Sensing compositions, methods, and devices for the detection of molecules using a nanopore device
The invention relates to compositions, methods, devices, systems, and kits for detecting and characterizing molecules using a nanopore device.
1. A method for detecting or characterization of a polynucleotide in a sample within a nanopore device comprising:
a. contacting a sample suspected of comprising a polynucleotide with a sensing solution comprising an effective amount of a polyether agent of Formula (I):
wherein:
m is 1-3;
n is 1-30;
each R 1 is independently H or methyl; and
R 2 and R 3 are each independently H or C (1-6) alkyl,
wherein the sensing solution is contacting a nanoporous membrane of a nanopore device, wherein the nanoporous membrane separates the space of the nanopore device into a cis volume and a trans volume;
b. applying a voltage across a nanopore of the nanoporous membrane thereby inducing translocation of the polynucleotide through the nanoporous membrane; and
c. detecting a current during the translocation of the polynucleotide in the nanopore device; and
(d) characterizing the polynucleotide as having a length of less than 500 base pairs (bps), wherein the nanopore device containing the sensing solution allows for discrimination of the polynucleotide by size.
2. The method of claim 1 , wherein the polyether agent is of Formula (Ia):
3. The method of claim 1 , wherein the polyether agent is of Formula (II):
wherein each R 4 is H or methyl.
4. The method of claim 3 , wherein n is either 1, 3, or 4, and each R 4 is H or is methyl.
5. The method of claim 1 , wherein the polyether agent is of Formula (III), (IIIa) or (IIIb):
wherein:
n is 1-30;
q is 1-29;
R 2 , R 3 and each R 4 are each independently H or methyl.
6. The method of claim 1 , wherein the sensing solution further comprises a salt, wherein the salt is a monovalent or divalent salt, and wherein the salt is selected from a group consisting of: LiCl, NaCl, MgCl 2 , CsCl, CaCl 2 , Li, Na, K, Mg, Cs, Ca, or a combination thereof, and is at a molar concentration of greater than 0.01M, 0.02M, 0.05M, 0.1M, 0.2M, 0.5M, 1M, 2M, 3M, 4M or 5M.
7. The method of claim 6 , wherein the salt is not KCl.
8. The method of claim 1 , further comprising a buffer solution selected from a group consisting of: Tris-HCl, Borate, CHES, Bis-tris propane, or CAPS, and wherein the buffer solution is at a concentration of at least 10 mM.
9. The method of claim 1 , further comprising a chelating agent, wherein the chelating agent is EDTA, EGTA or a combination thereof.
10. The method of claim 1 , wherein the effective amount is v/v 1%, 2%, 3%, 4% 5%, 6%, 7%, 8%, 9%, 10%, 11%, 12%, 13%, 14%, 15% or more.
11. The method of claim 1 , wherein the n is at least 3-4, or at least 4-5, at least 5-8, or at least 8-10, or at least 10-20, or at least 20-30.
12. The method of claim 1 , wherein characterizing further comprises discrimination of different lengths or sizes of the polynucleotide in the sample.
13. The method of claim 12 , wherein the different lengths or sizes of the polynucleotide in the sample is less than 300 bs, less than 200 bp, less than 100 bp, or less than 50 bp.
14. The method of claim 12 , wherein the discrimination is between a ssDNA, a dsDNA, a dsRNA, a RNA, a RNA/DNA hybrid, a PNA/DNA hybrid, or a RNA/PNA hybrid with length differences of less than 50 bp, 100 bp, 200 bp, 300 bp, or 400 bp.
15. The method of claim 1 , wherein characterizing further comprises one or more of: a quantity of the polynucleotide, a modification of the polynucleotide, a structure of the polynucleotide, a sequence of the polynucleotide, and a concentration of the polynucleotide.
16. The method of claim 1 , wherein the nanoporous membrane comprises a pore made from a solid state substrate or from a biological substrate.
17. The method of claim 1 , wherein the nanoporous membrane has a pore with a minimum diameter of greater than 4 nm, 5 nm, 6 nm, 7 nm, 8 nm, 9 nm, 10 nm, 15 nm, 20 nm, 25 nm, 30 nm, 35 nm, 40 nm, 45 nm, 50 nm, 55 nm, 60 nm, or 65 nm.
18. The method of claim 1 , wherein the nanoporous membrane has a pore with a minimum diameter of less than 70 nm, 75 nm, 80 nm, 85 nm, 90 nm, 95 nm, 100 nm, 105 nm, or 110 nm.
19. The method of claim 1 , wherein the nanoporous membrane has a pore with diameter of 20 nm to 60 nm.
20. The method of claim 1 , wherein the accuracy of the characterization is improved as compared to the same method performed in a standard running buffer.
