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US 2026/0120813 A1Published application
Methods and systems for single molecule tracking in cell-free systems
AssigneeEikon Therapeutics, Inc.
InventorsMarkus Seeger, Daniel Anderson, Stephanie Johnson, Zhengjiang Zhang
Life of this patent
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Abstract
The present disclosure relates to single molecule tracking methods, including high throughput methods, for analyzing molecules in cell-free samples. The present disclosure further provides systems for performing such methods.
Claims259
A method of identifying an interaction between a target molecule and a test molecule comprising:
- (a) contacting a cell-free sample comprising a plurality of the target molecule with a plurality of the test molecule;
- (b) tracking a plurality of the target molecules over time to provide a plurality of spatiotemporal trajectories and/or measurements of rotational motion;
- (c) analyzing the plurality of spatiotemporal trajectories and/or measurements of rotational motion to determine the target molecule's movement in the presence of the test molecule;
- and
- (d) comparing the target molecule's movement obtained in (c) with a reference target molecule's movement, wherein the reference target molecule's movement is the movement of the target molecule in the absence of the test molecule;
- wherein a change in the target molecule's movement compared to the reference target molecule's movement indicates an interaction between the target molecule and the test molecule.
3 more elements
A method for identifying an interaction between a test molecule and a target protein comprising a disordered domain comprising:
- (a) contacting a cell-free sample comprising a plurality of the target protein with a plurality of the test molecule;
- (b) tracking a plurality of the target protein over time to provide a plurality of spatiotemporal trajectories and/or measurements of rotational motion;
- (c) analyzing the plurality of spatiotemporal trajectories and/or measurements of rotational motion to determine the target protein's movement in the presence of the test molecule;
- and
- (d) comparing the target protein's movement obtained in (c) with a reference target protein's movement, wherein the reference target protein's movement is the movement of the target protein in the absence of the test molecule;
- wherein a change in the movement of the target protein comprising the disordered domain compared to the reference target protein's movement indicates an interaction between the target protein comprising the disordered domain and the test molecule.
3 more elements
A method for analyzing a target molecule in a test solution comprising:
- (a) tracking a plurality of the target molecules over time in the test solution to provide a plurality of spatiotemporal trajectories and/or measurements of rotational motion;
- (b) analyzing the plurality of spatiotemporal trajectories and/or measurements of rotational motion to determine the target molecule's movement in the test solution;
- and
- (c) comparing the target molecule's movement obtained in (b) with a reference target molecule's movement, wherein the reference target molecule's movement is the movement of the target molecule in a reference solution;
- wherein:
- (i) a change in the target molecule's movement compared to the reference target molecule's movement indicates that the target molecule is affected by the test solution;
- or (ii) no change in the target molecule's movement compared to the reference target molecule's movement indicates that the target molecule is not affected by the test solution.
4 more elements
A method for determining the form of a target molecule comprising:
- (a) tracking a plurality of the target molecules over time in a cell-free sample to provide a plurality of spatiotemporal trajectories and/or measurements of rotational motion;
- (b) analyzing the plurality of spatiotemporal trajectories and/or measurements of rotational motion to determine the target molecule's movement;
- and
- (c) comparing the target molecule's movement obtained in (b) with a reference target molecule's movement, wherein the reference target molecule's movement is the movement of one form of the target molecule;
- wherein:
- (i) a change in the target molecule's movement compared to the reference target molecule's movement indicates that the target molecule is of a different form than the reference target molecule;
- or (ii) no change in the target molecule's movement compared to the reference target molecule's movement indicates that the target molecule is of the same form as the reference target molecule.
4 more elements
A method for identifying a test molecule that can distinguish between at least two target molecules comprising:
- (a) contacting a cell-free sample comprising a plurality of a first target molecule with a plurality of the test molecule;
- (b) tracking a plurality of the first target molecules over time to provide a plurality of spatiotemporal trajectories and/or measurements of rotational motion;
- (c) analyzing the plurality of spatiotemporal trajectories and/or measurements of rotational motion to determine the first target molecule's movement in the presence of the test molecule;
- (d) contacting a cell-free sample comprising a plurality of a second target molecule with a plurality of the test molecule;
- (e) tracking a plurality of the second target molecules over time to provide a plurality of spatiotemporal trajectories and/or measurements of rotational motion;
- (f) analyzing the plurality of spatiotemporal trajectories and/or measurements of rotational motion to determine the second target molecule's movement in the presence of the test molecule;
- and
- (g) comparing the first and second target molecules' movement obtained in (c) and (f);
- wherein a change in the movement of the first and second target molecules indicates that the test molecule can distinguish between the two target molecules.
