AU761161B2 - High density immobilization of nucleic acids - Google Patents

Description

S&FRef: 459514D1

AUSTRALIA

PATENTS ACT 1990 COMPLETE SPECIFICATION FOR A STANDARD PATENT

ORIGINAL

Name and Address of Applicant: Actual Inventor(s): Address for Service: Sequenom, Inc.

11555 Sorrento Valley Road San Diego California 92121 United States of America Maryanne O'Donnell, Charles R. Cantor, Daniel P. Little, Hubert Koster, Spruson Ferguson St Martins Tower,Level 31 Market Street Sydney NSW 2000 (CCN 3710000177) High Density Immobilization of Nucleic Acids Invention Title: The following statement is a full description of this invention, including the best method of performing it known to me/us:- 0 5845c High Density Immobilization of Nucleic Acids [N:/Iibc]00384:bav BACKGROUND OF THE INVENTION In the fields of molecular biology and biochemistry, as well as in the diagnosis of diseases, nucleic acid hybridization has become a powerful tool for the detection, isolation and analysis of specific oligonucleotide sequences. Typically, such hybridization assays utilize an oligodeoxynucleotide probe that has been immobilized on a solid support; as for example in the reverse dot blot procedure (Saiki, R. Walsh, Levenson, C. and Erlich, H. A. (1989) Proc. Natl. Acad. Sci.

USA 86, 6230). More recently, arrays of immobilized DNA probes attached to a solid surface have been developed for sequencing by hybridization (SBH) (Drmanac, Labat, Brukner, and Crkvenjakov, R. (1989) Genomics, 4, 114-128), (Strezoska, Pauneska, T., S. Radosavljevic, Labat, Drmanac, and Crkvenjakov, R. (1991) Proc. Natl. Acad. Sci. USA, 88, 10089-10093). SBH uses an ordered 15 array of immobilized oligodeoxynucleotides on a solid support. A sample of unknown DNA is applied to the array, and the hybridization pattern is observed and analyzed to produce many short bits of sequence information simultaneously. An enhanced version of SBH, termed *positional SBH (PSBH), has been developed which uses duplex probes 20 containing single-stranded 3'-overhangs. (Broude, Sano, Smith, and Cantor, C.R. (1994) Proc. Natl. Acad. Sci. USA, 91, 3072- 3076). It is now possible to combine a PSBH capture approach with conventional Sanger sequencing to produce sequencing ladders detectable, for example by gel electrophoresis (Fu, Broude, N.E., ~25 K6ster, Smith, C.L. and Cantor, C.R. (1995) Proc. Nat/. Acad. Sci.

USA 92, 10162-10166).

For the arrays utilized in these schemes, there are a number of criteria which must be met for successful performance. For example, the immobilized DNA must be stable and not desorb during hybridization, washing or analysis. The density of the immobilized oligodeoxynucleotide must be sufficient for the ensuing anal ses. There must be minimal non-specific binding of the DNA to the surface. In addition, the immobilization process should not interfere with the ability of the immobilized probes to hybridize and to be substrates for enzymatic solid phase synthesis. For the majority of applications, it is best for only one point of the DNA to be immobilized, ideally a terminus.

In recent years, a number of methods for the covalent immobilization of DNA to solid supports have been developed which attempt to meet all the criteria listed above. For example, appropriately modified DNA has been covalently attached to flat surfaces functionalized with amino acids (Running, and Urdea, M.S. (1990) Biotechniques, 8, 276-277), (Newton, C. et al., (1993) Nucl. Acids.

Res., 21, 1155-1162.), (Nikiforov, and Rogers, Y.H. (1995) Anal.

15 Biochem., 227, 201-209), carboxyl groups, (Zhang, et al., (1991) Nucl. Acids. Res., 19 3929-3933), epoxy groups (Lamture, J.B. et al., (1994) Nucl. Acids. Res., 22, 2121-2125), (Eggers, et al., (1994) BioTechniques, 17, 516-524) or amino groups (Rasmussen, et al., (1991) Anal. Biochem., 198, 138-142). Although many of these methods were quite successful for their respective applications, the density of oligonucleotide bound (maximum of approximately 20 fmol of DNA per square millimeter of surface) (Lamture, et al., (1994) Nucl.

Acids. Res. 22, 2121-2125), (Eggers, et al., (1994) BioTechniques, 17, 516-524), was far less than the theoretical packing limit of DNA.

Therefore, a method for achieving higher densities of immobilized nucleic acids on a surface is needed. In particular, a method for achieving higher densities of surface immobilized nucleic acids which permits use, manipulation and further reaction of the immobilized nucleic acids, as well as analysis of the reactions, is needed.

In connection with the need for improved nucleic acid immobilization methods for use, for example, in analytical and diagnostic systems, is the need to develop sophisticated laboratory tools that will automate and expedite the testing and analysis of biological samples. At the forefront of recent efforts to develop better analytical tools is the goal of expediting the analysis of complex biochemical structures. This is particularly true for human genomic DNA, which is comprised of at least about one hundred thousand genes located on twenty four chromosomes. Each gene codes for a specific protein, which fulfills a specific biochemical function within a living cell. Changes in a DNA sequence are known as mutations and can result in proteins with altered or in some cases even lost biochemical activities; this in turn can cause a genetic disease. More than 3,000 genetic diseases are currently known.

~In addition, growing evidence indicates that certain DNA sequences may predispose an individual to any of a number of genetic diseases, such as diabetes, arteriosclerosis, obesity, certain autoimmune diseases and cancer. Accordingly, the analysis of DNA is a difficult but worthy pursuit *20 that promises to yield information fundamental to the treatment of many life threatening diseases.

Unfortunately, the analysis of DNA is made particularly cumbersome due to size and the fact that genomic DNA includes both coding and non-coding sequences exons and introns). As such, traditional techniques for analyzing chemical structures, such as the manual pipeting of source material to create samples for analysis, are of minimal value. To address the scale of the necessary analysis, scientists have developed parallel processing protocols for DNA diagnostics.

For example, scientists have developed robotic devices that eliminate the need for manual pipeting and spotting by providing a robotic arm that carries at its proximal end a pin tool device that.consists of a matrix of pin elements. The individual pins of the matrix are spaced apart from each other to allow each pin to be dipped within a well of a microtiter plate. The robotic arm dips the pins into the wells of the microtiter plate thereby wetting each of the pin elements with sample material. The robotic arm then moves the pin tool device to a position above a target surface and lowers the pin tool to the surface contacting the pins against the target to form a matrix of spots thereon.

Accordingly, the pin tool expedites the production of samples by dispensing sample material in parallel.

:Although this pin tool technique works well to expedite the production of sample arrays, it suffers from several drawbacks. First 15 during the spotting operation, the pin tool actually contacts the surface of the substrate. Given that .each pin tool requires a fine point in order that a small spot size is printed onto the target, the continuous contact of the pin tool against the target surface will wear and deform the fine "and delicate points of the pin tool. This leads to errors which reduce accuracy and productivity.

An alternative technique developed by scientists employs chemical attachment of sample material to the substrate surface. In one particular process, DNA is synthesized in situ on a substrate surface to produce a set of spatially distinct and diverse chemical products. Such techniques 25 are essentially photolithographic in that they combine solid phase chemistry, photolabile protecting groups and photo activated lithography.

Although these systems work well to generate arrays of sample material, they are chemically intensive, time consuming, and expensive.

It is further troubling that neither of the above techniques provide sufficient control over the volume of sample material that is .dispensed onto the surface of the substrate. Consequently, error can arise from the failure of these techniques to provide sample arrays with well controlled and accurately reproduced sample volumes. In an attempt to circumvent this problem, the preparation process will often dispense generous amounts of reagent materials. Although this can ensure sufficient sample volumes, it is wasteful of sample materials, which are often expensive and of limited availability.

Even after the samples are prepared, scientists still must confront the need for sophisticated diagnostic methods to analyze the prepared samples. To this end, scientists employ several techniques for identifying materials such as DNA. For example, nucleic acid sequences can be identified by hybridization with a probe which is complementary to the sequence to be identified. Typically, the nucleic acid fragment is labeled with a sensitive reporter function that can be radioactive, fluorescent, or chemiluminescent. Although these techniques can work well, they do suffer from certain drawbacks. Radioactive labels can be hazardous and the signals they produce decay over time. Nonisotopic fluorescent) labels suffer from a lack of sensitivity and fading of the signal when high intensity lasers are employed during the identification .e process. In addition, labeling is a laborious and time consuming error .prone procedure. Consequently, the process of preparing and analyzing arrays of a biochemical sample material is complex and error prone.

Therefore, it is an object herein to provide improved systems and methods for preparing arrays of sample material. It is a further object to provide systems that allow for the rapid production of sample arrays. It is a further object herein to provide supports to which high densities of nucleic acids molecules are linked.

SUMMARY OF THE INVENTION Processes for immobilizing a high density of nucleic acids on a surface, which are based on rapidly reacting a free thiol group of a modified surface or modified nucleic acid, under appropriate conditions, with a thiol-reactive functionality of the other component (surface or nucleic acid) are provided. This reaction may be direct or through a bifunctional cross-linking reagent. In a preferred embodiment, the modified nucleic acid includes a thiol group and the cross-linking reagent contains an iodoacetyl group.

Solid supports to which are linked "beads" which are linked to nucleic acid molecules are also provided. The beads are not necessarily spherical, but refer to particles that are conjugated to the solid support to o thereby increase the surface area of the solid support and/or to provide an alternative surface for conjuation of nucleic acids or other molecules.

15 The beads are preferably of a size of about 1 pm to 100 pm.

Compositions containing at least one bead conjugated to a solid support and further conjugated to at least one molecule, particularly a nucleic acid are provided. The bead is formed from any suitable matrix material *oo"i known to those of skill in the art, including those that are swellable and nonswellable. The solid support is any support known to those of skill in the art for use as a support matrix in chemical syntheses and analyses.

In such instances, the nucleic acid is linked to the "bead" via a sulfur o atom as described herein. In certain embodiments, the beads may be conjugated on the solid support in wells or pits on the surface, or the beads may be arranged in the form of an array on the support.

Preferably the bead is made of a material selected from materials that serve as solid supports for synthesis and for assays including but not limited to: silica gel, glass, magnet, polystyrene/l divinylbenzene resins, such as Wang resins, which are Fmoc-amino acid-4-(hydroxymethyl)phenoxymethylcopoly(styrene-1% divinylbenzene (DVD)) resin, chlorotrityl (2-chlorotritylchloride copolystyrene-DVB resin) resin, Merrifield (chloromethylated copolystyrene-DVB) resin metal, plastic, cellulose, cross-linked dextrans, such as those sold under the tradename Sephadex (Pharmacia) and agarose gel, such as gels sold under the tradename Sepharose (Pharmacia), which is a hydrogen bonded polysaccharide-type agarose gel, and other such resins and solid phase supports known to those of skill in the art. In a preferred embodiment, the bead is of a size in the range of about 0.1 to 500 pn, more preferably about 1 to 100 in diameter.

The solid support is in any desired form, including, but not limited to: a bead, capillary, plate, membrane, wafer, comb, pin, a wafer with pits, an array of pits or nanoliter wells and other geometries and forms known to those of skill in the art.

In another aspect, kits for immobilized nucleic acids on an insoluble support are provided. In one embodiment, the kit can comprise an appropriate amount of: i) a thiol-reactive cross-linking reagent; and ii) a surface-modifying reagent for modifying a surface with functionality which can react with the thiol-reactive cross-linking reagent. The kit can optionally include an insoluble support, a solid surface, magnetic microbeads or silicon wafers, for use in immobilizing nucleic acids. The kit can also optionally include appropriate buffers as well as instructions for use.

Use of these processes for immobilizing nucleic acid molecules 25 onto a solid support results in at least 12.5-fold higher immobilization than previously reported techniques. The processes are therefore particularly useful for forming nucleic acid launching pads for mass spectrometry.

.1 -9- The nucleic acids immobilized on a surface using the methods provided herein can be used in a variety of solid phase nucleic acid chemistry applications, including but not limited to nucleic acid synthesis (chemical and enzymatic), hybridization and/or extension, and in diagnostic methods based in nucleic acid detection and polymorphism analyses (see, U.S. Patent No. 5,605,798). Accordingly, further provided-herein are methods of reacting nucleic acid molecules in which the nucleic acid molecules are immobilized on a surface either by reacting a thiol-containing derivative of the nucleic acid molecule with an insoluble support containing a thiol-reactive group or by reacting a thiol-containing insoluble support with a thiol-reactive group-containing derivative of the nucleic acid molecule and thereafter further reacting the immobilized nucleic acid molecules.

a particular embodiment of the methods of reacting immobilized 15 nucleic acids, the immobilized nucleic acid is further reacted by ,r I hybridizing with a nucleic acid that is complementary to the immobilized S-nucleic acid or a portion thereof. Such hybridization reactions can be used to detect the presence of a specific nucleic acid in a sample. This S" is of particular use in the detection of pathogens in a sample, such as a biological sample, that may be employed in the diagnosis of diseases.

Therefore, also provided herein are methods of detecting a target nucleic acid in a sample wherein a thiol-containing nucleic acid complementary to the target nucleic acid is immobilized to a surface using the processes described herein and the sample is contacted with 25 the surface under conditions whereby target nucleic acid in the sample hybridizes to the immobilized nucleic acid. The hybridized target nucleic acid may be detected using a variety of methods, the preferred method being mass spectrometry. Further provided herein are methods of detecting alterations deletions, insertions and conversions) in the nucleotide sequence of the target nucleic acid. In these methods, the molecular weight of the hybridized target nucleic acid, as determined by mass spectrometry, is compared to the molecular weight expected for the target nucleic acid sequence. Deviations of the measured molecular weight from the expected molecular weight are indicative of an alteration in the nucleotide sequence of the target nucleic acid.

In other methods of detecting a target nucleic acid in a sample as provided herein, the target nucleic acid is immobilized to a surface containing thiol-reactive groups. In these methods, prior to immobilization, the target nucleic acid is amplified in a reaction in which an oligonucleotide primer contains a or 5'-disulfide linkage and the resulting product is reduced to generate a thiol-containing nucleic acid.

The thiol-containing nucleic acid is immobilized to a surface containing thiol-reactive groups and is contacted with a single-stranded nucleic acid 15 that is complementary to the immobilized nucleic acid or a portion thereof. Hybridization of the single-stranded nucleic acid may be detected by a variety of methods. For example, the single-stranded nucleic acid may be labeled with a readily detectable moiety, radioactive or chemiluminescent labels. In a preferred embodiment, the 20 single-stranded nucleic acid is detected by mass spectrometry.

In another embodiment of the methods of reacting immobilized nucleic acids, the immobilized nucleic acid is further reacted by extension of a nucleic acid that is hybridized to the immobilized nucleic acid or a portion thereof. Extension reactions such as these can be used, for 25 example, in methods of sequencing DNA molecules that are immobilized to an insoluble support using the processes described herein. Thus, also provided herein are methods of determining the sequence of a DNA molecule on a substrate in which a thiol-containing derivative of the DNA molecule is immobilized on the surface of an insoluble support containing -11thiol-reactive groups and hybridized with a single-stranded nucleic acid complementary to a portion of the immobilized DNA molecule prior to carrying out DNA synthesis in the presence of one or more dideoxynucleotides.

Extension of a nucleic acid primer that is hybridized to a nucleic acid immobilized to a surface as provided herein also can be used in the detection of nucleotide sequence alterations deletions, insertions, conversions) of a target nucleic acid. Accordingly, provided herein are methods of detecting alterations in a target nucleic acid sequence in which a single-stranded nucleic acid is hybridized to a thiol-containing target nucleic acid immobilized to a solid support according to the processes provided herein and the hybridized single-stranded nucleic acid is extended by addition of nucleotides to the 3' end of the molecule. The extension product is characterized by, for example, mass spectrometry to 15 determine whether its characteristics differ from those expected of a sequence complementary to the immobilized target nucleic acid. Thus, for example, the molecular weight of the extension product determined by mass spectrometry is compared to the expected molecular weight of a nucleic acid complementary to the target nucleic acid. Deviations from S. 20 the expected molecular weight are indicative of an alteration in the sequence of the target nucleic acid.

In particular embodiments of the methods of detecting alterations in a target nucleic acid sequence provided herein, the target nucleic acid may be amplified prior to immobilization to a thiol-reactive surface in a 25 reaction in which an oligonucleotide primer contains a or linkage. The resulting product is reduced to generate a thiol-containing target nucleic acid. The thiol-containing target nucleic acid is then immobilized to a surface containing thiol-reactive groups and the singlestranded complementary nucleic acid is hybridized thereto and extended.

-12- In a further embodiment of the methods of detecting alterations in a target nucleic acid sequence provided herein, a single-stranded nucleic acid complementary to the target nucleic acid is immobilized to a surface through a linkage that includes a thiol group-thiol reactive functionality bond and a cleavable linker moiety. The sample containing target nucleic acid is contacted with the surface under conditions whereby the target hybridizes with the immobilized single-stranded nucieic acid. The immobilized single-stranded nucleic acid is extended by addition of nucleotides to the 3' end of the molecule. Following extension, the double-stranded molecule is denatured and the single-stranded immobilized extension product is cleaved from the surface at the position of the linker. The extension product is characterized by, for example, *.*:mass spectrometry to determine whether its characteristics differ from those expected of a sequence complementary to the immobilized target 15 nucleic acid.

It is understood that all applications of the solid phase nucleic acid chemistry based on nucleic acids immobilized to a solid substrate according to the processes provided herein can be conducted with thiolcontaining nucleic acids and a thiol-reactive surface as well as with thiolo 20 reactive nucleic acids and a thiol-containing support.

Methods of forming an array of nucleic acids on a surface of a .substrate by contacting thiol-containing nucleic acids with an insoluble S°support containing thiol-reactive groups positioned in an ordered arrangement on the surface of the support are also provided herein. In 4: 25 an alternative method of forming an array of nucleic acids on a surface of *a substrate as provided herein, an insoluble support containing thiol functionalities positioned in an ordered arrangement on the surface of the support is contacted with nucleic acids containing a thiol-reactive group.

-13- Further provided herein are systems and methods for preparing a sample for analysis, and more specifically to systems and methods for dispensing low volumes of fluid material onto a substrate surface for generating an array of samples for diagnostic analysis. Systems and methods provided herein for preparing arrays of sample material are generally less expensive to employ and conserve reagent materials while allowing for the rapid production of highly reproducible sample arrays.

Provided herein with respect to systems and methods for dispensing low volumes of fluid material onto a substrate surface are serial and parallel dispensing tools that can be employed to generate multi-element arrays of sample material on a substrate surface. The substrate surfaces can be flat or geometrically altered to include wells of receiving material.

In one embodiment, the tool is one that allows the parallel 15 development of a sample array. To this end, the tool can be understood as an assembly of vesicle elements, or pins, wherein each of the pins can include a narrow interior chamber suitable for holding nanoliter volumes of fluid. Each of the pins can fit inside a housing that itself has an interior chamber. The interior housing can be connected to a pressure source that will control the pressure within the interior housing chamber to regulate the flow of fluid through the interior chamber of the pins.

This allows for the controlled dispensing of defined volumes of fluid from the vesicles.

In an alternative embodiment, the tool includes a jet assembly that 25 can include a capillary pin having an interior chamber, and a transducer element mounted to the pin and capable of driving fluid through the interior chamber of the pin to eject fluid from the pin. In this way, the tool can dispense a spot of fluid to a substrate surface by spraying the fluid from the pin. Alternatively, the transducer can cause a drop of fluid -14to extend from the capillary so that fluid can be passed to the substrate by contacting the drop to the surface of the substrate.

Further, the tool can form an array of sample material by dispensing sample material in a series of steps, while moving the pin to different locations above the substrate surface to form the sample array.

In a further embodiment, the prepared sample arrays are passed to a plate assembly that disposes the sample arrays for analysis by mass spectrometry. To this end, a mass spectrometer is provided that generates a set of spectra signal which can be understood as indicative of the composition of the sample material under analysis.

In one aspect, the dispensing apparatus provided herein for dispensing defined volumes of fluid, including nanovolumes and subnanovolumes of fluid, in chemical or biological procedures onto the surface of a substrate can include a housing having a plurality of sides ~15 and a bottom portion having formed therein a plurality of apertures, the walls and bottom portion of the housing defining an interior volume; one or more fluid transmitting vesicles, or pins, mounted within the apertures, having a nanovolume sized fluid holding chamber for holding oooo *nanovolumes of fluid, the fluid holding chamber being disposed in fluid communication with the interior volume of the housing, and a dispensing element that is in communication with the interior volume of the housing for selectively dispensing nanovolumes of fluid from the nanovolume o sized fluid transmitting vesicles when the fluid is loaded into the fluid holding chambers of the vesicles. As described herein, this allows the dispensing element to dispense nanovolumes of the fluid onto the surface of the substrate when the apparatus is disposed over and in registration with the substrate.

In one embodiment the fluid transmitting vesicle has an open proximal end and a distal tip portion that extends beyond the housing bottom portion when mounted within the apertures. In this way the open proximal end can dispose the fluid holding chamber in fluid communication with the interior volume when mounted with the apertures. Optionally, the plurality of fluid transmitting vesicles are removably and replaceably mounted within the apertures of the housing, or alternatively can include a glue seal for fixedly mounting the vesicles within the housing.

In one embodiment the fluid holding chamber includes a narrow bore dimensionally adapted for being filled with the fluid through capillary action, and can be sized to fill substantially completely with the fluid through capillary action.

In one embodiment, the plurality of fluid transmitting vesicles comprise an array of fluid delivering needles, which can be formed of metal, glass, silica, polymeric material, or any other suitable material.

15 In one embodiment the housing can include a top portion, and °.!mechanical biasing elements for mechanically biasing the plurality of fluid transmitting vesicles into sealing contact with the housing bottom portion. In one particular embodiment, each fluid transmitting vesicle has a proximal end portion that includes a flange, and further includes a seal 20 element disposed between the flange and an inner surface of the housing bottom portion for forming a seal between the interior volume and an external environment. The biasing elements can be mechanical and can include a plurality of spring elements each of which is coupled at one end to the proximal end of each of the plurality of fluid transmitting vesicles, and at another end to an inner surface of the housing top portion. The springs can apply a mechanical biasing force to the vesicle proximal end to form the seal.

In a further embodiment, the housing further includes a top portion, and securing element for securing the housing top portion to the -16housing bottom portion. The securing element can comprise a plurality of fastener-receiving apertures formed within one of the top and bottom portions of the housing, and a plurality of fasteners for mounting within the apertures for securing together the housing top and bottom portions.

In one embodiment the dispensing element can comprise a pressure source fluidly coupled to the interior volume of the housing for disposing the interior volume at a selected pressure condition. Moreover, in an embodiment wherein the fluid transmitting vesicles are filled through capillary action, the dispensing element can include a pressure controller that can vary the pressure source to dispose the interior volume of the housing at varying pressure conditions. This allows the controller varying element to dispose the interior volume at a selected ,o pressure condition sufficient to offset the capillary action to fill the fluid ,9o holding chamber of each vesicle to a predetermined height corresponding to a predetermined fluid amount. Additionally, the controller can further include a fluid selection element for selectively discharging a selected Sonanovolume fluid amount from the chamber of each vesicle;: In one particular embodiment, a pressure controller is included that operates under the controller of a computer program operating on a data 20 processing system to provide variable control over the pressure applied to the interior chamber of the housing.

in one embodiment the fluid transmitting vesicle can have a proximal end that opens onto the interior volume of the housing, and the fluid holding chamber of the vesicles are sized to substantially completely 25 fill with the fluid through capillary action without forming a meniscus at .e°the proximal open end. Optionally, the apparatus can have plural vesicles, wherein a first portion of the plural vesicles include fluid holding chambers of a first size and a second portion including fluid holding chambers of a second size, whereby plural fluid volumes can be dispensed.

In another embodiment, the dispensing apparatus can include a fluid selection element that has a pressure source coupled to the housing and in communication with the interior volume for disposing the interior volume at a selected pressure condition, and an adjustment element that couples to the pressure source for varying the pressure within the interior volume of the housing to apply a positive pressure in the fluid chamber of each of the fluid transmitting vesicles to vary the amount of fluid dispensed therefrom. The selection element and adjustment element can be computer programs operating on a data processing system that directs the operation of a pressure controller connected to the interior chamber.

