Abstract:
The present invention relates generally to a configurable array of probes for assaying targets within a fluid. The probes are contained within optical traps which allows for alterations in the selection and re-configuration of the quantity or quality of probes in the array. Moreover, the array is dynamic in that once configured the optical traps may allow for independent repositioning of a given optical trap and contained probe.

Description:
BACKGROUND OF THE INVENTION  
         [0001]    Throughout this application various publications are referenced within parentheses. The disclosures of these publications in their entireties are hereby incorporated by reference in this application in order to more fully describe the state of the art to which this invention pertains.  
           [0002]    1. Field of the Invention  
           [0003]    The present invention relates generally to arrays of probes. In particular, the invention relates to a system and method using a plurality of optical traps to form a configurable dynamic array of probes which may or may not be substrate bound.  
           [0004]    2. Discussion of the Related Art  
           [0005]    Arrays of potentially reactive probes have a long history of use in assays and other chemical and biological tests and experiments. For example, arrays are often used in the fields of genetics, biochemistry, and biology to assay a sample for biological or chemical material (known as a target). Often the sample being assayed is only available in relatively small quantities. This limited availability of some materials led to the development of microarrays useful to present a relatively high density of probes, in a small array, to assay for targets in a small quantity of a sample.  
           [0006]    Microarrays used in the testing of biological material are often referred to as bio-chips. Two principal applications of bio-chips are: extraction of sequence information about a specific nucleic acid i.e., whether that nucleic acid corresponds to an organism&#39;s entire genome, a singe gene, or a portion of a single gene (U.S. Pat. No. 6,025,136); and evaluation of gene expression. (See Schena, M. et al. “Quantitative monitoring of gene expression patterns with a complimentary DNA microarray,” Science 270 (5235):467-70 (Oct. 20, 1995); D. J. and Winzeler, E. A., “Genomics, gene expression and DNA arrays,” Nature 405(6788):827-836 (2000) and Ekins, R. and Chu, F. W., “Microarrays: their origins and applications;” Trends in Biotechnology 17:217-18 (1999).)  
           [0007]    Conventional microarrays are comprised of either a linear or a two-dimensional configuration of oligonucleotide probes, attached to the planar surface of a solid support (substrate). Different types of oligonucleotides are affixed to the substrate at predetermined locations. Consequently, once the microarray is formed, the location of the probes and hence the location of any targets that react with the probes is always known. The attachment of the probe is achieved by either direct synthesis of the oligonucleotide onto the substrate through a process known as in situ photolithography synthesis (U.S. Pat. Nos. 5,837,832 and 5,143,854), or attachment of the oligonucleotide after it has been synthesized.  
           [0008]    One drawback of such microarrays is that their linear or two dimensional configuration provides a limited surface area to which probes can be attached, thereby setting a limit on the density of the probes to assay for the targets. In the case of DNA hybridization between targets (DNA or DNA fragments) and probes (immobilized oligonucleotides) the rate of hybridization is controlled by the rate at which the targets are able to pass into contact with the probes. Accordingly, the higher the density of probes, the greater the rate of hybridization.  
           [0009]    A second drawback of such microarrays stems from the method of their configuration. Once a microarray is fabricated, the type and quantity of the probes become fixed.  
           [0010]    In an alterative approach to assaying for targets in a small quantity of a sample, probes are affixed to the surface of small bead-like substrates. (WO 00/61198 pending for Kambara &amp; Mitsuhashi.) Each bead containing a different probe is marked with a distinct label, thus permitting the identification of each probe and bound target by discerning which bead has what label after completion of the assay (See WO 00/71243).  
           [0011]    The identity of the bead and probe is maintained by physically transferring the bead with probe attached into a guide, capillary tube, groove, or holes within a sheet, then washing the beads with targets. While the non-flat nature of the beads does provide greater surface area for the targets to interact then does a microarray probe, the beads must still be held in some pre-determined order throughout the assay to maintain a record of the identity of what bead is supporting which probe or the bead probes must be collected and each bead probe examined after the assay to determine its identity.  
           [0012]    An additional drawback of both the microarray and the bead assays is the required physical attachment of the probe to a substitute. In some instances the attachment will in and of itself alter the probe, or affect the process that the probe is being used to assay. In other instances, during or after the initial assay, information may be obtained that would make for desirable alterations of the quality or quantity of the probes, if the identity of the probes was both known throughout the assay and the configuration of the array could be easily altered. However, such alters are not possible with either the microarray or bead assays.  
