Attorney Docket No.: 021766-0001 IOUS
`
`PATENT APPLICATION
`
`SYSTEMS AND METHODS FOR FLUORESCENCE DETECTION
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`WITH A MOVABLE DETECTION MODULE
`
`Inventors:
`
`Igor Kordunsky
`19 Payne Road
`Newton, MA 02461-1816
`Citizenship: U.S.A.
`
`Jeffrey A. Goldman
`24 Washington Drive
`Acton, MA 01720
`Citizenship: U.S.A.
`
`Michael J. Finney
`489 Douglass Street
`San Francisco, CA 94114
`Citizenship: U.S.A.
`
`Assignee:
`
`Bio-Rad Laboratories
`1000 Alfred Nobel Drive
`Hercules, CA
`
`Entity:
`
`Large
`
`TOWNSEND and TOWNSEND and CREW LLP
`Two Embarcadero Center, 8th Floor
`San Francisco, California 94111-3834
`Tel: 415-576-0200
`
`Agilent Exhibit 1207
`Page 1 of 447
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`

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`Attorney Docket No.: 021766-0001 lOUS
`
`PATENT
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`SYSTEMS AND METHODS FOR FLUORESCENCE DETECTION
`
`WITH A MOVABLE DETECTION MODULE
`
`5
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`CROSS-REFERENCES TO RELATED APPLICATIONS
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`[0001] This application is a continuation of Application No. 10/431,708, filed May 8, 2003,
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`entitled "Systems and Methods for Fluorescence Detection with a Movable Detection
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`Module," which disclosure is incorporated herein by reference for all purposes.
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`10
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`BACKGROUND OF THE INVENTION
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`[0002] The present invention relates in general to fluorescence detection systems and in
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`particular to a fluorescence detection system having a movable excitation/detection module
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`for use with a thermal cycler.
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`[0003] Thermal cyclers are known in the art. Such devices are used in a variety of
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`15
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`processes for creation and detection of various molecules of interest, e.g., nucleic acid
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`sequences, in research, medical, and industrial fields. Processes that can be performed with
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`conventional thermal cyders include but are not limited to amplification of nucleic acids
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`using procedures such as the polymerase chain reaction (PCR). Such amplification processes
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`are used to increase the amount of a target sequence present in a nucleic acid sample.
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`20
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`[0004] Numerous techniques for detecting the presence and/or concentration of a target
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`molecule in a sample processed by a thermal cycler are also known. For instance, fluorescent
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`labeling may be used. A fluorescent label (or fluorescent probe) is generally a substance
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`which, when stimulated by an appropriate electromagnetic signal or radiation, absorbs the
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`radiation and emits a signal (usually radiation that is distinguishable, e.g., by wavelength,
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`25
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`from the stimulating radiation) that persists while the stimulating radiation is continued, i.e. it
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`fluoresces. Some types of fluorescent probes are generally designed to be active only in the
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`presence of a target molecule (e.g., a specific nucleic acid sequence), so that a fluorescent
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`response from a sample signifies the presence of the target molecule. Other types of
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`fluorescent probes increase their fluorescence in proportion to the quantity of double-stranded
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`30 DNA present in the reaction. These types of probes are typically used where the
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`amplification reaction is designed to operate only on the target molecule.
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`Agilent Exhibit 1207
`Page 2 of 447
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`

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`[0005] Fluorometry involves exposing a sample containing the fluorescent label or probe to
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`stimulating (also called excitation) radiation, such as a light source of appropriate
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`wavelength, thereby exciting the probe and causing fluorescence. The emitted radiation is
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`detected using an appropriate detector, such as a photodiode, photomultiplier, charge-coupled
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`5
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`device (CCD), or the like.
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`[0006] Fluorometers for use with fluorescent-labeled samples are known in the art. One
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`type of fluorometer is an optical reader, such as described by Andrews et al. in U.S. Patent
`
`No. 6,043,880. A sample plate containing an array of samples is inserted in the optical
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`reader, which exposes the samples to excitation light and detects the emitted radiation. The
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`10
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`usefulness of optical readers is limited by the need to remove the sample plate from the
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`thermal cycler, making it difficult to monitor the progress of amplification.