~In a further alternative embodiment, the apparatus provided herein 6@ OS 15 is for dispensing a fluid in chemical or biological procedures into one or O.l@O more wells of a multi-well substrate. The apparatus can include a 5@55 o housing having a plurality of sides and a bottom portion having formed therein a plurality of apertures, the walls and bottom portion defining an interior volume, a plurality of fluid transmitting vesicles, mounted within 20 the apertures, having a fluid holding chamber disposed in communication with the interior volume of the housing, and a fluid selection and 5 dispensing means in communication with the interior volume of the 5 housing for variably selecting am amount of the fluid loaded within the fluid holding chambers of the vesicles to be dispensed from a single set r000 °o 25 of the plurality of fluid transmitting vesicles. Accordingly, the dispensing 6 means dispenses a selected amount of the fluid into the wells of the multi-well substrate when the apparatus is disposed over and in registration with the substrate.

-18- In yet another embodiment, provided herein is a fluid dispensing apparatus for dispensing fluid in chemical or biological procedures into one or more wells of a multi-well substrate, that comprises a housing having a plurality of sides and top and bottom portions, the bottom portion having formed therein a plurality of apertures, the walls and top and bottom portions of the housing-defining an interior volume, a plurality of fluid transmitting vesicles, mounted within the apertures, having a fluid holding chamber sized to hold nanovolumes of the fluid, the fluid holding chamber being disposed in fluid communication with the volume of the housing, and mechanical biasing element for mechanically biasing the plurality of fluid transmitting vesicles into sealing contact with the housing bottom portion.

General methods for preparing an array of sample material on a 'i surface of a substrate as described herein include the steps of providing

C.

15 a vesicle having an interior chamber containing a fluid, disposing the vesicle adjacent a first location on the surface of the substrate, controlling the vessel for delivering a nanoliter volume of a fluid at the first location of the surface of the substrate, and moving the vesicle to a ooo set of positions adjacent to the surface substrate whereby fluid is 20 dispensed at each location of the set of positions for forming an array of sample material.

Substrates employed during the general processes of preparing an array of sample material described herein can include flat surfaces for receiving the sample material as well as having the surfaces that include wells formed on the surface for defining locations for receiving the fluid that can be ejected from the chambers of the vesicles. Such substrates can be silicon, metal, plastic, a membrane, polymeric material, a metalgrafted polymer, as well as a substrate that is functionalized chemically, functionalized with beads, functionalized with dendrite trees of captured -19material, or any combinations of the above or any similar suitable material for receiving the dispensed fluid.

It is understood that in the general methods for preparing an array of sample material on a substrate surface described herein the apparatus can dispense both an analyte material as well as a support material, such as a matrix material, that aids in the analysis of the analyte. To this end the methods provided herein can include the steps of depositing a matrix material onto the substance of the substrate. Further the methods can also include a step of waiting a predetermined period of time to allow a solvent of the matrix material to evaporate. Once the solvent of the matrix material has evaporated, the methods herein can include a step of ejecting a volume of analyte fluid into the evaporated matrix material to dissolve with the matrix material and to form a crystalline structure on the substrate surface. It is understood that this step of redissolving the 15 matrix material with the analyte material aids in the analysis of the composition of the material during certain analytical processes, such as mass spectrometry.

In an alternative practice, the methods herein can include a step of ooo. dispensing a mixture that consists of the analyte material and the matrix material, as well as other material compositions. In this way the matrix and the analyte are delivered to the surface of the substrate as one 0* volume of material. In a further step, the prepared arrays of sample ooooo 0 material can be provided to a diagnostic tool for determining information that is representative of the composition of the sample material.

:25 Once such diagnostic tool can include a mass spectrometer. The 0 mass spectrometers can be time of flight mass spectrometers, fourier transform mass spectrometers or any other suitable type of mass spectrometer that allows the analysis of composition of the sample array.

In one practice of the methods, the step of providing a vesicle having an interior chamber includes the step of providing a vesicle having a piezo electric element for causing fluid to move through the chamber.

This method can also include the step of moving the vesicle by rasterizing the vesicle across the surface of the substrate, to form the array of sample material.

In an alternative practice of the methods, parallel processing protocols can be employed wherein the vesicle that is employed during the processing includes a vesicle assembly that has a plurality of vesicles arranged into a matrix for dispensing fluid to a first plurality of locations on the substrate surface. In this way in a single operation, the method provides for forming a matrix of a sample material on the substrate *.**surface. Offset printing can also be employed to form a large matrix of sample material by employing multiple printing steps with the vesicle 15 matrix. Other printing techniques can be employed by the present invention without departing from the scope thereof.

:I n another embodiment, fluid can be dispensed to the surface of the substrate by contacting the vesicle against the surface of the substrate to spot the surface of the substrate with sample material.

Alternatively, the methods provide for another non-contact printing approach wherein the processes of the invention cause a drop of fluid to o abe formed on at the distal tip of the vesicle. It is the drop of fluid that is contacted against the surface of the substrate for delivering sampling material thereto. This provides for the controlled delivery for the known 25 volume of fluid without resulting in the contacting of the vesicle against S" the surface of the substrate.

In further embodiments, vesicles are provided having an interior chamber that is dimensionally adapted to allow filling of the chamber by capillary action.

In another aspect, methods are provided for analyzing a material, that comprise the steps of providing a vesicle suitable for carrying a fluid having the material therein, disposing the vesicle adjacent a first location of the surface of the substrate, controlling the vesicle to deliver a nanoliter volume of the fluid to provide a defined and controlled volume of fluid at the first location of the surface of the substrate, moving the vesicle to a second position adjacent a second location on the surface on the substrate to dispense a defined and controlled volume of the material along an array of locations along the substrate surface, and performing mass spectrometry analysis of the material at each location of the array.

These methods can include the step of mixing a matrix material and an analyte material to form the fluid being delivered to the substrate surface.

Alternatively, this embodiment can include the steps of filling a chamber contained within the vesicle with a matrix material and dispensing the 15 matrix material to the array of locations. Subsequently, analyte can be dispensed. The step of performing mass spectrometry can include the S-step of performing a matrix assisted laser desorption ionization mass spectrometry, as well as time of flight mass spectrometry, or a fourier •transform spectrometry.

In another aspect, apparatus for forming an array of a sample material on a surface of a substrate are provided. Such apparatus will S° compromise a vesicle having a distal end suitable for carrying a fluid S" thereon, a movable arm having a distal portion mounted to the vesicle, a controller for moving the arm to dispose the vesicle adjacent a first location on the surface on the substrate and for controlling the vesicle to provide a nanoliter volume of the fluid at the first location of the surface of the substrate, and a diagnostic tool for analyzing the material to generate a composition signal that is representative of the chemical composition of the material. In this apparatus the vesicle can 22 comprise a solid shaft of material as well as a vesicle having an interior chamber suitable for carrying fluid as well as a chamber for carrying a fluid in a transducer element for ejecting fluid from that chamber.

Further provided herein are substrates having a surface for carrying an array of a matrix material and formed according to a process comprising the steps of a providing a vesicle suitable for transferring a fluid containing a matrix material, disposing the vesicle adjacent a first location on the surface on the substrate, controlling the vesicle to deliver the fluid to the first location of the surface of the substrate, and moving a vesicle to a set of positions adjacent the surface of the substrate and delivering fluid at each of these io locations to form an array of matrix material. This substrate itself can be a flat silicon chip as well as any other suitable material, and can be pitted, include wells, and have wells that have rough interior surfaces.

In particular embodiments, the methods of forming an array of nucleic acids on a surface of a substrate as provided herein include contacting predetermined positions of the surface of an insoluble support with thiol-containing nucleic acid solutions dispensed to the positions with a vesicle having an interior chamber containing the respective solutions whereby the predetermined positions incorporate thiol-reactive groups.

Alternatively, the entire surface of the substrate is derivatized with the thiol-reactive groups and thiol-containing nucleic acid is dispensed to predetermined positions on the surface in an array-forming manner. Also provided herein are substrates having a surface carrying an array of nucleic acids formed by the methods described herein.

According to a first embodiment of the invention there is provided a dispensing .o apparatus for dispensing nanoliter volumes of fluid in chemical or biological procedures 0o.ooi onto the surface of a substrate, comprising: a housing having a plurality of sides and a bottom portion having formed therein a plurality of apertures, wherein the sides and bottom portion of said housing define an interior volume, one or more fluid transmitting vesicles, mounted within said apertures, and having a S'fluid holding chamber of a size for holding and dispensing nanoliter volumes of fluid, said fluid holding chamber being disposed in fluid communication with said interior volume of said housing, and dispensing means in communication with said interior volume of said housing for S: selectively dispensing nanoliter volumes of fluid from said nanoliter volume sized fluid transmitting vesicles when fluid holding chambers of said vesicles are fully loaded, [R:\LIZZ]7143.doc:MQT 22a whereby said dispensing means dispenses nanoliter volumes of the fluid onto the surface of the substrate when the apparatus is disposed over and in registration with the surface of the substrate.

According to a second embodiment of the invention there is provided a fluid dispensing apparatus for dispensing nanoliter volumes of a fluid in chemical or biological procedures into one or more wells of a multi-well substrate, comprising: a housing having a plurality of sides and a bottom portion having formed therein a plurality of apertures, said sides and bottom portion defining an interior volume, a plurality of fluid transmitting vesicles for holding a nanoliter volume of a fluid, mounted within said apertures having a fluid holding chamber disposed in communication with said interior volume of said housing, a fluid volume selection and dispensing means in communication with said interior volume of said housing for variably selecting an amount of the fluid loaded into said fluid holding chambers of said vesicles to be dispensed from a single set of plurality of fluid transmitting vesicles, and whereby said dispensing means dispenses a selected amount of the fluid into the wells of the multi-well substrate when the apparatus is disposed over and in registration with the substrate, wherein the selected amount of fluid is a nanoliter volume.

According to a third embodiment of the invention there is provided a fluid dispensing apparatus for dispensing fluid in chemical or biological procedures into one or more wells of a multi-well substrate, said apparatus comprising: :i a housing having a plurality of sides and top and bottom portions, said bottom portion having formed therein a plurality of apertures, said sides and top and bottom portions of said housing defining an interior volume, a plurality of fluid transmitting vesicles, mounted within said apertures having a fluid holding chamber sized to hold nanoliter volumes of the fluid, said fluid holding chamber being disposed in fluid communication with said volume of said housing and mechanical biasing means for mechanically biasing said plurality of said transmitting vesicles into sealing contact with said housing bottom portion, wherein the o 30 apparatus dispenses nanoliter volumes of fluid.

According to a fourth embodiment of the invention there is provided a system, comprising the apparatus of the first embodiment, and further comprising: S.a robotic arm in attached to the housing, wherein the robotic arm is for holding and moving the housing to insert the vesicles into a fluid source for filling the vesicles with a nanoliter volume of fluid and for disposing said housing comprising said vesicles adjacent [R:\LBZZ]7143.doc:MQT 22b to the substrate to allow for dispensing fluid from the vesicles onto the surface of a substrate adjacent thereto.

According to a fifth embodiment of the invention there is provided a system for dispensing nanoliter volumes of fluid in chemical or biological procedures onto the surface of a substrate, comprising: a pin assembly having one or more apertures and one or more fluid transmitting pins, mounted within the apertures, wherein the pins comprise a solid shaft of material, wherein one end is for capturing a nanoliter volume of fluid thereon; and a robotic arm in contact with the pin assembly, wherein the robotic arm is for 1o holding and moving the assembly to insert the end of the pins into a fluid source for capturing fluid on the end of the pins or to dispose the pin assembly adjacent to the surface of a substrate to dispense fluid onto the surface of a substrate by contacting the fluid on the end of the pins with the surface of the substrate.

According to a sixth embodiment of the invention there is provided a system for dispensing nanoliter volumes of fluid in chemical or biological procedures onto the surface of a substrate, comprising: an assembly, comprising a capillary element for containing a volume of fluid to be dispensed through an orifice of the capillary and a transducer element in contact with the capillary for effecting physical deformation of the capillary causing ejectment of a nanoliter volume of fluid from the capillary; a robotic arm for holding an assembly and for aligning the assembly adjacent to the surface of the substrate to dispense nanoliter volumes of fluid from the capillary to the surface of the substrate aligned therewith; and mounting means for securing the robotic arm to the assembly.

The above and further features and advantages of the instant invention will become clearer from the following Figures, Detailed Description and Claims.

*.i o*9 •0.o.

SoS 5.5"5 [R:\LIBZZ]7143.doc:MQT BRIEF DESCRIPTION OF THE DRAWINGS Figure 1 illustrates a system for preparing arrays of a sample material for analysis.

Figure 2 illustrates a pin assembly suitable for use with the system depicted in Fig. 1 for implementing a parallel process of dispensing material to a surface of a substrate.

Figure 3 depicts a bottom portion of the assembly shown in Fig. 2.

Figure 4 depicts an alternative view of the bottom portion of the pin assembly depicted in Fig. 2.

Figures 5A-5D depict a method for preparing an array of sample material.

Figures 6A-6B depict an alternative assembly for dispensing material to the surface of a substrate.

Figure 7 is a schematic showing covalent attachment of 15 oligodeoxynucleotides to a silicon dioxide surface as described in the methods herein. In particular, silicon dioxide was reacted with 3aminopropyltriethoxysilane to produce a uniform layer of primary amino groups on the surface. A heterobifunctional crosslinking agent was then oe i reacted with the primary amine to incorporate an iodoacetamide-group.

An oligodeoxynucleotide containing a or 5'-disulfide (shown as the was treated with tris-(2-carboxyethyl) phosphine (TCEP) to reduce the disulfide to a free thiol, which was then coupled to the iodoacetamidosurface.

Figure 8 is a graph which plots conjugation of oligodeoxynucleotide probes to a silicon surface as a function of TCEP concentration used in the disulfide reduction.

Figure 9 is a matrix assisted laser desorbtion/ionization-time-offlight (MALDI-TOF) mass spectrum of a silicon wafer with the oligodeoxynucleotide sequence denoted "TCUC" GAATTCGAGCTCGGTACCCGG-3'; SEQ ID NO 1) covalently bound essentially as described in Figure 7 and the oligodeoxynucleotide sequence denoted "MJM6" (5'-CCGGGTACCGAGCTCGAATTC-3';

SEQ

ID NO 2) hybridized thereto.

Figure 10 is a schematic of the immobilization of specific thiolcontaining DNA targets generated by polymerase chain reaction (PCR) to the surface of a silicon wafer. An oligonucleotide [SEQ ID 'NO: 7] complementary to a portion of the DNA target sequence was hybridized to the immobilized DNA target and MALDI-TOF MS analysis was performed revealing a predominant signal at an observed mass-to-charge ratio of 3618.33 corresponding to the hybridized oligonucleotide, which has a the theoretical mass-to-charge ratio of 3622.4.

Figure 11 depicts one embodiment of a substrate having wells etched therein that are suitable for receiving material for analysis.

15 Figure 12 depicts one example of spectra obtained from a linear time of flight mass spectrometer instrument and representative of the material composition of the sample material on the surface of the substrate depicted in Fig. 11.

Figure 13 depicts molecular weights determined for the sample material having spectra identified in Fig. 12.

Figure 14 is a schematic of a 4 x 4 (16-location) DNA array on the surface of a silicon wafer with the thiol-containing oligonucleotide molecules denoted "Oligomer [5'-CTGGATGCGTCGGATCATCTTTTTT-(S)-3'; SEQ ID NO: Oligomer 2 (5'-(S)-CCTCTTGGGAACTGTGTAGTATT-3';

SEQ

25 ID NO:31 and "Oligomer 3" (SEQ ID NO: 1; a free thiol derivative "TCUC" oligonucleotide of EXAMPLE 1) covalently bound to 16 locations on the surface of the silicon wafer essentially as described in EXAMPLE 2.

Figure 15 is a schematic of the hybridization of specific oligonucleotides to each of the 16 locations of the DNA hybridization array of Figure 14 with the Oligomer 1 complementary oligonucleotide (5'-GATGATCCGACGCATCAGAATGT-3'; SEQ ID NO: 9) bound to Oligomer 1, the Oligomer 2 complementary oligonucleotide AATACTACACAG-3'; SEQ ID NO: 7) bound to Oligomer 2 and the Oligomer 3 complementary oligonucleotide CCGGGTACCGAGCTCGAATTC-3'; SEQ ID NO: 2) bound to Oligomer 3.

Figure 16 is a representative MALDI-TOF mass spectrum of a 4 x 4 (16-location) DNA array on a silicon wafer shown schematically in Figure The spectrum reveals a single, predominant signal of an experimental mass-to-charge ratio in each location corresponding to the specific hybridized oligonucleotides. The 2+ indicates the position of a doubly charged molecule used as a reference standard during MALDI-TOF MS analysis. The denotes residual amounts of contaminating S' oligonucleotide that remain on the surface of the chip following washing o. 15 procedures. The relative position of the signal reveals the approximate size of the contaminating oligonucleotide.

Figure 17 is a representative MALDI-TOF mass spectrum of an 8 x 8 (64-location) DNA array. The spectrum reveals a single, predominant signal of an experimental mass-to-charge ratio corresponding to the 20 predicted specific hybridized oligonucleotides. The denotes residual amounts of contaminating oligonucleotide that remain on the surface of the wafer following washing procedures. The relative position of the signal reveals the approximate size of the contaminating oligonucleotide.

Figure 18 is an illustration of nucleotide extension of a DNA primer 25 annealed to a thiol-containing DNA template immobilized to the surface of a SIAB-derivatized silicon wafer. A complementary 12-mer oligonucleotide primer [SEQ ID NO: 12] was hybridized to a 27-mer thiolcontaining oligonucleotide [SEQ ID NO: 111 immobilized to a silicon support through the SIAB crosslinker. The silicon surface containing the -26immobilized DNA duplex was incubated with DNA polymerase in the presence of dATP, dCTP, dGTP and ddTTP under extension conditions and subjected to MALDI-TOF MS analysis. The mass spectrum of the silicon wafer revealed the presence of two predominant signals; one of a mass-to-charge ratio equal to the unextended 12-mer oligonucleotide as well as a signal corresponding to a 15-mer DNA molecule that has been extended on the wafer by 3 nucleotides to the first position in the sequence in which a ddTTP was incorporated.

Figure 19 diagrams an experiment designed to test the effect of the distance between the SIAB-derivatized surface and the DNA duplex formed on primer extension reactions. Two thiol-containing oligonucleotides of different sequence [SEQ ID NOs: 8 11] were immobilized to a SIAB-derivatized silicon surface and incubated with specific oligonucleotides that form a DNA duplex with 0, 3, 6, 9 and 12 base spacers between the SIAB-derivatized surface and the DNA duplex formed by the oligonucleotide hybridized to the immobilized thiolcontaining DNA. The free 3'-end of the hybridized oligonucleotide was extended using either Sequenase DNA polymerase or ThermoSequenase DNA polymerase in the presence of the three deoxynucleotide triphosphates and the corresponding diddeoxynucleotide triphosphate under extension conditions and the resulting reaction products were subjected to MALDI-TOF MS analysis.

Figure 20 is a representative MALDI-TOF mass spectrum of the specific extension products of the primer extension experiment illustrated 25 in Figure 19. The spectra in the left-hand column are those resulting from MALDI-TOF MS analysis of the extension reactions in which Sequenase was used. The spectra in the right-hand column are those resulting from analysis of the extension reactions in which ThermoSequenase was used. ThermoSequenase DNA polymerase was

A

-27able to extend the 3'-end of the hybridized DNA primer where the distance between the DNA duplex and the surface of the derivatized silicon wafer varied between 0 to 12 nucleotides. Sequenase DNA polymerase also was able to extend the hybridized DNA where the distance between the DNA duplex and the silicon wafer was between 3 and 9 nucleotides.

DETAILED DESCRIPTION AND PREFERRED EMBODIMENTS Definitions Unless defined otherwise, all technical and scientific terms used herein have the same meaning as is commonly understood by one of skill in the art to which this invention belongs. All patents and publications referred to herein are incorporated by reference herein.

As used herein, the term "nucleic acid" refers to oligonucleotides or polynucleotides such as deoxyribonucleic acid (DNA) and ribonucleic 15 acid (RNA) as well as analogs of either RNA or DNA, for example, made from nucleotide analogs, any of which are in single or double-stranded form. Nucleic acid molecules can be synthetic or can be isolated from a particular biological sample using any number of procedures which are well-known in the art, the particular procedure chosen being appropriate 20 for the particluar biological sample.

As used herein, nucleotides include nucleoside mono-, di-, and triphosphates. Nucleotides also include modified nucleotides such as phosphorothioate nucleotides and deazapurine nucleotides. A complete set of chain-elongating nucleotides refers to four different nucleotides 25 that can hybridize to each of the four different bases comprising the DNA S, template.

As used herein, nucleic acid synthesis refers to any process by which oligonucleotides or polynucleotides are generated, including, but not limited to processes involving chemical or enzymatic reactions.

As used herein, the term "array" refers to an ordered arrangement of members or positions. The array may contain any number of members or positions and can be in any variety of shapes. In preferred embodiments, the array is two-dimensional and contains n x m members, wherein m and n are integers that can be the same or different. In particularly preferred embodiments, n and m are each 4 or a multiple thereof.

The term "cross-linking agent" is art-recognized, and, as used herein, refers to reagents which can immobilize a nucleic acid to an insoluble-support, preferably through covalent bonds. Thus, appropriate "cross-linking agents" for use herein includes a variety of agents that are capable of reacting with a functional group present on a surface of the insoluble support and with a functional group present in the nucleic acid molecule. Reagents capable of such reactivity include homo- and hetero- 15 bifunctional reagents, many of which are known in the art.

Heterobifunctional reagents are preferred.

As used herein, the term "thiol-reactive functionality," refers to a functionality which is capable of rapid reaction with a nucleophilic thiol moiety to produce a covalent bond a disulfide or thioether bond).

In general, thiol groups are good nucleophiles, and preferred thiol-reactive functionalities are reactive electrophiles. A variety of thiol-reactive functionalities are known in the art, and include, for example, haloacetyls (preferably iodoacetyl), diazoketones, epoxy ketones, a, I-unsaturated carbonyls a, I-enones) and other reactive Michael acceptors 25 (including maleimide), acid halides, benzyl halides, and the like. In certain embodiments, a free thiol group of a disulfide can react with a free thiol group by disulfide bond formation, including by disulfide.

exchange). A "thiol-reactive" cross-linking agent, as used herein, refers to a cross-linking reagent (or surface) which includes, or can be modified to include, at least one thiol-reactive functionality. It will be understood that reaction of a thiol group can be temporarily prevented by blocking with an appropriate protecting group, as is conventional in the art (see T.W. Greene and P.G.M. Wuts "Protective Groups in Organic Synthesis," 2nd ed. John Wiley Sons, (1991)).

As used herein, a selectively cleavable linker is a linker that is cleaved under selected conditions, such as a photocleavable linker, a chemically cleavable linker and an enzymatically cleavable linker a restriction endonuclease site or a ribonucleotide/RNase digestion). The linker is interposed between the support and immobilized DNA.

As used herein, the terms "protein", "polypeptide" and "peptide" are used interchangeably when referring to a translated nucleic acid (e.g.

gene product).

As used herein, "sample" shall refer to a composition containing a 15 material to be detected. In a preferred embodiment, the sample is a "biological sample" any material obtained from a living source (e.g.

human, animal, plant, bacteria, fungi, protist, virus). The biological sample can be in any form, including solid materials tissue, cell pellets and biopsies) and biological fluids urine, blood, saliva, 20 amniotic fluid and mouth wash (containing buccal cells)). Preferably solid materials are mixed with a fluid.

•As used herein, "substrate" shall mean an insoluble support onto •which a sample is deposited according to the materials as described herein. Examples of appropriate substrates include beads silica gel, controlled pore glass, magnetic, Sephadex/Sepharose, cellulose), capillaries, flat supports such as glass fiber filters, glass surfaces, metal surfaces (steel, gold, silver, aluminum, copper and silicon), plastic materials including multiwell plates or membranes of polyethylene, polypropylene, polyamide, polyvinylidenedifluoride), pins arrays of pins suitable for combinatorial synthesis or analysis or beads in pits of flat surfaces such as wafers silicon wafers) with or without plates.

In the particular methods of immobilizing nucleic acids to a substrate provided herein, preferred substrates are those which can support linkage of nucleic acids thereto at high densities, preferrably such that the covalently bound nucleic acids are present on the substrate at a density of at least about 20 fmol/mm 2 more preferably at least about 75 fmol/mm 2 still more preferably at least about 85 fmol/mm 2 yet more preferably at least about 100 fmol/mm 2 and most preferably at least about 150 fmol/mm 2 Among the most preferred substrates for use in the particular methods of immobilizing nucleic acids to substrates provided herein is silicon, whereas less preferred substrates include polymeric materials such as polyacrylamide. Substrates for use in methods of producing arrays provided herein include any of a wide 15 variety of insoluble support materials including, but not limited to silica gel, controlled pore glass, cellulose, glass fiber filters, glass surfaces, metal surfaces (steel, gold, silver, aluminum, silicon and copper), plastic

S

materials of polyethylene, polypropylene, polyamide, polyvinyldenedifluoride) and silicon.

