Devices and methods for target molecule characterization

• US 9,395,352 B2
• Filed: 04/07/2008
• Issued: 07/19/2016
• Est. Priority Date: 04/06/2007
• Status: Active Grant

• Current Assignee: Arizona Board of Regents (University of Arizona)
• Original Assignee: Arizona Board of Regents (University of Arizona)
• Inventors: Lindsay, Stuart, Zhang, Peiming
• Primary Examiner(s): Van, Luan
• Assistant Examiner(s): RUFO, LOUIS J
• Application Number:
  US12/594,366
• Publication Number:
  US 20100084276A1
• Time in Patent Office: 3,025 Days
• Field of Search: 205/80, 205/93, 204/450
• US Class Current: 1/1
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 2565/631 being a biochannel or pore
• CPC Class Codes: G01N 27/028 Circuits therefor measuring impedance per se G01R27/02
• CPC Class Codes: G01N 27/3276 being a hybridisation with immobilised receptors using a FET type sensor G01N27/4145; concerning the hybridisation C12Q1/68
• CPC Class Codes: G01N 27/3278 involving nanosized elements, e.g. nanogaps or nanoparticles nanopores G01N33/48721; magnetic beads G01N27/745
• CPC Class Codes: G01N 33/48721 Investigating individual macromolecules, e.g. by translocation through nanopores Coulter counters in general G01N15/12; fabrication methods for nanoscale apertures B81B1/00; sequencing of nucleic acids C12Q1/68

Abstract

The present invention provides a device having at least one constriction that is sized to permit translocation of only a single copy of the molecule. The device has a pair of spaced apart sensing electrodes that border the constriction, which may be a nanopore. The first electrode is connected to a first affinity element and the second electrode is connected to a second affinity element. The first and second affinity elements are configured to temporarily form hydrogen bonds with first and second portions of the target molecule as the latter passes through the constriction.

Claims

1. A molecular recognition device configured to identify at least one portion of a target molecule, the device comprising:

a partition having a first side, a second side, and a thickness therebetween;

at least one constriction having a first end open to the first side and a second end open to the second side, wherein;

the at least one constriction includes a diameter, an interior wall, a perimeter, and a length corresponding to at least the thickness, and

the diameter is configured to pass therethrough target molecules from the first side to the second side, a single target molecule at a time;

a single pair of first and second sensing electrodes arranged within the constriction between the first side and the second side of the partition, wherein

the first electrode encircling the perimeter of the interior wall and arranged at a first position along the length of the constriction,

the second electrode encircling the perimeter of the interior wall and arranged at a second position along the length of the constriction spaced away from the first position establishing a gap therebetween of between 0.5 and 10 nm, and

the partition material in the gap comprises an insulating material;

a first affinity element connected to the first electrode;

and

a second affinity element connected to the second electrode;

wherein the device is configured such that;

at least a portion of each target molecule translocating through the constriction forms one or more temporary non-covalent bonds with each of the first affinity element and the second affinity element upon passing adjacent the gap thereby establishing a temporary electrical circuit between the first electrode and the second electrode,

the circuit is configured to produce an observable current during the temporary binding, the current having one or more associated characteristics, and

the one or more characteristics of the current correspond to a signature of at least a portion of the target molecule for comparison against known signature currents for different target molecules or different portions of target molecules so as to identify at least the portion of each translocated target molecule.

2. The device of claim 1, wherein the partition is configured to separate a first chamber arranged to the first side of the partition and containing target molecules, from a second chamber arranged to the second side of the partition.

3. The device of claim 2, wherein at least one of the first chamber and the second chamber comprises a microfluidic channel.

4. The device according to claim 1, wherein the first sensing electrode is connected to the first affinity element via a first linker molecule.

5. The device according to claim 1, wherein:

the second sensing electrode is connected to the second affinity element via a second linker molecule.

6. The device according to claim 1, further comprising a pair of polarization electrodes configured to translocate a target molecule through the constriction.

7. The device according to claim 1, further comprising current monitoring means for monitoring the one or more characteristics of the current.

8. The device according to claim 7, wherein the current monitor means monitors at least one of a time-varying component of the electrical current and a strength component of the produced current.

9. The device according to claim 1, wherein the first affinity element is a phosphate grabber.

10. The device according to claim 9, wherein the phosphate grabber comprises a guanidinium moiety.

11. The device according to claim 1, wherein the first affinity element comprises 4-(mercaptomethyl)-1H-imidazole-2-carboxamide.

12. The device according to claim 1, further comprising first and second polarization electrodes for polarizing the constriction to translocate target molecules.

13. The device according to claim 1, wherein the device is further configured to process a sample containing target molecules at a speed of less than 5 mm/s.

14. The device according to claim 1, wherein the device is further configured to realize an observable current between about 10 pico-amps to about 1 nano-amp.

15. The device according to claim 1, wherein the first position of the first electrode is spaced from the first side of the partition, and wherein the partition material between the first side and the first position is an insulating material.

16. The device according to claim 15, wherein the second position of the second electrode is spaced from the second side of the partition, and wherein the partition material between the second side and the second position is an insulating material.

17. The device according to claim 1, wherein the partition adjacent at least the constriction comprises alternating layers of insulating material and the first and second electrodes.