|Publication number||US20060210449 A1|
|Application number||US 11/280,853|
|Publication date||Sep 21, 2006|
|Filing date||Nov 15, 2005|
|Priority date||Nov 16, 2000|
|Also published as||US6965433, US20020163642, WO2002041004A2, WO2002041004A3|
|Publication number||11280853, 280853, US 2006/0210449 A1, US 2006/210449 A1, US 20060210449 A1, US 20060210449A1, US 2006210449 A1, US 2006210449A1, US-A1-20060210449, US-A1-2006210449, US2006/0210449A1, US2006/210449A1, US20060210449 A1, US20060210449A1, US2006210449 A1, US2006210449A1|
|Inventors||Jim Zoval, Horacio Kido, Jorma Virtanen|
|Original Assignee||Zoval Jim V, Horacio Kido, Virtanen Jorma A|
|Export Citation||BiBTeX, EndNote, RefMan|
|Patent Citations (9), Referenced by (8), Classifications (59)|
|External Links: USPTO, USPTO Assignment, Espacenet|
This application is a continuation of U.S. application Ser. No. 09/999,274, filed on Nov. 15, 2001, which claims the benefit of U.S. Provisional Application No. 60/249,391, filed on Nov. 16, 2000, and U.S. Provisional Application No. 60/275,705, filed on Dec. 22, 2000, each of which are hereby expressly incorporated by reference in their entireties.
As shown in U.S. Pat. No. 6,030,581, an optical disc can be used to perform assays on biological or chemical samples. A sample can be provided in an opening and then moved by centrifugal force from one chamber or area to another chamber or area until it reaches an assay region where the sample (or a characteristic of the sample) can be observed. As shown in U.S. Pat. No. 5,892,577, which also is incorporated herein by reference, a beam can be scanned over a rotating disc. Radiation reflected from and/or transmitted through the disc can be detected by a detector and used to read encoded information and/or detect assays.
The embodiments of the present invention allow reflected light to be used both to read operational data and to detect a biological or chemical investigational feature and/or a characteristic thereof. One embodiment includes a biodisc with a substrate, a reflective layer over the substrate for encoding information, an opening in the reflective layer at a viewing window where an investigational feature can be provided, and a second reflective layer spaced from the first reflective layer and at least over the viewing window such that light passing through the substrate to the viewing window can be reflected by the second reflective layer. The first reflective layer can be directly on the substrate or separated by intermediate layers, such as a dye layer. Over the second reflective layer, a cap portion can be provided.
The disc can have different configurations for channels and chambers for moving a sample, such as a generally U-shaped circuit or a series of chambers. At the viewing window, the investigational feature can be detected by one of a number of methods, including colorimetry, fluorimetry, the use of reporters, such as beads, or the use of other methods by which a sample, or a characteristic of a sample, can be observed. The disc can be used for medical diagnostics, such as detecting cholesterol or glucose levels, or for blood typing, detection of antigens, or any other desired biological or chemical interaction. The disc can also be used for imaging small objects.
A biodisc and drive system as described herein can have one or more of a number of different advantages, including an ability to detect investigational features with reflected light, to read encoded data in addition to investigational features, and the ability to use the focusing of a standard disc reader at the reflective layer where information is encoded. This means that with the disc shown in the embodiments, a conventional optical drive may be usable with few changes. Other features and advantages will become apparent from the following detailed description, drawings, and claims.
Optical biodiscs for assays according to the present invention may have any suitable shape, diameter, or thickness, but preferably are implemented on a round disc with a diameter, thickness, and materials similar to those of a compact disc (CD), a recordable CD (CD-R), a digital versatile disc (DVD), or one of a number of other formats. Compact discs, DVDs, and other such discs have encoded informational (operational) data, such as audio information or software. A biodisc according to embodiments of the present invention has investigational features, and preferably both encoded operational data and investigative features. The operational information can include data for performing, controlling, and post-processing a test or assay on a biological or chemical material. This operational information can include, for example, information for controlling the rotation rate of the disc, the direction of rotation of the disc, timing for rotation, stopping and starting of the disc, delay periods, multiple rotation steps, locations of samples, and control of the power of the light source.