           [0013]    In an unrelated art, it is known to optically trap particles with multiple simultaneously generated optical tweezers. (See generally U.S. Pat. No. 6,055,106 issued to Grier &amp; Durfresne.) Optical tweezers use the gradient forces of a beam of light to trap particles based on the dielectric constant of a particle. To minimize its energy, a particle having a dielectric constant higher than the surrounding medium will move to the region of an optical tweezer when the electric field is the highest.  
           [0014]    Other types of traps that can be used to optically trap particles include, but are not limited to, optical vortices, optical bottles, optical rotators and light cages. An optical vortex produces a gradient surrounding an area of zero electric field which is useful to manipulate particles with dielectric constants lower than the surrounding medium or which are reflective, or other types of particles which are repelled by an optical tweezer. To minimize its energy such a particle will move to the region where the electric field is the lowest, namely the zero electric field area at the focal point of an appropriately shaped laser beam. The optical vortex provides an area of zero electric field much like the hole in a doughnut (toroid). The optical gradient is radial with the highest electric field at the circumference of the doughnut. The optical vortex detains a small particle within the hole of the doughnut. The detention is accomplished by slipping the vortex over the small particle along the line of zero electric field.  
           [0015]    The optical bottle differs from an optical vortex in that it has a zero electric field only at the focus and a non-zero electric field in all other directions surrounding the focus, at an end of the vortex. An optical bottle may be useful in trapping atoms and nanoclusters which may be too small or too absorptive to trap with an optical vortex or optical tweezer (J. Arlt and M. J. Padgett. “Generation of a beam with a dark focus surrounded by regions of higher intensity: The optical bottle beam,” Opt. Lett. 25, 191-193, 2000.)  
           [0016]    The optical rotator is a recently described optical tool which provides a pattern of spiral arms which trap objects. Changing the pattern causes the trapped objects to rotate. (L. Paterson M. P. MacDonald, J. Arlt, W. Sibbett, P. E. Bryant, and K. Dholakia, “Controlled rotation of optically trapped microscopic particles,” Science 292, 912-914, 2001.) This class of tool may be useful for manipulated non-spherical particles and driving MEMs devices or nano-machinery.  
           [0017]    The light cage, (Neal in U.S. Pat. No. 5,939,716) is loosely, a macroscopic cousin of the optical vortex. A light cage forms a time-averaged ring of optical tweezers to surround a particle too large or active to be trapped with dielectric constants lower than the surrounding medium. However, unlike a vortex, no-zero electric field area is created. An optical vortex, although similar in use to an optical tweezer, operates on an opposite principle.  
           [0018]    There exists a need for an assay method and system in which the interaction of the probes and targets can be evaluated absent attachment of the probe to a substrate. There also exists a need for a method and system of forming an array of probes which is configurable (and re-configurable), the method maintaining the identity of the probes throughout the assay irrespective of the location of the probe. The present invention satisfies these and other needs, and provides further related advantages.  
         SUMMARY OF THE INVENTION  
         [0019]    The present invention provides a novel and improved method and system to construct, configure and use three dimensional array of probes.  
           [0020]    Within a vessel optical traps are generated. The optical traps are produced by directing a beam of light such as a laser beam, at an optical element which alters the beam by patterning its phase to generate beamlets. The beamlets in turn are focused through a lens and produce the gradient conditions necessary for optical trapping. Probes, each with a known characteristic, are then added to the vessel. The probes for a given assay are chosen and than each is selected by containing it within an optical trap.  
           [0021]    The quantity and quality of probes forming the array are readily re-configurable by using the optical traps to add, discard, or replace probes. The arrangement of the probes, in the array, relative to one another is also dynamic because the spatial relationship of the probes to one another can be altered while maintaining the identity of the selected probes from which the array was configured. Accordingly, both the array and each of its probes are also movable in three dimensions and can be positioned, moved and re-positioned as a whole, or separately within the vessel.  
           [0022]    While a probe remains contained within an optical trap, regardless of whether it has been repositioned with the vessel and regardless of any change in it spatial position “order” in the array, the identity of the probe can be maintained by virtue of knowing the identity of the optical trap by which the probe is contained. Additionally, one optical trap can pass the probe to another optical trap and so on, while tracking the chain of optical trap custody of the probe thereby maintaining the identity of what probe is contained by which optical trap.  
           [0023]    Other features and advantages of the present invention will be set forth, in part, in the descriptions which follow and the accompanying drawings, wherein the preferred embodiments of the present invention are described and shown, and, in part will become apparent to those skilled in the art upon examination of the following detailed description taken in conjugation with the accompanying drawings, or may be learned by practice of the present invention. The advantages of the present invention may be realized and attained by means of the instrumentalities and combinations particularly pointed out in the appendant claims. 
