Bioarray chip reaction apparatus and its manufacture

• US 20050208646A1
• Filed: 11/22/2004
• Published: 09/22/2005
• Est. Priority Date: 06/08/1994
• Status: Abandoned Application

• Current Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Original Assignee: Affymetrix, Inc. (Thermo Fisher Scientific Incorporated)
• Inventors: Winkler, James L., Goss, Virginia W., Besemer, Donald M.
• Application Number:
  US10/995,882
• Publication Number:
  US 20050208646A1
• Time in Patent Office: Days
• US Class Current: 435/287.200
• CPC Class Codes: B01F 33/252 using bubbles as loose mixing element
• CPC Class Codes: B01F 33/30 Micromixers
• CPC Class Codes: B01F 33/40 Mixers using gas or liquid agitation, e.g. with air supply tubes
• CPC Class Codes: B01F 33/45 Magnetic mixers; Mixers with magnetically driven stirrers
• CPC Class Codes: B01F 33/452 using independent floating stirring elements
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/00286 Reactor vessels with top and bottom openings
• CPC Class Codes: B01J 2219/00353 Pumps
• CPC Class Codes: B01J 2219/00371 comprising electrodes
• CPC Class Codes: B01J 2219/00432 Photolithographic masks
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00529 DNA chips
• CPC Class Codes: B01J 2219/00531 essentially square
• CPC Class Codes: B01J 2219/00536 in the shape of disks
• CPC Class Codes: B01J 2219/0054 Means for coding or tagging the apparatus or the reagents
• CPC Class Codes: B01J 2219/00547 Bar codes
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/0059 Sequential processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/00608 : DNA chips
• CPC Class Codes: B01J 2219/0061 : The surface being organic
• CPC Class Codes: B01J 2219/00612 : the surface being inorganic
• CPC Class Codes: B01J 2219/00621 : by physical means, e.g. trenches, raised areas
• CPC Class Codes: B01J 2219/00626 : Covalent
• CPC Class Codes: B01J 2219/00637 : by coating it with another layer
• CPC Class Codes: B01J 2219/00641 : the porous medium being continuous, e.g. porous oxide substrates
• CPC Class Codes: B01J 2219/00659 : Two-dimensional arrays
• CPC Class Codes: B01J 2219/00662 : Two-dimensional arrays within two-dimensional arrays
• CPC Class Codes: B01J 2219/00689 : using computers
• CPC Class Codes: B01J 2219/00695 : Synthesis control routines, e.g. using computer programs
• CPC Class Codes: B01J 2219/00711 : Light-directed synthesis
• CPC Class Codes: B01J 2219/00722 : Nucleotides
• CPC Class Codes: B01J 2219/00725 : Peptides
• CPC Class Codes: B01J 2219/00731 : Saccharides
• CPC Class Codes: B01L 2200/025 : Align devices or objects to ensure defined positions relative to each other
• CPC Class Codes: B01L 2200/027 : for microfluidic devices
• CPC Class Codes: B01L 2200/0689 : Sealing
• CPC Class Codes: B01L 2200/12 : Specific details about manufacturing devices
• CPC Class Codes: B01L 2200/147 : Employing temperature sensors
• CPC Class Codes: B01L 2300/0636 : Integrated biosensor, microarrays
• CPC Class Codes: B01L 2300/0816 : Cards, e.g. flat sample carriers usually with flow in two horizontal directions
• CPC Class Codes: B01L 2300/0819 : Microarrays; Biochips
• CPC Class Codes: B01L 2300/0825 : Test strips
• CPC Class Codes: B01L 2300/0877 : Flow chambers
• CPC Class Codes: B01L 2300/1805 : Conductive heating, heat from thermostatted solids is conducted to receptacles, e.g. heating plates, blocks
• CPC Class Codes: B01L 2400/0439 : ultrasonic vibrations, vibrating piezo elements
• CPC Class Codes: B01L 2400/0442 : thermal energy, e.g. vaporisation, bubble jet
• CPC Class Codes: B01L 2400/0487 : fluid pressure, pneumatics
• CPC Class Codes: B01L 2400/0611 : duck bill valves
• CPC Class Codes: B01L 2400/065 : sliding valves
• CPC Class Codes: B01L 3/5027 : by integrated microfluidic structures, i.e. dimensions of channels and chambers are such that surface tension forces are important, e.g. lab-on-a-chip B01L3/5023 takes precedence; micromixers B01F33/30; microreactors for synthesis B01J19/0093; microcapillary devices in general B81B1/00
• CPC Class Codes: B01L 3/502707 : characterised by the manufacture of the container or its components by shaping or joining plastic parts B29C59/00, B29C65/00; by laminating B32B37/00; manufacture of microstructural devices in general B81C
• CPC Class Codes: B01L 3/502715 : characterised by interfacing components, e.g. fluidic, electrical, optical or mechanical interfaces
• CPC Class Codes: B01L 9/52 : Supports specially adapted for flat sample carriers, e.g. for plates, slides, chips
• CPC Class Codes: B01L 9/527 : for microfluidic devices, e.g. used for lab-on-a-chip
• CPC Class Codes: B82Y 30/00 : Nanotechnology for materials or surface science, e.g. nanocomposites
• CPC Class Codes: C07H 21/00 : Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 40/10 : Libraries containing peptides or polypeptides, or derivatives thereof
• CPC Class Codes: C40B 40/12 : Libraries containing saccharides or polysaccharides, or derivatives thereof
• CPC Class Codes: C40B 60/14 : for creating libraries
• CPC Class Codes: C40B 70/00 : Tags or labels specially adapted for combinatorial chemistry or libraries, e.g. fluorescent tags or bar codes
• CPC Class Codes: G01N 2035/00158 : Elements containing microarrays, i.e. "biochip"
• CPC Class Codes: H01L 21/67144 : Apparatus for mounting on conductive members, e.g. leadframes or conductors on insulating substrates
• CPC Class Codes: Y10T 436/25 : including sample preparation