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`[0007] One improvement integrates the optical reader with a thermal cycler, so that the
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`sample plate may be analyzed without removing it from the thermal cycler or interrupting the
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`PCR process. Examples of such combination devices are described in U.S. Patent No.
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`15
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`5,928,907, U.S. Patent No. 6,015,674, U.S. Patent No. 6,043,880, U.S. Patent No. 6,144,448,
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`U.S. Patent No. 6,337,435, and U.S. Patent No. 6,369,863. Such combination devices are
`
`useful in various applications, as described, e.g., in U.S. Patent No. 5,210,015, U.S. Patent
`
`No. 5,994,056, U.S. Patent No. 6,140,054, and U.S. Patent No. 6,174,670.
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`[0008] Existing fluorometers suffer from various drawbacks. For instance, in some
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`20
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`existing designs, different light sources and detectors are provided for different sample wells
`
`in the array. Variations among the light sources and/or detectors lead to variations in the
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`detected fluorescent response from one well to the next. Alternatively, the light source and/or
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`detector may be arranged in optical communication with more than one of the wells, with
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`different optical paths to and/or from each well. Due to the different optical paths, the
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`25
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`detected fluorescent response varies from one sample well to the next. To compensate for
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`such variations, the response for each sample well must be individually calibrated. As the
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`number of sample wells in an array increases, this becomes an increasingly time-consuming
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`task, and errors in calibration may introduce significant errors in subsequent measurements.
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`[0009]
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`In addition, existing fluorometers generally are designed such that the light sources
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`30
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`and detectors are fixed parts of the instrument. This limits an experimenter's ability to adapt
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`a fluorometer to a different application. For instance, detecting a different fluorescent label
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`generally requires using a different light source and/or detector. Many existing fluorometers
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`2
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`Agilent Exhibit 1207
`Page 3 of 447
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`

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`make it difficult for an experimenter to reconfigure light sources or detectors, thus limiting
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`the variety of fluorescent labels that may be used.
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`[0010]
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`It is also difficult to perform concurrent measurements of a number of different
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`fluorescent labels that may be present in a sample (or in different samples). As described
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`5
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`above, to maximize the data obtained in an assay, experimenters often include multiple
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`fluorescent labeling agents that have different excitation and/or emission wavelengths. Each
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`labeling agent is adapted to bind to a different target sequence, in principle allowing multiple
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`target sequences to be detected in the same sample. Existing fluorometers, however, do not
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`facilitate such multiple-label experiments. Many fluorometers are designed for a single
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`10
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`combination of excitation and emission wavelengths. Others provide multiple light sources
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`and detectors to allow detection of multiple labels; however, these configurations often allow
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`only one label to be probed at a time because the excitation wavelength of one label may
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`overlap the emission wavelength of another label; excitation light entering the detector would
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`lead to incorrect results. Probing multiple labels generally cannot be done in parallel,
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`15
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`slowing the data collection process.
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`[0011] Therefore, an improved fluorometer for a thermal cycler that overcomes these
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`disadvantages would be desirable.
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`BRIEF SUMMARY OF THE INVENTION
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`20
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`[0012] Embodiments of the present invention provide fluorescence detection in a thermal
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`cycling apparatus. According to one aspect of the invention, a fluorescence detection
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`apparatus for analyzing samples located in a plurality of wells in a thermal cycler includes a
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`support structure attachable to the thermal cycler and a detection module movably mountable
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`on the support structure. The detection module includes an excitation light generator and an
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`25
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`emission light detector, both disposed within the detection module. When the support
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`structure is attached to the thermal cycler and the detection module is mounted on the support
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`structure, the detection module is movable so as to be positioned in optical communication
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`with different ones of the plurality of wells.
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`[0013] According to another aspect of the invention, the detection module may include two
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`30
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`or more excitation light generators and two or more emission light detectors arranged to form
`
`two or more excitation/detection pairs. In one embodiment, the excitation/detection pairs are
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`arranged such that each excitation/detection pair is simultaneously positionable in optical
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`3
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`Agilent Exhibit 1207
`Page 4 of 447
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`

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`contact with a different one of the plurality of wells. In an alternative embodiment,
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`excitation/detection pairs are arranged such that when a first one of the excitation/detection
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`pairs is positioned in optical contact with any one of the plurality of wells, a different one of
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`the excitation/detection pairs is not in optical contact with any one of the plurality of wells.