       
    
    
     DESCRIPTION OF THE DRAWINGS  
       [0024]    [0024]FIG. 1 illustrates a partial cut-away side view of a system forming an array of configurable probes.  
         [0025]    [0025]FIG. 2 illustrates a view of a free-probe contained within an optical trap.  
         [0026]    [0026]FIG. 3 illustrates an overview of a system for forming an array of probes.  
         [0027]    [0027]FIG. 4 illustrates a beam altering element with multiple static regions.  
         [0028]    [0028]FIG. 5A illustrates a first operative movement of probes.  
         [0029]    [0029]FIG. 5B illustrates a second operative movement of probes.  
         [0030]    [0030]FIG. 6A illustrates a component view of a compact system to form optical traps.  
         [0031]    [0031]FIG. 6B illustrates an inverted microscope to which the compact system of FIG. 6A attaches. 
     
    
     DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS  
       [0032]    Particular embodiments of the invention are described below in considerable detail for the purpose of illustrating its principles and operation. However, various modifications may be made, and the scope of the invention is not limited to the exemplary embodiments described below. For example, while specific reference is made to biological systems and assays for gene sequencing and DNA hybridization, it can be appreciated that the method and system is of equal utility in such areas as optical circuit manufacturing and testing, nanocomposite material construction and testing, fabrication of opto-electronics, electronic components testing, assembly and testing of holographic data storage matrices, chemical assays, genomic assays, proteomics assays, facilitation of combinatorial chemistry, promotion of colloidal self-assembly, and probing non-biological materials.  
         [0033]    Certain terminology will be used in the following specification, for convenience and reference and not as a limitation. Brief definitions are provided below:  
         [0034]    A. “Beamlet” refers to a sub-beam of light or other source of energy that is generated by directing a beam of light or other source of energy, such as that produced by a laser or collimated output from a light emitting diode, through a medium which diffracts it into two or more sub-beams. An example of a beamlet would be a higher order laser beam diffracted off of a grating.  
         [0035]    B. “Phase profile” refers to the phase of light or other source of energy in a cross-section of a beam or a beamlet.  
         [0036]    C. “Phase pattering” refers to a patterned phase shift imparted to a beam of light, or a beamlet which alters its phase profile, including, but not limited to, diffracting, phase modulation, mode forming, splitting, converging, diverging, shaping and otherwise steering a section of a beam or a beamlet.  
         [0037]    D. “Probe” refers to a biological or other chemical material that selectively binds to, or reacts with, a target. Probes include, but are not limited to, oligonucleotides, polynucleotides, chemical compounds, proteins, peptides, lipids, polysaccharides, ligands, cells, antibodies, antigens, cellular organelles, lipids, blastomeres, aggregations of cells, microorganisms, cDNA, RNA and the like.  
         [0038]    E. “Target” refers to a biological or other chemical material whose presence or absence in a sample is detected by binding the target to or reacting the target with a probe. For example, the presence of a target formed of genetic material is detected by a reaction, such as a hybridization reaction, of the genetic material of the target with genetic material of a probe, which possesses the particular characteristic i.e., the complimentary structure, necessary for hybridization. Target materials also include, but are not limited to, oligonucleotides, polynucleotides, chemical compounds, proteins, lipids, polysaccharides, ligands, cells, antibodies, antigens, cellular organelles, lipids, blastomeres, aggregations of cells, microorganisms, peptides, cDNA, RNA and the like.  
         [0039]    As shown in FIG. 1, the probes  500 - 504  may be bound to or rated with, any suitable substrate, through any suitable binding process or protocol. An important characteristic of a suitable substrate is that it be a material, which can be contained by, and manipulated with, an optical trap. Representative dielectric substrates include beads, irregular small particles, or other regular small particles. Suitable substrates are constructed of materials, which include, but are not limited to, control pore glass, ceramics, silica, titanium dioxide, latex plastics, such as polystyrene, methylstyrene, polymethyl methacrylate, paramagnetic materials, thoriosol, graphite, Teflon, cross-linked dextrans, such as sepharose, cellulose, nylon, cross-linked micelles, liposomes, and vesicles.  