6 more elements
A method for identifying one or more test molecules that induce a conformational change in a target molecule comprising:
- (a) contacting cell-free samples comprising a plurality of the target molecule with a plurality of test molecules, where each sample is contacted with a different test molecule;
- (b) tracking a plurality of the target molecules in each sample over time to provide a plurality of spatiotemporal trajectories and/or measurements of rotational motion;
- (c) analyzing the plurality of spatiotemporal trajectories and/or measurements of rotational motion to determine the target molecule's movement in the presence of each of the different test molecules;
- and
- (d) comparing the target molecule's movement obtained in (c) with a reference target molecule's movement, wherein the reference target molecule's movement is the movement of the target molecule in the presence of a test molecule that does not induce a conformational change in the target molecule;
- wherein a change in the target molecule's movement compared to the reference target molecule's movement indicates an interaction between the target molecule and the one or more test molecules that induce a conformational change in the target molecule.
3 more elements
A method for determining a dose response for the interaction of a target molecule and a test molecule comprising:
- (a) contacting a plurality of cell-free samples comprising a plurality of the target molecule with the test molecule, where plurality of cell-free samples are contacted with a range of test molecule doses;
- (b) tracking a plurality of the target molecules over time in the presence of the range of doses of the test molecule to provide a plurality of spatiotemporal trajectories and/or measurements of rotational motion;
- (c) analyzing the plurality of spatiotemporal trajectories and/or measurements of rotational motion of the target molecules in the presence of the range of doses of the test molecule to determine the target molecule's movement at each dose of test molecule;
- (d) comparing the target molecule's movement obtained at different test molecule doses in step (c) to determine the dose response of the target molecule to the test molecule.
1 more element
A method for determining a difference in dose response to a test molecule by two target molecules comprising:
- (a) contacting a first plurality of cell-free samples comprising a plurality of the first target molecule with the test molecule, where first plurality of cell-free samples are contacted with a range of test molecule doses;
- (b) tracking a plurality of the target molecules over time in the presence of the range of doses of the test molecule to provide a first plurality of spatiotemporal trajectories and/or measurements of rotational motion;
- (c) analyzing the plurality of spatiotemporal trajectories and/or measurements of rotational motion of the target molecules in the presence of the range of doses of the test molecule to determine the first target molecule's movement at each concentration of test molecule;
- (d) comparing the target molecule's movement obtained at different test molecule doses in step (c) to determine the dose response of the target molecule to the test molecule;
- (e) repeating steps (a)-(d) with a second target molecule to determine the dose response of the second target molecule to the test molecule;
- and
- (f) comparing the dose response of the first target molecule to the dose response of the second target molecule to determine the difference in the response of the first and second target molecules to the test molecule.
4 more elements
A method for identifying a test molecule that can distinguish between at least two target molecules comprising:
- (a) contacting a cell-free sample comprising a plurality of a first target molecule and a plurality of a second target molecule with a plurality of the test molecule;
- (b) tracking a plurality of the first target molecules over time to provide a plurality of spatiotemporal trajectories and/or measurements of rotational motion;
- (c) analyzing the plurality of spatiotemporal trajectories and/or measurements of rotational motion to determine the first target molecule's movement in the presence of the test molecule;
- (d) tracking a plurality of the second target molecules over time to provide a plurality of spatiotemporal trajectories and/or measurements of rotational motion;
- (e) analyzing the plurality of spatiotemporal trajectories and/or measurements of rotational motion to determine the second target molecule's movement in the presence of the test molecule;
- and
- (f) comparing the first and second target molecules' movement obtained in (c) and (f);
- wherein a change in the movement of the first and second target molecules indicates that the test molecule can distinguish between the two target molecules.
5 more elements
A method for analyzing a test solution comprising a target molecule comprising:
- (a) tracking a plurality of a target molecule over time in the test solution to provide a plurality of spatiotemporal trajectories and/or measurements of rotational motion;
- (b) analyzing the plurality of spatiotemporal trajectories and/or measurements of rotational motion to determine the target molecule's movement in the test solution;
- and
- (c) comparing the target molecule's movement obtained in (b) with a reference target molecule's movement, wherein the reference target molecule's movement is the movement of the target molecule in a reference solution;
- wherein:
- the comparing of step (c) is used to determine a property of the test solution.
3 more elements
Dependencies are inferred from the claim text.