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`5
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`In some embodiments, the detection module is detachably mounted on the support structure,
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`thereby enabling a user to replace the detection module with a different detection module.
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`[0014] According to yet another aspect of the invention, a method for detecting the
`
`presence of a target molecule in a solution is provided. A plurality of samples is prepared,
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`each sample containing a fluorescent probe adapted to bind to a target molecule. Each
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`10
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`sample is placed in a respective one of a number of sample wells of a thermal cycler
`
`instrument, the thermal cycler instrument having a detection module movably mounted
`
`therein, the detection module including an excitation/detection channel, the
`
`excitation/detection channel including an excitation light generator disposed within the
`
`detection module and an emission light detector disposed within the detection module. The
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`15
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`thermal cycler instrument is used to stimulate a reaction, and the sample wells are scanned to
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`detect a fluorescent response by moving the detection module and activating the
`
`excitation/detection channel. During the scanning, the detection module is moved such that
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`the excitation/detection channel is sequentially positioned in optical communication with
`
`each of the plurality of sample wells. Where the detection module includes multiple
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`20
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`excitation/detection pairs or channels, channels may be active in parallel or sequentially.
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`[0015] The following detailed description together with the accompanying drawings will
`
`provide a better understanding of the nature and advantages of the present invention.
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`25
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`[0016) Fig. 1 is a perspective view of a thermal cycling apparatus according to an
`
`BRIEF DESCRIPTION OF THE DRAWINGS
`
`embodiment of the present invention;
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`[0017) Fig. 2 is an exploded view of a lid assembly for a thermal cycling apparatus
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`according to an embodiment of the present invention;
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`[0018] Fig. 3 is a bottom view of a fluorometer assembly for a thermal cycling apparatus
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`30
`
`according to an embodiment of the present invention;
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`4
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`Agilent Exhibit 1207
`Page 5 of 447
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`

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`[0019) Fig. 4 is a top view of detection module according to an embodiment of the present
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`invention;
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`[0020] Figs. 5A-B are bottom views of detection modules according to alternative
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`embodiments of the present invention;
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`5
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`[0021] Fig. 6 is a schematic diagram of an excitation/detection pair for a detection module
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`according to an embodiment of the present invention;
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`[0022] Fig. 7 is a block diagram illustrating electrical connections for a lid assembly for a
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`thermal cycling apparatus according to an embodiment of the present invention; and
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`[0023] Fig. 8 is a flow diagram of a process for using a thermal cycler having a
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`10
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`fluorescence detection system according to an embodiment of the present invention.
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`DETAILED DESCRIPTION OF THE INVENTION
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`[0024] An exemplary apparatus embodiment of the present invention will be described with
`
`reference to the accompanying drawings, in which like reference numerals indicate
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`15
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`corresponding parts. Methods of using the apparatus will also be described. It is to be
`
`understood that embodiments shown and described herein are illustrative and not limiting of
`
`the invention.
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`I. Exemplarv Apparatus
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`[0025] Fig. 1 is a perspective view of a thermal cycling apparatus 100 according to an
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`20
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`embodiment of the present invention. Apparatus 100 consists of a base unit 110 and a lid
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`assembly 112. Base unit 110, which may be of conventional design, provides power and
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`control functions for a thermal cycling process via conventional electronic components (not
`
`shown), such as programmable processors, clocks, and the like. Base unit 110 also provides
`
`a user interface 116 that may include a keypad 118 and an LCD display screen 120, enabling
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`25
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`a user to control and monitor operation of the thermal cycler. Base unit 110 connects to an
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`external power source (e.g., standard 120 V ac power) via a power cable 121. Some
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`examples of base unit 110 include the DNA Engine®, Dyad™, and TetradTM thermal cyders
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`sold by MJ Research, Inc., assignee of the present application.
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`[0026] Lid assembly 112 includes a sample unit and a fluorescence detection apparatus,
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`30
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`disposed within a lid 122; these components will be described below. Lid 122 has a handle
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`5
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`Agilent Exhibit 1207
`Page 6 of 447
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`

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`124 to aid in its placement on and removal from base unit 110, and ventilation holes 126. Lid
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`122 provides optical and thermal isolation for the components inside lid assembly 112.
