Photolithographic method and system for efficient mask usage in manufacturing DNA arrays
Systems, methods, and products are described for synthesizing probe arrays of polymers. A mask is used that includes reticle areas, each of which includes a number of reticles associated with a same synthesis area on a substrate. A method includes (a) aligning the mask with respect to the substrate so that a first reticle of a first reticle area is aligned with a first synthesis area and so that a second reticle of the first reticle area is aligned with a first discard area on the substrate; (b) coupling monomers on the first synthesis area at locations determined by the first reticle; (c) re-aligning the mask with respect to the substrate so that the second reticle is aligned with the first synthesis area; and (d) coupling monomers on the first synthesis area at locations determined by the second reticle. The monomers may be, for example, nucleotides, amino acids or saccharides.
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The present application claims priority from U.S. Provisional Patent Application Ser. No. 60/265,103, entitled “RAPID FLEXIBLE CONTENT ARRAY AND ONLINE ORDERING SYSTEM,” filed Jan. 29, 2001, hereby incorporated herein by reference in its entirety for all purposes.
FIELD OF THE INVENTIONThe present invention is related to systems, methods, and products providing lithographic masks used to form high-density probes of biological materials on a substrate.
BACKGROUNDU.S. Pat. No. 5,424,186 to Fodor, et al., describes a technique for, among other things, forming and using high density arrays of probes comprising molecules such as oligonucleotide, RNA, peptides, polysaccharides, and other materials. Arrays of oligonucleotides or peptides, for example, are formed on the surface by sequentially removing a photo-removable group from a surface, coupling a monomer to the exposed region of the surface, and repeating the process. Nucleic acid probe arrays synthesized in this manner, such as Affymetrix® GeneChip® probe arrays from Affymetrix, Inc. of Santa Clara, Calif., have been used to generate unprecedented amounts of information about biological systems. Analysis of these data may lead to the development of new drugs and new diagnostic tools.
A typical step in the process of synthesizing these probe arrays is to design a mask that will define the locations on a substrate that are exposed to light. Some systems and methods useful in the design and/or use of such masks are described in the following U.S. Pat. No. 5,571,639 to Hubbell, et al.; U.S. Pat. No. 5,593,839 to Hubbell, et al.; U.S. Pat. No. 5,856,101 to Hubbell, et al.; U.S. Pat. No. 6,153,743 to Hubbell, et al.; and U.S. Pat. No. 6,188,783 to Balaban, et al., each of which is hereby incorporated herein by reference for all purposes. Notwithstanding the advances described in these patents, it is desirable to identify additional techniques for designing and using masks in the manufacture of probe arrays.
SUMMARY OF THE INVENTIONSystems, methods, computer program products, masks, and probe arrays produced thereby, are described with reference to illustrative, non-limiting, embodiments. For example, while certain systems, methods, computer software products, masks, and probe arrays are described with respect to the manufacture and/or use of Affymetrix® GeneChip® probe arrays, these descriptions are merely illustrative. Other implementations are possible, for example, with respect to other types of probe arrays. Moreover, possible implementations are not limited to probe arrays. That is, the synthesized polymers need not be used as probes but may be employed with respect to any of a variety of conventional combinatorial chemistry purposes and uses.
In accordance with some embodiments, a method is described for synthesizing polymers on a substrate using one or more masks. In some implementations, the polymers synthesized on the substrate comprise probes in a probe array. The masks each include reticle areas made up of reticles. A reticle is made up of areas transparent to the photolithographic radiation (hereafter, simply referred to for convenience as “light”), and also is made up of occluded areas through which the light does not pass. The transparent areas are sometimes referred to as “flashes.” Each of the reticles in a particular reticle area is associated with the same synthesis area on the substrate. In those implementations in which the combinatorial chemistry is directed to producing probe arrays, the term “synthesis area” is used herein to refer to an area of the substrate on which probes are synthesized that are intended to be included in the synthesized probe arrays. In these implementations, a probe of a probe array generally may be a polymer having a sequence such that the probe is capable of hybridizing with potential targets, or having a sequence serving as a control to assess the hybridization process. In contrast, the term “discard area” is used herein to refer to an area on the substrate through which dicing lines may be cut to physically separate the substrate into two or more probe arrays. A part or all of a discard area may contain synthesized polymers that are not intended for use as probes (or, in implementations other than probe arrays, are not intended for the purpose of the combinatorial chemistry). That is, in the illustrated implementations, although polymers may be synthesized in discard areas, these polymers may be discarded or otherwise ignored or destroyed rather than used as probes in a synthesized probe array. The polymers in discard areas may have sequences suitable for hybridization or control, but need not. In some implementations, the term “discard area” may be used more broadly to also include areas not used for cutting but used for joining the substrate to packaging, or for other purposes not including the purpose of providing a synthesis area.