20 High density immobilization of nucleic acids to solid supports The methods described herein provide for high density immobilization of nucleic acid molecules on a insoluble solid) support. In general, nucleic acid molecules are immobilized on the insoluble support either directly or by means of cross-linking agents.

25 In embodiments of the methods in which a cross-linking reagent is not employed, a modified nucleic acid is reacted directly with a appropriately functionalized surface to yield immobilized nucleic acid.

Thus, for example, an iodoacetyl-modified surface (or other thiol-reactive -31surface functionality) can react with a thiol-modified nucleic acid to provide immobilized nucleic acids.

In accordance with the methods provided herein, the cross-linking agent is selected to provide a high density. of nucleic acids immobilized on the insoluble support. Without wishing to be bound by theory, it is believed that-the high density of immobilized nucleic acids described herein is due, at least in part, to a relatively rapid reaction occurring between the cross-linking agent and the nucleic acid a thiolmodified nucleic acid), compared to other reactions previously used to immobilize nucleic acids. In addition, high density may at least in part be due to a close spacing of the reactive groups amino groups of other reactive functionality) on the functionalized insoluble support.

Thus, reagents for modifying the surface will generally be selected to provide closely-spaced functionalities on the functionalized support. The cross-linking agent (and other reagents used to functionalize the support surface or the nucleic acid molecule) can be selected to provide any desired spacing of the immobilized nucleic acid molecules from the support surface, and to provide any desired spacing of the immobilized nucleic acids from each other. Thus, steric encumbrance of the nucleic 20 acid molecules can be reduced or eliminated by choice of an appropriate cross-linking agent. In certain embodiments, the cross-linking reagent can be selected to provide multiple reactive functionalities as used in dendrimer synthesis for attachment of multiple nucleic acids to a single cross-linking moiety. Preferably, the cross-linking agent is selected to be 25 highly reactive with the nucleic acid molecule, to provide rapid, complete, and/or selective reaction. In preferred embodiments, the reaction volume of the reagents the thiol group and the thiol-reactive functionality) is small.

-32- Nucleic acids and linkers Preferred nucleic acids for use herein are "thiol-modified nucleic acids," nucleic acids derivatized to contain at least one reactive thiol moiety. As described in further detail in Example 1, below, nucleic acids containing at least one reactive thiol are preferably made by treating a nucleic acid containing a 3' or 5' disulfide with a reducing agent, which preferably will not compete in subsequent reactions will not react with an iodoacetimido functionality. Disulfide-derivatized nucleic acids can be synthesized according to a variety of methods. For example, a nucleic acid can be modified at the or 5'-terminus by reaction with a disulfide-containing modifying a reagent. Alternatively, a thiolated primer can by enzymatically or non-enzymatically attached to the nucleic acid.

A 5'-phosphoramidate functionality can also provide an attachment point for a thiol or disulfide-containing cytosine or deoxycytosine. Examples of o.o. 15 reducing agents appropriate for reduction of a disulfide-modified nucleic acid include: tris-(2-carboxyethyl)phosphine (TCEP) (preferably a concentration in the range of 1-100mM (most preferably about 10mM)) is reacted at a pH in the range of 3-6 (most preferably about a temperature in the range of 20-45 0 C (most preferably about 37 0 C) for a 20 time period in the range of about 1 to about 10 hrs (most preferably for about 5 hrs); dithiothreitol (preferably a concentration in the range of to 100mM (depending on whether the reactant is isolated) is reacted at a pH in the range of 6-10 (most preferably about 8) and at a temperature in the range of 25-45 0 C (most preferably about 370C)) for a time in the 25 range of about 1 to about 10 hrs (most preferably about 5 hrs). TCE provides an advantage in the low pH at which it is reactive. This low pH effectively protonates thiols, thus suppressing nucleophilic reactions of thiols and resulting in fewer side reactions than with other disulfide reducing agents which are employed at higher pH.

-33- As further described in Example 1, below, a preferred bifunctional cross-linking agent is N-succinimidyl(4-iodacetyl) aminobenzcate (SIAB).

Other crosslinking agents include, but are not limited to, dimaleimide, dithio-bis-nitrobenzoic acid (DTNB), N-succinimidyl-S-acetyi-thioacetate (SATA), N-succinimidyl-3-(2-pyridyldithiol propionate (SPDP), succinimidyl 4-(N-maleimidomethyl)cyclohexane-1-carboxylate (SMCC) ad 6-hydrazinonicotimide (HYNIC) may also be used in the novel process.

For further examples of cross-linking reagents, see, Wong "Chemistry of Protein Conjugation and Cross-Linking," CRC Press (1991), and Hermanson, "Bioconiuqate Techniques" Academic Press (1995).

In preferred embodiments, the nucleic acid is immobilized using the I photocleavable linker moiety that is cleaved during mass spectrometry.

Exemplary photolabile cross-linker include, but are not limited to, 3- 15 amino-(2-nitrophenyl)propionic acid (Brown et al. (1995) Molecular Diversity, pp.4-12 and Rothschild et al. (1996) Nucleic Acids Res.

24:361-66).

In a further embodiment of the methods of detecting alterations in a target nucleic acid sequence provided herein and methods of 20 immobilization, a single-stranded nucleic acid complementary to the target nucleic acid is immobilized to a surface through a linkage that includes a thiol group-thiol reactive functionality bond and a cleavable, °preferably a selectively cleavable, linker moiety.

Linkers A target detection site can be directly linked to a solid support via a reversible or irreversible bond between an appropriate functionality on the target nucleic acid molecule and an appropriate functionality on the capture molecule. A reversible linkage can be such that it is cleaved under the conditions of mass spectrometry a -34photocleavable bond such as a charge transfer complex or a labile bond being formed between relatively stable organic radicals).

Photocleavable linkers are linkers that are cleaved upon exposure to light (see, Goldmacher et al. (1992) Bioconi. Chem. 3:104-107), thereby releasing the targeted agent upon exposure to light.

Photocleavable linkers that are cleaved upon exposure to light are known (see, ea, Hazum et al. (1981) in Pept.. Proc. Eur. Pept. Symp., 16th, Brunfeldt, K pp. 105-110, which describes the use of a nitrobenzyl group as a photocleavable protective group for cysteine; Yen et al.

(1989) Makromol. Chem 190:69-82, which describes water soluble photocleavable copolymers, including hydroxypropylmethacrylamide copolymer, glycine copolymer, fluorescein copolymer and methylrhodamine copolymer; Goldmacher et al. (1992) Bioconi. Chem.

3:104-107, which describes a cross-linker and reagent that undergoes 15 photolytic degradation upon exposure to near UV light (350 nm); and Senter et al. (1985) Photochem. Photobiol 42:231-237, which describes nitrobenzyloxycarbonyl chloride cross linking reagents that produce photocleavable linkages), thereby releasing the targeted agent upon exposure to light. In preferred embodiments, the nucleic acid is 20 immobilized using the photocleavable linker moiety that is cleaved during mass spectrometry.

Furthermore, the linkage can be formed with L' being a quaternary .ammonium group, in which case, preferably, the surface of the solid support carries negative charges which repel the negatively charged 25 nucleic acid backbone and thus facilitate the desorption required for analysis by a mass spectrometer. Desorption can occur either by the heat created by the laser pulse and/or, depending on by specific absorption of laser energy which is in resonance with the L' chromophore.

Thus, the L-L' chemistry can be of a type of disulfide bond (chemically cleavable, for example, by mercaptoethanol or dithioerythrol), a biotin/streptavidin system, a heterobifunctional derivative of a trityl ether group (see, K6ster et al. (1990) "A Versatile Acid-Labile Linker for Modification of Synthetic Biomolecules," Tetrahedron Letters 31:7095) that can be cleaved under mildly acidic conditions as well as under conditions of mass spectrometry, a levulinyl group cleavable under almost neutral conditions with a hydrjzinium/acetate buffer, an arginine-arginine or lysine-lysine bond cleavable by an endopeptidase enzyme like trypsin or a pyrophosphate bond cleavable by a pyrophosphatase, or a ribonucleotide bond in between the oligodeoxynucleotide sequence, which can be cleaved, for example, by a ribonuclease or alkali.

The functionalities, L and can also form a charge transfer complex and thereby form the temporary L-L' linkage. Since in many 15 cases the "charge-transfer band" can be determined by UV/vis spectrometry (see, Organic Charge Transfer Complexes by R.

Foster, Academic Press, 1969), the laser energy can be tuned to the corresponding energy of the charge-transfer wavelength and, thus, a specific desorption off the solid support can be initiated. Those skilled in 20 the art will recognize that several combinations can serve this purpose and that the donor functionality can be either on the solid support or coupled to the nucleic acid molecule to be detected or vice versa.

In yet another approach, a reversible L-L' linkage can be generated by homolytically forming relatively stable radicals. Under the influence of the laser pulse, desorption (as discussed above) as well as ionization will take place at the radical position. Those skilled in the art will recognize that other organic radicals can be selected and that, in relation to the dissociation energies needed to homolytically cleave the bond between them, a corresponding laser wavelength can be selected (see Reactive Molecules by C. Wentrup, John Wiley Sons, 1984).

When performing exonuclease sequencing using MALDI-TOF MS, a single stranded DNA molecule immobilized via its 5-end to a solid support is unilaterally degraded with a 3'-processive exonuclease and the molecular weight of the degraded nucleotide is determined sequentially.

Reverse Sanger sequencing reveals the nucleotide sequence of the immobilized DNA. By adding a selectively cleavable linker, not only can the mass of the free nucleotides be determined but also, upon removal of the nucleotides by washing, the mass of the remaining fragment can be detected by MALDI-TOF upon cleaving the DNA from the solid support.

Using selectively cleavable linkers, such as the photocleavable and chemical cleavable linkers provided herein, this cleavage can be selected to occur during the ionization and volatizing steps of MALDI-TOF.

15 The same rationale applies for a 5' immobilized strand of a double o stranded DNA that is degraded while in a duplex. Likewise, this also applies when using a 5'-processive exonuclease and the DNA is immobilized through the 3'-end to the solid support.

As noted, at least three version of immobilization are contemplated 20 herein: 1) the target nucleic acid is amplified or obtained (the target sequence or surrounding DNA sequence must be known to make primers to amplify or isolated); 2) the primer nucleic acid is immobilized to the solid support and the target nucleic acid is hybridized thereto (this is for detecting the presence of or sequencing a target sequence in a sample); or 3) a double stranded DNA (amplified or isolated) is immobilized through linkage to one predetermined strand, the DNA is denatured to eliminate the duplex and then a high concentration of a complementary primer or DNA with identity upstream from the target site is added and a strand displacement occurs and the primer is hybridized to the immobilized strand.

In the embodiments where the primer nucleic acid is immobilized on the solid support and the target nucleic acid is hybridized thereto, the inclusion of the cleavable linker allows the primer DNA to be immobilized at the 5'-end so that free 3'-OH is available for nucleic acid synthesis (extension) and the sequence of the "hybridized" target DNA'can be determined because the hybridized template can be removed by denaturation and the extended DNA products cleaved from the solid support for MALDI-TOF MS. Similarly for the immobilized DNA strand can be elongated when hybridized to the template and cleaved from the support. Thus, Sanger sequencing and primer oligo base extension t (PROBE), discussed below, extension reactions can be performed using gee S an immobilized primer of a known, upstreamn DNA sequence ecee 15 complementary to an invariable region of a target sequence. The nucleic .o:acid from the person is obtained and the DNA sequence of a variable region (deletion, insertion, missense mutation that cause genetic predisposition or diseases, or the presence of viral/bacterial or fungal ~DNA) not only is detected, but the actual sequence and position of the e20 mutation is also determined.

In other cases, the target DNA must be immobilized and the primer annealed. This requires amplifying a larger DNA based on known *sgee: O sequence and then sequencing the immobilized fragments the extended fragments are hybridized but not immobilized to the support as egos described above). In these cases, it is not desirable to include a linker C S because the MALDI-TOF spectrum is of the hybridized DNA; it is not necessary to cleave the immobilized template.

Any linker known to those of skill in the art for immobilizing nucleic acids to solid supports may be used herein to link the nucleic acid -38to a solid support. The preferred linkers herein are the selectively cleavable linkers, particularly those exemplified herein. Other linkers include, acid cleavable linkers, such as bismaleimideothoxy propane, acid-labile trityl linkers.

Acid cleavable linkers, photocleavable and heat sensitive linkers may also be used, particularly where it may be necessary to cleave the targeted agent to permit it to be more readily accessible to reaction.

Acid cleavable linkers include, but are not limited to, bismaleimideothoxy propane; and adipic acid dihydrazide linkers (see, e..Fattom et al.

(1992) Infection Immun. 60:584-589) and acid labile transferrin conjugates that contain a sufficient portion of transferrin to permit entry into the intracellular transferrin cycling pathway (see, Welh6ner et al. (1991) J. Biol. Chem. 266:4309-4314).

Photocleavable Linkers Photocleavable linkers are provided. In particular, photocleavable *linkers as their phosphoramidite derivatives are provided for use in solid phase synthesis of oligonucleotides. The linkers contain o-nitrobenzyl moieties and phosphate linkages which allow for complete photolytic cleavage of the conjugates within minutes upon UV irradiation. The UV wavelengths used are selected so that the irradiation will not damage the oligonucleotides and are preferrably about 350-380 nm, more preferably 365 nm. The photocleavable linkers provided herein possess comparable coupling efficiency as compared to commonly used phosphoramidite monomers (see, Sinha et al. (1983) Tetrahedron Lett. 24:5843-5846; 25 Sinha et al. (1984) Nucleic Acids Res. 12:4539-4557; Beaucage et al.

(1993) Tetrahedron 49:6123-6194; and Matteucci et al. (1981) J. Am.

Chem. Soc. 103:3185-3191).

In one embodiment, the photocleavable linkers have formula I: -39- R 200 (R

N

2 R 2-1 0 R 22 where R 20 is w-(4,4'-dimethoxytrityloxy)alky or w-hydroxyalkyl; R 21 is selected from hydrogen, alkyl, aryl, alkoxycarbonyl, aryloxycarbonyl and carboxy; R 22 is hydrogen or (dialkylamino)(w-cyanoalkoxy)P-; t is 0-3; and R 5 0 is alkyl, alkoxy, aryl or aryloxy.

In a preferred embodiment, the photocleavable linkers have formula 11: 202 R R0 *NO 2 S2.1 22I R O R where R 2 0 is w-(4,4'-dimethoxytrityloxy)alkyl, w-hydroxyalkyl or alkyl; R 2 1 is selected from hydrogen, alkyl, aryl, alkoxycarbonyl, aryloxycarbonyl and carboxy; R 22 is hydrogen or (dialkylamino)(w-cyanoalkoxy)P-; and X 20 is hydrogen, alkyl or OR 20 In particularly preferred embodiments, R 2 is d imethoxytrityloxy) propyl1, 3-hyd roxypropyl or methyl; R 21 is selected from hydrogen, methyl and carboxy; R 22 is hydrogen or (diisopropylamino)(2-cyanoethoxy)P-; and X 20 is hydrogen, methyl or

O

2 .In a more preferred embodiment,

R

2 is dimethoxytrityloxy)propyl; R 2 1 is methyl; R 22 is (diisopropylamino) (2cyanoethoxy)P-; and X 20 is hydrogen. In another more preferred embodiment, R 20 is methyl; R 2 1 is methyl; R 22 is (diisopropylamino) (2cyanoethoxy) and X 20 is 4 '-dimethoxytrityloxy)propoxy.

In another embodiment, the photocleavable linkers have formula IIl: 0 NO0 2 0

R

23 where R 23 is hydrogen or (dialkylamino)(w-cyanoalkoxy)P..; and R 2 is selected from w-hydroxyalkoxy, 4 '-d'imethoxytrityloxy)alkoxy, whydroxyalkyl and w-( 4 4 '-dimethoxytrityloxy) alkyl, and is unsubstituted or substituted on the alkyl or alkoxy chain with one or more alkyl groups; r and s are each independently 0-4; and R 50 is alkyl, alkoxy, aryl or aryloxy. In certain embodiments,

R

2 1 is w-hydroxyalkyl or -41dimethoxytrityloxy)alkyl, and is substituted on the alkyl chain with a methyl group.

In preferred embodiments,

R

23 is hydrogen or (diisopropylamino)(2cyanoethoxy)P-; and R 24 is selected from 3-hydroxypropoxy, dimethoxytrityloxy)propoxy, 4-hydroxybutyl, 3-hydroxy-1 -propyl, 1hydroxy-2-propyl, 3-hydroxy-2-methyl-l1-propyl, 2-hydroxyethyl, hydroxymethyl,.

4 4 4 '-dimethoxytrityloxy)butyl, dimethoxytrityloxy)-1 -propyl, 2 4 4 imetho xytrityloxy) ethyl, 1 dimethoxytrityloxy)-2-propyl, 3 4 4 '-dimethoxytriyloxy)-2-methyl-. 1 propyl and 4 4 '-dimethyoxytrityloxymethyl.

In more preferred embodiments, R 23 is (diisopropylamino)(2cyanoethoxy)P-; r and s are 0; and R 24 is selected from dimethoxytrityloxy)propoxy, 4 4 4 '-dimethoxytrityloxy)butyl, dimethoxytrityloxy)propyl, 2 4 4 1 -dimethoxytrityloxy)ethyl, 1 dimethoxytrityloxy)-2-propyl, 3 4 4 '-dimethoxytriyloxy)-2-methyl. 1 propyl and 4 4 '-dimethyoxytrityloxymethyl. R 24 is most preferably 3- (4,'-dimeth oxytrityloxy) pro poxy.

Preparation of the photocleavable linkers Preparation of photocleavable linkers of formulae I or 11 Photocleavable linkers of formulae I or 11 may be prepared by the methods described below, by minor modification of the methods by choosing the appropriate starting materials or by any other methods known to those of skill in the art.

In the photocleavable linkers of formula 11 where X 20 is hydrogen, the linkers may be prepared in the following manner. Alkylation of hydroxy-2-nitrobenzaldehyde with an w-hydroxyalkyl halide, 3hydroxypropyl bromide, followed by protection of the resulting alcohol as, a silyl ether, provides a 5-(w-silyloxyalkoxy)-2- -42nitrobenzaldehyde. Addition of an organometallic to the aldehyde affords a benzylic alcohol. Organometallics which may be used include trialkylaluminums (for linkers where R 21 is alkyl), such as trimethylaluminum, borohydrides (for linkers where R 2 1 is hydrogen), such as sodium borohydride, or metal cyanides (for linkers where R 21 is carboxy or alkoxycarbonyl), such as potassium cyanide. In the case of the metal cyanides, the product of the reaction, a cyanohydrin, would then be hydrolyzed under either acidic or basic conditions in the presence of either water or an alcohol to afford the compounds of interest.

The silyl group of the side chain of the resulting benzylic alcohols may then be exchanged for a 4,4'-dimethoxytriyl group by desilylation with, tetrabutylammonium fluoride, to give the corresponding alcohol, followed by reaction with 4,4'-dimethoxytrityl chloride. Reaction with, 2-cyanoethyl diisopropylchlorophosphoramidite affords the linkers where R 22 is (dialkylamino)(w-cyanoalkoxy)P-.

A specific example of a synthesis of a photocleavable linker of formula II is shown in the following scheme, which also demonstrates S use of the linker in oligonucleotide synthesis. This scheme is intended to be illustrative only and in no way limits the scope of the invention.

9• Experimental details of these synthetic transformations are provided in the Examples.

e *9 HO ~B r

K,CO,

0cat. K I HO O tBDMSCI tBDMSO,-O O E t 3NNO NO0 ImidazoleN0 CHO,

CHO

M e 3

A

tBDMS0-..',O n~

CH

2 O H BuNF CHS 0 Phosphorylatior

DMTCI

DMAP

D M TO-

NI

O 3 0H DMTO...-O N DNA synthesis

NO

2

CH

3 0 iPr 2 N 0 spacer NO 2 C H, 0 -0lig omner Synthesis of the linkers of formula 11 where X 2 0 is OR 20 3,4dihydroxyacetophenone is protected selectively at the 4-hydroxyl by -44reaction with, potassium carbonate and a silyl chloride. Benzoate esteres, propiophenones, butyrophenones, etc. may be used in place of the acetophenone. The resulting 4 -silyloxy-3-hydroxyacetophenone is then alkylated at the with an alkyl halide (for linkers where R 20 is alkyl) at the 3-hydroxyl and desilylated with, tetrabuylammonium fluoride to afford a 3 -alkoxy- 4 -hydroxyacetophenone. This compound is then alkylated at the 4-hydroxyl by reaction with an w-hydroxyalkyl halide, 3-hydroxypropyl bromide, to give a 4-(w-hydroxyalkoxy)-3alkoxyacetophenone. The side chain alcohol is then protected as an ester, an acetate. This compound is then nitrated at the with, concentrated nitric acid to provide the corresponding 2nitroacetophenones. Saponification of the side chain ester with, e.q., potassium carbonate, and reduction of the ketone with, sodium borohydride, in either order gives a 2 alkoxybenzylic alcohol.

Selective protection of the side chain alcohol as the corresponding 4 ,4'-dimethoxytrityl ether is then accomplished by reaction with 4,4'dimethoxytrityl chloride. Further reaction with, 2-cyanoethyl diisopropylchlorophosphoramidite affords the linkers where R 22 is (dialkylamino)(w-cyanoalkoxy)P-.

A specific example of the synthesis of a photocleavable linker of formula II is shown the following scheme. This scheme is intended to be illustrative only and in no way limit the scope of the invention. Detailed experimental procedures for the transformations shown are found in the 25 Examples.

*11t HO0 0

CH

3 O0 Ac 2 O0 I Et 3

I

H 3 C 0

OH

H 3 C 0 AcO

CH

3 O0

H

3

C

K 2 C0 3 cat. KI conc. HNO, A co AcO CH 3 0

C

NO 2 NO 2 K 2 C 03/ 0 H 3 0 NO 2 H 3 C 0 NaBH, D M T 0 0 H 3 C O H

DNA

1 0-

DNA

synthesis 0 0-CH 3 0 N NO 2 H 3C OH

I

iPr 2 N O -46- HO O AcO O

CH

3 O CH 3 0

NO

2 NO,

H

3 C 0 H 3 C OH NaBH,

K

2

CO,

DMTO O HO O

CH

3 O

CH

3 0

DMTCI

-2 D M A P N 2 NO-.

NO

2

H

3 C OH

H

3 C OH Phosphorylation B. Preparation of photocleavable linkers of formula III :*.*-Photocleavable linkers of formula III may be prepared by the methods described below, by minor modification of the methods by 5 choosing appropriate starting materials, or by other methods known to those of skill in the art.

In general, photocleavable linkers of formula III are prepared from w-hydroxyalkyl- or alkoxyaryl compounds, in particular w-hydroxy-alkyl or alkoxy-benzenes. These compounds are commercially available, or may 10 be prepared from an w-hydroxyalkyl halide 3-hydroxypropyl bromide) and either phenyllithium (for the w-hydroxyalkylbenzenes) or phenol (for the w-hydroxyalkoxybenzenes). Acylation of the w-hydroxyl group as an acetate ester) followed by Friedel-Crafts acylation of the aromatic ring with 2-nitrobenzoyl chloride provides a 4-(w-acetoxyalkyl or alkoxy)-2-nitrobenzophenone. Reduction of the ketone with, -47sodium borohydride, and saponification of the side chain ester are performed in either order to afford a 2-nitrophenyl-4-(hydroxy-alkyl or alkoxy)phenylmethanol. Protection of the terminal hydroxyl group as the corresponding 4,4'-dimethoxytrityl ether is achieved by reaction with 4,4'-dimethoxytrityl chloride. The benzylic hydroxyl group is then reacted with, 2-cyanoethyl diisopropylchlorophosphoramidite to afford linkers of formula II where R 23 is (dialkylamino)(w-cyanoalkoxy)P-.

Other photocleavable linkers of formula III may be prepared by substituting 2-phenyl-l-propanol or 2-phenylmethyl-l-propanol for the whydroxy-alkyl or alkoxy-benzenes in the above synthesis. These compounds are commercially available, but may also be prepared by reaction of, phenylmagnesium bromide or benzylmagnesium bromide, with the requisite oxirane propylene oxide) in the presence of catalytic cuprous ion.

