Biomolecular devices

• US 20070190656A1
• Filed: 05/04/2004
• Published: 08/16/2007
• Est. Priority Date: 05/03/2003
• Status: Abandoned Application

• Current Assignee: University of Edinburgh
• Original Assignee: University of Edinburgh
• Inventors: Campbell, Colin, Walton, Anthony, Mount, Andrew, Beattie, John, Ghazal, Peter, Evans, Stuart, Terry, Jonathan, Crain, Jason
• Application Number:
  US10/555,493
• Publication Number:
  US 20070190656A1
• Time in Patent Office: Days
• US Class Current: 436/63
• CPC Class Codes: B82Y 10/00 Nanotechnology for information processing, storage or transmission, e.g. quantum computing or single electron logic
• CPC Class Codes: G01N 33/54306 Solid-phase reaction mechanisms
• CPC Class Codes: G01N 33/54373 involving physiochemical end-point determination, e.g. wave-guides, FETS, gratings
• CPC Class Codes: G11C 13/0014 comprising cells based on organic memory material
• CPC Class Codes: G11C 13/0019 comprising bio-molecules
• CPC Class Codes: H10K 10/701 Organic molecular electronic devices
• CPC Class Codes: H10K 19/00 Integrated devices, or assemblies of multiple devices, comprising at least one organic element specially adapted for rectifying, amplifying, oscillating or switching, covered by group H10K10/00
• CPC Class Codes: H10K 85/761 Biomolecules or bio-macromolecules, e.g. proteins, chlorophyl, lipids or enzymes

Abstract

The present invention provides a macromolecular switch (51) suitable for use in a data acquisition and/or processing device. The switch comprises a macromolecular structure (10) having an ion binding site (14), and is flippable between a plurality of discretely different conformations corresponding to different ion binding conditions at the ion binding site (14). The macromolecular structure (10) is provided with at least one electrochemical input device (43) for applying such different ion binding conditions to the ion binding site (14) in response to corresponding external input signals. The invention also provides a method for data acquisition and/or processing, using a macromolecular structure switch of the invention.

Claims

1. a macromolecular switch suitable for use in a data acquisition and/or processing device, comprising:

a macromolecular structure having at least one ion binding site, and flippable between a plurality of discretely different conformations corresponding to different ion binding conditions at said at least one ion binding site, at least in the absence of any other binding to said macromolecular structure, said macromolecular structure being provided with at least one electrochemical input device formed and arranged for applying such different ion binding conditions to said ion binding site in response to corresponding external input signals.

2. A switch as claimed in claim 1 wherein said at least one input device is formed and arranged so as to be operable under the control of electrical external input signals.

3. A switch as claimed in claim 1 wherein said electrochemical input device comprises an ion reservoir and an ion reservoir control device formed and arranged for at least one of ion capture into and ion release from, said ion reservoir.

4. A switch as claimed in claim 3 wherein said ion reservoir control device comprises a redox system formed and arranged for said ion capture into and ion release from, said ion reservoir.

5. A switch as claimed in claim 1 wherein said at least one electrochemical input device is formed and arranged for reversible switching between said different ion binding conditions.

6. A switch as claimed in claim 1 wherein said macromolecular structure has at least one biomolecule analyte binding site formed and arranged for binding to a predetermined target biomolecule analyte.

7. A switch as claimed in claim 6 wherein are provided at least two said biomolecule analyte binding sites.

8. A switch as claimed in claim 1 wherein at least one said biomolecule analyte binding site has a competitor biomolecule bound thereto, which competitor biomolecule is substitutable by a said target biomolecule analyte in use of the switch, by means of competitive binding.

9. A switch as claimed in claim 8 wherein said competitor biomolecule is bound to said macromolecular structure so as to lock said structure in one of said conformations against flipping to a different said conformation.

10. A switch as claimed in claim 1 wherein said macromolecular switch is provided with at least one output device component of an output signal transmission system formed and arranged for use in reading of at least one of:

the conformational state of the macromolecular structure and the presence of a target biomolecule analyte bound to a said biomolecule analyte binding site.

11. A switch as claimed in claim 10 wherein said component comprises part of a separation sensitive output device.

12. A switch as claimed in claim 10 wherein said output device component comprises a fluorescent label.

13. A switch as claimed in claim 12 wherein said fluorescent label is suitable for use in a separation sensitive signal transmission system.

14. A switch as claimed in claim 13 wherein said separation sensitive signal transmission system is a FRET system.

15. A switch as claimed in claim 10 wherein said macromolecular structure is coupled to at least one solid state data signal processing component.

16. A switch as claimed in claim 15 wherein said at least one solid state data signal processing component comprises a component for transforming an optical signal into an electronic signal.

17. A switch as claimed in claim 1 wherein said macromolecular structure is coupled to at least one solid state data processing circuit, for transferring data substantially directly thereto.

18. A switch as claimed in claim 1 wherein said macromolecular structure is captively retained in proximity to said at least one input device.