The method includes the following steps: (a) for each reticle area, sequentially aligning two or more of the reticles of that reticle area with the associated synthesis area; and (b) for each sequential alignment, coupling monomers on the substrate at locations determined by the aligned reticles. The monomers of this method, and of other embodiments and implementations described herein, may include nucleotides, amino acids, or saccharides, for example.
In accordance with this method, the reticle areas are substantially contiguously arranged on the mask, and the plurality of reticles within each of the reticle areas are substantially contiguously arranged within the reticle area. The term “substantially contiguously” is used in this context to mean that reticles in a reticle area may abut each other, and that reticle areas may abut each other. That is, there generally need not be any spaces between the reticles or between the reticle areas. However, the term “substantially contiguously” is used broadly herein to include implementations, such as that illustrated in the detailed description below, in which narrow boundary areas are provided between reticles and/or between reticle areas. As described in greater detail below, these narrow boundary areas may be provided for a variety of practical reasons related to making masks, scanning labeled probe-target pairs, and other reasons. Notably, however, they are not provided for the reason of reserving, by themselves, a space on the substrate for dicing.
In some implementations of the method, each reticle area may be made up of reticles arranged in a particular pattern that is the same for all reticle areas. For example, the pattern may be an array of rows and columns in which the rows have a height H (which is the height of the reticles, plus a boundary area, if any) and the columns may have a width W (which is the width of the reticles, plus a boundary area, if any). In some aspects of these implementations, the sequential alignment of step (a) may include translating the mask with respect to the substrate by a sequence of steps. The translation distance at each step is determined by the height H or the width W. For example, a step may consist of a translation W to the right or, as another example, a translation W to the right and a translation H down. The translation between the mask and substrate is relative, and may thus be accomplished by moving the mask and keeping the substrate immobile, by moving the substrate and keeping the mask immobile, or by moving both to varying degrees.
In some implementations of the method, step (b) may include coupling a same monomer for each of the aligned reticles. Step (b) may also include directing light through the aligned reticles to de-protect the locations for coupling.
Other embodiments described herein are directed to systems for synthesizing polymers on a substrate. In one implementation, the system includes a mask having a plurality of reticle areas, wherein each reticle area includes two or more reticles, each of which is associated with a same synthesis area on the substrate. The system also has an aligner that, for each reticle area, sequentially aligns two or more of the reticles of that reticle area with the associated synthesis area. Another element of the system is a synthesizer that, for each sequential alignment, causes monomers to be coupled on the substrate at locations determined by the aligned reticles. In these implementations, the reticle areas are substantially contiguously arranged on the mask, and the reticles within each of the reticle areas are substantially contiguously arranged within the reticle area.
Further embodiments are directed to a mask for synthesizing polymers on a substrate. The mask has substantially contiguously arranged reticle areas and, within each reticle area, substantially contiguous reticles. Each of the reticles in a same reticle area is associated with a same synthesis area on the substrate and is constructed and arranged for synthesizing polymers by enabling the coupling of monomers on the same synthesis area at locations determined by the reticles.
Yet other embodiments are directed to a method for manufacturing a mask for synthesizing polymers on a substrate. The method includes the step of identifying two or more reticle areas substantially contiguously arranged on the mask. Another step is to construct and arrange two or more substantially contiguous reticles within each reticle area, each of which is associated with a same synthesis area on the substrate. The reticles further are constructed and arranged for synthesizing polymers by enabling the coupling of monomers on the same synthesis area at locations determined by the reticles of a particular reticle area.
Also described herein is a probe array including polymers synthesized on a substrate by a method that includes the steps of: (a) providing at least one mask having two or more reticle areas, wherein each reticle area comprises two or more reticles, each of which is associated with a same synthesis area on the substrate; (b) for each reticle area, sequentially aligning two or more of the plurality of reticles of that reticle area with the associated synthesis area; and (c) for each sequential alignment, coupling monomers on the substrate at locations determined by the aligned reticles. The two or more reticle areas are substantially contiguously arranged on the mask, and the two or more reticles within each of the reticle areas are substantially contiguously arranged within the reticle area.