15 Chemically cleavable linkers A variety of chemically cleavable linkers may be used to introduce a cleavable bond between the immobilized nucleic acid and the solid support. Acid-labile linkers are presently preferred chemically cleavable S.linkers for mass spectrometry, especially MALDI-TOF MS, because the acid labile bond is cleaved during conditioning of the nucleic acid upon addition of the 3-HPA matrix solution. The acid labile bond can be introduced as a separate linker group, the acid labile trityl groups or may be incorporated in a synthetic nucleic acid linker by introducing one or more silyl internucleoside bridges using diisopropylsilyl, thereby 25 forming diisopropylsilyl-linked oligonucleotide analogs. The diisopropylsilyl bridge replaces the phoshodiester bond in the DNA backbone and under mildly acidic conditions, such as trifluoroacetic acid (TFA) or 3-HPA/1% TFA MALDI-TOF matrix solution, results in the introduction of one or more intra-strand breaks in the DNA -48molecule. Methods for the preparation of diisopropylsilyl-linked oligonucleotide precursors and analogs are known to those of skill in the art (see Saha et al. (1993) J. Orq. Chem. 58:7827-7831). These oligonucleotide analogs may be readily prepared using solid state oligonucleotide synthesis methods using diisopropylsilyl derivatized deoxyribonucleosides.

Mass modification of nucleic acids In certain embodiments, nucleic acids modified at positions other than the or terminus can be used. Modification of the sugar moiety of a nucleotide at positions other than the 3' and 5' position is possible through concentional methods. Also, nucleic acid bases can be modified, by modification of C-5 of dT with a linker arm, as described in F. Eckstein, ed., "Oliaonucleotides and Analogues: A Practical Approach," IRL Press (1991). Such a linker arm can be modified to include a thiol moiety. Alternatively, backbone-modified nucleic acids phosoroamidate DNA) can be used so that the thiol group can be attached to the nitrogen center provided by the modified phosphate backbone.

e In preferred embodiments, modification of a nucleic acid, as described above, does not substantially impair the ability of the nucleic acid or nucleic sequence to hybridize to its complement. Thus, any modification should preferably avoid substantially modifying the functionalities of the nucleic acid which are responsible for Watson-Crick base pairing. The nucleic acid can be modified such that a non-terminal thiol group is present, and the nucleic acid, when immobilized to the support, is capable of self-complementary base pairing to form a "hairpin" structure having a duplex region.

I

-49- Solid supports and substrates Examples of insoluble supports and substrates for use herein include, but are not limited to, beads (silica gel, controlled pore glass, magnetic beads, Sephadex/Sepharose beads, cellulose beads, etc.), capillaries, flat supports such as glass fiber filters, glass surfaces, metal surfaces (steel, gold, silver, aluminum, silicon and copper), plastic materials including multiwell plates or membranes of polyethylene, polypropylene, polyamide, polyvinyldenedifluoride), wafers, combs, pins arrays of pins suitable for combinatorial synthesis or analysis) or beads in pits of flat surfaces such as wafers silicon wafers), with or without filter plates.

Mass spectrometry Once immobilized, the nucleic acids can be analyzed by any of a variety of means including, for example, spectrometric techniques such 15 as UV/VIS, IR, fluorescence, chemiluminescence, or NMR spectroscopy, mass spectrometry, or other methods know in the art, or combinations thereof. Preferred mass spectrometer formats include the ionization (I) techniques, such as matrix assisted laser desorption (MALDI), continuous or pulsed electrospray (ESI) and related methods lonstray or Thermospray), or massive cluster impact (MCI); these ion sources can be i* matched with detection formats including linear or reflectron time-offlight (TOF), single or multiple quadruple, single or multiple magnetic sector, Fourier Transform ion cyclotron resonance (FTICR), ion trap, and combinations thereof to yield a hybrid detector ion-trap/time-of- 25 flight). For ionization, numerous matrix/wavelength combinations (MALDI) or solvent combinations (ESI) can be employed.

Preparation of DNA arrays Methods and systems for preparing arrays of sample material for analysis by a diagnostic tool are provided herein. For example, Fig. 1 illustrates one system for preparing arrays of sample material for analysis by a diagnostic tool. Fig. 1 depicts a system 10 that includes a data processor 12, a motion controller 14, a robotic arm assembly 16, a monitor element 18A, a central processing unit 18B, a microliter plate of source material 20, a stage housing 22, a robotic arm 24, a stage 26, a pressure controller 28, a conduit 30, a mounting assembly 32, a pin assembly 38, and substrate elements 34. In the view shown by Fig. 1, it is also illustrated that the robotic assembly 16 can include a moveable mount element 40 and a horizontal slide groove 42. The robotic arm 24 can optionally pivot about a pin 36 to increase the travel range of the arm 24 so that arm 24 can disposes the pin assembly 38 above the source plate The data processor 12 depicted in Fig. 1 can be a conventional oo idigital data processing system such as an IBM PC compatible computer system that is suitable for processing data and for executing program instructions that will provide information for controlling the movement and operation of the robotic assembly 16. It will be apparent to one i skilled in the art that the data processor unit 12 can be any type of system suitable for processing a program of instructions signals that will operate the robotic assembly that is integrated into the robotic housing 16. Optionally the data processor 12 can be a micro-controlled assembly 25 that is integrated into robotic housing 16. In further alternative embodiments, the system 10 need not be programmable and can be a singleboard computer having a firmware memory for storing instructions for operating the robotic assembly 16.

-51- In the embodiment depicted in Fig. 1, there is a controller 14 that electronically couples between the data processor 12 and the robotic assembly 16. The depicted controller 14 is a motion controller that drives the motor elements of the robotic assembly 16 for positioning the robotic arm 24 at a selected location. Additionally, the controller 14 can provide instructions to the robotic assembly 16 to direct the pressure controller 28 to control the volume of fluid ejected from the individual pin elements of the depicted pin assembly 38. The design and construction of the depicted motion controller 14 follows from principles well known in the art of electrical engineering, and any controller element suitable for driving the robotic assembly 16 can be practiced without departing from the scope thereof.

The robotic assembly 16 depicted in Fig. 1 electronically couples to the controller 14. The depicted robotic assembly 16 is a gantry 15 system that includes an XY table for moving the robotic arm about a XY plane, and further includes a Z axis actuator for moving the robotic arm ~orthogonally to that XY plane. The robotic assembly 16 depicted in Fig.

~1 includes an arm 24 that mounts to the XY stage which moves the arm within a plane defined by the XY access. In the depicted embodiment, the XY table is mounted to the Z actuator to move the entire table along e the Z axis orthogonal to the XY plane. In this way, the robotic assembly "provides three degrees of freedom that allows the pin assembly 38 to be disposed to any location above the substrates 34 and the source plate i C20 which are shown in Fig. 1 as sitting on the stage 26 mounted to the S" 25 robotic assembly 16.

The depicted robotic assembly 16 follows from principles well i known in the art of electrical engineering and is just one example of a robotic assembly suitable for moving a pin assembly to locations adjacent a substrate and source plate such as the depicted substrate 34.

-52- Accordingly, it will be apparent to one of ordinary skill in the art that alternative robotic systems can be practiced following the descriptions herein without departing from the scope thereof.

Fig. .1 depicts an embodiment of a robotic assembly 16 that includes a pressure controller 28 that connects via a conduit 30 to the mount 32 that connects to the pin assembly 38. In this embodiment the mount 32 has an interior channel for fluidicly coupling the conduit 30 to the pin assembly 38. Accordingly, the pressure controller 28 is fluidicly coupled by the conduit 30 and the mount 32 to the pin assembly 38. In this way the controller 14 can send signals tothe pressure controller 28 to control selectively a fluid pressure delivered to the pin assembly 38.

Fig. 2 depicts one embodiment of a pin assembly 50 suitable for practice with the system depicted in Fig. 1 which includes the pressure controller 28. In the depicted embodiment, the pin assembly 50 includes a housing formed from an upper portion 52 and a lower portion 54 that o° ~are joined together by the crews 56A and 56B to define an interior ~chamber volume 58. Fig. 2 further depicts that to fluidicly seal the interior chamber volume 58 the housing can include a seal element depicted in Fig. 2 as an O-ring gasket 60 that sites between the upper block and the lower block 54 and surrounds completely the perimeter of o:o• ~the interior chamber volume 58. Fig. 2 further depicts that the pin assembly 50 includes a plurality of vesicles 62A-62D, each of which include an axial bore extending therethrough to form the depicted holding chambers 64A-64D. Each of the depicted vesicles extends through a 25 respective aperture 68A-68D disposed within the lower block 54 of the housing.

As further shown in the depicted embodiment, each of the vesicles 62A-62D has an upper flange portion that sits against a seal element 70A-70D to form a fluid-tight seal between the vesicle and the lower -53block 54 to prevent fluid from passing through the apertures 68A-68D.

To keep the seal tight, the depicted pin assembly 50 further includes a set of biasing elements 74A-74D depicted in Fig. 2 as springs which, in the depicted embodiments, are in a compressed state to force the flange element of the vesicles 62A-62D against their respective seal elements 70A-70D. As shown in Fig. 2, the biasing elements 74A-74D extend between the vesicles and the upper block 52. Each of the springs 74A- 74D can be fixedly mounted to a mounting pad 76A-76D where the spring elements can attach to the upper block 52. The upper block 52 further includes an aperture 78 depicted in Fig. 2 as a centrally disposed aperture that includes a threaded bore for receiving a swagelok 80 that can be rotatably mounted within the aperture 78.

As further depicted in Fig. 2, the swagelok 80 attaches by a conduit to a valve 82 than can connect the swagelok 80 to a conduit 84 that can be coupled to a pressure source, or alternatively can couple the swagelok 80 to a conduit 86 that provides for venting of the interior chamber 58. A central bore 88 extends through the swagelok 80 and couples to the tubing element which further connects to the valve 82 to thereby fluidicly and selectively couple the interior chamber volume 58 to either a pressure source, or a venting outlet.

i The pin assembly 50 described above and depicted in Fig. 2 disposed above a substrate element 90 that includes a plurality of wells 92 that are etched into the upper surface of the substrate 90. As illustrated by Fig. 2, the pitch of the vesicles 62A-62D is such that each 25 vesicle is spaced from the adjacent vesicles by a distance that is an integral multiple of the pitch distance between wells 92 etched into the upper surface of the substrate 90. As will be seen from the following description, this spacing facilitates the parallel dispensing of fluid, such that fluid can be dispensed into a plurality of wells in a single operation.

-54- Each of the vesicles can be made from stainless steel, silica, polymeric material or any other material suitable for holding fluid sample. In one example, 16 vesicles are employed in the assembly, which are made of hardened beryllium copper, gold plated over nickel plate. They are 43.2 mm long and the shaft of the vesicle is graduated to 0.46 mm outer diameter with a concave tip. Such a pin was chosen since the pointing accuracy can be approximately 501 micrometers. However, it will be apparent that any suitable pin style can be employed for the device, including but not limited to flat, star-shaped, concave, pointed solid, pointed semi-hollow, angled on one or both sides, or other such geometries.

Fig. 3 shows from a side perspective the lower block 54 of the pin assembly 50 depicted in Fig. 2. Fig. 3 shows approximate dimensions for one pin assembly. As shown, the lower block 54 has a bottom plate 98 and a surrounding shoulder 100. The bottom plate 98 is :approximately 3mm in thickness and the shoulder 100 is approximately or 5mm in thickness.

Fig. 4 shows from an overhead perspective the general structure and dimensions for one lower block 54 suitable for use with the pin 20 assembly for use with the pin assembly 50 shown in Fig. 2. As shown in Fig. 4, the lower block 54 includes a four-by-four matrix of apertures .4 68 to provide 16 apertures each suitable for receiving a vesicle. As described above with reference to Fig. 2, the spacing between the aperture 68 is typically an integral multiple of the distance between wells 25 on a substrate surface as well as the wells of a source plate.

Accordingly, a pin assembly having the lower block 54 as depicted in Fig. 4 can dispense fluid in up to 16 wells simultaneously. Fig. 4 also shows general dimensions of one lower block 54 such that each side of block 54 is generally 22 mm in length and the pitch between aperture 68 is approximately 4.5mm. Such a pitch is suitable for use with a substrate where fluid is to be dispensed at locations approximately 500 pm apart, as exemplified by the substrate 90 of Fig. 2. Fig. 4 also shows that the lower block 54 can include an optional 0-ring groove 94 adapted for receiving an 0-ring seal element, such as the seal element depicted in Fig. 2. It is understood that such a groove element 94 can enhance and improve the fluid seal formed by the seal element The pinblock can be manufactured of stainless steel as this material can be drilled accurately to about +25 pm, but a variety of probe materials can also be used, such as G10 laminate, PMMA or other suitable material. The pin block can contain any number of apertures and is shown with 16 receptacles which hold the 16 pins in place. To increase the pointing accuracy of each pin, an optional alignment place can be placed below the block so that about 6mm of the pin tip is left exposed to enable dipping into the wells of a microtiter plate. The layout of the probes in the depicted tool is designed to coordinate with a 384- ~well microtiter plate, thus the center-to-center spacing of the probes in 4.5mm. An array of 4 x 4 probes was chosen since it would produce an array that would fit in less than one square inch, which is the travel range of an xy stage of a MALDI TOF MS employed by the assignee.

The pintool assembly is completed with a stainless steel cover on the top side of the device which is then attached onto the Z-arm of the robot.

ol With references to Fig. 5, the robotic assembly 16 employs a pin tool assembly 38 that is configured similarly as the pin tool assembly 25 depicted in Figure 2. The pressure controller 28 selectively controls the pressure within chamber 58. With this embodiment, a control program operates on the data processor 12 to control the robotic assembly 16 in a way that the assembly 16 prints an array of elements on the substrates 34.

In a first step, Fig. 5A, the program can direct the robotic assembly 16 to move the pin assembly 38 to be disposed above the source plate 20. The robotic assembly 16 will then dip the pin assembly into the source plate 20 which can be a 384 well DNA source plate. As shown in Fig. 4 the pin assembly can include 16 different pins such that the pin assembly 50 will dip 16 pins into different 16 wells of the 384 well DNA source plate 20. Next the data processor 12 will direct the motion controller 14 to operate the robotic assembly 16 to move the pin assembly to a position above the surface of the substrate 34. The substrate 34 can be any substrate suitable for receiving a sample of material and can be formed of silicon, plastic, metal, or any other such suitable material. Optionally the substrate will have a flat surface, but can alternatively include a pitted surface, a surface etched with wells or any other suitable surface typography. The program operating on data processor 12 can then direct the robotic assembly, through the motion controller 14, to direct the pressure controller 28 to generate a positive t o pressure within the interior chamber volume 58. In this practice, the positive interior pressure will force fluid from the holding chambers of vesicles 62 to eject fluid from the vesicles and into a respective well 92 S* 20 of the substrate The program operating on data processor 12 can also direct the °4*S controller 14 to control the pressure controller 28 to control filling the holding chambers with source material from the source plate 20. The pressure controller 28 can generate a negative pressure within the

C

25 interior chamber volume 58 of the pin assembly. This will cause fluid to be drawn up into the holding chambers of the vesicles 62A-62D. The topressure controller 28 can regulate the pressure either by open-loop or closed-loop control to avoid having fluid overdrawn through the holding chambers and spilled into the interior chamber volume 58. Loop control -57systems for controlling pressure are well known in the art and any suitable controller can be employed. Such spillage could cause crosscontamination, particularly if the source material drawn from the source plate 20 varies from well to well.

In an alternative practice of the invention, each of the holding chambers 64A-64D is sufficiently small to allow the chambers to be filled by capillary action. In such a practice, the pin assembly can consist of an array of narrow bore needles, such as stainless steel needles, that extend through the apertures of the lower block 54. The needles that are dipped into source solutions will be filled by capillary action. In one practice, the length of capillary which is to be filled at atmospheric pressure is determined approximately by: H= 2v

PGR

where H equals Height, gamma equals surface tension, P equals solution density, G equals gravitational force and R equals needle radius. Thus the volume of fluid held by each vesicle can be controlled by selecting *the dimensions of the interior bore. It is understood that at room 0 temperature water will fill a 15 cm length of 100 pm radius capillary.

O. *20 Thus, a short bore nanoliter volume needle will fill to full capacity, but should not overflow because the capillary force is understood to be too small to form a meniscus at the top of the needle orifice. This prevents *06O cross-contamination due to spillage. In one embodiment, the vesicles of the pin assembly can be provided with different sized interior chambers S° 25 for holding and dispensing different volumes of fluid.

In an alternative practice, to decrease the volume of liquid that is drawn into the holding chambers of the vesicles, a small positive 0505 pressure can be provided within the interior chamber volume 58 by the 000000 pressure controller 28. The downward force created by the positive pressure can be used to counter the upward capillary force. In this way, -58the volume of fluid that is drawn by capillary force into the holding chambers of the vesicles can be controlled.

Fig. 5B shows that fluid within the holding chambers of the needle can be dispensed by a small positive pressure introduced through the central bore 88 extending through a swagelok 80. By regulating the pressure pulse that is introduced into the interior chamber volume 58, fluid can be ejected either as a spray or by droplet formation at the needle tip. It is understood that the rate of dispensing, droplet versus °•spray, depends in part upon the pressure applied by the pressure 10 controller 28. In one practice, pressure is applied in the range of l* between 10 and 1,000 Torr of atmospheric pressure.

To this end the data processor 12 can run a computer program ~that controls and regulates the volume of fluid dispensed. The program *can direct the controller 28 to eject a defined volume of fluid, either by generating a spray or by forming a drop that sits at the end of the :.vesicle, and can be contacted with the substrate surface for dispensing the fluid thereto.

Figures 5C and 5D show the earlier steps shown in Figs. can again be performed, this time at a position on the substrate surface 20 that is offset from the earlier position. In the depicted process, the pin tool is offset by a distance equal to the distance between two wells 92.

It will be apparent that other offset printing techniques can be employed without departing from the scope of the invention.

It will be understood that several advantages of the pin assembly depicted in Fig. 2 are achieved. For example, rinsing between dispensing events is straightforward, requiring only single or multiple pin fillings and emptying events with a rinse solution. Moreover, since all holding chambers fill to full capacity, the accuracy of the volumes dispensed varies only according to needle inner dimensions which can be carefully -59controlled during pin production. Further the device is cost effective, with the greatest expense attributed to the needles, however because no contact with a surface is required, the needles are exposed to little physical strain or stress, making replacement rare and providing long life.

Alternatively, deposition of sample material onto substrate surface can include techniques that employ pin tool assemblies that have solid pin elements extending from a block wherein a robotic assembly dips the solid pin elements of the pin assembly into a source of sample material to So-o wet the distal ends of the pins with the sample materials. Subsequently ~10 the robotic assembly can move the pin assembly to a location above the substrate and then lower the pin assembly against the surface of the substrate to contact the individual wetted pins against the surface for spotting material of the substrate surface.

Figures 6A and 6B depict another alternative system for dispensing material on or to the surface of the substrate. In particular, Figure 6A °ooo depicts a jet printing device 110 which includes a capillary element 112, o*oo a transducer element 114 and orifice (not shown) 118, a fluid conduit 122, and a mount 124 connecting to a robotic arm assembly, such as the robotic arm 24 depicted in Figure 1. As further shown in Figure 6A the jet assembly 110 is suitable for ejecting from the orifice 118 a series of drops 120 of a sample material for dispensing sample material onto the surface 128.

The capillary 112 of the jet assembly 110 can be a glass capillary, a plastic capillary, or any other suitable housing that can carry a fluid sample and that will allow the fluid sample to be ejected by the action of a transducer element, such as the transducer element 114. The transducer element 114 depicted in Figure 6A is a piezo electric transducer element which forms around the parameter of the capillary 112 and can transform an electrical pulse received from the pulse generator within a robotic assembly 16 to cause fluid to eject from the orifice 118 of the capillary 112. One such jet assembly having a piezoelectric transducer element is manufactured by MicroFab Technology, Inc., of Germany. Any jet assembly, however, that is suitable for dispensing defined and controlled the volumes of fluid can be used herein including those that use piezoelectric transducers, electric *o".transducers, electrorestrictive transducers, magnetorestrictive .transducers, electromechanical transducersor any other suitable transducer element. In the depicted embodiment, the capillary 112 has a 10 fluid conduit 122 for receiving fluid material. In an optional embodiment, fluid can be drawn into the capillary by action of a vacuum pressure that will draw fluid through the orifice 118 when the orifice 118 is submerged in a source of fluid material. Other embodiments of the jet assembly 110 *can be practiced with the invention without departing from the scope thereof.

Figure 6B illustrates a further alternative assembly suitable for p •being carried on the robotic arm of a robotic assembly, such as the assembly 16 depicted in Figure 1. Figure 6B illustrates four jet assemblies connected together, 130A-130D. Similar to the pin assembly *20 in Figure 2, the jet assembly depicted in Figure 6B can be employed for the parallel dispensing of fluid material. It will be obvious to one of ordinary skill in the art of electrical engineering, that each of the jet assemblies 130A-130D can be operated independently of the others, for allowing the selective dispensing of fluid from select ones of the jet assemblies. Moreover, each of the jet assemblies 130A-1300 can be independently controlled to select the volume of fluid that is dispensed from each respected one of the assembly 130A-130D. Other modifications and alterations can be made to the assembly depicted in Figure 6B without departing from the scope of the invention.

I -61- Methods for rapidly analyzing sample materials are also provided.

To this end sample arrays can be formed on a substrate surface according to any of the techniques discussed above. The sample arrays are then analyzed by mass spectrometry to collect spectra data that is representative of the composition of the samples in the array. It is understood that the above methods provide processes that allow for rapidly dispensing definite and controlled volumes of analyte material. In particular these processes allow for dispensing sub to low nanoliter volumes of fluid. These low volume deposition techniques generate 10 sample arrays well suited for analysis by mass spectrometry. For example, the low volumes yield reproducibility of spot characteristics, such as evaporation rates and reduced dependence on atmospheric S• conditions such as ambient temperature and light.

~Continuing with the example shown in Fig. 5, the arrays can be prepared by loading oligonucleotides (0.1-50 ng/lll) of different sequences or concentrations into the wells of a 96 well microtiter source Splate 20; the first well can be reserved for holding a matrix solution. A substrate 34, such as a pitted silicon chip substrate, can be placed on the stage 26 of the robotics assembly 16 and can be aligned manually to orient the matrix of wells about a set of reference axes. The control program executing on the data processor 12 can receive the coordinates of the first well of the source plate 20. The robotic arm 12 can dip the pin assembly 38 into source plate 20 such that each of the 16 pins is dipped into one of the wells. Each vesicle can fill by capillary action so that the full volume of the holding chamber contains fluid. Optionally, the program executing on the data processor 12 can direct the pressure controller to fill the interior chamber 58 of the pin assembly 38 with a positive bias pressure that will counteract, in part, the force of the -62capillary action to limit or reduce the volume of fluid that is drawn into the holding chamber.

Optionally, the pin assembly 38 can be dipped into the same 16 wells of the source plate 20 and spotted on a second target substrate.

This cycle can be repeated on as many target substrates as desired.

Next the robotic arm 12 can dip the pin assembly 38 in a washing *solution, and then dip the pin assembly into 16 different wells of the source plate 20, and spot onto the substrate target offset a distance from the initial set of 16 spots. Again this can be repeated for as many 10 target substrates as desired. The entire cycle can be repeated to make a ~2x2 array from each vesicle to produce an 8x8 array of spots (2x2 elements/vesicle x 16 vesicles 64 total elements spotted). However, it will be apparent to anyone of ordinary skill in the art that process suitable for forming arrays can be practiced with the present invention without departing from the scope thereof.

Oligonucleotides of different sequences or concentrations can be loaded into the wells of up to three different 384-well microtiter source plates; one set of 16 wells can be reserved for matrix solution. The wells of two plates are filled with washing solution. Five microtiter Oe,20 plates can be loaded onto the stage of the robotic assembly 16. A plurality of target substrates can be placed abutting an optional set of banking or registration pins disposed on the stage 26 and provided for aligning the target substrates along a set of reference axes. If the matrix and oligonucleotide are not pre-mixed, the pin assembly can be employed to first spot matrix solution on all desired target substrates. In a subsequent step the oligonucleotide solution can be spotted in the same pattern as the matrix material to re-dissolve the matrix. Alternatively, a sample array can be made by placing the oligonucleotide solution on the -63wafer first, followed by the matrix solution, or by pre-mixing the matrix and oligonucleotide solutions.

After depositing the sample arrays onto the surface of tne substrate, the arrays can be analyzed using any of a variety of means spectrometric techniques, such as UV/VIS, IR, fluorescence, chemiluminescence, NMR spectrometry or mass spectrometry. For example, subsequent to either dispensing process, sample loaded substrates can be placed onto a MALDI-TOF source plate and held there with a set of beveled screw mounted polycarbonate supports. In one 10 practice, the plate can be transferred on the end of a probe to be held onto a 1/m resolution, 1" travel xy stage (Newport) in the source region of a time-of-flight mass spectrometer. It will be apparent to one of ordinary skill in the art that any suitable mass spectrometry tool can be employed with the present invention without departing from the scope thereof.