         [0040]    As shown in the alternative embodiment illustrated in FIG. 2, the method of the instant invention also includes using one or using more optical traps  1005  (one shown) to contain one or more probes  505  (one shown) that are unbound to a substrate. It should be understood that the configurable arrays may contain only bound probes, only unbound probes, or a combination of bound and unbound probes. Selection of what mixture, if any, of bound and unbound probes may in part be influenced by a probe&#39;s physical properties. Specifically, the properties of certain probes, such as skin cells, may be altered absent adhesion to a substrate. Conversely, the action of other probes, such as proteins, may be better served by maintaining the tertiary structure of the probe/protein by eliminating the substrate.  
         [0041]    [0041]FIG. 1 illustrates a configurable array  8  of substrate-bound probes  500 - 504  for assaying a biological material. The probes are configured within a subject cell  10  using movable optical traps  1000 - 1004  constructed from focused beamlets  2000 - 2004 . The subject cell  10  is a vessel constructed of a substantially transparent material, which allows the beamlets to pass through and which does not interfere with the formation of the optical traps.  
         [0042]    Illustrated in FIG. 3 is an overview of a system to generate and alter the position of the configurable array of probes, generally designated as  20 . Movable optical traps  1000 - 1004  (FIG. 1) are generated within the vessel  10  by passing a collimated light, preferably a laser beam  100 , produced by a laser  102  to area A′ on a beam splitter  30 . One of the light beams, beam  31 , originates from the laser  102  and is redirected so that it proceeds from the area A′ on the beam split  30  to area A on the phase patterning optical element  22 . Each beamlet created by the phase patterning optical element  22  then passes through area B at the back aperture  28  of the focusing lens  12 . Beamlets are converged by the focusing lens  12  The resulting focused beamlets form the optical traps  1000 - 1004  by producing the gradient conditions necessary to contain and manipulate the probes in three dimensions. For clarity, only five sets of probes, beamlets, and optical traps are shown in FIG. 1, but it should be understood that a greater or lesser number can be provided depending on the nature, scope, and other parameters of the assay and the capabilities of the system generating the optical traps.  
         [0043]    Any suitable laser can be used as the source of the laser beam  100 . Useful lasers include solid state laser; diode pumped lasers, gas lasers, dye lasers, alrexanderite lasers, free electron lasers, VCSEL lasers, diode lasers, Ti-Sapphire lasers, doped YAG lasers, doped YLF laser, diode pumped YAG lasers; and flash lamp-pumped YAG lasers. Diode-pumped Nd:YAG lasers operating between 10 mW and 5 W are preferred. The preferred wavelengths of the laser beam  100  used to form arrays for investigating biological material include the infrared, near infrared, visible red, green, and visible blue wavelengths, with wavelengths from about 400 nm to about 1060 nm being most preferred.  
         [0044]    The beam splitter  30  is constructed of a dichroic mirror, photonic band gap mirror, omni directional mirror, or other similar device. The beam splitter  30  selectively reflects the wavelength of light used to form the optical traps and transmits other wavelengths. The portion of light reflected from area A′ of the beam splitter is then passed through an area A of an encoded phase patterning optical element  22  disposed substantially in a plane  24  conjugate to a planar back aperture  28  of a focusing lens  12 .  
         [0045]    When the laser beam  100  directed through the phase patterning optical element  22 , the phase patterning optical element produces a plurality of beamlets having an altered phase profile. Depending on the number and type of optical traps desired, the alteration may include diffraction, wavefront shaping, phase shifting, steering, diverging and converging. Based upon the phase profile chosen the phase patterning optical element can be used to generate optical traps in the form of optical tweezers, optical vortices, optical bottles, optical rotators, light cages, and combinations of two or more of these forms.  
         [0046]    In those embodiments in which the phase profile of the beamlets is less intense at the periphery and more intense at regions inward from the periphery, overfilling the back aperture  28  by less than about 15 percent is useful to form optical traps with greater intensity at the periphery of the optical traps than optical traps formed without overfilling the back aperture  28 .  
         [0047]    Suitable phase patterning optical elements are characterized as transmissive or reflective depending on how they direct the focused beam of light or other source of energy. Transmissive diffractive optical elements transmit the beam of light or other source of energy, while reflective diffractive optical elements reflect the beam.  