Investigational features can include any chemical or biological material providing a test result. In one embodiment, target sequences, such as capture DNA strands or antibodies, are attached to a disc surface in a viewing window (also referred to as a viewing window). In the DNA example, a reporter is attached to a target DNA sequence, which is complementary to a capture DNA sequence. In the presence of a target sequence, the complementary capture DNA strand will hybridize with the target, thereby attaching DNA target sequences to the disc surface. In a subsequent wash step, unbound reporters are removed. A beam of light focused on the viewing window will determine the presence, or lack thereof, of a target sequence. Such a system is described in more detail in U.S. Provisional Application Ser. No. 60/257,705, filed Dec. 12, 2000, which is expressly incorporated by reference.
Other techniques for observing a sample or a characteristic of a sample include colorimetry and fluorimetry. In the case of colorimetry, a sample is provided in a viewing window, and the beam of light is directed to the sample. From the amount of light that is detected, information about the sample is derived.
An optical biodisc may generally be reflective, transmissive, and/or have some combination of reflective and transmissive portions. In the case of a reflective disc or in a reflective portion, an incident light beam may be focused onto a reflective surface of the disc, reflected by the reflective surface, and returned through optical elements to a detector as it would be in a conventional informational disc. In a transmissive disc or transmissive portion of a disc, light passes through the disc to a detector on the other side of the disc from the light source. The transmissive portions could be partially reflective. A transmissive disc is described in more detail in U.S. Provisional Application Ser. Nos. 60/255,233, filed Dec. 12, 2000; 60/294,051, filed May 29, 2001; 60/306,266, filed Jul. 18, 2001; 60/306,599, filed Jul. 19, 2001; and 60/291,233, filed May 16, 2001, each of which is incorporated herein by reference.
The embodiments of the present invention relate mainly to reflective biodiscs which provide both operational and investigative features, but the disc could include transmissive portions as well.
A light source 202 provides light to optical components 212 to produce an incident light beam 204, which may be collimated or non-collimated. In the case of a reflective portion of disc 100, incident light beam 204 is reflected off disc 100 to produce a return beam 206. Return beam 206 passes through optical components 212, and then to a detector 210. This detector can be a conventional optical disc drive detector or a modified detector.
Optical components 212 can include a lens, a beam splitter, and a quarter wave plate that changes the polarization of the light beam so that the beam splitter directs a reflected beam through the lens to focus the reflected beam onto the detector. These are conventional components in optical disc drives. An astigmatic element, such as a cylindrical lens, may be provided between the beam splitter and detector to introduce astigmatism in the reflected light beam.
Data from detector 210 is provided to a computer 236, including a processor 220 and an analyzer 222, and then to a monitor 224 to display an image or results. This computer 236 can represent a desktop computer, programmable logic, or some other processing device, and also can include a connection (such as over the Internet) to other processing and/or storage devices. A drive motor 226 and a controller 228, which can be connected to computer 236, are provided for controlling the rotation of disc 100. Thus if encoded operational data on disc 100 indicates that disc 100 is to be rotated at a certain rate, computer 236 can direct controller 228 to drive motor 226 at that rate. Computer 236 and controller 228 can be on the same computer.
The disc can have a physical mark referred to as a trigger mark 120. A hardware trigger sensor 218 is used to detect trigger mark 120. Trigger sensor 218 provides a signal to computer 236 that controls the collection and/or use of detected data by computer 236. In one embodiment, computer 236 only stores and analyzes data relating to investigational features when trigger sensor 218 detects trigger mark 120. In this case, data regarding investigational features is collected and analyzed when the trigger is detected. The trigger is preferably aligned radially with viewing windows. Trigger sensor 218 and trigger mark 120 can be located under disc 100 and on the bottom side of disc 100, respectively.
With a transmissive disc, there would also be a top detector on the other side of the disc from the light source. Transmissive disc detection is shown, for example, in U.S. Provisional Application Ser. Nos. 60/270,095, filed Feb. 20, 2001; 60/292,108, filed May 18, 2001; 60/292,110, filed May 18, 2001; 60/313,917, filed Aug. 21, 2001; and in Gordon, U.S. Pat. No. 5,892,577, filed Apr. 6, 1999, each of which is incorporated herein, by reference.
