Patent Publication Number: US-2004053295-A1

Title: Linear array device

Description:
[0001] The present invention(s) relate to devices apparatus and sensor mechanisms for the detection of target biomaterials in a fluid sample. These will generally be of use in screening and assay techniques with particular relevance to the fields of molecular biology; pharmacology and genomic or otherwise diagnostics in healthcare markets.  
       [0002] Physical arrays of binding agents or probes, such as oligonucleotides and polynucleotides, have become an increasingly important tool in the biotechnology industry and related fields. These arrays, in which a plurality of binding agents are deposited onto a solid support surface in the form of an array or pattern, find use in a variety of applications, including drug screening, nucleic acid sequencing, mutation analysis, and the like.  
       [0003] There are many different approaches to creating these so-called “genomic-chip” arrays or biological arrays and many references to methods of both attachment of biomaterials to solid surfaces in matrix arrays and their interrogation and measurement.  
       [0004] In terms of attachment of biomaterials to solid surface to produce such arrays for screening, U.S. Pat No. 5,412,087 describes how spatially addressable immobilisation of oligonucleotides and other Biological polymers of surfaces may be achieved—references therein discuss various methodologies that may be exploited.  
       [0005] The technology drivers in genomic analysis are pushing towards carrying out parallel hybridisation on array formats of biological probe-targets. In for example DNA sequencing by hybridisation; DNA fingerprinting and genetic mapping, so-called chip-array technologies are becoming the industry standard.  
       [0006] Technology advances are pushing better methods of attachment of materials at predefined sections of surface and for better (more specific) methods of measuring any binding to these sites during experiments.  
       [0007] Other than a few low-end systems that use radioactive or chemiluminescent tagging, most microarrays use fluorescent tags as their means of identification. These labels can be delivered to the DNA units in several different ways. Hence, these arrays are typically interrogated optically (e.g. U.S. Pat. No. 5,071,248), although there have been attempts to measure other physical properties, e.g.: electrical properties of these addressable sites (either conductively in liquid; U.S. Pat. No: 4,713,347, or capacitively U.S. Pat. No: 4,543,646 or as part of a field effect transistor U.S. Pat. No: 4,233,144).  
       [0008] The present invention provides a method of detecting the presence of at least one target analyte in a fluid sample, said method comprising the steps of:  
       [0009] a) providing a linear array device comprising an elongate substrate having a linear array of different spatially addressable probe moieties anchored thereto, said substrate having a leading end portion and a trailing end portion;  
       [0010] b) bringing said device into contact with said sample under conditions conducive to selective binding interaction between the target analyte and a said probe moiety which is specific therefor;  
       [0011] c) providing a microstructure reading apparatus;  
       [0012] d) providing relative translation of said device and said reading apparatus for providing linear spatial address data for said probe moieties anchored to said substrate;  
       [0013] e) reading said device so as to detect signal indicating the presence of bound analyte; and  
       [0014] f) correlating the address data with bound analyte signal data so as to determine the linear spatial address of any probe moiety having analyte bound thereto, thereby to determine the identity of said probe moiety.  
       [0015] In another aspect the present invention provides a linear array device suitable for use in a method according to the present invention, said device comprising an elongate substrate having a linear array of different spatially addressable probe moieties anchored thereto, said substrate having a leading end portion and a trailing end portion, wherein said device has at least one, longitudinally indexable, microstructure characteristic which is readable so as to provide linear spatial addresses for said probe moieties, said substrate having a tensile strength sufficient to allow stable transportation of said device through a sample contacting station and a reading station in use of said device, by means of at least one of: supporting said device with leading and trailing end portions thereof secured to spaced apart portions of a support structure, with said device extending under tension between said leading and trailing end portions, and providing relative translation between said supported device and said stations; and pulling on said leading end portion of said device.  
       [0016] Novel devices and methods of interrogation are provided for the diagnostic screening of liquid samples for particular biomaterials. The devices are string-like, linear arrays onto which are deposited (immobilised) spatially-addressable, “probe” biomaterials. The base material from which the string is manufactured will in general a polymer material (e.g. polyurethanes, polyesters, polycarbonates, polyureas, polyamides, polyethyleneimines, polyarylene sulfides, polysiloxanes, polyimides, polyacetates, pvdf), although these may be glass, metal, or ceramic or combinations thereof.  
