through the opening that is less than the average translocation velocity at which the analyte translocates through the opening in the absence of modification and alteration, and wherein the modified analyte comprises a modified nucleic acid.
2 . The method of claim 1 , wherein the modified nucleic acid is a modified DNA.
3 . The method of claim 1 , wherein the modified nucleic acid comprises a linker joining the nucleic acid to an arresting construct.
4 . The method of claim 1 , wherein at least one arresting construct is an insert arresting construct.
5 . The method of claim 4 , wherein the insert arresting construct is a duplex nucleic acid.
6 . The method of claim 4 , wherein the modified analyte is a single-stranded DNA (ssDNA) modified with at least two or more insert arresting constructs each further defined as a duplex DNA.
7 . The method of claim 1 , wherein at least one arresting construct is a pendant arresting construct.
8 . The method of claim 1 , wherein the modified analyte comprises a translocation initiation tail.
9 . The method of claim 8 , wherein the translocation initiation tail is a single-stranded DNA.
10 . The method of claim 9 , wherein the single-stranded DNA is a homopolymeric DNA.
11 . The method of claim 1 , wherein application of an electric field or physical pressure causes the analyte to enter the nanopore.
12 . The method of claim 1 , wherein a magnetic bead is attached to the analyte on the trans side, and alteration is caused by a magnetic force causing the analyte to move through the nanopore.
13 . The method of claim 1 , wherein the alteration is caused by a voltage pulse, a voltage ramp, a light pulse, or a mechanical force pulse.
14 . The method of claim 1 , wherein the alteration comprises dissociation of at least one arresting construct.
15 . The method of claim 1 , wherein the alteration comprises conformational change of at least one arresting construct.
16 . The method of claim 1 , wherein the nanopore is inserted into a bilayer, membrane, thin film, or solid-state aperture.
17 . The method of claim 16 , wherein the nanopore is contained within an artificial membrane comprising a mycolic acid.
18 . The method of claim 1 , wherein the nanopore is a Mycobacterium smegmatis porin (Msp) or mutant thereof, or α-hemolysin or a variant thereof.