Tuning and calibration features of sequence-detection system

Patent metadata

Field	Value
Publication number	US-11976322-B2
Application number	US-201816623634-A
Country	US
Kind code	B2
Filing date	Sep 14, 2018
Priority date	Sep 15, 2017
Publication date	May 7, 2024
Grant date	May 7, 2024

Abstract

The current document discusses electromechanical sequence detectors that transduce changes in the shape of a shape-change sensor component into an electrical signal from which one or more derived values are generated. In a disclosed implementation, the sequence-detection system comprises a mechanical-change sensor that changes shape when specifically interacting with entities within a target, a shape-to-signal-transduction component that transduces changes in the shape of the mechanical-change sensor into an electrical signal, an analysis subsystem that determines the types of entities within the target using the electrical signal, and a control subsystem that continuously monitors operational characteristics of the sequence-detection system and adjusts sequence-detection system operational parameters.

First claim

The invention claimed is:

1. A sequence-detection system comprising:
a mechanical-change sensor that exhibits one or more mechanical changes when specifically interacting with entities within a target, each entity having a type;
a mechanical-change-to-signal transducer that transduces the one or more mechanical changes into a signal;
an analysis subsystem that determines a sequence of entity types within the target using the signal; and
a control subsystem that
is configured to initialize the sequence-detection system in accordance with one or more operational parameters,
initializes the sequence-detection system in accordance with one or more operational parameters,
is configured to control the sequence-detection system to generate, collect samples of, and analyze the signal to determine the sequence of entity types within the target, and
controls the sequence-detection system to generate, collect samples of, and analyze the signal to determine the sequence of entity types within the target,
wherein the target is a primer-associated nucleic-acid template polymer;
wherein the entities are nucleotide monomers;
wherein the mechanical-change sensor is a nucleic-acid-polymerase mechanical-change sensor contained within a first solution-containing chamber; and
wherein the mechanical-change-to-signal transducer further comprises
a variable resistor that regulates flow of an electrical current through a porin channel that provides fluid communication between the first solution-containing chamber and a second solution-containing chamber,
a mechanical coupler that couples the nucleic-acid-polymerase mechanical-change sensor to the variable resistor, and
a current-to-voltage converter that outputs a voltage signal that varies in correspondence with a rate of flow of the electrical current through the porin channel,
wherein the one or more operational parameters include:
a voltage magnitude of a read voltage applied across the porin channel and a polarity of the read voltage;
a voltage magnitude of a noise-inhibition voltage applied across the porin channel and a polarity of the noise-inhibition voltage; and
a voltage magnitude of a configuration voltage applied across the porin channel and a polarity of the configuration voltage.

2. The sequence-detection system of claim 1
wherein the polarity of the noise-inhibition voltage is opposite from the polarity of the read voltage; and
wherein the polarity of the noise-inhibition voltage is opposite from the polarity of the configuration voltage.

3. The sequence-detection system of claim 1 wherein the control subsystem configures the sequence-detection system by:
applying the configuration voltage across the porin channel with the configuration polarity to seat the nucleic-acid-polymerase mechanical-change sensor within the porin.

4. The sequence-detection system of claim 3 wherein, following configuration of the sequence-detection system, the control subsystem adjusts the read voltage magnitude to position a reporter region of a nucleic-acid-polymer tether at a reference displacement.

5. The sequence-detection system of claim 1 wherein, following configuration of the sequence-detection system, the control subsystem controls the sequence-detection system to generate, collect samples of, and analyze the signal to determine the sequence of entity types within the target by:
iteratively
applying the read voltage across the porin channel with the polarity of the read voltage for a first time period, during which the voltage output signal is sampled, stored in a memory, and analyzed by the analysis subsystem, and
applying the noise-inhibition voltage across the porin channel with the polarity of the noise-inhibition voltage for a second time period
until a termination condition occurs.

6. The sequence-detection system of claim 5 wherein lengths of the first and second time periods are specified by operational parameters.

7. The sequence-detection system of claim 5 wherein termination conditions include:
a power-off event; and
a decrease in a rate of sequence-information generation below a threshold level by the sequence-detection system.

8. The sequence-detection system of claim 1 wherein the operational parameters include:
temperature;
pH of solutions in the first and second solution-containing chambers; and
contents of the solutions in the first and second solution-containing chambers.

9. The sequence-detection system of claim 8 wherein the operational parameter related to the contents of the solutions in the first and second solution-containing chambers encompasses one or more of:
one or more types of ionized salts in the solutions;
concentrations of the one or more types of ionized salts in the solutions;
one or more types of nucleotide polyphosphates in the solution in the first solution-containing chamber;
concentrations of the one or more types of nucleotide polyphosphates in the solution in the first solution-containing chamber;
one or more types of primer-associated nucleic-acid template polymers in the solution in the first solution-containing chamber;
concentrations of the one or more types of primer-associated nucleic-acid template polymers in the solution in the first solution-containing chamber; and
a type and structure of a nucleic-acid-polymer tether.

10. The sequence-detection system of claim 8 wherein the operational parameter related to the contents of the solution in the solution in the first solution-containing chamber is adjusted to control the rate of sequential specific interaction of the mechanical-change sensor with entities within the target.

11. The sequence-detection system of claim 8 wherein a primer with a 3′ dideoxynucleotide monomer is employed to constrain the sequence-detection system to specifically interact with a single entity.

12. The sequence-detection system of claim 1 wherein a signal response of the sequence-detection system is configured by selecting a reporter region with a nucleotide-monomer sequence corresponding to the signal response.

Assignees

• Illumina Inc

Inventors

• Mandell Jeffrey G
• Gunderson Kevin L
• Keehan Michael Gregory
• Garcia Erin Christine

Classifications

• C12Q1/6869 Primary

  Methods for sequencing · CPC title

• B01L3/502707

  characterised by the manufacture of the container or its components · CPC title

• B01L3/502715

  characterised by interfacing components, e.g. fluidic, electrical, optical or mechanical interfaces · CPC title

• G01N27/44791

  Microapparatus (sample containers with integrated microfluidic structures B01L3/5027) · CPC title

• G01N33/48721

  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) · CPC title