       [0017] The addressability may be achieved through monitoring of the spatial change, created locally by the deposited/immobilised probe; which may in addition be considered in reference to other fiducial markings on the string; which may or may not be random surface textures. Such fiducial features may be exploited using correlation techniques to achieve absolute position measurement/indexing along said string and hence can allow interrogation of the biomaterial functionalised site at that position on the string. Such markings as included for position sensing may in addition contain encoded data appropriate for the string or measurement.  
       [0018] The string may be functionalised using a variety of techniques, however, to maximise sensitivity it is envisaged that coating said string cylindrically with biomaterials will exploit the larger surface area that this will afford when drawn through a liquid analyte.  
       [0019] In general, such biomaterial functionalised addressable linear-string-arrays may be used to exploit a wide variety of ligand-antiligand-type reactions. For example, direct binding assays may be performed to detect the affinity of various ligand type biomaterials (e.g. but not restricted to cell membrane receptors, monocolonal antibodies, hormones, drugs, oligonucleotides, peptides, enzymes, cofactors, lectins, sugars, oligosaccharides, cills, cellular membranes and organelles).  
       [0020] The result of such simultaneous screening of a liquid analyte for affinity binding to an addressable probe, anti-ligand site on the string may be interrogated, measured in a variety of ways. For example, the traditional assay techniques of auto-radiography, where one of the moieties is radio actively labelled. Fluorescence or optical measurement may also be used to measure binding to a site.  
       [0021] The string-like nature of the detection arrays and the small circumferential dimensions of strings lend themselves to particular local optical and/or electrical methods for measuring binding.  
       [0022] More generally, the linear-aspect of the string-array provides easy relative movement with respect to:  
       [0023] the analyte in screening;  
       [0024] the deposition station/mechanism in coating with Biomaterial and  
       [0025] the reader/detection mechanism.  
       [0026] In particular, in many cases the simplicity and symmetry of the system lend itself to either movement of the string relative to various other devices, however, as similar affect could have been achieved with the string stationary and moving the devices. Therefore, in further discussion of movement of the string, it will be implied, unless explicitly stated to the contrary, that this also includes such equivalent effects as could have been achieved by reciprocal movement of the device relative to a stationary string.  
       [0027] This simple linear transport scheme lends itself to reduction in complexity of all parts of such an array detection system. In particular:  
       [0028] achieving addressability/indexing and putting additional encoded information on the string—features are exploited that are unique to a point on the string; Such features may be artefacts from the production of the string, or they may be subsequently manufactured by (but not limited to) embossing, attaching, printing, imbedding, (plasma or wet) etching, abrading—either separately or in combination—which will all giving rise to a local surface or subsurface modification that may be random or periodic. These features are then used as a reference to a particular location (address) on the string. Moreover, various combinations of these methods of manufacture can be used to place either explicit or covert codes onto the strings, which may be used for identification and traceability (e.g. traceability backwards for quality control and history and forward traceability for use in subsequent bioinformatic analysis) and/or to give instructions to automated handling systems. Such codes can be either like “Gray codes” with a varying mark/space ratio or can be effectively simple “bar codes”.  
       [0029] deposition of the biomaterial “probes” onto the strings—the robes are deposited onto the strings relative to the index features mentioned previously. In one embodiment, this may be achieved using cylindrically depositing “drop on demand” mechanisms (e.g. ink-jet technologies);  
       [0030] the testing of a liquid analyte sample for “targets” simply by drawing the string through the sample (which will typically be a small volume &lt;=200 μL and held in a loop by surface tension) or bending or folding said string into a small contained volume.  
       [0031] Surface binding of materials in the analyte may be challenged by ‘plucking’ or mechanically vibrating the string and/or the analyte—this provides enhanced specificity of binding detection. In addition, such agitation of the analyte/string ensures homogenous mixing of the analyte; This can be achieved using either some shaker mechanism (e.g. a piezoceramic—typically a bimorph driven at resonance of around a 20 kHz or an electromagnetic coil—like a loudspeaker coil driven at similar frequencies. Moreover, sound may be used to resonantly couple to the string or its holder and provided agitation thereby.  
       [0032] Reading/detecting binding—again the positioning infrastructure can be simple by drawing the ‘tested’ string through an interrogation volume where a local electrical an/or optical measurement is used to detect affinity binding.  