In other embodiments, a computer program product is described for synthesizing polymers on a substrate using a mask having a plurality of reticle areas, wherein each reticle area comprises two or more reticles, each of which is associated with a same synthesis area on the substrate. The product includes a computer usable medium storing control logic that, when executed on a computer system, performs a method including the steps of: (a) for each reticle area, sequentially aligning two or more of the reticles of that reticle area with the associated synthesis area; and (b) for each sequential alignment, coupling monomers on the substrate at locations determined by the aligned reticles. The reticle areas are substantially contiguously arranged on the mask, and the reticles within each of the reticle areas are substantially contiguously arranged within the reticle area.
Also described herein is a method for synthesizing probe arrays of polymers on a substrate using a mask having two or more reticle areas, wherein each reticle area includes two or more reticles, each of which is associated with a same synthesis area on the substrate. The method includes the following steps: (a) aligning the mask with respect to the substrate so that a first reticle of a first reticle area is aligned with a first synthesis area associated with the two or more reticles of the first reticle area, and so that a second reticle of the first reticle area is aligned with a first discard area on the substrate; (b) coupling monomers on the first synthesis area at locations determined by the first reticle; (c) re-aligning the mask with respect to the substrate so that the second reticle is aligned with the first synthesis area; and (d) coupling monomers on the first synthesis area at locations determined by the second reticle.
In general, the preceding steps may be repeated so that each of the reticles of a reticle area is aligned during a synthesis step with the synthesis area associated with that reticle area. When a reticle is aligned with the synthesis area, the other reticles of the same reticle area typically are not aligned with that, or another, synthesis area. Rather, they typically are aligned with a discard area. A further step in some implementations of the method is to dice the substrate. The dicing is done at least partially within the first discard area. Typically, the dicing physically separates a probe array, including the first synthesis area on the substrate, from at least one other synthesis area on the substrate.
A further embodiment described herein consists of a system for synthesizing probe arrays of polymers on a substrate. The system includes a mask having two or more reticle areas, wherein each reticle area comprises a plurality of reticles, each of which is associated with a same synthesis area on the substrate. Also included in the system is an aligner that (i) aligns the mask with respect to the substrate so that a first reticle of a first reticle area is aligned with a first synthesis area associated with the plurality of reticles of the first reticle area, and so that a second reticle of the first reticle area is aligned with a first discard area on the substrate, and (ii) re-aligns the mask with respect to the substrate so that the second reticle is aligned with the first synthesis area. Another element of the system is a synthesizer that (i) couples monomers on the first synthesis area at locations determined by the first reticle when the first reticle is aligned with the first synthesis area, and (ii) couples monomers on the first synthesis area at locations determined by the second reticle when the second reticle is aligned with the first synthesis area. Typically, the synthesizer further is constructed and arranged to direct light through the aligned reticles to de-protect the locations for coupling.
Yet another embodiment consists of a probe array comprising polymers synthesized on a substrate by a method that includes the following steps: (a) providing at least one mask having a plurality of reticle areas, wherein each reticle area comprises a plurality of reticles, each of which is associated with a same synthesis area on the substrate; (b) aligning the mask with respect to the substrate so that a first reticle of a first reticle area is aligned with a first synthesis area associated with the plurality of reticles of the first reticle area, and so that a second reticle of the first reticle area is aligned with a first discard area on the substrate; (c) coupling monomers on the first synthesis area at locations determined by the first reticle; (d) re-aligning the mask with respect to the substrate so that the second reticle is aligned with the first synthesis area; and (e) coupling monomers on the first synthesis area at locations determined by the second reticle. A further embodiment is a computer program product for synthesizing polymers on a substrate using a mask having a plurality of reticle areas. Each reticle area includes a plurality of reticles, each of which is associated with a same synthesis area on the substrate. The product includes a computer usable medium storing control logic that, when executed on a computer system, performs a method including: (a) aligning the mask with respect to the substrate so that a first reticle of a first reticle area is aligned with a first synthesis area associated with the plurality of reticles of the first reticle area, and so that a second reticle of the first reticle area is aligned with a first discard area on the substrate; (b) coupling monomers on the first synthesis area at locations determined by the first reticle; (c) re-aligning the mask with respect to the substrate so that the second reticle is aligned with the first synthesis area; and (d) coupling monomers on the first synthesis area at locations determined by the second reticle.