         [0048]    The phase patterning optical element can also be categorized as having a static or a dynamic surface. Examples of suitable static phase patterning optical elements include those with one or more fixed surface regions, such as gratings, including diffractions gratings, reflective gratings, and transmissive gratings, holograms, including polychromatic holograms, stencils, light shaping holographic filters, polychromatic holograms, lenses, mirrors, prisms, waveplates and the like. The static, transmissive phase patterning optical element  40 , as shown in FIG. 4, is characterized by a fixed surface  41 . However, in some embodiments, the phase patterning optical element itself is movable, thereby allowing for the selection of one more of the fixed surface regions  42 - 46  by moving the phase patterning optical element relative to the laser beam to select the appropriate region. The static phase patterning optical element may be attached to a spindle  47  and rotated with a controlled electric motor (not shown). The static phase patterning optical element in the embodiment shown in FIG. 4 has a fixed surface  41  and discreet regions  42 - 46 . In other embodiments of static phase patterning optical elements, either transmissive or reflective, the fixed surface  41  has a non-homogeneous surface containing substantially continuously varying regions, or a combination of discreet regions, and substantially continuously varying regions.  
         [0049]    Examples of suitable dynamic phase patterning optical elements having a time dependent aspect to their function include computer generated diffractive patterns, phase shifting materials, liquid crystal phase shifting arrays, micro-mirror arrays, including piston mode micro-mirror arrays, spatial light modulators, electro-optic deflectors, accousto-optic modulators, deformable mirrors, reflective MEMS arrays and the like. With a dynamic phase patterning optical element, the medium which comprises the phase patterning optical element encodes a hologram which can be altered, to impart a patterned phase shift to the focused beam of light which results in a corresponding change in the phase profile of the focused beam of light such as diffraction, or convergence. Additionally, the medium can be altered to produce a change in the location of the optical traps. It is an advantage of dynamic phase patterning optical elements, that the medium can be altered to independently move each optical trap.  
         [0050]    Preferred dynamic optical elements include phase-only spatial light modulators such as the “PAL-SLM series X7665”, manufactured by Hamamatsu, of Japan or the “SLM 512N15′ and SLM 512SA7,” both manufactured by Boulder Nonlinear Systems of Layafette Colo. The phase patterning optical elements are computer controlled to generate the beamlets  2000 - 2004  (FIG. 1) by a hologram encoded in the medium which can be varied to the beamlets and select the form of the beamlets.  
         [0051]    In some embodiments, the form of the optical traps and/or the locations of optical traps used to form the array are altered and hence configured and re-configured. The form can be changed from its original form to that of an optical tweezer, an optical, a vortex, an optical bottle, an optical rotator or a light cage. The optical trap can be moved in two or three dimensions.  
         [0052]    The patterning optical element is also useful to impart a particular topological mode to the laser light, for example, by converting a Gaussian into a Gauss-Laguerre mode. Accordingly, one beamlet may be formed into a Gauss-Laguerre mode while another beamlet may be formed in a Gaussian mode.  
         [0053]    The probes are configured within a vessel  10 . The vessel  10  is a subject cell constructed of a substantially transparent material, which allows the beamlets to pass through and which does not interfere with the formation of the optical traps. In those embodiments, where the substrate is labeled with a wavelength specific dye, the subject cell should be transparent to the specific wavelength. Furthermore, the subject cell should be constructed of a material that is inert to the substrate. For example, biological substrates such as cells, proteins, and DNA should not stick to the surface of the subject cell and must not be changed or destroyed by the material.  
         [0054]    Probes which possess the particular characteristics necessary for binding and/or reacting with the target of interest are selected for addition to the vessel and inclusion in the configurable array. In some of the embodiments, where the probe is bond to a substrate, the substrate is labeled with a marker (such as a wavelength specific dye) to facilitate selection of the probe. In preferred embodiments, all the substrate bound probes that have the same binding or reactivity characteristic are labeled with the same type of markers. When the substrate is labeled with a wavelength specific marker, the selection of probes  500 - 504  can be accomplished by adding the probes bound to the labeled substrate to the vessel  10 . Then, as illustrated in FIG. 3, spectral measurement of the probe&#39;s labeled substrate can be used to select (or not to select) a probe for inclusion in the array. In some embodiments (FIG. 2) the probe may be unbound to a substrate and may also be labeled.  
         [0055]    In embodiments where unlabeled probes are chosen to form all or part of the array, the probes can be added to the vessel  10  in a sequential order. In sum a case the identity of a probe is known by its load order or a probe&#39;s identify can be known on the basis of the time that the probe is added. Alternatively, the probes having binding or reactivity characteristics that differ from one another, can be segregated to different predetermined locations, based on the difference in properties. The probes are then selected on the basis of their location within the vessel.  