Preferred mass spectrometer formats for use with the arrays decsribed herein include ionization techniques including but not limited to matrix assisted laser desorption (MALDI), continuous or pulsed electrospray (ESI) and related methods lonspray or Thermospray), or S* 20 massive cluster impact (MCI); those ion sources can be matched with detection formats including linear or non-linear reflectron time-of-flight (TOF), single or multiple quadruple, single or multiple magnetic sector, Fourier Transform ion cyclotron resonance (FTICR), ion trap, and combinations thereof ion-trap/time-of-flight). For ionization, numerous matrix/wavelength combinations (MALDI) or solvent combinations (ESI) can be employed. Subattomole levels of protein have been detected for example, using ESI (Valaskovic, G. A. et al., (1996) Science 273: 1199-1202) or MALDI (Li, L. et al., (1996) J. Am. Chem.

Soc 118: 1662-1663) mass spectrometry.

Thus, it will be understood that in processes described herein a completely non-contact, high-pressure spray or partial-contact, low pressure dro, let formation mode can be employed. In the latter, the only contact that v.ill occur is between the droplet and the walls of the well or a hydrophilic flat surface of the substrate 34. In neither practice need there be any contact between the needle tip and the surface.

Preferred embodiments In one preferred embodiment, a nucleic acid molecule can be covalently immobilized on a silica support by functionalization of the 10 support with an amino functionality derivatization of the support with a reagent such as 3-aminopropyl-triethoxysilane (Aldrich Chemical Co., Milwaukee, WI); see Figure Other functionalized oxysilanes or orthosilicates can be used, and are commercially available from S* Gelest, Inc., Tullytown, PA). For example, 3-mercaptopropyltriethoxysilane can be used to functionalize a silicon surface with thiol groups.

The amino-functionalized silica can then be reacted with a heterobifunctional reagent such as N-succinimidyl (4-iodacetyl) aminobenzoate (SIAB) (Pierce, Rockford, IL). Other homo- and heterobifunctional reagents which can be employed are available commercially, 20 from Pierce. Finally, a nucleic acid functionalized with a thiol group at the 5'-terminus) is covalently bound to the derivatived silica support by reaction of the thiol functionality of the nucleic acid molecule with the iodoacetyl functionality of the support.

In certain embodiments, the nucleic acid can be reacted with the cross-linking reagent to form a cross-linker/nucleic acid conjugate, which is then reacted with a functionalized support to provide an immobilized nucleic acid. Alternatively, the cross-linker can be combined with the nucleic acid and a functionalized solid support in one pot to provide substantially simultaneous reaction of the cross-linking reagent with the nucleic acid and the solid support. In this embodiment, it will generally be necessary to use a heterobifunctional cross-linker, a cross-linker with two different reactive functionalities capable of selective reaction with each of the nucleic acid and the functionalized solid support.

The methods provided herein are useful for producing spatiallyaddressable arrays of nucleic acids immobilized on insoluble supports.

For example, the methods can be used to provide arrays of different nucleic acids immobilized on pins arranged in an array. In another *embodiment, a photo-cleavable protecting group on the insoluble support 10 can be selectively cleaved by photolithography) to provide portions of a surface activated for immobilization of a nucleic acid. For example, a silicon surface, modified by treatment with 3-mercaptopropyltriethoxysilane to provide thiol groups, can be blocked with a photocleavable protecting group (for examples of photocleavable protecting groups, see, PCT Publication WO 92/10092, or McCray et a..(1989) Ann. Rev. Biophvs. Bioohys. Chem. 18:239-270), and be selectively deblocked by irradiation of selected areas of the surface, e.q., by use of a photolithography mask. A nucleic acid modified to contain a thiol-reactive group can then be attached directly to the support, or, 20 alternatively, a thiol-reactive cross-linking reagent can be reacted with the thiol-modified support, followed by (or substantially simultaneously with) reaction with a nucleic acid to provide immobilized nucleic acids. A nucleic acid base or sequence, once immobilized on a support according to the methods described herein, can be further modified according to known methods, for example, the nucleic acid sequence can be lengthened by performing solid-phase nucleic acid synthesis according to conventional techniques, including combinatorial techniques.

Insoluble supports comprising nucleic acids are provided herein.

Preferably the nucleic acids are covalently bound to a surface of the insoluble support through at least one sulfur atom, the nucleic acids are covalently bound to the surface through a linker moiety which includes at least one sulfur atom. Such covalently bound nucleic acids are readily produced by the methods described herein. The insoluble supports can be used in a variety of applications including those that involve hybridization and sequencing. Exemplary applications are illustrated in the Examples.

In preferred embodiments, the covalently bound nucleic acids are a present on the surface of the insoluble support at a density of at least 10 about 20 fmol/mm 2 more preferably at least about 75 fmol/mm 2 still S- more preferably at least about fmol/mm 2 yet more preferably at least about 100 fmol/mm 2 and most preferably at least about 150 fmol/mm 2 In another aspect, combinatorial libraries of immobilized nucleic acids, covalently bound to a solid support as described above are provided.

In still another aspect, a kit for immobilized nucleic acids on a solid "support is provided. In one embodiment, the kit comprises an appropriate amount of: i) a thiol-reactive cross-linking reagent; and ii) a surface-modifying reagent for modifying a surface with a functionality 20 (preferably other than a thiol) which can react with the thiol-reactive cross-linking reagent. The kit can optionally include an insoluble support, a solid surface, magnetic microbeads, for use in immobilized nucleic acids. The kit can also include a reagent for modifying a nucleic acid with a thiol functionality.

In another embodiment, the kit comprises a reagent for modifying the surface of a support with a thiol moiety, and a thiol-reactive crosslinking reagent which can react with a thiol moiety of a support. In certain embodiments, the kit also includes an insoluble support, a -67solid surface, magnetic microbeads, for use in immobilizing nucleic acids.

The kits described herein can also optionally include appropriate buffers; containers for holding the reagents; and/or instructions for use.

In yet another embodiment, the insoluble supports covalently bound with nucleic acids, the entire surface or spatially addressable or pre-addressable array formats, can be used in a variety of solid phase nucleic acid chemistry applications, including but not limited to nucleic acid synthesis (chemically and enzymatically), hybridization and/or 10 extension, and in diagnostic methods based in nucleic acid detection and polymorphism analyses (see, U.S. Patent No. 5,605,798).

Accordingly, further provided herein are methods of reacting nucleic acid molecules in which the nucleic acid molecules are immobilized on.a surface either by reacting a thiol-containing derivative of the nucleic acid molecule with an insoluble support containing a thiol-reactive group or by reacting a thiol-containing insoluble support with a thiol-reactive groupcontaining derivative of the nucleic acid molecule and thereafter further reacting the immobilized nucleic acid molecules.

In a particular embodiment, the immobilized nucleic acid is further reacted by hybridizing with a nucleic acid that is complementary to the immobilized nucleic acid or a portion thereof. In another embodiment, the immobilized nucleic acid is further reacted by extension of a nucleic acid that is hybridized to the immobilized nucleic acid or a portion thereof. Extension reactions such as these can be used, for example, in methods of sequencing DNA molecules that are immobilized to an insoluble support using the processes described herein. Thus, also provided herein are methods of determining the sequence of a DNA molecule on a substrate in which a thiol-containing derivative of the DNA molecule is immobilized on the surface of an insoluble support containing -68thiol-reactive groups and hybridized with a single-stranded nucleic acid complementary to a portion of the immobilized DNA prior to carrying out DNA synthesis in the presence of one or more dideoxynucleotides.

The present invention is further illustrated by the following Examples, which area intended merely to further illustrate and should not be construed as limiting. The entire contents of all the of the references (including literature references, issued patents, published patent applications, and co-pending patent applications) cited throughout this application are hereby expressly incorporated by reference.

10 EXAMPLE 1 High Density Attachment of DNA to Silicon Wafers Materials and Methods All reagents, unless otherwise noted, were obtained from Aldrich Chemical, Milwaukee, WI.

Silicon Surface Preparation Silicon wafers were washed with ethanol, flamed over bunsen burner, and immersed in an anhydrous solution of 25% (by volume) 3aminopropyltriethoxysilane in toluene for 3 hours. The silane solution was then removed, and the wafers were washed three times with 20 toluene and three times with dimethyl sulfoxide (DMSO). The wafers were then incubated in a 10mM anhydrous solution of N-succinimidyl (4iodoacetyl) aminobenzoate (SIAB) (Pierce Chemical, Rockford, IL) in anhydrous DMSO. Following the reaction, the SIAB solution was removed, and the wafers were washed three times with DMSO.

Since it was impossible to monitor the condensation of SIAB and the amino group while on the solid support of the wafer, the reaction was performed in solution to determine the optimal reaction time. Thin layer chromatography (TLC) (glass backed silica plates with a 254 nm fluorescent indicator) (Baker, Phillipsburg, NF) was employed using 95:5 -69chloroform:methanol (Baker, Phillipsburg, NJ) which enabled separation of the two starting materials. It was possible to visualize the SIAB starting material under long wave ultraviolet light (302 nm); 3aminopropyltriethoxysilane was not active under ultraviolet light, therefore, the plate was sprayed with a solution of ninhydrin which reacts with primary amines to reveal a purple spot upon heating. A microscale reaction was run in chloroform/DMSO using a slight molar excess of SIAB in comparison to 3-aminopropyltriethoxysilane and monitored with the above mentioned TLC conditions.

10 Oligonucleotide Modifications Reduction of the disulfide from or oligodeoxynucleotides (Operon Technologies, Alameda, CA or Oligo Etc., Wilsonville, OR) was monitored using reverse-phase FPLC (Pharmacia, Piscataway, NJ); a shift can be seen in the retention time of the oligodeoxynucleotide upon cleavage of the disulfide. Various reduction methods were investigated to determine the optimal conditions. In one case, the disulfide-containing oligodeoxynucleotide (31.5nmol, was incubated with dithiothreitol (DTT) (Pierce Chemical, Rockford, IL) (6.2mmol, 100 mM) as pH 8.0 and 37 0 C. With the cleavage reaction 20 essentially complete, the free thiol-containing oligodeoxynucleotide was isolated using a Chromaspin-10 column (Clontech, Palo Alto, CA) since DTT may compete in the subsequent reaction. Alternatively, tris-(2carboxyethyl) phosphine (TCEP) (Pierce Chemical, Rockford, IL) has been used to cleave the disulfide. The disulfide-containing oligodeoxynucleotide (7.2nmol, 0.36mM) was incubated with TCEP in pH buffer at 370C. It is not necessary to isolate the product following the reaction since TCEP does not competitively react with the iodoacetamido functionality. Varying concentrations of TCEP were used for the cleavage reaction to determine the optimal conditions for the conjugation reaction.

Probe Coupling To each wafer which had been derivatized to contain the iodoacetamido functionality as described above was added a aqueous solution of the free-thiol containing oligodeoxynucleotide in 100mM phosphate buffer, pH 8; the reaction was allowed to proceed for a minimum of five hours at room temperature in 100% relative humidity.

Following the reaction, the oligodeoxynucleotide solution was removed, 10 and the wafers were washed two times in 5 X SSC buffer sodium citrate, 750mM sodium chloride, pH 7) with 50% formamide (USB, Cleveland, OH) at 65 0 C for 1 hour each.

Radiochemical Determination of Probe Density In order to determine the amount of DNA covalently attached to a surface or the amount of a complementary sequence hybridized, radiolabeled probes were employed. In cases where a *i containing oligodeoxynucleotide was to be immobilized, the 3'-terminus was radiolabeled using terminal transferase enzyme and a radiolabeled dideoxynucleoside triphosphate; in a standard reaction, 15pmol (0.6pM) 20 of the 5'-disulfide-containing oligodeoxynucleotide was incubated with (16.5pmol, 0.66pM) of [a- 32 P] (ddATP) (Amersham, Arlington Height, IL) in the presence of 0.2mM 2mercaptoethanol. Upon the addition of 40 units of the terminal deoxynucleotidyl transferase enzyme (USB, Cleveland, OH), the reaction was allowed to proceed for one hour at 37°C. After this time, the reaction was stopped by immersion of the vial in 75°C water bath for ten minutes, and the product was isolated using a Chromaspin-10 column (Clontech, Palo Alto, CA). Similarly, a oligodeoxynucleotide was radiolabeled with 35

S.

-71- In cases where a 3'-disulfide-containing oligodeoxynucleotide was to be immobilized, the 5'-terminus was radiolabeled using T4 polynucleotide kinase and a radiolabeled nucleoside triphosphate. For example, 1 5pmol (0.6pM) of the 3'-disulfide-containing oligodeoxynucleotide was incubated with 50pCi (16.5pmol, 0.66pM) of

[A

32 p adenosine-5'triphosphate (ATP) (Amersham, Arlington Height, IL) in the presence of 50mM Tris-HCI, pH 7.6, 10mM MgCI,, 10mM 2mercaptoethanol. Following the addition of 40 units of T4 polynucleotide kinase, the reaction was allowed to proceed for 1 hour at 37 0 C. The 10 reaction was stopped by immersion of the vial in a 75 0 C water bath for ten minutes; the product was then isolated using a column (Clontech, Palo Alto, CA).

To determine the density of covalently immobilized probe, the disulfide-containing oligodeoxynucleotide of choice was added to a trace amount of the same species than had been radiolabeled as described above. The disulfide was cleaved, the probe was immobilized on iodoacetamido-functionalized wafers, the wafers were washed, and then exposed to a phosphorimager screen (Molecular Dynamics, Sunnyvale, CA). For each different oligodeoxynucleotide utilized, reference spots 20 were made on polystyrene in which the molar amount of oligodeoxynucleotide was known; these reference spots were exposed to the phosphorimager screen as well. Upon scanning the screen, the quantity (in moles) of oligodeoxynucleotide bound to each chip was determined by comparing the counts to the specific activities of the references.

Hybridization and Efficiency To a wafer that had been functionalized with an immobilized probe was added a solution of a complementary sequence (10pM) in 1M NaCI and TE buffer. The wafer and solution were heated to 75°C and allowed to cool to room temperature over 3 hours. After this time, the solution was removed, and the wafer was washed two times with TE buffer To determine the amount of oligonucleotide hybridized, immobilization of the probe was first carried out as described above except that the probe was labeled with 35 S rather than 3 2 P. The density of immobilized probe was determined with the phosphorimager. Next, the same wafer was incubated in TE buffer, 1 M NaCI, and its complementary strand (10pM) which had been radiolabeled with 3 2

P.

Hybridization was carried out as previously described. Following a wash to remove non-specific binding, the wafer and reference were exposed to a phosphorimager screen with a piece of copper foil between the screen and the wafer. The copper foil serves to block the signal from 35 S, while allowing the 32 P signal to pass freely. The molar amount of hybridized oligonucleotide is then determined, thus revealing the percent of covalently immobilized probe that is available for hybridization.

20 MALDI-TOF Mass Spectrometric Analysis As described above, wafers containing non-radiolabeled immobilized oligodeoxynucleotide (name: TCUC; sequence: GAATTCGAGCTCGGTACCCGG; molecular weight; 6455Da; SEQ ID NO.

1) were synthesized, and a complementary sequence (name: MJM6; sequence: CCGGGTACCGAGCTCGAATTC; molecular weight: 6415Da; SEQ ID NO. 2) was hybridized. The wafers were washed in ammonium citrate buffer for cation exchange to remove sodium and potassium ions on the DNA backbone (Pieles, U. et al., (1993) Nucl.

Acids Res., 21:3191-3196). A matrix solution of 3-hydroxypicolinic acid (3-HPA, 0.7 M in 50% acetonitrile, 10% ammonium citrate; Wu, et al. (1993) Rapid Commun. Mass Spectrom., 7:142-146) was spotted onto the wafer and allowed to dry at ambient temperature. The wafers were attached directly to the sample probe of a Finnigan MAT (Bremen, Germany) Vision 2000 reflectron TOF mass spectrometer using a conducting tape. The reflectron possesses a 5 keV ion source and keV post-acceleration; a nitrogen laser was employed; and all spectra were taken in the positive ion mode.

Results 10 Surface Chemistry Employing standard silicon dioxide modification chemistry, a silicon wafer was reacted with 3-aminopropyltriethoxysilane to produce a uniform layer of primary amino groups on the surface. As shown in Figure 7, the surface was then exposed to a heterobifunctional crosslinker resulting in iodoacetamido groups on the surface. It was possible to determine the optimal reaction time of this reaction in solution using TLC. The SIAB crosslinker was visualized under long wave ultraviolet light (302nm) to reveal a spot with an Rf value of 0.58. 3aminopropyltriethoxysilane was not active under ultraviolet light, 20 therefore, ninhydrin was used to reveal a purple spot indicating the presence of a primary amine at the baseline. A microscale reaction was run using a slight molar excess of SIAB in comparison to 3aminopropyltriethoxysilane; TLC analysis after approximately one minute revealed a new spot visible under long wave ultraviolet light with an R, value of 0.28. There was no evidence of a purple spot upon spraying with ninhydrin, thus all the 3-aminopropyltriethoxysilane starting material had been consumed in the reaction. UV light also revealed the excess SIAB which remained following the reaction. From these results, it was determined the reaction is complete after approximately one minute. In -74all cases, the iodoacetamido-functionalized wafers were used immediately to minimize hydrolysis of the labile iodoacetamidofunctionality. Additionally, all further wafer manipulations were performed in the dark since the iodoacetamido-functionality is light sensitive.

Disulfide reduction of the modified oligonucleotide was monitored by observing a shift in retention time on reverse-phase FPLC. It was *determined that after five hours in the presence of DTT (100mM) or TCEP (10mM), the disulfide was fully reduced to a free thiol. If the DTT 10 reaction was allowed to proceed for a longer time, an oligonucleotide dimer formed in which pairs of free thiols had reacted. Such dimerization was also observed when the DTT was removed following the completion of the cleavage reaction. This dimerization was not observed when TCEP was employed as the cleavage reagent since this reaction is performed at pH 4.5, thus the free thiols were fully protonated inhibiting dimerization.

Immediately following disulfide cleavage, the modified oligonucleotide was incubated with the iodacetamido-functionalized 'wafers. To ensure complete thiol deprotonation, the coupling reaction 20 was performed at pH 8.0. The probe surface density achieved by this chemistry of silicon wafers was analyzed using radiolabeled probes and a phosphorimager. The probe surface density was also monitored as a function of the TCEP concentration used in the disulfide cleavage reaction (Figure Using 10mM TCEP to cleave the disulfide and the other reaction conditions described above, it was possible to reproducibly yield a surface density of 250 fmol per square mm of surface. Identical experiments as described above were performed except that the oligonucleotide probe lacked a thiol modification; surface densities of less than 5 fmol per square mm of surface proved that non-specific binding is minimal and that probe coupling most likely occurred as proposed in Figure 7.

Hybridization After attaching 35 S-labeled probes to the surface of wafers and determining conjugation density as described above, hybridization of 32

P-

labeled oligonucleotides was carried out; hybridization efficiency and density were determined using the phosphorimager and copper foil. It SI" was determined experimentally that copper foil blocks 98.4% of an 3S signal, while fully allowing a 32P signal to be detected. The 10 complementary sequence reproducibly hybridized to yield 105 fmol per square mm of surface; this corresponds to approximately 40% of the Sconjugated probes available for hybridization. Similarly, a noncomplementary sequence was employed in this scheme yielding less than fmol per square mm of surface in non-specific binding.

It is hypothesized that stearic interference between the tightly packed oligonucleotide on the flat surface inhibits hybridization efficiencies higher that 40%. With this in mind, a spacer molecule was

I

incorporated between the terminus of the hybridizing region of the oligonucleotide and the support. The chosen spacers were a series of 20 poly dT sequences ranging in length from 3 to 25. Upon examination of these samples with radiolabels and the phosphorimager, it was determined that 40% was still the maximum hybridization that could be achieved.

MALDI-TOF MS Analysis Wafers were functionalized with probes, complementary sequences were hybridized, and the samples were analyzed under standard MALDI conditions as described above. Analysis revealed that only the annealed strand (MJM6) was observed in the mass spectrum with an experimental mass-to-charge ratio of 6415.4; the theoretical mass-to-charge ratio is 6415 (Figure Since there was no signal at a mass-to-charge ratio of 6455, it was determined that the waferconjugated strand (TCUC) was not desorbed thus the iodoacetamido linkage was stable enough to withstand the laser and remain intact.

There was an additional signal observed at a mass-to-charge ration of 6262.0. This signal results from a depurination of guanosines since it is known that DNA is susceptible to the loss of purine bases during the MALDI process, (Nordoff, et (1992) Rapid Commun. Mass Spectrom. 6:771-776). The sample crystals on the wafer were not 10 homogeneously distributed, thus it was necessary to hunt for a good spot Because of this non-homogeneity, the mass resolution varied, but it generally ranged from 200-300 for the desorbed oligonucleotide in the mass spectra. In one set of experiments, non-complementary sequences were hybridized to the wafer; following a wash as previously described, analysis by MALDI-TOF MS revealed that minimal non-specific annealing o.o.I* had taken place since no signal was detected.

EXAMPLE 2 Immobilization of amplified DNA targets to silicon wafers The SIAB-conjugated silicon wafers were also used to analyze 20 speciic free thiol-containing DNA fragments of a particular amplified DNA target sequence.

As shown in Figure 10, a 23-mer oligodeoxynucleotide containing a 5'-disulfide linkage (purchased from Operon Technologies; SEQ ID NO: 3] that is complementary to the 3'-region of a 112 bp human genomic DNA template [Genebank Acc. No.: Z52259; SEQ ID NO: 4] was used as a primer in conjunction with a commercially available 49-mer primer, which is complementary to a portion of the 5'-end of the genomic DNA [purchased from Operon Technologies; SEQ ID NO: in PCR reactions -77to amplify a 135 bp DNA product containing a 5'-disulfide linkage attached to only one strand of the DNA duplex [SEQ ID NO: 6].

The PCR amplification reactions were performed using the Amplitaq GoldKit [Perkin Elmer Cataolog No. N808-0249]. Briefly, 200 ng 112 bp human genomic DNA template was incubated with 10 pM of 23-mer primer and 8pM of commercially available 49-mer primer, 10 mM dNTPs, 1 unit of Amplitaq Gold DNA polymerase in the buffer provided by the manufacturer and PCR was performed in a thermocycler.

o. The 5'-disulfide bond of the resulting PCR product was fully 10 reduced using 10 mM TCEP as described in EXAMPLE 1 to generate a free 5'-thiol group. The DNA strand containing free-thiol group was conjugated to the surface of the silicon wafer through the SIAB linker essentially as outlined in Figure 7.

The silicon wafer conjugated with the 135 bp thiol-containing DNA was incubated with a complementary 12-mer oligonucleotide [SEQ ID NO: 7] and specifically hybridized DNA fragments were detected using MALDI-TOF MS analysis. The mass spectrum revealed a signal with an observed experimental mass-to-charge ratio of 3618.33; the theoretical mass-to-charge ratio of the 12-mer oligomer sequence is 3622.4 Da.

20 Thus, a specific DNA target molecule that contain a linkage can be amplified. The molecules are immobilized on a SIABderivatized silicon wafer using the methods described herein and specific complementary oligonucleotides may be hybridized to these target molecules and detected using MALDI-TOF MS analysis.

Example 3 Spectrochip mutant detection in ApoE gene This example describes the hybridization of an immobilized template, primer extension and mass spectrometry for detection of the wildtype and mutant Apolipoprotein E gene for diagnostic purposes. This example demonstrates that immobilized DNA molecules containing a specific sequence can be detected and distinguished using primer extension of unlabeled allele specific primers and analysis of the extension products using mass spectrometry.

A 50 base synthetic DNA template complementary to the coding sequence of allele 3 of the wildtype apolipoprotein E gene: GCCTGGTACACTGCCAGGCGCTTCTGCAGGTCATCGGCATCGCGGAGGAG -3' [SEQ ID NO: 17] or complement to the mutant apolipoprotein E gene carrying a G -*A transition at codon 158: 5'-GCCTGGTACACTGCCAGGCACTTCTGCAGGTCATCGGCATCGCGGAGGAG-3' [SEQ ID NO: 18] containing a 3'-free thiol group was coupled to separate SIAB-derivatized silicon wafers essentially as outlined in Figure 7 and as described in 15 Examples 1 and 2.

