# US 8,784,736 B2 · Systems and devices for isothermal biochemical reactions and/or analysis > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 8,784,736 B2 - Document ID: US8784736B2 - Status: Granted - Kind: B2 - Application number: 13/415,709 - Filed: 2012-03-08 - Published: 2012-07-05 - Granted: 2014-07-22 - Earliest claimed: 2007-03-22 - Assignees: Keck Graduate Institute - Applicants: Robert W. Doebler, II; Christopher Cooney; Anna Hickerson; James D. Sterling; Ali Nadim - Inventors: Robert W. Doebler, II; Christopher Cooney; Anna Hickerson; James D. Sterling; Ali Nadim - Web page: https://patentgrep.com/patent/US8784736B2 ## CPC - B01L 7/52: {with provision for submitting samples to a predetermined sequence of different temperatures, e.g. for treating nucleic acid samples} - C12Q 1/6844: Nucleic acid amplification reactions - G01N 21/0332: {with temperature control (control of temperature G05D23/00; cryostats F17C3/08)} - G01N 21/6428: {Measuring fluorescence of fluorescent products of reactions or of fluorochrome labelled reactive substances, e.g. measuring quenching effects, using measuring "optrodes" (in vivo A61B5/00; immunoassay G01N33/53)} - G01N 21/6486: {Measuring fluorescence of biological material, e.g. DNA, RNA, cells (G01N21/6428 takes precedence)} - B01L 2200/147: Employing temperature sensors - B01L 2300/0609: Holders integrated in container to position an object - B01L 2300/0654: Lenses; Optical fibres - B01L 2300/0681: Filter - B01L 2300/18: Means for temperature control - B01L 2300/1805: Conductive heating, heat from thermostatted solids is conducted to receptacles, e.g. heating plates, blocks - B01L 2300/1827: using resistive heater - G01N 2201/06153: the sources being LED's - Y10T 436/12: Condition responsive control - Y10T 436/25: including sample preparation - B01L: CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE - C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES - G01N: INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES (measuring or testing apparatus or processes other than immunoassay, involving enzymes or microorganisms C12M, C12Q) - Y10T: TECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION ## Abstract An isothermal reaction and analysis system may include a receiver to receive sample holders, a thermal control subsystem to control a temperature of the receiver, an excitation subsystem, a detection subsystem and an analysis subsystem. Excitation sources and/or detectors are positioned to enhance data collection. Sample holders may include filters, selectively blocking and passing wavelengths or bands of electromagnetic radiation. ## Claims ### Claim 1 A system to support biochemical reactions, comprising: a receiver having a plurality of receptacles formed therein, each of the receptacles sized to at least partially receive and support a respective one of a plurality of sample holders; an excitation subsystem including at least a first plurality of excitation sources each with a respective axis of emission and positioned at least partially in the receiver to direct electromagnetic energy toward at least a portion of a respective one of the sample holders received in a respective one of the receptacles of the receiver, the excitation subsystem operable to emit electromagnetic energy with a first wavelength sufficient to excite fluorescence in each of a number of samples contained in respective ones of a plurality of the sample holders while the sample holders are received and supported by the receiver; a detection subsystem that includes a plurality of detectors, each of the detectors having a respective line of sight and positioned to detect fluorescence emission of electromagnetic energy at wavelength that is different from the first wavlength, emitted by a respective sample contained in a respective one of the sample holders that are received and supported by the receiver, each of the detectors positioned such that the respective line of sight of the detector and the respective axis of emission of the respective excitation source are arranged at an angle to reduce the detection of emission directly from the excitation sources; and a thermal control subsystem operable to at least approximately maintain an at least approximately uniform temperature of the receiver at least approximately constant for a period of time sufficient to perform an isothermal reaction on the samples. ### Claim 2 (depends on 1) The system of claim 1 wherein at least one of the plurality of detectors is positioned such that the line of sight of the detector and the axis of emission of the respective excitation source are not coaxial. ### Claim 3 (depends on 1) The system of claim 1 wherein the excitation subsystem includes a second plurality of excitation sources, each of the excitation sources of the second plurality of excitation sources positioned at least partially in the receiver to direct the electromagnetic energy toward at least a portion of a respective one of the sample holders received in a respective one of the receptacles of the receiver, the electromagnetic energy directed by the excitation sources of the second plurality of excitation sources being of a different wavelength than the electromagnetic energy directed by the excitation sources of the first plurality of excitation sources. ### Claim 4 (depends on 3) The system of claim 3 wherein each of the excitation sources is positioned completely within a respective passage in the receiver to direct the electromagnetic energy