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`[0027] Fig. 2 is an exploded view of the inside oflid assembly 112. Shown are a sample
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`unit 202, a lid heater 204, and a fluorometer assembly 206. Sample unit 202 contains a
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`5
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`number of sample wells 210 arranged in a regular array (e.g., an 8x12 grid). In one
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`embodiment, each sample well 210 holds a removable reaction vessel (not shown), such as a
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`tube, that contains a nucleic acid sample to be tested, together with appropriate PCR reactants
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`(buffers, primers and probes, nucleotides, and the like) including at least one fluorescent label
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`or probe adapted to bind to or otherwise respond to the presence of a target nucleic acid
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`10
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`sequence. The reaction vessels are advantageously provided with transparent sample caps
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`(not shown) that fit securely over the tops of the vessels to prevent cross-contamination of
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`samples or spillage during handling. Reaction vessels may also be sealed in other ways,
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`including the use of films such as Microseal®B (made by MJ Research, Inc.), wax products
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`such as Chill-out™ (made by MJ Research, Inc.), or mineral oil. In an alternative
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`15
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`configuration, a removable sample tray (not shown) that holds one or more distinct samples
`
`at locations corresponding to sample wells 210 is used. The sample tray may also be sealed
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`in any of the ways described above.
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`[0028] Sample unit 202 also includes heating elements (e.g., Peltier-effect thermoelectric
`
`devices), heat exchange elements, electrical connection elements for connecting the heating
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`20
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`elements to base unit 110, and mechanical connection elements. These components (not
`
`shown) may be of conventional design. Sample unit 202 also provides electrical connections
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`for lid heater 204 and fluorometer assembly 206 via multiwire cables 212, which are
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`detachably connected to connectors 214.
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`[0029] Lid heater 204 has holes 220 therethrough, matching the size and spacing of the
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`25
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`sample wells 210, and electronically controlled heating elements (not shown). Lid heater 204
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`is coupled to lid 122. The coupling mechanism (not shown) is advantageously movable (e.g.,
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`lid heater 204 may be attached to lid 122 by a hinge) in order to provide access to fluorometer
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`assembly 206 when lid 122 is removed from sample unit 202. When lid 122 is in place on
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`sample unit 202, supports 224 hold lid heater 204 in position. Lower portions 226 of
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`30
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`supports 224 are advantageously designed to compress lid heater 204 toward sample unit 202,
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`thereby reducing the possibility of sample evaporation during operation of apparatus 100.
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`This compression also allows reaction vessels of different sizes to be used. Lid heater 204 is
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`6
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`Agilent Exhibit 1207
`Page 7 of 447
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`

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`used to control the temperature of the sample caps (or other sealants) of reaction vessels
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`sample wells 210, in order to prevent condensation from forming on the caps during thermal
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`cycling operation.
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`[0030] Lid heater 204 advantageously includes one or more calibration elements 222
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`5
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`positioned between selected ones of holes 220 or in other locations away from the holes, such
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`as near the periphery of lid heater 204. Calibration elements 222 provide a known
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`fluorescence response and may be used to calibrate fluorescence detectors in fluorometer
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`assembly 206. Calibration elements 222 may be made, e.g., of a fluorescent coating on a
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`glass or plastic substrate, or they may consist of a plastic with a dye impregnated in it,
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`10
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`fluorescent glass, or a fluorescent plastic such as polyetherimide (PEI). Neutral-density or
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`other types of filters may be placed over the fluorescent material in order to avoid saturating
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`the fluorescence detectors. In general, any material may be used, provided that its
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`fluorescence characteristics are sufficiently stable over time with the application of light
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`(photo-bleaching) and heat. To the extent practical, the effect of temperature on the
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`15
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`fluorescence response is advantageously minimized. Where multiple calibration elements
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`222 are provided, different materials may be used for different ones of the calibration
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`elements. In an alternative embodiment, lid heater 204 may be omitted, and calibration
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`elements 222 may be disposed on the surface of sample unit 202.
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`[0031] Sample unit 202 and lid heater 204 may be of conventional design. Examples of
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`20
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`suitable designs include sample unit and lid heater components of the various Alpha TM
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`modules sold by MJ Research, Inc., assignee of the present application.