A 21-mer oligonucleotide primer: GCC GAT GAC CTG CAG AAG-3' [SEQ ID NO: 19] was hybridized to each of the immobilized templates and the primer was extended using a commercially available kit Sequenase or Thermosequenase, U.S. Biochemical Corp]. The addition of Sequenase DNA polymerase or Thermosequenase DNA polymerase in the presence •of three deoxyribonucleoside triphosphates (dNTPs; dATP, dGTP, dTTP) and dideoxyribonucleoside cytosine triphosphate (ddCTP) in buffer *according to the instructions provided by the manufacturer resulted in a S* 25 single base extension of the 21-mer primer bound to the immobilized template encoding the wildtype apolipoprotein E gene and a three base extension of the 21-mer primer bound to the immobilized template encoding the mutant form of apolipoprotein E gene.

-79- The wafers were analyzed by mass spectrometry as described herein. The wildtype apolipoprotein E sequence results in a mass spectrum that distinguishes the primer with a single base extension (22mer) with a mass-to-charge ratio of 6771.17 Da (thetheoretical mass to charge ratio is 6753.5 Da) from the original 21-mer primer with a massto-charge ratio of 6499.64 Da. The mutant apolipoprotein E sequence results in a mass spectrum that distinguishes the primer with a three base extension (24-mer) with a mass-to-charge ratio of 7386.9 (the theoretical mass charge is 7386.9) from the original 21-mer primer with a mass to charge ration of 6499.64 Da.

EXAMPLE 4 Preparation of DNA arrays using serial and parallel dispensing tools Robot-driven serial and parallel pL-nL dispensing tools were used to generate 10-103 element DNA arrays on square chips with flat or 15 geometrically altered with wells) surfaces for matrix assisted laser desorption ionization mass spectrometry analysis. In the former, a 'piezoelectric pipette' (70 pm id capillary) dispenses single or multiple -0.2 nL droplets of matrix, and then analyte, onto the chip; spectra from as low as 0.2 fmol of a 36-mer DNA have been acquired using this procedure. Despite the fast sec) evaporation, micro-crystals of 3hydroxypicolinic acid matrix containing the analyte are routinely produced resulting in higher reproducibility than routinely obtained with larger volume preparations; all of 100 five fmol spots of a 23-mer in 800 pm wells yielded easily interpreted mass spectra, with 99/100 parent ion signals having signal to noise ratio of In a second approach, probes from 384 well microtiter plate are dispensed 16 at a time into chip wells or onto flat surfaces using an array of spring loaded pins which transfer nL to the chip by surface contact; MS analysis of array elements deposited with the parallel method are comparable in terms of sensitivity and resolution to those made with the serial method.

Description of the piezoelectric serial dispenser The experimental system developed from a system purchased from Microdrop GmbH, Norderstedt Germany and can include a piezoelectric element driver which sends a pulsed signal to a piezoelectric element bonded to and surrounding a glass capillary which holds the solution to be dispensed; a pressure transducer to load (by negative pressure) or empty (by positive pressure) the capillary; a robotic xyz stage and robot driver to maneuver the capillary for loading, unloading, dispensing, and cleaning, a stroboscope and driver pulsed at the frequency of the piezo element to enable viewing of 'suspended' droplet characteristics; separate stages for source and designation plates or sample targets (i.e.

Si chip); a camera mounted to the robotic arm to view loading to :15 designation plate; and a data station which controls the pressure unit, xyz robot, and piezoelectric driver.

Description of the parallel dispenser The robotic pintool consists of 16 probes housed in a probe block and mounted on an X Y, 2 robotic stage. The robotic stage was a gantry system which enables the placement of sample trays below the arms of the robot. The gantry unit itself is composed of X and Y arms which move 250 and 400 mm, respectively, guided by brushless linear servo motors with positional feedback provided by linear optical encoders. A lead screw driven Z axis (50 mm vertical travel) is mounted to the xy axis 25 slide of the gantry unit and is controlled by an in-line rotary servo motor with positional feedback by a motor-mounted rotary optical encoder. The work area of the system is equipped with a slide-out tooling plate that holds five microtiter plates (most often, 2 plates of wash solution and 3 plates of sample for a maximum of 1152 different oligonucleotide -81solutions) and up to ten 20x20 mm wafers. The wafers are placed precisely in the plate against two banking pins and held secure by vacuum. The entire system is enclosed in plexi-glass housing for safety and mounted onto a steel support frame for thermal and vibrational damping. Motion control is accomplished by employing a commercial motion controller which was a 3-axis servo controller and is integrated to a computer; programming code for specific applications is written as needed.

Samples were dispensed with the serial system onto several surfaces which served as targets in the MALDI TOF analysis including [1] A flat stainless steel sample target as supplied for routine use in a Thermo Bioanalysis Vision 2000; the same design stainless steel target with micromachined nanopits; flat silicon (Si) wafers; [4] polished flat Si wafers; Si wafers with rough (3-6 pLm features) pits; 15 12x12 or 18x18) mm Si chips with 10x10 (or 16x16) arrays of chemically etched wells, each 800x80011m on a side with depths ranging from 99-400 (or(b) 120) micrometer, pitch 1.0 (or(b) 1.125) mm; 15x15 mm Si chips with 28x28 arrays of chemically etched wells, each 450x450 micrometer on a side with depths ranging from 48-300 micrometer, pitch 0.5 mm; [8]flat polycarbonate or other plastics; gold and other metals; [10] membranes; [11] plastic surfaces sputtered with gold or other conducting materials. The dispensed volume is controlled from 10 '0 to 10 6 L by adjusting the number of droplets dispensed.

Sample Preparation and Dispensing 1. Serial Oligonucleotides (0.1-50 ng/microliter of different sequence or concentrations were loaded into wells of a 96 well microtiter plate; the first well was reserved for matrix solution. A pitted chip (target 6a in -82- MALDI targets' section) was placed on the stage and aligned manually.

Into the (Windows-based) robot control software were entered the coordinates of the first well, the array size (ie number of spots in x and y) and spacing between elements, and the number of 0.2 nL drops per array element. The capillary was filled with 10 microL rinse H 2 0, automatically moved in view of a strobe light-illuminated camera for checking tip integrity and cleanliness while in continuous pulse mode, and emptied. The capillary was then filled with matrix solution, again checked at the stroboscope, and then used to spot an array onto flat or pitted surfaces. For reproducibilty studies in different MS modes, typically a 10x10 array of 0.2-20 nL droplets were dispensed. The capillary was emptied by application of positive pressure, optionally rinsed with H 2 0, and led to the source oligo plate where 5pL of 0.05- 2.0/M synthetic oligo were drawn. The capillary was then rastered in 15 series over each of the matrix spots with 0.2-20 nL aqueous solution added to each.

2. Parallel Parallel Programs were written to control array making by offset printing; to make an array of 64 elements on 10 wafers, for example, the tool was dipped into 16 wells of a 3 84 well DNA source plate, moved to the target Si, plastic, metal), and the sample spotted by surface contact. The tool was then dipped into the same 16 wells and spotted on the second target; this cycle was repeated on all ten wafers. Next the tool was dipped in washing solution, then dipped into 16 different wells of the source plate, and spotted onto the target 2.25mm offset from the initial set of 16 spots; again this was repeated on all 10 wafers; the entire cycle was repeated to make a 2x2 array from each pin to produce an 8x8 array of spots (2x2 elements/pin X 16 pins 64 total elements spotted).

-83- To make arrays for MS analysis, olegonucleotides of different sequences or concentrations were loaded into the wells of up to three different 384-well microtiter plates, one set of 16 wells was reserved for matrix solution. The wells of two plates were filled with washing solution. The five microtiter plates were loaded onto the slide-out tooling plate. Ten wafers were placed abutting the banking pins on the tooling plate, and the vacuum turned on. In cases where matrix and oligonucleotide were hot pre-mixed, the pintool was used to spot matrix solution first on all desired array elements of the ten wafers. For this example, a 16 x 16 array was created, thus the tool must spot each of the ten wafers 16 times, with an offset of 1.125mm. Next, the oligonucleotide solution was spotted in the same pattern to re-dissolve the matrix. Similarly, an array could be made by placing the oligonucleotide solution on the wafer first, followed by the matrix 15 solution, or by pre-mixing the matrix and oligonucleotide solutions.

Mass spectrometry Subsequent to either dispensing scheme, loaded chips were held onto a MALDI-TOF source plate with a set of beveled screw mounted polycarbonated supports. The plate was transferred on the end of a probe to be held onto a 1 pm resolution, 1" travel xy stage (Newport) in the source region of a time-of-flight mass spectrometer. The instrument, normally operated with 18-26 kV extraction, could be operated in linear or curved field reflectron mode, and in continuous or delayed extraction mode.

-84-

RESULTS

Serial dispensing with the piezoelectric pipette While delivery of a saturated 3HPA solution can result in tip clogging as the solvent at the capillary-air interface evaporates, premixing DNA and matrix sufficiently dilutes the matrix such that it remains in solution while stable sprays which could be maintained until the capillary was emptied were obtained; with 1:1 diluted (in H 2 0) matrix solution, continuous spraying for 10 minutes was possible. Turning off the piezo element so that the capillary sat inactive for 5 minutes, and reactivating the piezo element also did not result in a clogged capillary.

Initial experiments using stainless steel sample targets as provided by Finnigan Vision 2000 MALDI-TOF system run in reflectron mode utilized a pre-mixed solution of the matrix and DNA prior to dispensing 15 onto the sample target. In a single microtiter well, 50pL saturated matrix solution, 25/JL of a 51pL solution of the 12-mer (ATCG)3, and 25pL of a 51pL solution of the 28-mer (ATCG)7 were mixed. A set of 10x10 "o arrays of 0.6pL drops was dispensed directly onto a Finnigan Vision 2000 sample target disk; MALDI-TOF mass spectrum was obtained from a single array element which contained 750 attomoles of each of the two oligonucleotides. Interpretable mass spectra has been obtained for DNAs as large as a 53-mer (350 amol loaded, not shown) using this method.

Mass spectra were also obtained from DNAs microdispensed into the wells of a silicon chip. Figure 11 shows a 12x12mm silicon chip with 100 chemically etched wells; mask dimensions and etch time were set such that fustum inverted flat top pyramidal) geometry wells with 8 0 0x800pm (top surface) and 100pm depth were obtained.

Optionally, the wells can be roughed or pitted. As described above, the chip edge was aligned against a raised surface on the stage to define the x and y coordinate systems with respect to the capillary. (Alternatives include optical alignment, artificial intelligence pattern recognition routines, and dowel-pin based manual alignment). Into each well was dispensed 20 droplets 5 nL) of 3-HPA matrix solution without analyte; for the 50% CH 3 CN solution employed, evaporation times for each droplet were on the order of 5-10 seconds. Upon solvent evaporation, each microdispensed matrix droplet as viewed under a 120X stereomicroscope generally appeared as an amorphous and 'milky' flat disk; such appearances are consistent with those of droplets from which the Figure 3b spectrum was obtained. Upon tip emptying, rinsing, and refilling with a 1.4pm aqueous solution of a 23-mer DNA (Mr(calc) 6967 Da), the capillary was directed above each of the 100 spots of matrix where 5nL of the aqueous DNA solution was dispensed directly on S: top of the matrix droplets. Employing visualization via a CCD camera, it appeared that the aqueous analyte solution mixed with and re-dissolved the matrix (complete evaporation took 10 sec at ambient temperature and humidity). The amorphous matrix surfaces were converted to true micro-crystalline surfaces, with crystalline features on the order of 1pom.

Consistent with the improved crystallization afforded by the matrix •re-dissolving method, mass spectrum acquisition appeared more reproducible than with pre-mixed matrix plus analyte solutions; each of the 100 five fmol spots of the 23-mer yielded interpreted mass spectra (Figure 12), with 99/100 parent ion signals having signal to noise ratios of such reproducibility was also obtained with the flat silicon and metallic surfaces tried (not shown). The Figure 12 spectra were obtained on a linear TOF instrument operated at 26 kV. Upon internal calibration of the top left spectrum (well using the singly and doubly charged molecular ions, and application of this calibration file to all other 99 spectra as an external calibration (Figure 13), a standard deviation of <9 Da from the average molecular weight was obtained, corresponding to a relative standard deviation of Parallel dispensing with the robotic pintool Arrays were made with offset printing as described above. The velocity of the X and Y stages are 35 inches/sec, and the velocity of the Z stage is 5.5 inches/sec. It is possible to move the X and Y stages at maximum velocity to decrease the cycle times, however the speed of the Z stage is to be decreased prior to surface contact with the wafer to avoid damaging it. At such axes speeds, the approximate cycle time to spot 16 elements (one tool impression of the same solutions) on all ten wafers is 20 seconds, so to make an array of 256 elements would take -5.3 minutes. When placing different oligonucleotide solutions on the array, an additional washing step much be incorporated to clean the pin 15 tip prior to dipping in another solution, thus the cycle time would increase to 25 seconds or 6.7 minutes to make 10 wafers.

Sample delivery by the tool was examined using radio-labeled solutions and the phosphorimager as described previously; it was determined that each pin delivers approximately 1nL of liquid. The spotto-spot reproducibility is high. An array of 256 oligonucleotide elements of varying sequence and concentration was made on flat silicon wafers using the pintool, and the wafer was analyzed by MALDI-TOF MS.

EXAMPLE Use of High Density Nucleic Acid Immobilization to Generate Nucleic Acid 25 Arrays Employing the high density attachment procedure described in EXAMPLE 1, an array of DNA oligomers amenable to MALDI-TOF mass spectrometry analysis was created on a silicon wafer having a plurality of locations, depressions or patches, on its surface. To generate the -87array, a free thiol-containing oligonucleotide primer was immobilized only at the selected locations of the wafer see Figure 14]. Each location of the array contained one of three different oligomers. To demonstrate that the different immobilized oligomers could be separately detected and distinguished, three distinct oligonucleotides of differing lengths that are complementary to one of the three oligomers were hybridized to the array on the wafer and analyzed by MALDI-TOF mass spectrometry.

Oligodeoxynucleotides Three sets of complementary oligodeoxynucleotide pairs were synthesized in which one member of the complementary oligonucleotide pair contains a or 5'-disulfide linkage [purchased from Operon Technologies or Oligos, Etc.]. For example, Oligomer 1 (:[d(CTGATGCGTCGGATCATCTTTTTT-SS); SEQ ID NO: 8] contains a 3'- 15 disulfide linkage whereas Oligomer 2 [d(SS- CCTCTTGGGAACTGTGTAGTATT); a 5'-disulfide derivative of SEQ ID NO: 3] and Oligomer 3 [d(SS-GAATTCGAGCTCGGTACCCGG); a disulfide derivative of SEQ ID NO: 1] each contain a 5'-disulfide linkage.

The oligonucleotides complementary to Oligomers 1-3 were designed to be of different lengths that are easily resolvable from one S* another during MALDI-TOF MS analysis. For example, a 23-mer S• oligonucleotide [SEQ ID NO: 9] was synthesized complementary to a portion of Oligomer 1, a 12-mer oligonucleotide [SEQ ID NO: 7] was synthesized complementary to a portion of Oligomer 2 and a 21-mer [SEQ ID NO: 2; sequence denoted "MJM6" in EXAMPLE 1] was synthesized complementary to a portion of Oligomer 3. In addition, a fourth 29-mer oligonucleotide [SEQ ID NO: 10] was synthesized that lacks complementarity to any of the three oligomers. This fourth oligonucleotide was used as a negative control.

-88- Silicon surface chemistry and DNA immobilization 4 x 4 (16-location) array A 2 X 2 cm 2 silicon wafer having 256 individual depressions or wells in the form of a 16 X 16 well array was purchased from a commercial supplier [Accelerator Technology Corp., College Station, Texas i. The wells were 800 X 800 /m 2 120 pm deep, on a 1.125 pitch. The silicon wafer was reacted with 3 -aminopropyltriethoxysilane to produce a uniform layer of primary amines on the surface and then exposed to the heterobifunctional crosslinker SIAB resulting in iodoacetamido functionalities on the surface see Figure 7].

To prepare the oligomers for coupling to the various locations of the silicon array, the disulfide bond of each oligomer was fully reduced using 10 mM TCEP as depicted in EXAMPLE 1, and the DNA resuspended at a final concentration of 10 M in a solution of 100 mM 15 phosphate buffer, pH 8.0. Immediately following disulfide bond reduction, the free-thiol group of the oligomer was coupled to the iodoacetamido functionality at 16 locations on the wafer using the probe coupling conditions essentially as described in Figure 7. To accomplish the separate coupling at 16 distinct locations of the wafer, the entire surface of the wafer was not flushed with an oligonucleotide solution but, instead, an -30-nl aliquot of a predetermined modified oligomer was added in parallel to each of 16 locations depressions) of the 256 wells on the wafer to create a 4 x 4 array of immobilied DNA using a pin tool as described herein (see the Detailed Description and 25 Example 4 provided herein).

Thus, as shown in Figure 14, one of modified Oligomers 1-3 was covalently immobilized to each of 16 separate wells of the 256 wells on the silicon wafer thereby creating a 4 x 4 array of immobilized DNA. For example, Oligomer 1 was conjugated at a well position in the upper left -89hand corner of the 4 x 4 array and Oligomer 2 was conjugated to the adjacent location, and so forth. An illustration of the completed array is shown in Figure 14.

In carrying out the hybridization reaction, the three complementary oligonucleotides and the negative control oligonucleotide were mixed at a final concentration of 10 pM for each oligonucleotide in 1 ml of TE buffer mM Tris-HCI, pH 8.0, 1 mM EDTA] supplemented with 1 M NaCI, and the solution was heated at 65°C for 10 min. Immediately thereafter, the entire surface of the silicon wafer was flushed with 800 pl of the heated oligonucleotide solution. The complementary oligonucleotides were annealed to the immobilized oligomers by incubating the silicon array at ambient temperature for 1 hr, followed by incubation at 4°C for at least 10 min. Alternatively, the oligonucleotide solution can be added to the wafer which is then heated and allowed to cool for hybridization.

15 An illustration of the complementary oligonucleotides annealed to the specific oligomers covalently immobilized at each location is shown in Figure The hybridized array was then washed with a solution of 50 mM ammonium citrate buffer for cation exchange to remove sodium and potassium ions on the DNA backbone (Pieles, U. et al., (1993) NucL.

SAcids Res., 21:3191-3196). A 6-ni aliquot of a matrix solution of 3- Shydroxypicolinic acid [0.7 M 3-hydroxypicolinic acid-10 ammonium citrate in 50 acetonitrile; see Wu et Rapid Commun. Mass Spectrom. 7:142-146 (1993)] was added to each location of the array using a piezoelectric pipette as described herein.

The solution was allowed to dry at ambient temperature and thereafter a 6-nl aliquot of water was added to each location using a piezoelectric pipette to resuspend the dried matrix-DNA complex, such that upon drying at ambient temperature the matrix-DNA complex forms a uniform crystalline surface on the bottom surface of each location.

MALDI-TOF MS analysis The MALDI-TOF MS analysis was performed in series on each of the 16 locations of the hybridization array illustrated in Figure essentially as described in EXAMPLE 1. The resulting mass spectrum of oligonucleotides that specifically hybridized to each of the 16 locations of the DNA hybridization array is shown in Figure 16. The mass spectrum revealed a specific signal at each location representative of observed experimental mass-to-charge ratio corresponding to the specific complementary nucleotide sequence.

For example, in the locations that have only Oligomer 1 conjugated thereto, the mass spectrum revealed a predominate signal with an observed experimental mass-to-charge ratio of 7072.4 approximately 15 equal to that of the 23-mer; the theoretical mass-to-charge ratio of the 23-mer is 7072.6 Da. Similarly, specific hybridization of the 12-mer oligonucleotide to the array, observed experimental mass-to-charge ratio .e of 3618.33 Da (theoretical 3622.4 Da), was detected only at those locations conjugated with Oligomer 2 whereas specific hybridization of MJM6 (observed experimental mass-to-charge ratio of 6415.4) was detected only at those locations of the array conjugated with Oligomer 3 f [theoretical 6407.2 Da].

None of the locations of the array revealed a signal that corresponds to the negative control 2 9-mer oligonucleotide (theoretical mass-to-charge ratio of 8974.8) indicating that specific target DNA molecules can be hybridized to oligomers covalently immobilized to specific locations on the surface of the silicon array and a plurality of hybridization assays may be individually monitored using MALDI-TOF MS analysis.

8 x 8 (64-location) array A 2 X 2 cm 2 silicon wafer having 256 individual depressions or wells that form a 16 X 16 array of wells was purchased from a commercial supplier [Accelerator Technology Corp., College Station, Texas The wells were 800 X 800 pm 2 120 pm deep, on a 1.125 pitch. The silicon wafer was reacted with 3-aminopropyltriethoxysilane to produce a uniform layer of primary amines on the surface and then exposed to the heterobifunctional crosslinker SIAB resulting in iodoacetamido functionalities on the surface see Figure 7].

Following the procedures described above for the preparation of the 16-location DNA array, Oligomers 1-3 were immobilized to 64 locations forming an 8 X 8 array on the 256 well silicon wafer, hybridized to complementary oligonucleotides and analyzed by MALDI- TOF MS analysis. Figure 17 shows the mass spectrum of the 64- 15 location DNA array analyzed in series by MALDI-TOF analysis. As shown for the 16-location array, specific hybridization of the complementary oligonucleotide to each of the immobilized thiol-containing oligomers was observed in each of the locations of the DNA array.

EXAMPLE 6 Extension of hybridized DNA primers bound to DNA templates immobilized on a silicon wafer The SIAB-derivatized silicon wafers can also be employed for primer extension reactions of the immobilized DNA template using the procedures essentially described in U.S. Patent NO. 5,605,798.

25 As shown in Figure 18, a 27-mer oligonucleotide [SEQ ID NO: 111 containing a 3'-free thiol group was coupled to a SIAB-derivatized silicon wafer as described above, for example, in Example 1. A 12-mer oligonucleotide primer [SEQ ID NO: 12] was hybridized to the immobilized oligonucleotide and the primer was extended using a -92commercially available kit Sequenase or ThermoSequenase,

U.S.

Biochemical Corp]. The addition of Sequenase DNA polymerase or ThermoSequenase DNA polymerase in the presence of three deoxyribonucleoside triphosphates (dNTPs; dATP, dGTP, dCTP) and dideoxyribonucleoside thymidine triphosphate (ddTTP) in buffer according to the instructions provided by the manufacturer resulted in a 3-base extension of the 12-mer primer while still bound to the silicon wafer.

The wafer was then analyzed by MALDI-TOF mass spectrometry as described above. As shown in Figure 18, the mass spectrum results clearly distinguish the 15-mer [SEQ ID NO: 13] from the original unextended 12-mer thus indicating that specific extension can be performed on the surface of a silicon wafer and detected using MALDI- TOF MS analysis.

*EXAMPLE 7 15 Effect of linker length on polymerase extension of hybridized DNA primers bound to DNA templates immobilized on a silicon wafer S* The effect of the distance between the SIAB-conjugated silicon surface and the duplex DNA formed by hybridization of the target DNA to the immobilized oligomer template was investigated, as well as choice of enzyme see Figure 19].

Two SIAB-derivatized silicon wafers were conjugated to the 3'-end of two free thiol-containing oligonucleotides of identical DNA sequence except for a 3-base poly dT spacer sequence incorporated at the 3'-end [SEQ ID NOs: 8 11]. These two oligonuclotides were synthesized and 25 each was separately immobilized to the surface of a silicon wafer through the SIAB cross-linker see Figure 71. Each wafer was incubated with a 12-mer oligonucleotide [SEQ ID NOs: 12, 14 and complementary to portions of the nucleotide sequences common to both of the oligonucleotides by denaturing at 75 °C and slow cooling the

I

-93silicon wafer. The wafers were then analyzed by MALDI-TOF mass spectrometry as described above.

As previously shown in Figure 18, a 3-base specific extension of the bound 12-mer oligonucleotide was observed using the oligomer primer where there is a 9-base spacer between the duple-: and the surface [SEQ ID NO: 12]. As shown in Figure 19, similar results were observed when the DNA spacer lengths between the S'AB moiety and the DNA duplex were 0, 3, 6 and 12. The results of MALDI-TOF mass spectrometry analysis of the wafers are shown in Figure 20. In addition, Figure 19 also shows that the extension reaction may be performed using a variety of DNA polymerases. Thus, the SIAB linker may be directly ~coupled to the DNA template or may include a linker sequence without effecting primer extension of the hybridized DNA.

:'EXAMPLE 8 15 Detection of Double-Stranded Nucleic Acid Molecules via Strand Displacement and Hybridization to an Immobilized Complementary Nucleic Acid This example describes immobilization of a 24-mer primer and the specific hybridization of one strand of a duplex DNA molecule, thereby permitting amplification of a selected target molecule in solution phase and permitting detection of the double stranded molecule.