toward only a base portion of the respective sample holder when the sample holder is positioned in the respective one of the receptacles, the base portion at least proximate a bottom of the sample holder when supported by the receiver. ### Claim 5 (depends on 1) The system of claim 1, further comprising: at least one filter positioned between at least one excitation source and the at least one of the sample holders when the at least one of the sample holders is received by the respective receptacle of the receiver. ### Claim 6 (depends on 1) The system of claim 1, further comprising: at least one filter positioned between at least one of the detectors and the at least one of the sample holders when the at least one of the sample holders is received by the respective receptacle of the receiver, the at least one filter operative to filter at least a portion of the electromagnetic energy emitted by at least one of the excitation sources. ### Claim 7 (depends on 1) The system of claim 1 wherein the thermal control subsystem includes at least one temperature sensor operable to detect a temperature at least proximate the sample holders that is indicative of a temperature of a biochemical reaction within the sample holders and at least one heater element operable to provide heat to the receiver in response to a difference between the detected temperature and at least one set temperature. ### Claim 8 (depends on 7) The system of claim 7 wherein the at least one heater element is conductively thermally coupled to the receiver to provide heat to the sample holders via the receiver. ### Claim 9 (depends on 8) The system of claim 8 wherein the receiver has a large thermal mass with respect to the samples. ### Claim 10 (depends on 1) The system of claim 1 wherein the excitation subsystem includes a number of light emitting diodes at least some of which are operable to emit electromagnetic energy in at least two distinct bands. ### Claim 11 (depends on 1) The system of claim 1 wherein the detectors of the detection subsystem include a number of photodiodes that are responsive to electromagnetic energy in a portion of the electromagnetic spectrum between an ultraviolet portion of the electromagnetic spectrum and an infrared portion of the electromagnetic spectrum, inclusive. ### Claim 12 (depends on 1) The system of claim 1 wherein the excitation subsystem includes a number of light emitting diodes at least some of which are operable to emit electromagnetic energy in a portion of the electromagnetic spectrum between an ultraviolet portion of the electromagnetic spectrum and an infrared portion of the electromagnetic spectrum, inclusive. ### Claim 13 (depends on 1) The system of claim 1, further comprising: the plurality of sample holders, wherein each of the sample holders comprises a material that filters out a portion of electromagnetic energy emitted by the excitation subsystem and passes a portion of electromagnetic energy emitted by the excitation subsystem. ### Claim 14 (depends on 1) The system of claim 1 wherein the receptacles are spaced from one another by a distance selected from 2.25 mm, 4.5 mm and 9 mm. ### Claim 15 (depends on 1) The system of claim 1, further comprising: at least one controller configured to provide control signals to at least one of modulate or pulsate the excitation sources and to select a component of a response signal from the detection elements based on the modulation or pulsation of the excitation sources. ### Claim 16 (depends on 1) The system of claim 1 wherein the at least one controller is configured to perform Fourier transformation on the response signal to improve a signal-to-noise ratio of the system. ### Claim 17 (depends on 1) The system of claim 1, further comprising: at least one controller configured to provide respective control signals to at least one of modulate or pulsate the excitation sources at respective frequencies and to select a component of a response signal from the detection elements based on the modulation or pulsation of the excitation sources. ### Claim 18 (depends on 1) The system of claim 1 wherein there are at least two excitation sources and one detector per receptacle, where each of at least two of the excitation sources per receptacle emit at different wavelengths, and further comprising: at least one controller configured to operate a first one of the two excitations sources of a first receptacle at a first frequency and a second one of the excitation sources of the first receptacle at a second frequency, different from the first frequency, and to demodulate a response signal from the detector based on the first and the second frequencies. ### Claim 19 (depends on 18) The system of claim 18 wherein the at least one controller is configured to determine at least one piece of information about a first biochemical reaction occurring in the first receptacle and at least one piece of information about a second biochemical reaction occurring in the first receptacle based on the demodulated response signal. ### Claim 20 (depends on 1) The system of claim 1, further comprising: at least one controller configured to vary a current supplied to the excitation sources to cause each of the excitation sources to emit a first wavelength at a first time and a second wavelength different from the first wavelength at a second time. ### Claim 21 (depends on 1) The system of claim 1 wherein the biochemical reaction is an isothermal amplification reaction and the sample comprises nucleic acids.