         [0056]    As seen in FIG. 3, spectroscopy of a sample of biological material can be accomplished with an imaging illumination source  39  suitable for either spectroscopy or polarized light back scattering, the former being useful for assessing chemical identity, and the later being suited for measuring dimensions of internal structures such as the nucleus size. Using such spectroscopic method; in some embodiments, cells are interrogated and the array of probes created from selected interrogated cells. For instance, a computer  38  can be used to analyze the spectral data and to identify suspected cancerous, pre-cancerous and/or non-cancerous cell types. The computer then can apply the information to direct optical traps to contain selected cell types. The contained cells then may be used as the probes in assays, based on the reaction or binding of the contained cells with targets such as other cells, antibodies, antigens, and other biological material, or drugs and other chemicals. Those skilled in the art will recognize that the methodology used to interrogate and concentrate cells based on parameters specific to cancerous cells, may be altered, without departing from the scope of the invention, for use with interrogating and/or separating blastomeres, cells, or other material.  
         [0057]    In other embodiments, labeled or unlabeled probes, such as unlabeled probes having differing binding or reactivity characteristics may be placed in a series of sub-cells  16  disposed within the vessel  10 . In FIG. 1, for clarity, only one sub-cell is shown. However, it should be understood that a plurality of such sub-cells can be provided. In some embodiments, the boundaries of a sub-cell are constructed with optical traps. A number of optical traps placed in the ring orientation create an optical sub-cell which can perform the same functions as the physical sub-cell  16 .  
         [0058]    Placement of the probe in a sub-cell  16  is by any suitable means including movement by optical traps, through flow channels, through micro-capillaries or by other equivalent mechanism. In each sub-cell, one or more probes having the same binding or reactivity characteristics are placed. Section of the probes for inclusion in the array is then made on the basis of the sub-cell in which the probe is contained.  
         [0059]    The optical traps  1000 - 1004  are then used to trap the selected probes  500 - 504  by containing the probes within the optical traps  1000 - 1004 . A group of such contained probes are thereby configured to form an array.  
         [0060]    The inventive method and system lends itself to a semi-automated or automated process for tracking the movement and contents of each optical trap. The movement can be monitored, via video camera, spectrum, or an optical data stream and which provides a computer controlling the selection of probes and generation of optical traps information useful to adjusting the type of probes contained by the optical traps and the composition of the probes forming the array. In other embodiments, the movement is tracked based on predetermined movement of each optical trap caused by encoding the phase patterning optical element. Additionally, in some embodiments, a computer is used to maintain a record of each probe contained in each optical trap.  
         [0061]    Returning to the beam splitter  30 , the beam split  30  also provides a light beam  32  originating from the imaging illumination source  39  which passes through the subject cell  10  forming an optical data stream corresponding to the location of one or more of the beamlets, derived from the location and position of a probe contained by an optical trap.  
         [0062]    The optical data stream can then be viewed, converted to a video signal monitored, or analyzed by visual inspection  34   a  of an operator  36 , spectroscopically  34   b,  and/or video monitoring  34   c.  The optical data stream  32  may also be processed by a photodetector to monitor intensity, or any suitable device to convert the optical data stream to a digital data stream adapted for use by a computer  38 .  
         [0063]    To construct the array, the operator  36  and/or the computer  38  will adjust the hologram encoded by the phase patterning optical element  22  to direct the movement of each optical trap to acquire the selected probe and trap it. The plurality of optical traps with contained probes form the composition of the configured array that may be reconfigured as to the composition or position of the probes depending on the needs of the user. Using the optical data stream, the position of one or more of the trapped probes can be identified and their positions monitored. Based on such information, the surface of the phase patterning optical element can be altered, in some embodiments independently, to change the form of one or more of the optical traps containing the probes.  
         [0064]    Additionally, the position of one or more of the trapped probes in the array can be tracked by monitoring the position of the optical trap which contains it. Then using such information, any given probe in the array may be independently repositioned within the subject cell by altering the surface of the phase patterning optical element and the identity of each probe remains known by the optical trap in which it is contained irrespective of where the optical trap positions the probe.  
         [0065]    In a preferred embodiment, the computer  38  controls the movement of the optical traps both before and after the probes are trapped. In other embodiments, the optical data stream is first converted to a video signal which is then used to produce an image corresponding to the array and the operator views the image to control the movement of at least one of the optical traps based on the image.  
         [0066]    Referring to both FIGS. 1 and 3, to perform an assay, a first batch of targets T 1 -T 5  is added to new subject cell  10 , which also contains a fluid medium  3000 , via an inlet port  14 . The array of probes  500 - 504  is suspended in the medium  3000  via their containment by the optical traps  1000 - 1004 . To increase the opportunity for interaction with the targets T 1 -T 5 , the probes may be moved about the subject cell corresponding to movement of the optical traps.  