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`[0032] Fluorometer assembly 206 includes a support frame or platform 230 fixedly
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`mounted inside lid 122. Movably mounted on the underside of support frame 230 is a shuttle
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`232, which holds a detection module 234. Shuttle 232 is movable in two dimensions so as to
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`25
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`position detection module 234 in optical communication with different ones of the sample
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`wells 210 in sample unit 202 through the corresponding holes 220 in lid heater 204. Support
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`frame 230 and supports 224 are advantageously dimensioned such that when lid 122 is
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`positioned in base unit 110 and closed, detection module 234 is held in close proximity to lid
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`heater 204; one of skill in the art will appreciate that this arrangement reduces light loss
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`30
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`between the sample wells and the detection module.
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`[0033] Fig. 3 is a bottom view of fluorometer assembly 206, showing a movable mounting
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`of shuttle 232 and detection module 234. In this embodiment, translation stages driven by
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`7
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`Agilent Exhibit 1207
`Page 8 of 447
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`

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`stepper motors are used to move the shuttle 232, to which detection module 234 is detachably
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`coupled, to a desired position. Specifically, support platform 230 has an x-axis stepper motor
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`302 and a lead screw 304 attached thereto. Stepper motor 302 operates to tum lead screw
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`304, thereby moving a translation stage 306 along the x direction (indicated by arrow). Limit
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`5
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`switches 308 are advantageously provided to restrict the motion of translation stage 306 to an
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`appropriate range, large enough to allow detection module 234 to be placed in optical contact
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`with any of the wells while preventing translation stage 306 from contacting other system
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`components, such as stepper motor 302.
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`[0034] Translation stage 306 has a y-axis stepper motor 316 and a lead screw 318 mounted
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`10
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`thereon. Stepper motor 316 operates to tum lead screw 318, thereby moving shuttle 232
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`along they direction (indicated by arrow). Limit switches 320 are advantageously provided
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`to restrict the motion of shuttle 232 to an appropriate range, large enough to allow detection
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`module 234 to be placed in optical contact with any of the wells, while preventing shuttle 232
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`from contacting other system components, such as stepper motor 316.
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`15
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`[0035] Stepper motors 302, 316, lead screws 304, 318, and limit switches 308, 320 may be
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`of generally conventional design. It will be appreciated that other movable mountings may
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`be substituted. For example, instead of directly coupling the motors to the lead screws,
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`indirect couplings such as chain drives or belt drives may be used. Chain drives, belt drives,
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`or other drive mechanisms may also be used to position the detection module without lead
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`20
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`screws, e.g., by attaching a translation stage to the chain, belt, or other drive mechanism.
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`Other types of motors, such as servo motors or linear motors, may also be used. Different
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`drive mechanisms may be used for different degrees of freedom.
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`[0036] Shuttle 232 holds detection module 234 via connectors 330, 331. Connectors 330,
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`331 which may vary in design, are configured to support and align detection module 234 on
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`25
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`the underside of shuttle 232. The connectors are advantageously adapted to allow easy
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`insertion and removal of detection module 234, to facilitate replacement of the detection
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`module. In one embodiment, connectors 330 provide mounting for a cylindrical member (not
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`shown) that pivotably holds an edge of detection module 234, while connectors 331 include
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`ball plungers mounted on shuttle 232 that are insertable into corresponding receptacles on
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`30
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`detection module 234. Electrical connections (not shown) between shuttle 232 and detection
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`module 234 may also be provided, as will be described below.
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`8
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`Agilent Exhibit 1207
`Page 9 of 447
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`[0037] Fig. 4 is a top view of detection module 234. Detection module 234 includes
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`fittings 420 that couple to corresponding connectors 330 on the underside of shuttle 232,
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`thereby securing detection module 234 in place so that it moves as a unit with shuttle 232.
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`Detection module 234 also includes an electrical connector 424 that couples to a
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`5
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`corresponding electrical connector on the underside of shuttle 232, thereby allowing control
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`and readout signals to be provided to and obtained from detection module 234.