Disc drive system 200 is thus employed to rotate disc 100, read and process any encoded operational information stored on the disc, and detect chemical, biological, or biochemical investigational features in an assay region of the disc. Optionally, in a system such as a CD-R, disc drive system 200 can be used to write information to disc 100 either before or after the material in the assay zone is analyzed by the read beam of the drive.
A channel layer 104, also referred to as an adhesive layer, has fluidic circuits 128 formed therein preferably by stamping or cutting desired shapes from the layer. The channel layer can be over a capture layer where an investigational feature can bind. Each fluidic circuit 128 can have a flow channel 130 and a return channel 132. A fluidic circuit can include other microfluidic channels and chambers, such as preparatory regions and a waste region, as shown, for example, in the incorporated U.S. Pat. No. 6,030,581.
Substrate 106 is made up primarily of a layer of polycarbonate, and has a reflective layer deposited on the top of the polycarbonate layer. Viewing windows 140 are openings in the reflective layer that may be formed by removing portions of the reflective layer in any desired shape, or by masking viewing windows 140 before applying the reflective layer. One viewing window or a plurality of such windows can be oriented along one or more radii from the center of the disc. The reflective layer on substrate 106 is preferably formed from a metal, such as aluminum or gold, and can be configured with the rest of substrate 106 to encode operational information that is read with incident light.
In operation, samples are provided through inlet ports 110. When rotated, the sample moves outwardly from inlet ports 110 along a fluidic circuit 128. Through one of a number of biological or chemical reactions or processes, detectable investigational features may then be present in viewing windows 140.
The disc may be designed so that investigational features are captured to be in the focal plane coplanar with the reflective layer that has encoded information. This reflective layer is where an incident beam is typically focused conventionally through optical components and the optical properties of the substrate; alternatively, investigational features may be captured at a location in front of or at the focal plane, i.e., farther from the light source. The former configuration is referred to as a “proximal” type disc (see
Trigger marks 120 may be included on the surface of the reflective layer, and may include a clear window in all three layers of the biodisc, an opaque area, or a reflective or semi-reflective area encoded with information. The use of the trigger marks is described in conjunction with
Substrate layer 106 may be impressed with a spiral track that starts at an innermost readable portion of the disc and then spirals out to an outermost readable portion of the disc. In a non-recordable disc such as a CD, this track is made up of a series of embossed pits with varying length, each typically having a depth of approximately one-quarter the wavelength of the light that is used to read the disc. The varying lengths and spacing between the pits encode the operational data. The spiral groove of a recordable CD-R disc has a detectable dye rather than pits.
Numerous designs and configurations of an optical pickup and associated electronics may be used in the context of the embodiments of the present invention. Further details and alternative designs for compact discs and readers are described in Compact Disc Technology, by Nakajima and Ogawa, IOS Press, Inc. (1992); The Compact Disc Handbook, Digital Audio and Compact Disc Technology, by Baert et al. (eds.), Books Britain (1996) and CD-Rom Professional's CD-Recordable Handbook: The Complete Guide to Practical Desktop CD, Starrett et al. (eds.), ISBN: 0910965188 (1996); all of which are incorporated herein in their entirety by reference.
The layer of substrate 168 in
The path of an incident beam 152 is directed toward disc 100 from the light source. Incident beam 152 is focused on a point in a focal plane coplanar with reflective layer 148 and continues upwardly traversing through viewing window 140 to eventually fall incident onto reflective surface 148. At this point, incident beam 152 is reflected back and thereby forms a return beam 154. Without reflective layer 148 being added, the viewing window would be transmissive. This model applies for the behavior of the light beams for
A sample can thus be provided to reservoir 132, provided through reservoirs 134 and 136 to capillary channel 142 to viewing window 140. The movement from reservoir 132 to viewing window 140 can be all at once, or in a series of stages governed by physical resistance and different speeds of rotation—in other words, rotation at a first rotation rate moves the sample from reservoir 132 to 134, rotation at a second rotation rate moves the sample from reservoir 134 to 136, and then rotation at a third rotation rate moves the sample from reservoir 136 to viewing window 140. Delays for heating, incubating, or some other purpose can be provided between steps.