         [0067]    For example, in one embodiment, the probes  500 - 504  are trolled through the medium  3000  containing the targets T 1 -T 5 . By containing the probes optically, as opposed to physically, and moving the probes within the subject cell  10 , the opportunity for interaction of a probe with each target is increased, thus improving the speed and efficiency of the assay.  
         [0068]    The movement of an array of probes  500 - 502  via the sequential creation of sets of optical traps is illustrated in FIGS. 5A and 5B. In the embodiment illustrated in FIG. 5A, there is shown a simple linear movement of the array of probes, configured along a line P 1  representing a first set of predetermined positions. Movement is accomplished by transferring the probes from a fast set of optical traps to a second, third, and then fourth set. Referring additionally to FIG. 4, the first set of optical traps is generated by directing a laser beam at a first region  42  of the phase patterning optical element  40 . When the beamlets emanating from the first region  42  pass through a focusing lens, they form the first set of optical traps at a first position P 1  containing the probes  500 - 503 .  
         [0069]    To move the probes  500 - 502  from the first position P 1  to a second position P 2 , the static phase patterning optical element  40  is rotated around a spindle  47  to align the laser beam with a second region  43  which generates the second set of optical traps at a corresponding second set of predetermined positions P 2 . By constructing the second set of optical traps in the appropriate proximity to the first position P 1 , the probes can be passed from the first set of optical traps to the second set of optical traps. The sequence may continue passing the probes from the second set of predetermined positions P 2  to a third set of predetermined positions P 3 , from the third set of positions P 3  to a fourth set of predetermined positions P 4 , and from the fourth set of predetermined positions P 4  to a fifth set of predetermined positions P 5  by the rotation of the phase patterning optical element to align the appropriate region  42 - 46  corresponding to the desired position P 1 -P 5 . The time interval between the termination of one set of optical traps and the generation of the next should be of a duration to ensure that the probes are transferred to the next set of optical traps before they drift away.  
         [0070]    Such movement of the probes can be useful to troll the probes through the medium thereby enhancing the opportunity to have targets within the medium interact with the probes. This type of simple movement may also be useful in moving the probes from a sub-cell  16  (FIG. 1) to another area of the subject cell  10 , or segregating probes into a sub-cell  16 .  
         [0071]    In the embodiment illustrated in FIG. 5B there is shown a staggered movement of the probes from a wide to narrow proximity. The staggered movement of the probes occurs in a similar fashion as described in reference to FIG. 5A. However, the first region  42  now produces staggered optical traps with two probes  500  and  502  configured along a line P 1 , while a third probe  501  is configured at P 2 , a position between the two probes, but spaced apart from the line P 1 . As the probes are passed from a first set of optical traps to a second set and moved to second and subsequent positions, the staggered arrangement of the probes allows the probes to be packed densely without placing a set of traps in too close a proximity to two probes at the same time which could cause the probes to be contained by the wrong optical trap.  
         [0072]    Once a target has interacted with a probe, spectral methods can be used to investigate the target. The spectrum of those probes which had positive results (i.e., those probes which reacting with or bonded with the targets) can be obtained by using imaging illumination  39  such as that suitable for either inelastic spectroscopy or polarized light back scattering. The computer  38  can analyze the spectral data to identify the desired targets and direct the phase patterning optical element to segregate those desired targets. Those skilled in the art will recognize that the methodology used to segregate targets based on spectral data may be altered, without departing from the scope of the invention, to identify and/or segregate targets based on other information obtained from the targets and/or the optical data stream.  
         [0073]    Upon completion of the assay, selection can be made, via computer  38  and/or operator  36 , of which probes to discard and which to collect. The reconfigurable nature of the array allows for selective movement of a given optical trap and contained probe. In some cases the medium  3000  and unbound targets will be removed or flushed from the subject cell  10  through an outlet port  18  and the assay will be completed. In other cases, at least some of the probes still contained by optical traps, are reused with additional targets to perform further assays. This technique can be useful in the case of probes that tested positive or negative, depending on the parameters of the assay. In yet other cases, because the array of probes is reconfigurable as to the quantity and characteristics of the probes forming the array, the optical traps can be used to discard unbound probes and acquire additional probes for further experimentation.  
         [0074]    In some embodiments, it is not necessary to generate beamlets from each region of the static beam altering optical element  40 , or move the beam altering optical element  40  in a set direction. Instead, changing the order of the regions will change the location of the sets of optical traps.  