The preceding embodiments and implementations are not necessarily inclusive or exclusive of each other and may be combined in any manner that is non-conflicting and otherwise possible, whether they be presented in association with a same, or a different, embodiment or implementation. The description of one embodiment or implementation is not intended to be limiting with respect to others. Also, any one or more function, step, operation, or technique described elsewhere in this specification may, in alternative embodiments or implementations, be combined with any one or more function, step, operation, or technique described in the summary. Thus, the above embodiments and implementations are illustrative rather than limiting.
BRIEF DESCRIPTION OF THE DRAWINGS The above and other embodiments and implementations will be more clearly appreciated from the following detailed description when taken in conjunction with the accompanying drawings. In the drawings, like reference numerals indicate like structures or method steps and the leftmost digit of a reference numeral indicates the number of the figure in which the referenced element first appears (for example, the element 120 appears first in
Detailed descriptions are now provided with respect to systems, methods, software program products, masks produced thereby, probe arrays produced thereby, and combinations thereof.
Synthesized Probe ArraysVarious techniques and technologies may be used for synthesizing dense arrays of biological materials on or in a substrate or support. For example, Affymetrix® GeneChip® arrays are synthesized in accordance with techniques sometimes referred to as VLSIPS™ (Very Large Scale Immobilized Polymer Synthesis) technologies. Some aspects of VLSIPS™ technologies are described in the following U.S. Pat. No. 5,424,186 to Fodor, et al.; U.S. Pat. No. 5,143,854 to Pirrung, et al.; U.S. Pat. No. 5,445,934 to Fodor, et al.; U.S. Pat. No. 5,744,305 to Fodor, et al.; U.S. Pat. No. 5,831,070 to Pease, et al.; U.S. Pat. No. 5,837,832 to Chee, et al.; U.S. Pat. No. 6,022,963 to McGall, et al.; and U.S. Pat. No. 6,083,697 to Beecher, et al. Each of these patents is hereby incorporated by reference in its entirety. The probes of these arrays in some implementations consist of oligonucleotides, which are synthesized by methods that include the steps of activating regions of a substrate and then contacting the substrate with a selected monomer solution. The regions are activated with a light source shown through a mask in a manner similar to photolithography techniques used in the fabrication of integrated circuits. Other regions of the substrate remain inactive because the mask blocks them from illumination. By repeatedly activating different sets of regions and contacting different monomer solutions with the substrate, a diverse array of polymers is produced on the substrate. Various other steps, such as washing unreacted monomer solution from the substrate, are employed in various implementations of these methods.
Additional techniques for synthesizing and using high-density probe arrays are described in U.S. Pat. No. 5,384,261 to Winkler, et al. These techniques include systems for mechanically protecting portions of a substrate and selectively de-protecting and coupling materials to the substrate using light-directed methods. Still further techniques for probe array synthesis are provided in U.S. Pat. No. 6,121,048 to Zaffaroni, et al. The '261 and '048 patents also are incorporated herein by reference for all purposes.
The probes of these synthesized probe arrays typically are used in conjunction with tagged biological samples such as cells, proteins, genes or EST's, other DNA sequences, or other biological elements. These samples, referred to herein as “targets,” are processed so that, typically, they are spatially associated with certain probes in the probe array. For example, one or more chemically tagged biological samples, i.e., the targets, are distributed over the probe array. Some targets hybridize with at least partially complementary probes and remain at the probe locations, while non-hybridized targets are washed away. These hybridized targets, with their “tags” or “labels,” are thus spatially associated with the targets' complementary probes. The hybridized probe and target may sometimes be referred to as a “probe-target pair.” Detection of these pairs can serve a variety of purposes, such as to determine whether a target nucleic acid has a nucleotide sequence identical to or different from a specific reference sequence. See, for example, U.S. Pat. No. 5,837,832, referred to and incorporated above. Other uses include gene expression monitoring and evaluation (see, e.g., U.S. Pat. No. 5,800,992 to Fodor, et al.; U.S. Pat. No. 6,040,138 to Lockhart, et al.; and International App. No. PCT/US98/15151, published as WO99/05323, to Balaban, et al.), genotyping (U.S. Pat. No. 5,856,092 to Dale, et al.), or other detection of nucleic acids. The '992, '138, and '092 patents, and publication WO99/05323, are incorporated by reference herein in their entireties for all purposes.