19. A switch as claimed in claim 18 wherein said macromolecular structure is anchored to a solid substrate.

20. A switch as claimed in claim 1 wherein said macromolecular structure comprises an HJ-like structure in which at least part of the four HJ arm structures is comprised by non-polynucleotide material, which is not incompatible with the operation and application of the conformation switching of the macromolecular structure, and wherein the branch point of the HJ-like macromolecular structure has at least the four interacting polynucleoside dimer sequence elements of an HJ branch point.

21. A switch as claimed in claim 20 wherein said four interacting polynucleoside dimer sequence elements of an HJ branch point are comprised by:

TC, GT, AG, and CA.

22. A switch as claimed in claim 1 wherein said macromolecular structure comprises at least one polynucleotide.

23. A switch as claimed in claim 22 wherein said macromolecular structure is a Holliday-Junction.

24. A switch as claimed in claim 1 wherein said macromolecular structure comprises at least one polypeptide.

25. A switch assembly comprising a plurality of switches according to claim 1, provided with an input signal device formed and arranged for applying external input signals to said input devices of said switches, in temporally separated manner.

26. A switch assembly comprising a plurality of switches according to claim 1, wherein said switches have different biomolecule analyte binding sites and are disposed in substantially direct proximity to each other so that one said switch can interact with a neighboring said switch.

27. A switch as claimed in claim 26 wherein said switches are formed and arranged so that said one switch is coupled to a said neighboring switch via a biomolecule binding to respective biomolecule analyte binding sites thereof.

28. A switch as claimed in claim 1 comprising a bio-interactive “

transistor”

for controlling transmission of a data carrier signal, said device comprising

a) a biological macromolecule structure,

b) which structure has, at least, a first conformation and a second conformation different from said first conformation,

c) said structure being anchored to a fixed substrate in a fluid interfaceable condition,

d) so as to permit transformation between said first and second conformations in response to a control signal input,

e) first and second parts of said macromolecule structure mounting respective interacting, first and second, portions of a separation sensitive data carrier signal transmission portion of said transistor device,

f) said first and second parts of said macromolecule structure having different separation distances in said first and second conformations of the structure, and

g) wherein different output signals are obtainable from said signal transmission portion in said first and second conformations of said structure, whereby different control signal inputs can provide different output signals.

33. A method as claimed in claim 29 wherein is provided a switch assembly according to claim 21, in which method said external input signals are applied to said input devices of said switches in temporally separated manner.

29. A method for data acquisition and/or processing, which method includes the steps of:

providing a macromolecular structure having at least one biomolecule analyte binding site, and having at least one ion binding site, and flippable between a plurality of discretely different conformations corresponding to different ion binding conditions at said at least one ion binding site,

at least in the absence of any binding to said biomolecule analyte binding site, said macromolecular structure being provided with at least one electrochemical input device formed and arranged for applying such different ion binding conditions to said ion binding site in response to corresponding external input signals, and said macromolecular structure being in a first said conformation; and

applying an external input signal to said at least one input device so as to change the ion binding conditions at said ion binding site so that said macromolecular structure is flipped from said first conformation to a second said conformation.

30. A method as claimed in claim 29 wherein is provided a said macromolecular structure provided with a said input device comprising an ion reservoir and an ion reservoir control device formed and arranged for at least one of ion capture into and ion release from, said ion reservoir, and wherein said external input signal is applied to said at least one input device so as to capture ions into or release ions from, said ion reservoir.

31. A method as claimed in claim 29 which includes the step of contacting said macromolecular structure with a sample containing a biomolecule analyte.

32. A method as claimed in claim 31 wherein is provided a said macromolecular switch provided with at least one output device component formed and arranged for use in reading of at least one of:

the conformational state of the macromolecular structure and the presence of a target biomolecule analyte bound to a said biomolecule analyte binding site, which method includes the step of reading at least one of;

the conformational state of the macromolecular structure and the presence of a target biomolecule analyte bound to a said biomolecule analyte binding site.

34. A method for detecting a target biomolecule analyte, which method comprises the steps of:

providing a macromolecular structure having at least one biomolecule analyte binding site formed and arranged for binding to a said target biomolecule analyte, and having at least one ion binding site, and flippable between a plurality of discretely different conformations corresponding to different ion binding conditions at said at least one ion binding site, at least in the absence of any binding to said biomolecule analyte binding site, said macromolecular structure being provided with at least one electrochemical input device formed and arranged for applying such different ion binding conditions to said ion binding site in response to corresponding external input signals;

contacting said macromolecular structure with a sample containing a biomolecule analyte; and

probing said macromolecular structure for the presence of biomolecule analyte bound to said biomolecule analyte binding site.

35. A method as claimed in claim 34 wherein is provided a said macromolecular switch provided with at least one output device component comprises part of a separation sensitive output device formed and arranged for use in providing different output signals in said different conformations of said macromolecular structure in use thereof, which method includes the step of reading said separation sensitive output device.

36. A method as claimed in claim 34 which includes the step of applying an external input signal to said at least one input device so as to change the ion binding conditions at said ion binding site so that said macromolecular structure is flipped from one said conformation to a second said conformation.

37. A method as claimed in claim 34 wherein is provided a macromolecular structure formed and arranged so as to be non-enabled for target biomolecule analyte binding in one said conformation and enabled in another said conformation, which method includes the step of switching said macromolecular structure from said non-enabled conformation, to said enabled conformation.