         [0075]    Shown in FIG. 6A is an elevational view of a compact system for forming the optical traps, generally designated  50 . The phase patterning optical element  51  is a dynamic optical element, with a reflective, dynamic surface which is also a phase only spatial light modulator such as the “PAL-SLM series X7665,” manufactured by Hamamatsu of Japan the “SLM 512SA7” or the “SLM 512SA15” both manufactured by Boulder Nonlinear Systems of Lafayette, Colo. These dynamic optical elements have an encodable reflective surface in which a computer controls a hologram formed therein.  
         [0076]    [0076]FIG. 6A shows a compact system for forming the optical traps, the optical element  51  is aligned with, or attached to, a housing  52  through which a first light channel  53   a  is provided. One end  53   b  of the first light channel is in close proximity to the optical element  51 , the other end  53   c  of the first light channel intersects with and communicates with a second light channel  53   d  formed perpendicular thereto. The second light channel is formed within a base  54   a  of a microscope lens mounting turret or “nosepiece”  54   b.  The nosepiece  54   b  is adapted to fit into a Nixon TE 200 series microscope (not shown). The second light channel communicates with a third light channel  55   a  which is also perpendicular to the second light channel. The third light channel  55   a  traverses from the top surface of the nosepiece  54   b  through the base of the nosepiece  54   a  and is parallel to an objective lens focusing lens  56 . The focusing lens has a top and a bottom forming a back aperture  57 . Interposed in the third light channel the second light channel and the back aperture  57  of the focusing lens is a dichroic mirror beam splitter  58 . Other components within the compact system for forming the optical traps  50  include a first mirror M 1 , which reflects the beamlets emanating from the phase patterning optical element through the first light channel, a first set of transfer optics TO 1  disposed within the first light channel, aligned to receive the beamlets reflected by the first mirror M 1 , a second set of transfer optic TO 2  disposed within the first light channel, aligned to receive the beamlets passing through the first set of transfer lenses TO 1 , and a second mirror M 2 , positioned at the intersection of the first light channel and the second light channel, aligned to reflect beamlets passing through the second set of transfer optics TO 2  and through the third light channel  55   a.    
         [0077]    To generate the optical traps, a laser been (not shown) is directed through an optical  150  out a collimator end  151  and reflected off the dynamic surface  59  of the optical element  51 . The beam of light (not shown) exiting the collimator end  151  of the optical fiber  150  is diffracted by the dynamic surface  59  of the optical element  51  into a plurality of beamlets (not shown). The number type and direction of each beamlet may be controlled and varied by altering the hologram encoded in the dynamic surface medium  59 . The beamlets then reflect off the first mirror M 1  through the first set of transfer optics TO 1  down the first light channel  53   a  through the second set of transfer optics TO 2  to the second mirror M 2 ; and are directed at the dichroic mirror  58  up to the back aperture  57  of the objective lens  56 , are converged through the objective lens  56 , thereby producing the optical gradient conditions necessary to form the optical traps. That portion of the light which is split through the dichroic mirror  58 , for imaging, passes through the lower portion of the third light channel  55   b  forming an optical data stream (not shown).  
         [0078]    In those embodiments in which the phase profile of the beamlets is less intense at the periphery and more intense at regions inward from the periphery, overfilling the back aperture  57  by less than about 15 percent is useful to form optical traps with greater intensity at the periphery of optical traps than optical traps formed without overfilling the back aperture  57 .  
         [0079]    Shown in FIG. 6B is an elevational view of a Nixon TE 200 series microscope into which the compact system for forming the optical traps  50  has been mounted, generally designated  60 . The nosepiece  54  with the attached a housing  52  fits directly into the microscope via the mount (not shown) for the nosepiece  54   a  and  54   b.  The housing and its contents and attached optical element  51  are secured to the nosepiece  54   a  and  54   b  require few or no alterations or modifications to the remainder of the microscope. For imaging, an illumination source  61  may be provided above the objective lens  56 .  
         [0080]    The first and second set of transfer optics TO 1  and TO 2  are shown containing two lens elements each. The lenses can be either convex or concave. Different and varying types and quantity of lenses such as symmetrical air space singlets, symmetrical air spaced doublets and/or additional lenses or groups of lenses, can be chosen to achieve the image cage transfer from the first mirror M 1  to the second mirror M 2 . In some embodiments the first and second set of transfer optics are symmetrical air spaced doublets, spaced at a distance to act in combination as a telephoto lens.  
         [0081]    Since certain changes may be made in the above systems apparatus and methods without departing from the scope of the invention herein involved, it is intended that all matter contained in the above description, as shown in the accompanying drawings specification shall be interpreted in an illustrative, and not a limiting sense.