21. The method of claim 1 , wherein the characterization has improved accuracy as compared to characterization from the same method performed in a standard buffer.
22. The method of claim 21 , wherein the standard buffer comprises LiCl, KCl, NaCl or a monovalent ion thereof.
23. The method of claim 21 , wherein the standard buffer comprises LiCl, KCl, or NaCl or a monovalent ion thereof and does not contain a polyether agent of Formula (I), (II), (III), (IV), or a combination therefore.
24. The method of claim 1 , wherein the cis volume and the trans volume comprise the same sensing solution.
25. The method of claim 1 , wherein the cis volume and the trans volume comprise a sensing solution that are different.
26. The method of claim 1 , wherein the cis volume comprises the sensing solution, and the trans volume comprises at least a 10% carbohydrate solution.
27. The method of claim 1 , wherein the cis volume comprises a 10% carbohydrate solution and the trans volume comprises a sensing solution of any one of claim 1 .
28. The method of claim 1 , wherein the nanopore device comprises electrodes for applying a voltage across the nanopore and for monitoring the current.
29. The method of claim 1 , wherein the cis volume and trans volume are in fluidic communication through the pore.
30. The method of claim 1 , wherein the contacting step further comprises a probe comprising a residue conjugated to a voltage-sensitive moiety, that binds to the polynucleotide.
31. The method of claim 1 , wherein the current is an ionic current.
32. The method of claim 1 , wherein the current is a tunneling current.
33. The method of claim 1 , wherein the polynucleotide is a double-stranded polynucleotide.
34. A nanopore device for detecting or characterizing a polynucleotide in a sample when mixed with a sensing solution, comprising:
a. a nanopore formed within a nanoporous membrane;
b. the nanoporous membrane, wherein the nanoporous membrane separates an interior space of the nanopore device into a cis volume and a trans volume;
c. a sensor comprising a set of electrodes for applying a voltage across the nanopore and for monitoring an ionic current through the nanopore;
d. a sensing solution within the nanoporous membrane comprising an effective amount of a polyether agent of Formula (I):
wherein:
m is 1-3;
n is 1-30;
each R 1 is independently H or methyl; and
R 2 and R 3 are each independently H or C (1-6) alkyl,
wherein the sensor is configured to measure ionic current across the nanopore, and characterize the polynucleotide within the sensing solution as having a length of less than 500 base pairs (bps) as the polynucleotide translocates through the nanopore under the applied voltage, wherein the nanopore device containing the sensing solution allows for discrimination of the polynucleotide by size.
35. The device of claim 34 , wherein the cis volume and the trans volume each comprise the same sensing solution.
36. The device of claim 34 , wherein the cis volume and the trans volume each comprise a different sensing solution.
37. The device of claim 34 , wherein the device further comprises a voltage-clamped amplifier.
38. The device of claim 34 , wherein device is a biological nanopore device.
39. The device of claim 34 , wherein device is a solid-state nanopore device.
40. The device of claim 34 , wherein device is a hybrid nanopore device.
41. A system for detecting or characterizing a polynucleotide in a sample comprising:
a. a sensing solution and a nanopore device, wherein the sensing solution comprises:
an effective amount of a polyether agent of Formula (I):
wherein:
m is 1-3;
n is 1-30;
each R 1 is independently H or methyl; and
R 2 and R 3 are each independently H or C (1-6) alkyl,
and wherein the nanopore device comprises a nanopore formed within a nanoporous membrane, wherein the nanoporous membrane separates the space of the nanopore device into a cis volume and a trans volume;
b. a sensor for detecting a current from a polynucleotide in the nanopore device;
c. a processor; and
d. a computer readable medium for storing code that detects translocation of the polynucleotide through the nanopore device when executed by the processor, wherein the code further stores an algorithm that identifies one or more current signatures, that when executed by the processor, causes the processor to characterize the polynucleotide as having a length of less than 500 base pairs (bps) as the polynucleotide translocates through the nanopore of the nanopore device under the applied voltage, wherein the nanopore device containing the sensing solution allows for discrimination of the polynucleotide by size.
42. A kit for detection or characterization of a polynucleotide in a sample using a nanopore device comprising:
a. a sensing solution and a nanopore device, wherein the sensing solution comprises:
an effective amount of a polyether agent of Formula (I):
wherein:
m is 1-3;
n is 1-30;
each R 1 is independently H or methyl; and
R 2 and R 3 are each independently H or C (1-6) alkyl,
and wherein the nanopore device comprises a nanoporous membrane, wherein the nanoporous membrane separates the space of the nanopore device into a cis volume and a trans volume; and
b. instructions for using the sensing solution with the nanopore device to detect or characterize the polynucleotide in the sample.