Probes typically are able to detect the expression of corresponding genes or EST's by detecting the presence or abundance of mRNA transcripts present in the target. This detection may, in turn, be accomplished by detecting labeled cRNA that is derived from cDNA derived from the mRNA in the target. In general, a group of probes, sometimes referred to as a probe set, contains sub-sequences in unique regions of the transcripts and does not correspond to a full gene sequence. Further details regarding the design and use of probes are provided in U.S. Pat. No. 6,188,783, incorporated above, and in PCT Application Ser. No. PCT/US 01/02316, filed Jan. 24, 2001, and hereby incorporated herein in its entirety for all purposes.
Labeled targets in hybridized probe arrays may be detected using various commercial devices, sometimes referred to as “scanners.” Scanners image the targets by detecting fluorescent or other emissions from the labels, or by detecting transmitted, reflected, or scattered radiation. A typical scheme employs optical and other elements to provide excitation light and to selectively collect the emissions. Also generally included are various light-detector systems employing photodiodes, charge-coupled devices, photomultiplier tubes, or similar devices to register the collected emissions. For example, a scanning system for use with a fluorescent label is described in U.S. Pat. No. 5,143,854, incorporated by reference above. Other scanners or scanning systems are described in U.S. Pat. Nos. 5,578,832; 5,631,734; 5,834,758; 5,936,324; 5,981,956; 6,025,601; 6,141,096; 6,185,030; and 6,201,639, and in PCT Application PCT/US99/06097 (published as WO99/47964), each of which is hereby incorporated by reference in its entirety for all purposes.
Mask Design System 101 and Mask Manufacturing System 150
As will be appreciated by those of ordinary skill in the relevant art, mask specification files 112 include data specifying a layout of reticles on one or more masks consistent with desired mask characteristics 106 and probe information 107. As also will be appreciated by those of ordinary skill in the relevant art, probe specification files 114 include information specifying the order in which monomers may be applied in a probe array synthesizer that synthesizes probe arrays using masks 155. Although the word “files” is used for convenience of illustration with respect to files 112 and 114, the word is used broadly to include any type of data structure or technique for storing or transmitting data in any form or format.
Mask manufacturing system 150 may be any of a variety of conventional systems for producing masks, or a mask-producing system of a type that may be developed in the future. Masks 155 produced by system 150 typically comprise lithographic members such as chrome on glass, as one illustrative and non-limiting example. Reticles on the mask selectively direct light to a substrate during an exposure in accordance with known techniques. As noted above with respect to an illustrative example, the light may activate linker molecules at sites on the substrate determined by openings in the reticles through which the light passes. Mask manufacturing system 150 is capable of producing masks 155 of conventional design or of an improved design in accordance with aspects of the present invention, depending on whether desired mask characteristics 106 are conventional or otherwise.
Probe Arrays Synthesized Using Masks of FIGS. 2A-B
As indicated in
In accordance with conventional techniques well known to those of ordinary skill in the relevant art, a number of masks having reticles arranged in the fashion shown in
A second light-exposure step is represented in
These synthesis cycles may continue using dozens of masks 155A, each of which has reticles 210 arranged in a same configuration and aligned over the same areas of wafer 240. The last of these dozens of masks is represented in
Notably, the dicing operation in accordance with this conventional approach typically requires that a significant portion of masks 155A be set aside for dicing offsets 212. The example of 3-millimeter offset areas separating each probe array area is typical in order to accommodate the thickness of the cut made by conventional techniques. Also, the number of masks needed in accordance with the conventional approach of
Thus, while the number of masks used to synthesize probe arrays 330A through 330D is one-fourth the number used to synthesize probe arrays 230A through 230Y of the previous example, the number of probe arrays from the mask set is reduced from 25 to four. As is now evident, both the number of probe arrays synthesized with a mask set and the number of masks in a mask set can be altered by changing the size and/or geometry of the mask and reticles. As one of many possible examples, mask 155B could have been made with four groups of nine reticles (i.e., 36 reticles per mask for the synthesis of nine probe arrays using four light-exposure steps per mask) by increasing the size of the mask and/or reducing the size of the reticles. Similarly, the mask of this alternative example could consist of nine groups of four reticles (i.e., 36 reticles per mask for the synthesis of four probe arrays using nine light-exposure steps per mask).
Many arrangements of reticles are possible that allow multiple synthesis cycles to be accomplished using each mask. One alternative arrangement is illustrated in FIGS. 4A-E.