       [0033] With regard to the reading technology to topology of the string lends itself to exploiting electrical and/or optical measurement of affinity binding. This may make use of high ‘Q’ cavity structures through which the string is drawn. Measurement of a characteristic parameter of the cavity may then give a measure of the amount of binding at a site on the string. The measurement more generally may look at either absorption of stimulating energy; or in leakage of some near-field phenomena—typically a loss-type measurement. The use of a high ‘Q’ cavity provides additional amplification potential in the system that may enhance the detection sensitivity.  
       [0034] The present invention exploits a string or fibre, which may be of any material (e.g. polymer, metal, wire) or a composite thereof (e.g. plastic fibre with metal core of a textile)—generally it will be a linear cylindrical structure that will have ideally a high degree of flexibility. Onto this string, a spatial addressable array of biomaterials are deposited.  
       [0035] The scale of the strings will ideally be of a small diameter (typically &lt;0.5 mm diameter) to allow small bending radii. The addressability of the string (to spatially locate the biomaterial with respect to the string itself) may exploit some fiducial marking which may be structured or merely some random surface texturing on the string with using some correlation measurement can give an absolute position marker/measurement along the string. Clearly a ‘tape’ could also be included.  
       [0036] Indexing/addressing of bio-arrays for DNA sequencing, genetic testing and diagnostics is necessary to ensure correct identification of bio-targets and to improve the efficiency of the assay process. For fluorescence detection of hybridisation of bio-molecules, it is desirable to use optical methods for indexing as this will reduce the complexity and the cost of the resultant sensor instrumentation. One method is to use a sacrificial fluorescent dye to produce an additional colour for indexing, i.e. this colour is different from those used for fluorescent labelling of probe and target molecules. Two techniques can be used to deposit the indexing dye molecules on a bio-string. The first technique involves covalent bonding of the dye molecules to the surface of the string through a linkage that is chemically added to the molecules which can be the same as that for probe immobilisation, the deposition can be realised using robotic spotting as for the probe molecules. In the second technique, the dye molecules are doped in a resin and the mixture is deposited along a fibre/string. A UV curable resin is preferred.  
       [0037] The second method is to produce optical elements along a bio-string for indexing. One element is an optical grating device which can be fabricated on the string. The diffraction of an optical beam can be detected and used to index the string. For polymer fibre, the fabrication methods described in the section on microstructure production will be preferred. For glass optical fibre, grating elements can be created by periodically modifying the refractive index of the fibre by projection of light from a UV laser through a phase mask or an interference pattern produced using a UV laser.  
       [0038] In both of the indexing methods for fluorescence detection, the indexing dye/optical grating need to be arranged in a particular periodic fashion or to follow a particular mathematical function to enable easy identification of probe locations on a string.  
       [0039] One simple and flexible approach involves attaching a fluorophore such as fluorescein or Cy3 to the oligonucleotide “probe” layer. Techniques for detecting fluorescence have become almost routine.  
       [0040] Various methods can be used to create microstructures on a string/fibre for indexing/addressing, namely hot embossing and laser micromachining. The embossing method is particularly useful for a polymer string/fibre. In this method, a master is created with the desired microstructures (e.g. optical grating for optical indexing) using UV lithography and electroforming, silicon micromaching, or precision engineering [ 1 ]. The microstructures on the master are then transferred onto a fibre by hot embossing. In this process, the polymer material is heated to a temperature around its glass transition temperature, the master is then pressed against the fibre and the fibre is cooled so a replica of the microstructures on the master is created on the surface of the fibre which can be used to index the fibre for bio-analysis.  
       [0041] Laser micromaching can also be used to fabricate microstructures for indexing by ablation of the surface of a fibre [ 2 ]. Light from a UV laser is projected to the fibre surface through a mask with a pattern of the desired microstructure. The transmitted light ablates the fibre surface to form a microstructure. The indexing microstructure can also be fabricated by scanning a focussed laser spot on the fibre surface.  
       [0042] Both of the above methods rely on the removal of some surface material to form the indexing microstructures. Alternatively simple indexing structures, such as polymer “bumps” can be produced on a fire/string by depositing additional material locally. For example, an UV curable resin may be deposited using techniques similar to that of an ink jet. Lamination through a mask can also be used for producing indexing microstructures for one dimensional bio-analysis.  