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`[0038] Fig. 5A is a bottom view of one embodiment of detection module 234, showing four
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`openings 502, 504, 506, 508 for four independently controlled fluorescent
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`excitation/detection channels (also referred to as "excitation/detection pairs") arranged inside
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`10
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`the body of detection module 234. Examples of excitation/detection channels will be
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`described below. The spacing of openings 502, 504, 506, 508 corresponds to the spacing of
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`sample wells 210. Thus, when opening 502 is placed in optical communication with one of
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`the sample wells 210, openings 504, 506, and 508 are each in optical communication with a
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`different one of the sample wells 210. Openings 502, 504, 506, 508 may simply be holes
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`15
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`through the bottom surface of detection module 234, or they may be made of any substance
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`that has a high degree of transparency to the excitation and detection light wavelengths of
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`their respective channels.
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`[0039] Fig. 5B is a bottom view of a detection module 234' according to an alternative
`
`embodiment of the invention. In this embodiment, four openings 512, 514, 516, 518 are
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`20
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`provided, but they are arranged in a staggered fashion so that only one opening at a time may
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`be in optical communication with any of the sample wells. This configuration is useful for
`
`reducing cross-talk between the excitation/detection pairs.
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`[0040] Fig. 6 is a schematic diagram illustrating a configuration of optical elements for an
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`excitation/detection channel (or excitation/detection pair) 600 according to an embodiment of
`
`25
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`the invention. Detection module 234 may include one or more instances of
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`excitation/detection pair 600, each of which provides an independent fluorescence detection
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`channel. Excitation/detection pair 600 is arranged inside opaque walls 602, which provide
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`optical isolation from other excitation/detection pairs that may be included in detection
`
`module 234, as well as from external light sources. An excitation light path 604 includes a
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`30
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`light-emitting diode (LED) or other light source 606, a filter 608, a lens 610, and a beam
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`splitter 612. A detection light path 620 includes beam splitter 612, a filter 624, a lens 626,
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`and a photodiode or other photodetector 628. Beam splitter 612 is advantageously selected to
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`9
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`Agilent Exhibit 1207
`Page 10 of 447
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`

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`be highly transparent to light of the excitation wavelength and highly reflective of light at the
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`detection (fluorescent response) wavelength.
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`[0041] The components of excitation light path 604 are arranged to direct excitation light of
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`a desired wavelength into a reaction vessel 616 held in a sample well 210 of sample block
`
`5
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`202. The desired wavelength depends on the particular fluorescent labeling agents included
`
`in reaction vessel 616 and is controlled by selection of an appropriate LED 606 and filter 608.
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`Optical communication between the excitation/detection pair 600 and reaction vessel 616 is
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`provided by opening 502 in opaque walls 602 and a hole 220 through lid heater 204, as
`
`described above. To maximize light transmission to and from excitation/detection pair 600,
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`10
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`the space between opening 502 and lid heater 204 is advantageously made small during
`
`operation.
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`[0042] Excitation light that enters reaction vessel 616 excites the fluorescent label or probe
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`therein, which fluoresces, thereby generating light of a different wavelength. Some of this
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`light exits reaction vessel 616 on detection light path 620 and passes through opening 502.
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`15
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`Beam splitter 612 directs a substantial portion of the fluorescent light through filter 624,
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`which filters out the excitation frequency, and lens 626, which focuses the light onto the
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`active surface of photodiode 628. Photodiode 628 generates an electrical signal in response
`
`to the incident light. This electrical signal is transmitted by a readout signal path 630 to
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`circuit board 634, which routes the signal to electrical connector 424 for readout. Circuit
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`20
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`board 634 and/or signal path 630 may also include other components, such as pre-amplifiers,
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`for shaping and refining the electrical signal from photodiode 628.
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`[0043] LED 606 and photodiode 628 may be controlled by signals received via connector
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`424, as indicated by respective control signal paths 636, 638. Control signals for LED 606
`
`may operate to activate and deactivate LED 606 at desired times; control signals for
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`25
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`photodiode 628 may operate to activate and deactivate photodiode 628 at desired times,
`
`adjust a gain parameter, and so on.
`
`[0044] While Fig. 6 shows one excitation/detection pair 600, it is to be understood that an
`
`embodiment of detection module 234 may contain any number of such pairs, each of which is
`
`advantageously in optical isolation from the others and has its own opening for optical
`
`30
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`communication with the sample wells (e.g., openings 504, 506, 508 of Fig. 5). The various
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`excitation/detection pairs are independently controlled and independently read out, but their
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`respective control and readout paths may all be coupled to circuit board 634.