Thus, in all of the preceding variations noted with respect to FIGS. 3A-F and 4A-E, the disadvantage remains that reticles are separated by dicing offsets 312 and 412. As noted, these dicing offsets are reserved for the purpose of allowing dicing of probe arrays through locations on wafers 340 and 440, respectively, as determined by the separation of reticles in the same group (i.e., reticles exposed during the same light-exposure step). The inclusion of dicing offsets 312 and 412 reduce the area of masks 155B and 155C, respectively, that can be dedicated to reticles.
Probe Arrays Synthesized Using Masks of FIGS. 5A-C, 6I, 6K, and 6L A number of advantages, as compared for instance to the previous mask examples, can be attained by employing a mask design such as that now described in relation to FIGS. 5A-C, 6I, 6K, and 6L. For convenience, and for reasons that will be described below, this advantageous design may sometimes be referred to hereafter as the “interleaved” design, and masks having this design are sometimes referred to as “interleaved” masks. Significantly, the interleaved design need not reserve areas of the mask so that those reserved areas will provide, by themselves, an area on a wafer through which dicing cuts may be made. Rather, as shown in
Interleaved mask 155D of
There are a variety of practical reasons, not related to providing discard areas on a wafer, for optionally providing boundaries of non-zero width. One reason for providing non-zero-width boundaries is related to the process of scanning probe arrays. As shown in
When irradiated by a scanner, any labeled targets that have hybridized with polymers in discard areas around the first synthesis area will provide detectable excitation radiation. This excitation radiation may interfere with the identification of intended probes within the first synthesis area. For example, a human operator or a software algorithm attempting to identify corners of the probe array created from the first synthesized area may be confused by emissions detected from labeled targets that happened to hybridize with the polymer in discard areas near the corners. Identification of corners of a probe array is a typical method for imposing an “alignment grid” to help in identifying probes from scanned images, as described in greater detail in U.S. Pat. No. 6,090,555 to Fiekowsky, et al., which is hereby incorporated by reference herein in its entirety for all purposes. By providing a small boundary between reticles, a small separation is provided between a synthesis area and its surrounding discard areas, and thus the likelihood of confusion may be reduced. However, providing a non-zero boundary for this reason is optional and need not be implemented in various implementations.
Another reason for optionally providing boundaries of non-zero width is that the design of the machinery used to handle, align, and/or synthesize masks and/or wafers may make it convenient to employ masks and/or wafers of particular outside dimensions. For instance, a mask or wafer having the 45 millimeter by 45 millimeter dimensions of the present example may be more convenient than one of 40 millimeters on a side. Thus, whereas 100 reticles of 4 millimeters by 4 millimeters each could fit on a square mask of 40 millimeters on a side and such an implementation is optional, this arrangement of abutting reticles would merely leave empty space on the edges of a square mask or wafer having 45 millimeters on a side. Thus, a separation of 0.5 millimeters may be provided between reticles of this size on a square mask of 45 millimeters on a side without affecting the efficiency of mask usage. It may be advantageous in some cases to increase the size of each reticle from 4.0 to 4.5 millimeters on a side, thus allowing the synthesis of additional probes using abutting reticles. However, it also is possible that the smaller reticle size is sufficient for synthesis of the desired number of probes, and there thus may be no reason to increase the reticle size. Also, the equipment used for packaging, handling, or processing (e.g., hybridizing, washing, scanning) probe arrays may make it convenient to have probe arrays of a particular size. Thus, while larger reticles and thus larger probe arrays might be possible for masks or wafers of a particular size, there may be no reason to use the larger reticles.
Yet another practical reason that boundaries of non-zero width may be employed is if the width of a discard area is less than the minimum width needed for dicing, and each synthesis area is separated from its neighboring synthesis areas by no more than one discard area. For example, if each reticle is a square having sides of 2.53 millimeters, and the interleaved reticle areas have four reticles that abut each other, then the discard areas around each synthesis area on a wafer will be 2.53 millimeters. For implementations in which the area reserved for the dicing cut must be no less than 3 millimeters wide, then an addition of 0.5 millimeters increases the effective size of the discard area to provide the extra margin for dicing.