A 24-mer DNA primer CTGATGCGTC GGATCATCTT TTTT [SEQ ID NO: containing a 3'-free thiol group was coupled to a •SIAB-derivatized silicon wafer essentially as outlined in Figure 7 and 25 described in Examples 1 and 2.

An 18-mer synthetic oligonucleotide CTGATGCGTCGGATCATC-3' [SEQ ID NO: 16] was premixed with a 12mer oligonucleotide 5'-GATGATCCGACG-3' [SEQ ID NO: 12] that has a sequence that is complementary to 12 base portion of the 18-mer oligonucleotide. The oligonucleotide mix was heated to 75 0 C and cooled -94slowly to room temperature to faciliate the formation of a duplex molecule: 5'-CTGATGCGTCGGATCATC-3' [SEQ ID NO: 16] GCAGCCTAGTAG-5' ISEQ ID NO: 12].

The specific hybridization of the 12-mer strand of the duplex molecule -o the immobilized 24-mer primer was carried out by mixing 1pM of the duplex molecule using the hybridization conditions described in Example 6.

The wafers were analyzed by mass spectrometry as described above. Specific hybridization was detected in a mass spectrum of the 12-mer with a mass-to-charge ratio of 3682.78 Da.

EXAMPLE 9 1-( 2 -Nitro-5-(3-O-4,4'-dimethoxytritylpropoxy)phenyl)-1-0-((2cyanoethoxy)-diisopropylaminophosphino)ethane 15 A. 2 -Nitro-5-(3-hydroxypropoxy)benzaldehyde 3-Bromo-l-propanol (3.34 g, 24 mmol) was refluxed in 80 ml of anhydrous acetonitrile with 5-hydroxy-2-nitrobenzaldehyde (3.34 g, mmol), K 2

CO

3 (3.5 and KI (100 mg) overnight (15 The reaction mixture was cooled to room temperature and 150 ml of methylene 20 chloride was added. The mixture was filtered and the solid residue was washed with methylene chloride. The combined organic solution was evaporated to dryness and redissolved in 100 ml methylene chloride.

The resulted solution was washed with saturated NaCI solution and dried .over sodium sulfate. 4.31 g of desired product was obtained after removal of the solvent in vacuo.

R, 0.33 (dichloromethane/methanol, 95/5).

UV (methanol) maximum: 313, 240 (shoulder), 215 nm; minimum: 266 nm.

'H NMR (DMSO-d 6 6 10.28 1H), 8.17 1H), 7.35 1H), 7.22 (s, 1H), 4.22(t, 2H), 3.54 2H), 1.90 2H).

3 C NMR (DMSO-d 6 6 189.9, 153.0, 141.6, 134.3, 127.3, 118.4, 114.0, 66.2, 56.9, 31.7.

B. 2 -Nitro-5-( 3 -0-t-butyldimethylsilylpropoxy)benzaldehyde 2 -Nitro-5-(3-hydroxypropoxy)benzaldehyde(1 g, 4.44 mmol) was dissolved in 50 ml anhydrous acetonitrile. To this solution, it was added 1 ml of triethylamine; 200 mg of imidazole, and 0.8 g (5.3 mmol) of tBDMSCI. The mixture was stirred at room temperature for 4 h.

Methanol (1 ml) was added to stop the reaction. The solvent was removed in vacuo and the solid residue was redissolved in 100 ml methylene chloride. The resulted solution was washed with saturated sodium bicarbonate solution and then water. The organic phase was dried over sodium sulfate and the solvent was removed in vacuo. The crude mixture was subjected to a quick silica gel column with methylene chloride to yield 1.44 g of 2-nitro-5-(3-O-t- 15 butyldimethylsilylpropoxy)benzaldehyde.

Rf 0.67 (hexane/ethyl acetate, 5/1).

UV (methanol), maximum: 317, 243, 215 nm; minimum: 235, 267 nm.

'H NMR (DMSO-d 6 6 10.28 1H), 8.14 1H), 7.32 1H), 7.20 (s, 1H), 4.20 2H), 3.75 2H), 1.90 2H), 0.85 9H), 0.02 6H).

13 C NMR (DMSO-d 6 6 189.6, 162.7, 141.5, 134.0, 127.1, 118.2, 113.8, 65.4, 58.5, 31.2, 25.5, -5.7.

C. 1 2 -Nitro-5-(3-0-t-butyldimethylsilylpropoxy)phenyl)ethanol High vacuum dried 2-nitro-5-(3-O-tbutyldimethylsilylpropoxy)benzaldehyde (1.02 g, 3 mmol) was dissolved 50 ml of anhydrous methylene chloride. 2 M Trimethylaluminium in toluene (3 ml) was added dropwise within 10 min and keeped the reaction mixture at room temperature. It was stirred further for 10 min and the mixture was poured into 10 ml ice cooled water. The emulsion was separated from water phase and dried over 100 g of sodium sulfate -96to remove the remaining water. The solvent was removed in vacuo and the mixture was applied to a silica gel column with gradient methanol in methylene chloride. 0.94 g of desired product was isolated.

0.375 (hexane/ethyl acetate, 5/1).

UV (methanol), maximum: 306, 233, 206 nm; minimum: 255, 220 nm.

'H NMR (DMSO-d 6 6 8.00 1H), 7.36 1H), 7.00 1H), 5.49 (b, OH), 5.31 1H), 4.19 2H), 3.77 2H), 1.95 2H), 1.37 (d, 3H), 0.86 9H), 0.04 6H).

3 C NMR (DMSO-d 6 6 162.6, 146.2, 139.6, 126.9, 112.9, 112.5, 64.8, 63.9, 58.7, 31.5, 25.6, 24.9, -5.8.

D. 1 2 -Nitro-5-(3-hydroxypropoxy)phenyl)ethanol S. 1-(2-Nitro-5-(3-0-t-butyldimethylsilylpropoxyphenyl)ethanol (0.89 g, 2.5 mmol) was dissolved in 30 ml of THF and 0.5 mmol of nBu 4

NF

was added under stirring. The mixture was stirred at room temperature 15 for 5 h and the solvent was removed in vacuo. The remaining residue was applied to a silica gel column with gradient methanol in methylene chloride. 1-( 2 -Nitro-5-( 3 -hydroxypropoxy)phenyl)ethanol (0.6 g (99%) was obtained.

Rf 0.17 (dichloromethane/methanol, 95/5).

UV (methanol), maximum: 304, 232, 210 nm; minimum: 255, 219 nm.

1 H NMR (DMSO-d 6 6 8.00 1H), 7.33 1H), 7.00 1H), 5.50 (d, OH), 5.28 OH), 4.59 1H), 4.17 2H), 3.57 2H), 1.89 (m, 2H), 1.36 2H).

1 C NMR (DMOS-d 6 6162.8, 146.3, 139.7, 127.1, 113.1, 112.6, 65.5, 25 64.0, 57.0, 31.8, 25.0.

-97- E. 1-( 2 -Nitro-5-( 3

-O-

4 ,4'-dimethoxytritylpropoxy)phenyl)ethanol 1-(2-Nitro-5-(3-hydroxypropoxy)phenyl)ethanol (0.482 g, 2 mmol) was co-evaporated with anhydrous pyridine twice and dissolved in 20 ml anhydrous pyridine. The solution was cooled in ice-water bath and 750 mg (2.2 mmol) of DMTCI was added. The reaction mixture was stirred at room temperature overnight and 0.5 ml methanol was added to stop the reaction. The solvent was removed in vacuo and the residue was coevaporated with toluene twice to remove trace of pyridine. The final residue was applied to a silica gel column with gradient methanol in methylene chloride containing drops of triethylamine to yield 0.96 g of the desired product 1-( 2 -nitro-5-(3-O-4,4'-dimethoxytritylpropoxy)phenyl)ethanol.

Rf= 0.50 (dichloromethane/methanol, 99/1).

SUV (methanol), maximum: 350 (shoulder), 305, 283, 276 (shoulder), 233, 208 nm; minimum: 290, 258, 220 nm.

'H NMR (DMSO-d 6 6 8.00 1H), 6.82-7.42 (ArH), 5.52 OH), 5.32 1H), 4.23 2H), 3.71 6H), 3.17 2H), 2.00 2H), 1.37 3H).

3 "C NMR (DMOS-d) 6 162.5, 157.9, 157.7, 146.1, 144.9, 140.1, 20 139.7, 135.7, 129.5, 128.8, 127.6, 127.5, 127.3, 126.9, 126.4, 113.0, 112.8, 112.6, 85.2, 65.3, 63.9, 59.0, 54.8, 28.9, 24.9.

F. 1-( 2 -Nitro-5-(3-O-4,4'-dimethoxytritylpropoxy)phenyl)-1-O- 2 -cyanoethoxy)-diisopropylaminophosphino)ethane 1-( 2 -Nitro-5-( 3 -O-4,4'-dimethoxytritylpropoxy)phenyl)ethanol (400 mg, 0.74 mmol) was dried under high vacuum and was dissolved in :ml of anhydrous methylene chloride. To this solution, it was added ml N,N-diisopropylethylamine and 0.3 ml (1.34 mmol) of 2-cyanoethyl- N,N-diisopropylchlorophosphoramidite. The reaction mixture was stirred at room temperature for 30 min and 0.5 ml of methanol was added to -98stop the reaction. The mixture was washed with saturated sodium bicarbonate solution and was dried over sodium sulfate. The solvent was removed in vacuo and a quick silica gel column with 1% methanol in methylene chloride containing drops of triethylamine yield 510 mg (93%) the desired phosphoramidite.

0.87 (dichloromethane/methanol, 99/1).

EXAMPLE 1 -(4-(3-0-4,4'-Dimethoxytritylpropoxy)-3-methoxy-6-nitrophenyl) cyanoethoxy)-diisopropylaminophosphino)ethane A. 4 3 -Hydroxypropoxy)-3-methoxyacetophenone 3-Bromo-l-propanol (53 ml, 33 mmol) was refluxed in 100 ml of anhydrous acetonitrile with 4 -hydroxy-3-methoxyacetophenone (5 g, mmol), K 2

CO

3 (5 and KI (300 mg) overnight (15 h).

Methylenechloride (150 ml) was added to the reaction mixture after 15 cooling to room temperature. The mixture was filtered and the solid residue was washed with methylene chloride. The combined organic solution was evaporated to dryness and redissolved in 100 ml methylene chloride. The resulted solution was washed with saturated NaCI solution and dried over sodium sulfate. 6.5 g of desired product was obtained after removal of the solvent in vacuo.

oo* Rf,=0.41 (dichloromethane/methanol, 95/5).

UV (methanol), maximum: 304, 273, 227, 210 nm: minimum: 291, 244, 214 nm.

*o 1 H NMR (DMSO-de) 67.64 1H), 7.46 1H), 7.04 1H), 4.58 (b, OH), 4.12 2H), 3.80 3H), 3.56 2H), 2.54 3H), 1.88 2H).

13 C NMR (DMSO-d) 6 196.3, 152.5, 148.6, 129.7, 123.1, 111.5, 110.3, 65.4, 57.2, 55.5, 31.9, 26.3.

B. 4 3 -Acetoxypropoxy)- 3 -methoxyacetophenone 4 3 -Hydroxypropoxy)-3-methoxyacetophenone (3.5 g, 15.6 mmol) was dried and dissolved in 80 ml anhydrous acetonitrile. This mixture, 6 ml of triethylamine and 6 ml of acetic anhydride were added. After 4 h, 6 ml methanol was added and the solvent was removed in vacuo. The residue was dissolved in 100 ml dichloromethane and the solution was washed with dilute sodium bicarbonate solution, then water. The organic phase was dried over sodium sulfate and the solvent was removed. The solid residue was applied to a silica gel column with methylene chloride to yield 4.1g of 4 -(3-acetoxypropoxy)-3methoxyacetophenone Rf=0.22 (dichloromethane/methanol, 99/1).

UV (methanol), maximum: 303, 273, 227, 210 nm; minimum: 290, 243, 214 nm.

15 'H NMR (DMSO-d 6 J7.62 1H), 7.45 1H), 7.08 1H), 4.12 (m, 4H, 3.82 3H), 2.54 3H), 2.04 2H), 2.00 3H).

e 1 3 C NMR (DMSO-d 6 6 196.3, 170.4, 152.2, 148.6, 130.0, 123.0, e* o 111.8, 110.4, 65.2, 60.8, 55.5, 27.9, 26.3, 20.7.

C. 4 3 -Acetoxypropoxy)-3-methoxy-6-nitroacetophenone 20 4 3 -Acetoxypropoxy)-3-methoxyacetophenone (3.99 g, 15 mmol) o was added portionwise to 15 ml of 70% HNO 3 in water bath and keep the reaction temperature at the room temperature. The reaction mixture was stirred at room temperature for 30 min and 30 g of crushed ice was added. This mixture was extracted with 100 ml of dichloromethane and the organic phase was washed with saturated sodium bicarbonate solution. The solution was dried over sodium sulfate and the solvent was removed in vacuo. The crude mixture was applied to a silica gel column with gradient methanol in methylene chloride to yield 3.8 g of desired product 4 3 -acetxyroxypropoxy)-3-methoxy-6- -100nitroacetophenone and 0.38 g of ipso-substituted product 5-(3a cetoxypropoxy)-4..metho xyl 1, 2 -d initro benzene.

Side ipso-substituted product 5-( 3 -acetoxypropoxy)-4methoxy-1 ,2dlinitrobenzene: Rf =0.47 (dichloromethane/methanol, 99/1).

UIV (methanol), maximum: 334, 330, 270, 240, 212 nm; minimum: 310, 282, 263, 223 nm.

'H NMR (GDCI 3 &67.36 1 7.34 1 4.28 2H), 4.18 2H), 4.02 3H), 2.20 (in, 2H), 2.08 3H).

3 C NMVR (GDCI 3 6 170.9, 152.2, 151.1, 117.6, 111.2, 107.9, 107.1, 66.7, 60.6, 56.9, 28.2, 20.9.

Desired product 4 3 -acetoxypropoxy)-3-methoxy..6.nitroacetophenone: Rf 0.29 (dichloromethane/methanol, 99/1).

UV (methanol), maximum: 344, 300, 246, 213 nm; minimum: 320, 270, 227 nm.

0 1 1 H NMR (CDCI 3 6 7.62 1 6.74 1 4.28 2H), 4.20 2H), 3.96 3H), 2.48 3H), 2.20 (in, 2H), 2.08 3H).

13 C NMVR (CDCI 3 6 200.0, 171.0, 154.3, 148.8, 138.3, 133.0, 108.8, 108.0, 66.1, 60.8, 56.6, 30.4, 28.2, 20.9.

D. l-( 4 3 -Hydroxypropoxy)-3-methoxy-6.nitrophenyl)ethano 4 3 -Acetoxypropoxy)-3-methoxy.6.nitroacetophenone (3.73 g, 12 minol) was added 150 ml ethanol and 6.5 g of K 2 C0 3 The mixture was stirred at room temperature for 4h and TLC with 5% methanol in dichioromethane indicated the completion of the reaction. To this same reaction mixture, it was added 3.5 g of NaBH 4 and the mixture was stirred at room temperature for 2h. Acetone (10 ml) was added to react with the remaining NaBH 4 The solvent was removed in vacuo and the residue was uptaken into 50 g of silica gel. The silica gel mixture was applied on the top of a silica gel column with 5% methanol in methylene -101chloride to yield 3.15 g of desired product hyd roxypro poxy) -3-methoxy- 6-nitrop henyl1) eth an ol1 Intermediate product 4-(3-hydroxypropoxy)-3-methoxy-6nitroacetophenone after deprotection: R, =0.60 (dichloromethane/methanol, 95/5).

Final product 1 (-3hdoyrpoy--ehx--itohnlehnl R= 0.50 (dichloromethane/methanol, 95/5).

UV (methanol), maximum: 344, 300, 243, 219 nm: minimum: 317, 264, 233 nm.

1 H NMVR (DMSO-d 6 J7.54 1 7.36 1 5.47 OH), 5.27 (in, 1 4.55 OH), 4.05 Ct, 2H), 3.90 3H), 3.55 2H), 1.88 (in, 2H), 1. 37 3 H).

13 C NMR (DMSO-d 6 6 153.4, 146.4, 138.8, 137.9, 109.0, 108.1, 68.5, 65.9, 57.2, 56.0, 31.9, 29.6.

E. 1 .(4-(3-O-4,4'-Dimethoxytritylpropoxy)-3-methoxy-6nitrophenyl)ethanol *1 -(4-(3-Hydroxypropoxy)-3-methoxy-6-nitrophenyl)ethanoI (0.325 g, 1 .2 inmol) was co-evaporated with anhydrous pyridine twice and dissolved in 1 5 ml anhydrous pyridine. The solution was cooled in icewater bath and 450 mg (1.33 minol) of DMTCI was added. The reaction mixture was stirred at room temperature overnight and 0.5 ml methanol was added to stop the reaction. The solvent was removed in vacuo and the residue was co-evaporated with toluene twice to remove trace of pyridine. The final residue was applied to a silica gel column with gradient methanol in methylene chloride containing drops of triethylamine to yield 605 mg of desired product dimethoxytritylpropoxy)-3-metho xy-6- nitrophenyl) ethanol.

R= 0.50 (dichloromethane/methanol, 95/5).

-102- UV (methanol), maximum: 354, 302, 282, 274, 233, 209 nm; minimum: 322, 292, 263, 222 nm.

'H NMR (DMSO-d 6 6 7.54 1H), 6.8-7.4 (ArH), 5.48 OH), 5.27 (in, 1 4.16 2H), 3.85 3H), 3.72 6H), 3.15 2H), 1.98 2H), 1. 37 3 H).

130C NMVR (DMSO-d 6 65157.8, 153.3, 146.1,' 144 138.7, 137.8, 135.7, 129.4, 128.7, 127.5, 127.4, 126.3, 112.9i 11 2.6, 108.9, 108.2, 85.1, 65.7, 63.7, 59.2, 55.8, 54.8, 29.0, 25.0.

F. 1-4(--,'Dmtoyrtlrpx)3mtoy6 nitrophenyl)-1 2 -cyanoethoxy).

diisopropylaminophosphino) ethane l-( 4 3

-O-

4 4'.Dimethoxytritylpropoxy) .thy 6 nitrophenyl)ethanol (200 mg, 3.5 minol) was dried under high vacuum and was dissolved in 15 ml of anhydrous methylene chloride. To this solution, it wa s added 0.5 ml N,N-diisopropylethylamine and 0.2 ml (0.89 mmol) of 2 -cybnioethyl-N,NdiisopropylchlorophosphoramiditeTh reaction mixture was stirred at room temperature for 30 min and 0.5 ml of methanol was added to stop the reaction. The mixture was washed with saturated sodium bicarbonate solution and was dried over sodium .20 sulfate. The solvent was removed in vacuo and a quick silica gel column with 1 methanol in methylene chloride containing drops of triethylamine yield 247 mg the desired phosphoramidite 0- O 4 4 'd im eth oxytrityl pro p oxy) 3methcx y6-n itro ph e I -1 cyan oeth oxy)-d iiso pro pylamino phosphino) eth ane.

R, =0.87 (dichloromethane/methanol, 99/i).

-103- EXAMPLE 11 Oligonucleotide synthesis The oligonucleotide conjugates containing photocleavable linker were prepared by solid phase nucleic acid synthesis (see: Sinha et al.

Tetrahedron Lett. 1983, 24, 5843-5846; Sinha et al. Nucleic Acids Res.

1984, 12, 4539-4557; Beaucage et al. Tetrahedron 1993, 49, 6123- 6194; and Matteucci et al. J. Am. Chem. Soc. 1981, 103, 3185-3191) under standard conditions. In addition a longer coupling time period was employed for the incorporation of photocleavable unit and the 5' terminal amino group. The coupling efficiency was detected by measuring t e absorbance of released DMT cation and the results indicated a comparable coupling efficiency of phosphoramidite 1-(2-nitro-5-(2-O-4,4'dimethoxytritylpropoxy)phenyl)-1-0-((2-cyanoethoxy)diisopropylaminophosphino)ethane or 15 dimethoxytritylpropoxy)-3-methoxy-6-nitrophenyl)-1-0-((2-cyanoethoxy)diisopropylaminophosphino)ethane with those of common nucleoside phosphoramodites. Deprotection of the base protection and release of the conjugates from the solid support was carried out with concentrated ammonium at 55 oC overnight. Deprotection of the base protection of 20 other conjugates was done by fast deprotection with AMA reagents.

Purification of the MMT-on conjugates was done by HPLC (trityl-on) using 0.1 M triethylammonium acetate, pH 7.0.and a gradient of acetonitrile to 25% in 20 minutes). The collected MMT or DMT protected conjugate was reduced in volume, detritylated with aqueous acetic acid (40 min, 0 oC), desalted, stored at -20 0

C.

-104- EXAMPLE 12 Photolysis study In a typical case, 2 nmol of oligonucleotide conjugate containing photocleavable linker in 200 pl distilled water was irradiated with a long wavelength UV lamp (Blak Ray XX-1 5 UV lamp, Ultraviolet products, San Gabriel, CA) at a distance of 10 cm (emission peak 365 nm, lamp intensity 1.1 mW/cm 2 at a distance of 31 cm). The resulting mixture was analyzed by HPLC (trityl-off) using 0.1 M triethylammonium acetate, pH 7.0 and a gradient of acetonitrile. Analysis showed that the conjugate was cleaved from the linder within minutes upon UV irradiation.

Equivalents Those skilled in the art will recognize, or be able to ascertain using no more than routine experimentation, numerous equivalents to the 15 specific procedures described herein. Such equivalents are considered to be within the scope of this invention and are covered by the following claims.

-105- SEQUENCE LISTING GENERAL INFORMATION

APPLICANT:

NAME: SEQUENOM, INC.

STREET: 11555 Sorrento Valley Road CITY: San Diego STATE: California COUNTRY: USA POSTAL CODE (ZIP): 92121

INVENTOR/APPLICANT:

NAME: Maryanne J. O'Donnell STREET: 3855 Nobel Drive CITY: San Diego STATE: California COUNTRY: USA POSTAL CODE (ZIP): 92122

INVENTOR/APPLICANT:

NAME: Charles R. Cantor STREET: 11 Bay State Road CITY: Boston STATE: Massachusetts COUNTRY: USA POSTAL CODE (ZIP): 02215

INVENTOR/APPLICANT:

S* NAME: Daniel P. Little STREET: 393 Glendale Lake Rd.