       [0043] Encoded information may take a variety of codes be that either simple colour coding of the strings to the eye; or the inclusion of encoded information in either applied structures (in the form of simple bar-codes or gray-codes) or other features. These codes may be used for whatever purposes—e.g. batch control; history, etc. The codes may be interlaced along the length of the string in a similar manner to that used on compact disks to provide enhanced data integrity—this can also be achieved using multiply redundant codes; in general a 128-bit code should be easily achievable, but clearly other codes are covered (figure needed)  
       [0044] Key advantages of this embodiment of a one dimensional flexible array will be that the biomaterial may be simply transported through liquid analytes, and detection/measurement systems.  
       [0045] This can allow for simplification of the mechanisms for fluidic handling of the liquid sample to be analysed and the phenomena and mechanism to be exploited. In its simplest form the string will be mounted taught on a rigid carrier which is then moved relative to some datum structure. Utilising close contact of the string with respect to simple kinematically constrained geometries e.g. v-groove technology in silicon processing will allow very precise +/−1 μm positioning of string relative to any reader—whilst allowing movement along the string. More complicatedly, the string may be included in a cassette and or may have a ferrite or magnetically-coated end that will allow dragging forces to be applied using an external magnetic field.  
       [0046] Generally, the liquid analyte will be less than 500 μL in volume and will exploit surface tension in its coating of the string. In one embodiment, the analyte will be sitting on a surface with controlled circular hydrophilic regions—the string is then pulled through the resulting meniscus.  
       [0047] Another embodiment makes use of a droplet held in a loop, or a droplet of analyte attached to and shaken along the string.  
       [0048] The measurement or detection of binding events is envisaged as being again simplified as the topology and scale of the string together with the simplicity of transport of the said string make it easy to exploit local measurements at a point in space. One preferred mechanism is to measure some electrical/optical property of the string, which may be ‘dry’ or in aqueous solution for the measurement. Having the string pass through a high ‘Q’ resonant cavity (at some suitable frequency—RF or optical or both) can allow for gain in the measurement performed, which can increase the sensitivity of detection. Also since the cylindrical cross-section of the string with material circumferentially around it, measurement is integrating through the whole volume of the material which again can lead to increased sensitivity.  
       [0049] The string-like nature of the arrays are also ideally suited to mechanically challenging the affinity binding reactions—by mechanically vibrating the string in solution (possibly just plucking it) additional mixing can be assured and also non-specific (—non affinity bound) materials may be challenged from attachment to a site. This can lead to an increase in specificity of the assays. 
     
    
    
     [0050] Further preferred features and advantages of the invention will appear from the following detailed description given by way of example of some preferred embodiments illustrated with reference to the accompanying drawings in which:  
     [0051]FIG. 1 is a schematic view of a sample testing system of the invention;  
     [0052] FIGS.  2  to  4  are schematic views of different linear array devices of the invention;  
     [0053]FIG. 5 is a schematic view showing reading of the random microstructure of an elongate substrate used in a device of the invention;  
     [0054]FIG. 6 is a schematic view of another linear array device of the invention;  
     [0055]FIG. 7 is a schematic view of a supported linear array device of the invention;  
     [0056] FIGS.  8  to  10  are schematic views showing alternative sample contacting arrangements;  
     [0057] FIGS.  11  to  13  are schematic views showing use of alternative forms of reading apparatus; and  
     [0058]FIG. 14 is a schematic view of an apparatus for manufacture of a linear array device of the invention by attaching probe moieties to the substrate. 
    
    
     [0059]FIG. 1 shows a sample testing system  1  comprising a sample contacting station  2  and a reading station  3 , and a transport mechanism  4  for drawing a linear array device  5  successively past said sample contacting station  2  and said reading station  3 . The linear array device  5  comprises an elongate substrate  6  having a series of different oligonucleotide probe moieties  7  anchored thereto. At the sample contacting station  2  a wire loop  8  is used to support a small volume of fluid sample  9  containing various labelled analytes  10 . The loop  8  has a small opening  11  through which the linear array  5  can be passed so as to immerse part  12  of the device  5  in the sample  9 . When a probe moiety  13  encounters a target analyte  14  which specifically binds thereto, this remains bound thereto when the device is withdrawn from the fluid sample  9 . Normally a washing station  15  would be provided to ensure complete removal of any other parts of sample which might have become entrained with the device. Alternatively and/or additionally there could be provided a wiping or doctor device  16  for preventing entrainment of fluid from the sample contact station as the device is withdrawn from it.  