The use of interleaved masks to synthesize polymers on a substrate is now further described in relation to
It will be understood that the examples of
As will now be appreciated, a significant advantage of using interleaved masks is that the number of masks in a mask set generally may be substantially reduced as compared to designs in which portions of the mask are dedicated to dicing offsets. At the same time, the productivity of interleaved masks generally need not be compromised in terms of the number of probe arrays synthesized. These advantages are demonstrated, for example, by comparing conventional mask 155A of
As is evident, increasing the number of light-exposure steps implemented on each mask, assuming the mask size remains the same, generally is accomplished by reducing the size of the reticles. Smaller reticles generally results in smaller synthesis areas, which generally means, assuming a constant probe density, that fewer probes may be synthesized on each synthesis area and thus fewer probes are included in the resulting probe arrays. However, this effect is ameliorated by at least two considerations. First, the mask area is efficiently used in accordance with the interleaved design because little or no space need be provided between reticles. Thus, more information can generally be carried by an interleaved mask than by conventional masks in which dicing offsets, generally carrying no information, are included.
Second, there are important applications in which the savings in time and money achieved by using interleaved masks far outweighs any reduction in the number of probes in the resulting probe arrays. For example, there is considerable demand among users for custom-made arrays that can be provided relatively quickly and inexpensively. A user of custom-made arrays may not require that tens of thousands of genes or EST's be probed in a single array. Rather, the user may require probe arrays representing far fewer sequences, e.g., 100 to 1,000 genes or EST's. Moreover, the user may not need large numbers of the customized arrays. For example, a dozen arrays may be sufficient. For user demand of this type, the previous example of a reticle of 2.53 millimeters on a side generally provides sufficient probe density using conventional probe synthesis technology while producing sufficient number of probe arrays using far fewer masks as compared to conventional mask designs. For example, if the boundary area between reticles has a width of 0.47 millimeters (so that the boundary area plus discard area is sufficient for a 3 millimeter dicing cut), then the illustrative square mask of 45 millimeters on a side can accommodate 15×15=225 reticles. If these 225 reticles are applied to 15 light-exposure steps, then a mask set generally produces 15 square synthesis areas of 2.53 millimeters on a side and 15 probe arrays of this size. It is illustratively assumed that 75 light-exposure steps are used for complete synthesis of probes (e.g., 25-mer oligonucleotides). Thus, only five interleaved masks (75 divided by 15) are required in the illustrative mask set. Using the conventional approach represented by mask 155A, 75 masks would be needed. The fifteen-fold reduction in the size of the mask set achieved using the interleaved masks provides significant savings in time and cost while satisfying user demand with respect to probe density and number of probe arrays supplied.
The foregoing steps, and others that may be used in numerous variations of the interleaved mask design, may be implemented, for example, in the form of computer instructions and data such as represented by desired mask characteristics 106 of
System 800 includes a computer or controller 810, which may be any type of general purpose computer, as described above with respect to computer 100, or a dedicated processor or controller. System 800 also includes aligner 820 that, typically under the control of computer or controller 810, performs the sequential alignments of masks and substrates as specified, for example, by aspects of mask specification files 112. Thus, alignment steps of
Having described various embodiments and implementations, it should be apparent to those skilled in the relevant art that the foregoing is illustrative only and not limiting, having been presented by way of example only. Many other schemes for distributing functions among the various functional elements of the illustrated embodiment are possible. The functions of any element may be carried out in various ways in alternative embodiments. For example, some or all of the functions described as being carried out by computer or controller 810 could be carried out by aligner 820 and/or synthesizer 830.
Also, the functions of several elements may, in alternative embodiments, be carried out by fewer, or a single, element. Similarly, in some embodiments, any functional element may perform fewer, or different, operations than those described with respect to the illustrated embodiment. Also, functional elements shown as distinct for purposes of illustration may be incorporated within other functional elements in a particular implementation. Also, the sequencing of functions or portions of functions generally may be altered. Certain functional elements, files, data structures, and so on, may be described in the illustrated embodiments as located in system memory of a particular computer. In other embodiments, however, they may be located on, or distributed across, computer systems or other platforms that are co-located and/or remote from each other. For example, any one or more of data files or data structures described as co-located on and “local” to a server or other computer may be located in a computer system or systems remote from the server or other computer. In addition, it will be understood by those skilled in the relevant art that control and data flows between and among functional elements and various data structures may vary in many ways from the control and data flows described above or in documents incorporated by reference herein. More particularly, intermediary functional elements may direct control or data flows, and the functions of various elements may be combined, divided, or otherwise rearranged to allow parallel processing or for other reasons. Also, intermediate data structures or files may be used and various described data structures or files may be combined or otherwise arranged. Numerous other embodiments, and modifications thereof, are contemplated as falling within the scope of the present invention as defined by appended claims and equivalents thereto.
