Method for nanopore RNA characterisation
The invention relates to a new method of characterizing a target RNA polynucleotide by taking one or more measurements as the target RNA polynucleotide moves with respect to a transmembrane pore. The movement is controlled by a DNA helicase. The invention also relates to a modified RNA construct wherein the RNA polynucleotide has been modified to increase DNA helicase binding thereto.
1. A method of characterising a target RNA polynucleotide comprising:
a) providing (i) an RNA polynucleotide wherein the RNA polynucleotide is modified to comprise a non-RNA polynucleotide and (ii) a DNA helicase enzyme; wherein the DNA helicase comprises a modification to reduce the size of an opening in the polynucleotide binding domain through which in at least one conformational state the RNA polynucleotide can unbind from the helicase
b) contacting the RNA polynucleotide and DNA helicase enzyme provided in a) with a transmembrane pore such that the DNA helicase controls the movement of the RNA polynucleotide through the transmembrane pore;
c) taking one or more measurements as the RNA polynucleotide moves with respect to the transmembrane pore, wherein the measurements are indicative of one or more characteristics of the RNA polynucleotide, and thereby characterising the target RNA polynucleotide.
2. A method according to claim 1 wherein the non-RNA polynucleotide comprises a DNA helicase binding site or a DNA adaptor.
3. A method according to claim 2 wherein the DNA helicase binding site or the DNA adaptor comprises a leader sequence.
4. A method according to claim 3 wherein the leader sequence preferentially threads into the pore.
5. A method according to claim 1 wherein the non-RNA polynucleotide is covalently attached to the RNA polynucleotide.
6. A method according to claim 1 wherein the non-RNA polynucleotide is ligated to the RNA polynucleotide.
7. A method according to claim 1 wherein the non-RNA polynucleotide is hybridised to the RNA polynucleotide.
8. A method according to claim 1 , wherein the one or more characteristics are selected from (i) length of the RNA polynucleotide, (ii) identity of the RNA polynucleotide, (iii) the sequence of the RNA polynucleotide, (iv) the secondary structure of the RNA polynucleotide and (v) whether or not the RNA polynucleotide is modified.
9. A method according to claim 1 wherein the one or more characteristics of the RNA polynucleotide are measured by electrical and/or optical measurement.
10. A method according to claim 1 , wherein step c) comprises measuring the current passing through the transmembrane pore as the RNA polynucleotide moves with respect to the transmembrane pore wherein the current is indicative of one or more characteristics of the RNA polynucleotide and thereby characterising the RNA polynucleotide.
11. A method according to claim 1 , wherein the RNA polynucleotide comprises modification by methylation, by oxidation, by damage, with one or more proteins, base analogues or with one or more labels, tags or spacers.
12. A method according to claim 1 , wherein the RNA polynucleotide is coupled to the membrane using one or more anchors.
13. A method according to claim 1 , wherein the movement is controlled by a series of one of more DNA helicases.
14. A method according to claim 1 , wherein the one or more helicases are a) Hel308 helicases, RecD helicases, XPD helicases or Dda helicases (b) helicases derived from any of the helicases in (a); or (c) a combination of any of the helicases in (a) and/or (b).
15. A method according to claim 1 , wherein the transmembrane pore is a protein pore or a solid state pore.
16. A method according to claim 15 , wherein the transmembrane protein pore is a protein pore and is derived from a hemolysin, leukocidin, Mycobacterium smegmatis porin A (MspA), MspB, MspC, MspD, CsgG, lysenin, outer membrane porin F (OmpF), outer membrane porin G (OmpG), outer membrane phospholipase A, Neisseria autotransporter lipoprotein (NalP) and WZA.
17. A method of characterising an RNA polynucleotide comprising:
a) providing (i) an RNA polynucleotide wherein the RNA polynucleotide is modified to comprise a non-RNA polynucleotide, (ii) a DNA helicase enzyme, and (iii) one or more molecular brakes that are derived from helicases and are modified such that they bind the polynucleotide but do not function as a helicase;
b) contacting the RNA polynucleotide and DNA helicase enzyme provided in a) with a transmembrane pore such that the DNA helicase controls the movement of the RNA polynucleotide through the transmembrane pore;
c) taking one or more measurements as the RNA polynucleotide moves with respect to the transmembrane pore, wherein the measurements are indicative of one or more characteristics of the RNA polynucleotide, and thereby characterising the RNA polynucleotide.
18. A method according to claim 17 wherein the non-RNA polynucleotide comprises a DNA helicase binding site or a DNA adaptor.
19. A method according to claim 18 wherein the DNA helicase binding site or the DNA adaptor comprises a leader sequence.
20. A method according to claim 19 wherein the leader sequence preferentially threads into the pore.
21. A method according to claim 17 wherein the non-RNA polynucleotide is covalently attached to the RNA polynucleotide.
22. A method according to claim 17 wherein the non-RNA polynucleotide is ligated to the RNA polynucleotide.
23. A method according to claim 17 wherein the non-RNA polynucleotide is hybridised to the RNA polynucleotide.
24. A method according to claim 17 , wherein the one or more characteristics are selected from (i) length of the RNA polynucleotide, (ii) identity of the RNA polynucleotide, (iii) the sequence of the RNA polynucleotide, (iv) the secondary structure of the RNA polynucleotide and (v) whether or not the RNA polynucleotide is modified.
25. A method according to claim 17 wherein the one or more characteristics of the RNA polynucleotide are measured by electrical and/or optical measurement.
26. A method according to claim 17 , wherein step c) comprises measuring the current passing through the transmembrane pore as the RNA polynucleotide moves with respect to the transmembrane pore wherein the current is indicative of one or more characteristics of the RNA polynucleotide and thereby characterising the RNA polynucleotide.
27. A method according to claim 17 , wherein the RNA polynucleotide comprises modification by methylation, by oxidation, by damage, with one or more proteins, base analogues or with one or more labels, tags or spacers.
28. A method according to claim 17 , wherein the RNA polynucleotide is coupled to the membrane using one or more anchors.
29. A method according to claim 17 , wherein the movement is controlled by a series of one of more DNA helicases.
30. A method according to claim 17 , wherein the one or more helicases are a) Hel308 helicases, RecD helicases, XPD helicases or Dda helicases (b) helicases derived from any of the helicases in (a); or (c) a combination of any of the helicases in (a) and/or (b).
31. A method according to claim 17 , wherein the transmembrane pore is a protein pore or a solid state pore.
32. A method according to claim 31 , wherein the transmembrane protein pore is a protein pore and is derived from a hemolysin, leukocidin, Mycobacterium smegmatis porin A (MspA), MspB, MspC, MspD, CsgG, lysenin, outer membrane porin F (OmpF), outer membrane porin G (OmpG), outer membrane phospholipase A, Neisseria autotransporter lipoprotein (NalP) and WZA.