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`10
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`Agilent Exhibit 1207
`Page 11 of 447
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`

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`[0045] The configuration of excitation/detection pairs may be varied from that shown, and
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`the excitation and detection light paths may include additional components, fewer
`
`components, or any combination of desired components. The optics may be modified as
`
`appropriate for a particular application (e.g., the optical path may be shorter in embodiments
`
`5 where lid heater 204 is not included) and use any number and combination of components
`
`including but not limited to lenses, beam splitters, mirrors, and filters. While LEDs provide a
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`compact and reliable light source, use of other types of coherent or incoherent light sources,
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`such as laser diodes, flash lamps, and so on, is not precluded. Similarly, the detectors are not
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`limited to photodiodes; any type of photodetector may be substituted, including
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`10
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`photomultipliers and charge-coupled devices (CCDs). Each excitation/detection pair is
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`advantageously configured as a self-contained assembly, requiring only external electrical
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`connections to make it operational. Because the length of the excitation and detection optical
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`paths do not vary from one experiment to the next, it is desirable to fixedly mount and
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`optimize the various optical components of each excitation/detection pair 600 inside
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`15
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`detection module 234 during manufacture so that further adjustments during operation are not
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`required.
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`[0046] Fig. 7 is a block diagram illustrating electrical connections for lid assembly 112. A
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`main processing board 702 is mounted in lid assembly 112. Main processing board 702
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`includes a primary signal processor 704, a stepper motor driver unit 706, a connection 708 for
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`20
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`electrical power, and a connection 710 for an external computer (e.g., a personal computer, or
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`PC). Main processing board 702 also provides connectors 214 for cables 212 that provide
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`transmission of electrical signals to and from lid 122.
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`[0047] Lid 122 includes a secondary processing board 720 that facilitates communication
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`between main processing board 702 and stepper motors 302, 316, as well as shuttle 232.
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`25
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`Secondary processing board 720 includes connectors 722 for cables 212, a connector 724 that
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`connects a cable 726 to shuttle 232, and connectors 732 and 734 for cables 736, 738 that
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`provide control signals to the x and y stepper motors 302, 316. Routing paths (not shown) in
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`secondary processing board 720 establish appropriate signal connections between the various
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`connectors.
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`30
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`[0048] Cable 726 is used to communicate control signals for detection module 234, such as
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`activating and deactivating individual light sources, and to receive signals from the
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`photodetectors included in detection module 234. Electrical connector 730 is provided on
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`Agilent Exhibit 1207
`Page 12 of 447
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`shuttle 232 for passing signals to and from detection module 234. Electrical connector 730
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`accepts the mating connector 424 on the top surface of detection module 234 when detection
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`module 234 is mounted on shuttle 232. In an alternative embodiment, cable 726 may attach
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`directly to detection module 234.
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`5
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`[0049] As mentioned above, main processing board 702 provides a connection 710 to an
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`external computer (not shown). The external computer may be used to control the motion of
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`shuttle 232 and the operation of detection module 234, as well as for readout and analysis of
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`fluorometry data obtained from detection module 234.
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`[0050] As described above, detection module 234 is designed to be self-contained and
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`10
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`detachable from shuttle 232. This allows for a reconfigurable fluorometry system, in which
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`an experimenter is able to change detection modules as desired to perform different
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`measurements. For instance, different detection modules may be optimized for different
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`fluorescent labeling agents (or combinations of agents). If the experimenter wishes to study a
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`different agent, she simply installs the appropriate detection module. Installation is a matter
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`15
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`of attaching electrical connector 424 and mechanical connectors 420 on the top of the desired
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`detection module 234 to corresponding connectors on the underside of shuttle 234. In some
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`embodiments, the connectors are designed such that the electrical connection is made
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`automatically as the mechanical connection is engaged. As noted above, lid heater 204 is
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`advantageously movably mounted so as to allow access to fluorescence assembly 230,
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`20
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`thereby allowing experimenters to change detection modules.
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`[0051]
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`It will be appreciated that the apparatus described herein is illustrative and that
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`variations and modifications are possible. For instance, the base and sample unit may be
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`designed as an integrated system or separated further into smaller modular components. The
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`fluorometer assembly need not be attached or otherwise integrated into the lid, so long as it is
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`25 mountable in a fixed position