Claims
1-28. (canceled)
29. A method for synthesizing probe arrays of polymers on a substrate using a mask having a plurality of reticle areas, wherein each reticle area comprises a plurality of reticles, each of which is associated with a same synthesis area on the substrate, the method comprising the steps of:
- (a) aligning the mask with respect to the substrate so that a first reticle of a first reticle area is aligned with a first synthesis area associated with the plurality of reticles of the first reticle area, and so that a second reticle of the first reticle area is aligned with a first discard area on the substrate;
- (b) coupling monomers on the first synthesis area at locations determined by the first reticle;
- (c) re-aligning the mask with respect to the substrate so that the second reticle is aligned with the first synthesis area; and
- (d) coupling monomers on the first synthesis area at locations determined by the second reticle.
30. The method of claim 29, wherein:
- when the first reticle is aligned with the first synthesis area, every reticle of the first reticle area other than the first reticle is aligned with a discard area on the substrate.
31. The method of claim 29, further comprising the step of:
- dicing the substrate at least partially within the first discard area.
32. The method of claim 31, wherein:
- the dicing physically separates a probe array, including the first synthesis area on the substrate, from at least one other synthesis area on the substrate.
33. The method of claim 31, wherein:
- the plurality of reticles in each reticle area are arranged in a same pattern.
34. The method of claim 33, wherein:
- the pattern comprises rows and columns of reticles.
35. The method of claim 34, wherein:
- the dicing of the substrate is done in a straight line lying entirely within one or more discard areas including the first discard area.
36. The method of claim 29, wherein:
- the monomers are selected from the group consisting of nucleotides, amino acids or saccharides.
37. The method of claim 29, wherein:
- step (b) further comprises coupling a first monomer and step (d) further comprises coupling the first monomer or a second monomer.
38. The method of claim 29, wherein:
- steps (b) and (d) each further comprise directing light through the aligned reticles to de-protect the locations for coupling.
39. A system for synthesizing probe arrays of polymers on a substrate, comprising:
- (a) a mask having a plurality of reticle areas, wherein each reticle area comprises a plurality of reticles, each of which is associated with a same synthesis area on the substrate;
- (b) an aligner constructed and arranged to (i) align the mask with respect to the substrate so that a first reticle of a first reticle area is aligned with a first synthesis area associated with the plurality of reticles of the first reticle area, and so that a second reticle of the first reticle area is aligned with a first discard area on the substrate, and (ii) re-align the mask with respect to the substrate so that the second reticle is aligned with the first synthesis area; and
- (c) a synthesizer constructed and arranged to (i) couple monomers on the first synthesis area at locations determined by the first reticle when the first reticle is aligned with the first synthesis area, and (ii) couple monomers on the first synthesis area at locations determined by the second reticle when the second reticle is aligned with the first synthesis area.
40. The system of claim 39, wherein:
- the monomers are selected from the group consisting of nucleotides, amino acids or saccharides.
41. The system of claim 39, wherein:
- the synthesizer further is constructed and arranged to direct light through the aligned reticles to de-protect the locations for coupling.
42-48. (canceled)
49. A computer program product for synthesizing polymers on a substrate using a mask having a plurality of reticle areas, wherein each reticle area comprises a plurality of reticles, each of which is associated with a same synthesis area on the substrate, the product comprising a computer usable medium storing control logic that, when executed on a computer system, performs a method comprising the steps of:
- (a) aligning the mask with respect to the substrate so that a first reticle of a first reticle area is aligned with a first synthesis area associated with the plurality of reticles of the first reticle area, and so that a second reticle of the first reticle area is aligned with a first discard area on the substrate;
- (b) coupling monomers on the first synthesis area at locations determined by the first reticle;
- (c) re-aligning the mask with respect to the substrate so that the second reticle is aligned with the first synthesis area; and
- (d) coupling monomers on the first synthesis area at locations determined by the second reticle.
50. The computer program product of claim 49, wherein the method further comprises the step of:
- (e) dicing the substrate at least partially within the first discard area.
51. The computer program product of claim 49, wherein:
- the monomers are selected from the group consisting of nucleotides, amino acids or saccharides.
Type: Application
Filed: May 26, 2005
Publication Date: Nov 24, 2005
Applicant: Affymetrix, INC (Santa Clara, CA)
Inventors: Michael Mittmann (Palo Alto, CA), Earl Hubbell (Los Angeles, CA)
Application Number: 11/138,840