     [0060] The reading station  3  includes a signal reading apparatus  17  for detecting the presence of labelled target analyte  14  bound to a probe moiety  13  on the device  5 , and a microstructure reading apparatus  18  for obtaining address data for said probe moiety  13  with target analyte bound thereto. This address data can then be used to identify the particular probe moiety  13  having analyte bound thereto, thereby confirming the presence of a particular target analyte  14  which hybridises with said oligonucleotide probe.  
     [0061] The linear array device  5  also has at its leading end portion  19  a traction engagement device in the form of a magnetic bead  20  which can be engaged by a magnetic traction device  4  to pull the linear array device  5  through the sample contacting and reading stations  2 , 3 .  
     [0062]FIG. 2 shows a linear array device  19  in the form of a generally cylindrical filament  20  with a series of annular probe moiety deposits  21  extending therealong. In FIG. 3 there is shown a linear array device  22  wherein the substrate  23  is in the form of a tape. This type of substrate is particularly advantage for use with microstructure reading apparatus based on electrical capacitance measurements as this allows the separation of the capacitor plates of the reading apparatus to be minimized and the area thereof maximized. In the linear array device  24  of FIG. 4 the probe moiety deposits  25  have a generally spherical surface (by use of a beaded substrate onto which probe material is applied or by building up the amount of probe material on a regular cross-section substrate) so as to maximize the probe area presented to the sample.  
     [0063]FIG. 5 shows a substrate  26  which has a random microstructure characteristic  27  which is recorded during a first pass. In a subsequent pass of the linear array device containing said substrate  26 , by using suitable reading apparatus  27  provided with a correlation processing device  28 , unique address data can be obtained.  
     [0064]FIG. 6 shows schematically a linear array device  29  with a series of probe moieties  30  and with a bar coded section  31  providing identification data for the individual device  29 .  
     [0065]FIG. 7 shows a linear array device  32  supported on a bow support structure  33  to facilitate handling etc.  
     [0066] FIGS.  8  to  10  are schematic views showing alternative sample contacting arrangements. In FIG. 8 the linear array device  34  is allowed to adopt a compact form  35  for complete immersion in a fluid sample  36  in a vessel  37 . In FIG. 9 a fluid sample  38  is constrained in a well  39  on a plate  40  which has a groove  41  extending across it and intersecting the well  39 . The groove acts as a kinematic constraint for a linear array device  42  as it is pulled along the groove  41  and through the fluid sample  38 .  
     [0067] In FIG. 9 a drop of fluid sample  43  is applied to the leading end portion  44  of a vertically extending linear array device  45  and allowed to flow down the length of the linear array device  45 . The linear array device  45  is mechanically perturbed by application of a suitable vibrational frequency from an ultrasonic sound apparatus  46  so as to encourage the fluid sample drop  43  to flow down the linear array device  45  whilst at the same time challenging to a greater or lesser degree the binding of analyte to the probe moieties.  
     [0068] FIGS.  11  to  13  are schematic views showing use of alternative forms of reading apparatus. FIG. 11 shows a linear array device  47  being drawn through a Fabry-Perot cavity  48  formed in one arm  49  of a Mach-Zender planar light guide interferometer  50 . FIG. 12 shows a fibre optic reading apparatus  51  being used to read a linear array device  52  as it is drawn through a kinematic constraint guide support device  53  comprising a plate  54  with a groove  55  therein for receiving the linear array device  52 . FIG. 13 shows schematically a reading apparatus  56  together with a kinematic constraint guide support device  53  similar to that in FIG. 12, with a reading device  57  suitable for use in changes in electrical capacitance as the linear array device  52  is drawn past it.  
     [0069]FIG. 14 shows schematically a linear array device production apparatus  58  based on ink-jet writing technology, which uses an annular array  59  of fluid jet ejection nozzles  60  to deposit in controlled manner an annular layer of probe material  61  onto an elongate substrate  62  as this is drawn through the array  59 .  
     [0070] Literature References  
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     [0073] U.S. Pat. No. 5,071,248: “Optical sensor for selective detection of substances and/or for the detection of  
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