Viewing window 140 is created by removing a portion of reflective layer 164. A reflective layer 148 is at the top of viewing window 140.
The test sample is injected or deposited into flow channel 141 through an inlet port 232. As flow channel 141 is further filled with test sample, reporters 240 with DNA sequences 242 flow in flow channel 141 as illustrated in
In this manner, reporters 240 are retained within the viewing windows 234. Hybridization may be further facilitated by rotating disc 100 so that reporters 240 slowly move or tumble down flow channel 141. Slow movement allows ample time for additional hybridization. After hybridization, the disc may be rotated further to clear the viewing windows 234 of unattached reporters 240.
Interrogation beam 152 may then be scanned through viewing windows 234 to determine the presence of reporters 240 as illustrated in
As the light beam moves along the tracks, the amount of reflected light is high outside of the viewing window. Within the viewing window, where the reflective layer under the cap is spaced from the focal point, the amount of reflected light declines. Within the viewing window, more light is reflected when the light beam reflects off the reporter. The analysis software thus looks for a drop—and then increase in the amount of reflected light to detect the bounds of the viewing window. Within the viewing window, the analysis software looks for peaks that exceed a threshold and counts these peaks. The light then moves to the next track to be used, which may be several tracks away from the previously read track. Such a reading system is shown, for example, in U.S. Provisional Application Ser. No. 60/270,095, filed Feb. 20, 2001, which is expressly incorporated herein by reference.
Other detection methods may be used. The counting can be performed in hardware with edge detection circuitry. Other hardware and software methods can be used, including imaging and using image recognition software to detect individual reporters. Other detection methods may be more oriented to a yes/no decision. The boundary of the window can be determined from encoded information in the reflective layer near the window.
Having described several embodiments of the present invention, it should be apparent that modifications can be made without departing from the scope of the invention as defined by the appended claims. For example, the testing can be used for medical diagnostics, biological agent detection (including biological warfare), environmental testing, and forensic DNA analysis. A CD-type system can image microstructures, detect and count cells, detect microbeads (e.g., 1-6 microns) used in DNA and immuno-assays, detect colorimetric substrates used in enzymatic assays, and detect new or reported nanogold and nanocarbon. Assay techniques include Ab-Ag reaction, hybridization, enzyme cascade, chelation, binding to surface markers, and imaging by cell identification and agglutination. The references to physical relationship, such as one layer being “over” another, or light being provided to the “bottom” of the disc, are meant as terms of reference, but are not meant to literally be “over” necessarily; rather, the light could be directed from above with the structure upside down, or the disc could be on its side.
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|U.S. Classification||422/400, 435/287.2, 435/288.7, 435/288.5, 422/82.09, 436/164, 356/246, 435/6.19, 435/5|
|International Classification||B01L3/00, G01N21/07, G01N35/00, B01J19/00, C40B50/14, C12M1/34, C40B60/14, C40B40/06, G01N21/00, B32B27/12, B81B1/00|
|Cooperative Classification||G01N21/07, B01J2219/00605, B01J2219/00648, B01J2219/00695, B01L2300/0806, B01L2200/12, B01L2300/0887, B01J2219/00659, B01J2219/00675, B01J2219/00722, B01L2300/021, B01L2400/0409, B01J2219/00596, B01L3/5025, B01J2219/00702, C40B40/06, C40B60/14, B01J2219/00689, C40B50/14, B01J2219/00536, B01L3/502753, B01J19/0046, B01J2219/00637, B82Y30/00, B01J2219/005, G01N35/00069, B01J2219/00585, B01L2300/0636, B01J2219/00317, B01J2219/00707, B01J2219/0061, B01L2300/168, B01L3/5027|
|European Classification||B82Y30/00, B01L3/5025, B01L3/5027, G01N21/07, G01N35/00C2, B01J19/00C|