CITY: Patton STATE: Pennsylvania COUNTRY: USA POSTAL CODE (ZIP): 18668

INVENTOR/APPLICANT:

NAME: Hubert Koster STREET: 8636 Via Mallorca Drive CITY: La Jolla STATE: California S(D) COUNTRY: USA POSTAL CODE (ZIP): 92037 (ii) TITLE OF INVENTION: METHODS OF HIGH DENSITY IMMOBILIZATION OF NUCLEIC ACIDS AND SYSTEMS AND METHODS FOR PREPARING AND ANALYZING LOW VOLUME ANALYTE ARRAY ELEMENTS 9 (iii) NUMBER OF SEQUENCES: (iv) CORRESPONDENCE ADDRESS: ADDRESSEE: Brown, Martin, Haller McClain STREET: 1660 Union Street CITY: San Diego STATE: CA COUNTRY: USA ZIP: 92101-2926 COMPUTER READABLE FORM: MEDIUM TYPE: Diskette -106- S~ *e

V

0O.*

V

0. 0 COMPUTER: IBM Compatible OPERATING SYSTEM: DOS SOFTWARE: None (vi) CURRENT APPLICATION

DATA:

APPLICATION NUMBER: Attorney Docket No. 7 352-2001PC FILING DATE: 06-NOV-1997

CLASSIFICATION:

(vii) PRIOR APPLICATION

DATA:

APPLICATION NUMBER: Attorney Docket No. 73 5 2-2001B FILING DATE: 08-OCT-1997

CLASSIFICATION:

(vii) PRIOR APPLICATION

DATA:

APPLICATION NUMBER: 08/746,055 FILING DATE: 11/06/96 (vii) PRIOR APPLICATION

DATA:

APPLICATION NUMBER: 08/786,988 FILING DATE: 01/23/97 (vii) PRIOR APPLICATION

DATA:

APPLICATION NUMBER: 08/787,639 FILING DATE: 01/23/97 (viii) ATTORNEY/AGENT

INFORMATION:

NAME: Seidman, Stephanie

L

REGISTRATION NUMBER: 33,779 REFERENCE/DOCKET NUMBER: 7 3 52-2001PC (ix) TELECOMMUNICATION

INFORMATION:

TELEPHONE: 619-238-0999 TELEFAX: 619-238-0062

TELEX:

INFORMATION FOR SEQ ID NO:1: SEQUENCE

CHARACTERISTICS:

LENGTH: 21 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: unknown (ii) MOLECULE TYPE: cDNA (iii) HYPOTHETICAL:

NO

(iv) ANTISENSE:

NO

FRAGMENT

TYPE:

(vi) ORIGINAL

SOURCE:

(xi) SEQUENCE DESCRIPTION: SEQ ID NO: 1: GAATTCGAGC TCGGTACCCG G 21 INFORMATION FOR SEQ ID NO:2: SEQUENCE

CHARACTERISTICS:

LENGTH: 21 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: unknown" 0

.OVOOV

V

S

-107- (ii) MOLECULE TYPE: cDNA (iii) HYPOTHETICAL: NO (iv) ANTISENSE: NO FRAGMENT TYPE: (vi) ORIGINAL SOURCE: (xi) SEQUENCE DESCRIPTION: SEQ ID NO:2: CCGGGTACCG AGCTCGAATT C 21 INFORMATION FOR SEQ ID NO:3: SEQUENCE CHARACTERISTICS: LENGTH: 23 base pairs TYPE: nucleic acid STRANDEDNESS: unknown TOPOLOGY: unknown (ii) MOLECULE TYPE: cDNA (iii) HYPOTHETICAL: NO (iv) ANTISENSE: NO FRAGMENT TYPE: (vi) ORIGINAL SOURCE: (xi) SEQUENCE DESCRIPTION: SEQ ID NO:3: CCTCTTGGGA ACTGTGTAGT ATT 23 INFORMATION FOR SEQ ID NO:4: SEQUENCE CHARACTERISTICS: LENGTH: 112 base pairs S: TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: unknown (ii) MOLECULE TYPE: cDNA (iii) HYPOTHETICAL: NO (iv) ANTISENSE: NO FRAGMENT TYPE: ORIGINAL SOURCE: (xi) SEQUENCE DESCRIPTION: SEQ ID NO:4: AGGCTGTCTC TCTCCCTCTC TCATACACAC ACACACACAC ACACACACAC ACACACACAC ACACACACAC TCACACTCAC CCACANNNAA ATACTACACA GTTCCCAAGA GG o 112 INFORMATION FOR SEQ ID SEQUENCE CHARACTERISTICS: LENGTH: 49 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: unknown (ii) MOLECULE TYPE: cDNA (iii) HYPOTHETICAL: NO (iv) ANTISENSE: NO FRAGMENT TYPE: I

I

-108- (vi) ORIGINAL SOURCE: (xi) SEQUENCE DESCRIPTION: SEQ ID TAATACGACT CACTATAGGG CGA.AGGCTGT CTCTCTCCCT CTCTCATAC 49 INFORMATION FOR SEQ ID NO:6: SEQUENCE CHARACTERISTICS: LENGTH: 135 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: unknown (ii) MOLECULE TYPE: cDNA (iii) HYPOTHETICAL:

NO

(iv) ANTISENSE: NO FRAGMENT TYPE: (vi) ORIGINAL SOURCE: (xi) SEQUENCE DESCRIPTION: SEQ ID No:6: TAATACGACT CACTATAGGG CGAAGGCTGT CTCTCTCCT CTCTCATACA cACACACACA CACACACACA CACACACACA CACACACACA CACTCACACr CACCCACANN NAAATACTAC 120 ACAGTTCCCA

AGAGG

135 (2 INFORATIO FOR SEQ ID £Nu:7: SEQUENCE CHARACTERISTICS: LENGTH: 12 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: unknown (ii) MOLECULE TYPE: cDNA (iii) HYPOTHETICAL: No (iV) ANTISENSE: NO FRAGMENT TYPE: (vi) ORIGINAL SOURCE: (xi) SEQUENCE DESCRIPTION: SEQ ID NO: 7: AATACTACAC AG 12 INFORM ATION FOR SEQ ID NO:8: SEQUENCE CHARA~CTERISTICS: LENGTH: 24 base pairs TYPE: nucleic acid STRANDEDNESS: unknown TOPOLOGY: unknown (ii) MOLECULE TYPE: cDNA (iii) HYPOTHETICAL:

NO

(iv) ANTISENSE: NO FRAGMENT TYPE: (vi) ORIGINAL SOURCE: -109- (xi) SEQUENCE DESCRIPTION: SEQ ID NO:8: CTGATGCGTC GGATCATCTT TTTT 24 INFORMATION FOR SEQ ID NO:9: SEQUENCE CHARACTERISTICS: LENGTH: 23 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: unknown (ii) MOLECULE TYPE: cDNA (iii) HYPOTHETICAL: NO (iv) ANTISENSE: NO FRAGMENT TYPE: (vi) ORIGINAL SOURCE: (xi) SEQUENCE DESCRIPTION: SEQ ID NO:9: GATGATCCGA CGCATCAGAA TGT 23 INFORMATION FOR SEQ ID SEQUENCE CHARACTERISTICS: LENGTH: 29 base pairs TYPE: nucleic acid STRANDEDNESS: unknown TOPOLOGY: unknown (ii) MOLECULE TYPE: cDNA (iii) HYPOTHETICAL: NO (iv) ANTISENSE: NO FRAGMENT TYPE: (vi) ORIGINAL SOURCE: (xi) SEQUENCE DESCRIPTION: SEQ ID GATCTAGCTG GGCCGAGCTA GGCCGTTGA 29 INFORMATION FOR SEQ ID NO:11: SEQUENCE CHARACTERISTICS: LENGTH: 27 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: unknown (ii) MOLECULE TYPE: cDNA (iii) HYPOTHETICAL: NO (iv) ANTISENSE: NO FRAGMENT TYPE: (vi) ORIGINAL SOURCE: (xi) SEQUENCE DESCRIPTION: SEQ ID NO:11: CTGATGCGTC GGATCATCTT TTTTTTT 27 INFORMATION FOR SEQ ID NO:12: SEQUENCE CHARACTERISTICS: -110- LENGTH: 12 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: unknown (ii) MOLECULE TYPE: cDNA (iii) HYPOTHETICAL: NO (iv) ANTISENSE: NO FRAGMENT TYPE: (vi) ORIGINAL SOURCE: (xi) SEQUENCE DESCRIPTION: SEQ ID NO:12: GATGATCCGA CG 12 INFORMATION FOR SEQ ID NO:-13: SEQUENCE CHARACTERISTICS: LENGTH: 15 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: unknown (ii) MOLECULE TYPE: cDNA (iii) HYPOTHETICAL: NO (iv) ANTISENSE: NO FRAGMENT TYPE: (vi) ORIGINAL SOURCE: (xi) SEQUENCE DESCRIPTION: SEQ ID NO:13: GATGATCCGA CGCAT INFORMATION FOR SEQ ID NO:14: SEQUENCE CHARACTERISTICS: LENGTH: 12 base pairs S* TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: unknown (ii) MOLECULE TYPE: cDNA (iii) HYPOTHETICAL: NO (iv) ANTISENSE: NO FRAGMENT TYPE: (vi) ORIGINAL SOURCE: (xi) SEQUENCE DESCRIPTION: SEQ ID NO:14: AAAAAAGATG AT 12 INFORMATION FOR SEQ ID SEQUENCE

CHARACTERISTICS:

LENGTH: 12 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: unknown (ii) MOLECULE TYPE: cDNA (iii) HYPOTHETICAL:

NO

111- (iv) ANTISENSE:

NO

FRAGMENT

TYPE:

(vi) ORIGINAL

SOUJRCE:

(xij) SEQUENCE DESCRIPTION: SEQ ID NO:1S: GATCCGACGC AT 12 INFORMATION FOR SEQ ID NO:16: SEQUENCE

CHARACTERISTICS:

LENGTH: 18 base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: unknown (ii) MOLECULE TYPE:

CDNA

(iii) HYPOTHETICAL:

NO

(iv) ANTISENSE:

NO

FRAGMAENT

TYPE:

(vi) ORIGINAL

SOURCE:

(xi) SEQUENCE DESCRIPTION: SEQ ID NO:16: CTGATGCGTC GGATCATC 1 INFORMATION FOR SEQ ID NO:17: SEQUENCE

CHARACTERISTICS:

LENGTH: 50 base pairs TYPE: nucleic- acid STRANDEDNESS: single TOPOLOGY: unknown (ii) MOLECULE TYPE: cDNA (iii) HYPOTHETICAL:

NO

(iv) ANTISENSE:

NO

FRAMET

TYPE:

(vi) ORIGINAL

SOURCE:

(xi) SEQUENCE DESCRIPTION: SEQ ID NO:17: GCCTGGTACA CTGCCAGGCG_ CTTCTGC.AGG TCATCGGCAT CGCGGAGGAG INFORM;LTION FOR SEQ ID NO:18: SEQUENCE

CHARACTERISTICS:

LENGTH: SO base pairs TYPE: nucleic acid STRANDEDNESS: single TOPOLOGY: unknown (ii) MOLECULF TYPE: cDNA (iii) HypOTHETICAL:

NO

(iv) ANTISENSE:

NO

FRAGMENT

TYPE:

(vi) ORIGINAL,

SOURCE:

(xi) SEQUENCE DESCR-IPTION: SEQ ID NO:18: GCCTGGTACA CTGCCAGGA CTGCAGG TCATCGG3CAT CGCGGAGGAG

I

-112- INFORMATION FOR SEQ ID NO:l9: SEQUENCE CHARACTERISTICS: LENGTH: 21 base pairs TYPE: nucleic acid STRAZ4DEDNESS: single TOPOLOGY: unknown (ii) MOLECULE TYPE: cDNA (iii) HYPOTHETICAL: NO (iv) ANTISENSE: NO FRAGMENT TYPE: (vi) ORIGINAL SOURCE: (xi) SEQUENCE DESCRIPTION: SEQ ID NO:19: GATGCCGATG ACCTGCAGAAG 21.

Claims (42)

1. A dispensing apparatus for dispensing nanoliter volumes of fluid in chemical or biological procedures onto the surface of a substrate, comprising: a housing having a plurality of sides and a bottom portion having formed therein a plurality of apertures, wherein the sides and bottom portion of said housing define an interior volume, one or more fluid transmitting vesicles, mounted within said apertures, and having a fluid holding chamber of a size for holding and dispensing nanoliter volumes of fluid, said fluid holding chamber being disposed in fluid communication with said interior volume of said housing, and dispensing means in communication with said interior volume of said housing for selectively dispensing nanoliter volumes of fluid from said nanoliter volume sized fluid transmitting vesicles when fluid holding chambers of said vesicles are fully loaded, whereby said dispensing means dispenses nanoliter volumes of the fluid onto the surface 15 of the substrate when the apparatus is disposed over and in registration with the surface of 0the substrate.

2. The apparatus of claim 1, wherein each said fluid transmitting vesicle has an open proximal end and a distal tip portion that extends beyond said housing bottom portion when mounted within said apertures, said open proximal end disposing said fluid S 20 holding chamber in fluid communication with said interior volume when mounted with the apertures.

3. The apparatus of claim 1, wherein said one or more fluid transmitting vesicles are removably and replaceably mounted within said apertures of said housing. The apparatus of claim 1, wherein said one or more fluid transmitting vesicles include a glue seal for fixedly mounting said vesicles within said housing. The apparatus of claim 1, wherein said fluid holding chamber includes a bore that is sufficiently narrow to be filled with fluid through capillary action.

6. The apparatus of claim 1, wherein each said fluid holding chamber of said one or more fluid transmitting vesicles are sized to cause said fluid holding chamber to be substantially filled with the fluid through capillary action.

7. The apparatus of claim 1, comprising a plurality of fluid transmitting vesicles, wherein said plurality of fluid transmitting vesicles comprise an array of fluid delivering needles.

8. The apparatus of claim 7, wherein said fluid delivering needles are fabricated from metal. [R:\LIBZZ]04374.doc:mrr 114

9. The apparatus of claim 7, wherein said fluid delivering needles are fabricated from glass. The apparatus of claim 7, wherein said fluid delivering needles are fabricated from silica.

11. The apparatus of claim 7, wherein said fluid delivering needles are fabricated from polymeric material.

12. The apparatus of claim 1, wherein the number of said one or more fluid transmitting vesicles is less than or equal to the number of wells of a multi-well substrate.

13. The apparatus of claim 1, comprising a plurality of fluid transmitting vesicles, and further comprising mechanical biasing means of mechanically biasing said plurality of fluid transmitting vesicles into sealing contact with said housing bottom portion, wherein the house further comprises a top portion.

14. The apparatus of claim 13, wherein each of the fluid transmitting vesicles has a proximal end portion that includes a flange, and further comprising a sealer element disposed between the flange and an inner surface of the housing bottom portion for forming a seal between the interior volume and an external environment. The apparatus of claim 14, wherein said mechanical biasing means includes a plurality of spring elements each of which are coupled at one end to said proximal end of each said one or more fluid transmitting vesicles, and at another end to an inner surface of said housing top portion, said spring element applying a mechanical biasing force to said S: vesicle proximal end to form said seal. :i 16. The apparatus of claim 1, wherein said housing further includes a top portion, and further comprising securing means for securing said housing top portion to said oo.o•i housing bottom portion.

17. The apparatus of claim 16, wherein said securing means comprises a plurality of fastener-receiving apertures formed within one of said top and bottom portions or said housing, and a plurality of fasteners for mounting within said apertures for securing together said housing top and bottom portions.

18. The apparatus of claim 1, wherein said dispensing means comprises a S 30 pressure source fluidly coupled to said interior volume of said housing for disposing said interior volume at a selected pressure condition.

19. The apparatus of claim 18, wherein said fluid transmitting vesicles are filled through capillary action, and wherein said dispensing means further comprises means for varying said pressure source to dispose said interior volume of said housing at varying pressure conditions, said means for varying disposing said interior volume at a selected [R:\LIBZZ]7143.doc:MQT 115 pressure condition sufficient to offset said capillary action to fill the fluid holding chamber of each vesicle to a predetermined height corresponding to a predetermined fluid amount. The apparatus of claim 19, wherein said means for varying further comprises fluid selection means for selectively discharging a selected nanoliter volume fluid amount from said chamber of each said vesicle.

21. The apparatus of claim 1, wherein said fluid transmitting vesicle has a proximal end that opens onto said interior volume of sid housing, and wherein said fluid holding chamber of said vesicles are sized to cause said fluid holding chamber to be substantially filled with the fluid through capillary action without forming a meniscus at said proximal open end.

22. The apparatus of claim 1, wherein said dispensing means comprises fluid selection means for selectively varying the amount of fluid dispensed from said fluid holding chamber of each vesicle. Is 23. The apparatus according to claim 1, comprising a plurality of vesicles, wherein a first portion thereof includes fluid holding chambers of a first size and a second ooooo Sportion includes fluid holding chambers of a second size, whereby a plurality of fluid •volumes can be dispensed.

24. The apparatus of claim 22, wherein said fluid selection means comprises a S 20 pressure source coupled to said housing and in communications with said interior volume for disposing said interior volume at a selected pressure condition, and adjustment means coupled to said pressure source for varying said pressure within said interior volume of said housing to apply a positive pressure in said fluid chamber of each said fluid transmitting vesicle to vary the amount of fluid dispensed therefrom.

25. A fluid dispensing apparatus for dispensing nanoliter volumes of a fluid in chemical or biological procedures into one or more wells of a multi-well substrate, comprising a housing having a plurality of sides and a bottom portion having formed therein a plurality of apertures, said sides and bottom portion defining an interior volume, a plurality of fluid transmitting vesicles for holding a nanoliter volume of a fluid, mounted within said apertures having a fluid holding chamber disposed in communication with said interior volume of said housing, a fluid volume selection and dispensing means in communication with said interior volume of said housing for variably selecting an amount of the fluid loaded into said fluid [R:\LIBZZ]04374.doc:nrr 116 holding chambers of said vesicles to be dispensed from a single set of plurality of fluid transmitting vesicles, and whereby said dispensing means dispenses a selected amount of the fluid into the wells of the multi-well substrate when the apparatus is disposed over and in registration with the substrate, wherein the selected amount of fluid is a nanoliter volume.

26. The fluid dispensing apparatus of claim 25, wherein said fluid volume selection and dispensing means is adapted to select various amounts of fluid to be dispensed from said single set of vesicles.

27. The fluid dispensing apparatus of claim 25, wherein said fluid volume selection and dispensing means comprises a pressure source fluidly coupled to said interior volume of said housing for dispensing said interior volume at a selected pressure condition.

28. The fluid dispensing apparatus of claim 27, further compromising means for varying the pressure within the interior volume of the housing to select the amount of 15 fluid to dispense from said fluid transmitting vesicles.

29. The fluid dispensing apparatus of claim 27, wherein said fluid transmitting vesicles are filled with the fluid through capillary action, and further comprising means for varying said pressure source to dispose said interior volume of said housing at varying pressure conditions, said means for varying dispensing said interior volume at a pressure S 20 condition sufficient to offset said capillary action to fill the fluid holding chamber of each vesicle to a predetermined height corresponding to a predetermined fluid amount. The fluid dispensing apparatus of claim 25, wherein said fluid selection means comprises a pressure source coupled to said housing and in communication with said interior volume for dispensing said interior volume at a selected pressure condition, and adjustment means coupled to said pressure source for varying said pressure within said interior volume of said housing to apply a positive pressure in said fluid chamber of each said fluid transmitting vesicle to vary the amount of fluid dispensed therefrom.

31. A fluid dispensing apparatus for dispensing fluid in chemical or biological procedures into one or more wells of a multi-well substrate, said apparatus comprising a housing having a plurality of sides and top and bottom portions, said bottom portion having formed therein a plurality of apertures, said sides and top and bottom portions of said housing defining an interior volume, [R:\LIBZZ]04374.doc: rrT 117 a plurality of fluid transmitting vesicles, mounted within said apertures having a fluid holding chamber sized to hold nanoliter volumes of the fluid, said fluid holding chamber being disposed in fluid communication with said volume of said housing and mechanical biasing means for mechanically biasing said plurality of said transmitting vesicles into sealing contact with said housing bottom portion, wherein the apparatus dispenses nanoliter volumes of fluid.

32. The fluid dispensing apparatus of claim 31, wherein each said fluid transmitting vesicle has a proximal end portion that includes a flange, and further comprising a sealer element disposed between the flange and an inner surface of the housing bottom portion for forming a pressure and fluid seal between the internal and external environment.

33. The fluid dispensing apparatus of claim 31, wherein said mechanical biasing means includes a plurality of spring elements each of which are coupled at one end to said means includes a plurality of spring elements each of which are coupled at one end to said i proximal end of said fluid transmitting vesicle, and at another end to an inner surface of S•said housing top portion, said spring elements applying a mechanical biasing force to said vesicle proximal end to form said fluid and pressure seal.

34. The fluid dispensing apparatus of claim 31, further comprising securing means for securing said housing top portion to said housing bottom portion. ooo•• S 20 35. The fluid dispensing apparatus of claim 34, wherein said securing means comprises a plurality of fastener-receiving apertures formed within one of said top and bottom portions of said housing, and a plurality of fasteners for mounting within said apertures for securing said housing top and bottom portions together.

36. The fluid dispensing apparatus of claim 31, further comprising dispensing means in communication with said interior volume of said housing for selectively dispensing the fluid from said fluid transmitting vesicles when the fluid is loaded within said fluid holding chambers of said vesicles, whereby said dispensing means dispenses the fluid into the wells of the multi-well substrate when the apparatus is disposed over an in registration with the substrate.

37. The fluid dispensing apparatus of claim 36, wherein said dispensing means comprises a pressure source fluidly coupled to said interior volume of said housing for dispensing said interior volume at a selected pressure condition.

38. The fluid dispensing apparatus of claim 31, wherein said plurality of fluid transmitting vesicles are removably and replaceably mounted within said apertures of said housing. [R:\LIBZZ]04374.doc:nrr 118

39. The fluid dispensing apparatus of claim 31, wherein said plurality of fluid transmitting vesicles comprises an array of fluid delivering needles. The fluid dispensing apparatus of claim 36, wherein said fluid transmitting vesicles are filled with the fluid through capillary action, and wherein said dispensing means further comprises means for varying said pressure source to dispense said interior volume of said housing at varying pressure conditions, said means for varying disposing said interior volumes at a selected pressure condition sufficient to offset said capillary action to fill the fluid holding chamber of each vesicle to a predetermined height corresponding to a predetermined fluid amount.

41. The fluid dispensing apparatus of claim 36, wherein said dispensing means comprises fluid selection means for selectively varying the amount of fluid dispensed from said fluid holding chamber of each vesicle.

42. The fluid dispensing apparatus of claim 31, further comprising a pressure Ssource coupled to the housing and in communication with the interior volume for 15s dispensing the interior volume at a selected pressure condition, and :6o000 adjustment means coupled to the pressure source for varying the pressure within the oi Sinterior volume of the housing to apply a positive pressure to the fluid chamber of each :0 the fluid transmitting vesicle to vary the amount of fluid dispensed therefrom.

43. The apparatus of claim 1, comprising a plurality of fluid transmitting vesicles. 0 20 44. A system, comprising the apparatus of claim 1, and further comprising: a robotic arm in attached to the housing, wherein the robotic arm is for holding and moving the housing to insert the vesicles into a fluid source for filling the vesicles with a nanoliter volume of fluid and for disposing said housing comprising said vesicles adjacent to the substrate to allow for dispensing fluid from the vesicles onto the surface of a o 25 substrate adjacent thereto. The system of claim 44, further comprising a central processing means for processing data and for executing program instructions to provide information for controlling the movement and operation of the robotic arm.

46. The system of claim 44, wherein the substrate is for performing mass spectrometry on samples deposited thereon.

47. A system for dispensing nanoliter volumes of fluid in chemical or biological procedures onto the surface of a substrate, comprising: a pin assembly having one or more apertures and one or more fluid transmitting pins, mounted within the apertures, wherein the pins comprise a solid shaft of material, wherein one end is for capturing a nanoliter volume of fluid thereon; and [R:\LIBZZ]04374.doc:rr 119 a robotic arm in contact with the pin assembly, wherein the robotic arm is for holding and moving the assembly to insert the end of the pins into a fluid source for capturing fluid on the end of the pins or to dispose the pin assembly adjacent to the surface of a substrate to dispense fluid onto the surface of a substrate by contacting the fluid on the end of the pins with the surface of the substrate.

48. The apparatus of claim 47, further comprising a central processing means for processing data and for executing program instructions to provide information for controlling the movement and operation of the robotic arm.

49. The apparatus of claim 47, wherein the end of the pins for capturing a nanoliter lo volume of fluid comprises a shape selected from the group consisting of flat, star-shaped, concave, pointed solid, pointed semi-hollow, and angled on one or both sides. The apparatus of claim 47, wherein the pin assembly comprises a plurality of pins in an array.

51. A system for dispensing nanoliter volumes of fluid in chemical or biological procedures onto the surface ofa substrate, comprising: an assembly, comprising a capillary element for containing a volume of fluid to be oi dispensed through an orifice of the capillary and a transducer element in contact with the capillary for effecting physical deformation of the capillary causing ejectment of a nanoliter volume of fluid from the capillary; S 20 a robotic arm for holding an assembly and for aligning the assembly adjacent to the surface of the substrate to dispense nanoliter volumes of fluid from the capillary to the surface of the substrate aligned therewith; and mounting means for securing the robotic arm to the assembly.

52. The system of claim 51, further comprising a central processing means for 25 processing data and for executing program instructions to provide information for controlling the movement and operation of the robotic arm.

53. The system claim 51, wherein the transducer element is selected from the group consisting of a piezoelectric, electric, electrorestrictive, magnetorestrictive, and electromechanical transducer.

54. A dispensing apparatus for dispensing nanoliter volumes of fluid in chemical or biological procedures onto the surface of a substrate, said apparatus being substantially as hereinbefore described with reference to the accompanying drawings. A fluid dispensing apparatus for dispensing nanoliter volumes of a fluid in chemical or biological procedures into one or more wells of a multi-well substrate, said [R:\LIBZZ]04374.doc:mrr 120 apparatus being substantially as hereinbefore described with reference to the accompanying drawings.

56. A system for dispensing nanoliter volumes of fluid in chemical or biological procedures onto the surface of a substrate, said system being substantially as hereinbefore described with reference to the accompanying drawings. Dated 25 March, 2003 Sequenom, Inc. Patent Attorneys for the Applicant/Nominated Person SPRUSON FERGUSON 0O So 000 S.. 0 S *55500 0 555* S*o 0 S *0 i 5 0 S S7.. S 0 S* S 00 8 00 [R \LIBZZ]7143.doc:MQT