Abstract

A body 300 having a cavity 310 for mounting a substrate 120 fabricated with probe sequences at known locations according to the methods disclosed in U.S. Pat. No. 5,143,854 and PCT WO 92/10092 or others, is provided. The cavity includes inlets 350 and 360 for introducing selected fluids into the cavity to contact the probes. Accordingly, a commercially feasible device for use in high throughput assay systems is provided.

Claims

1-92. -92. (canceled)

93. A holder for a transparent slide having front and rear surfaces, and carrying moieties on at least a portion of the rear surface which is opposite a first portion on the front surface, comprising:

(a) a backer member, (b) front and rear clamp sets which can be moved apart to receive the slide therebetween in an enclosed an protected environment on the holder, and which are urged against the enclosed and protected slide out of contact with the moieties and the first portion of the front surface to retain the slide with the moieties facing, and spaced apart from, the backer member.

94. A holder according to claim 93, wherein the clamp members are positioned such that the holder can receive and retain a slide having an area of no more than 200 cm.sup.2.

95. A holder according to claim 94, wherein the moieties on the rear side of the retained slide are spaced from the backer member by between 0.1 mm to 10 mm.

96. A holder according to claim 93, wherein the holder is rectangular in shape with a maximum area of a side of no more than 100 cm.sup.2.

97. A holder according to claim 95, wherein the clamp members are resiliently urged against the enclosed and protected slide.

98. A holder according to claim 96, wherein the clamp members are urged against the slide front and rear surfaces adjacent a periphery of the slide.

99. A holder according to claim 96, wherein the backer is opaque.

100. A holder according to claim 93, additionally comprising a body having a channel, wherein the backer member comprises a bottom surface of the channel.

101. A holder for a transparent slide having front and rear surfaces, and carrying moieties on at least a portion of one of the surfaces which is opposite a first portion on the other of the surfaces, comprising:

(a) a body having side portions and a channel intermediate the side portions and extending in a direction between ends of the body;

(b) front and rear clamp member sets with members disposed about the channel, one set of which is fixed to the body side portions while the other set is movable to an open position away from the fixed set so as to receive the slide between the sets and urge the enclosed and protected slide against the fixed set to retain the slide between the sets, wherein both clamp sets are out of contact with the moieties and the first portion of the enclosed and protected slide.

102. A holder according to claim 101, additionally comprising two spaced apart guides extending from the body adjacent respective sides of the channel so as to guide the sliding of the slide into the enclosed and protected environment while allowing a user'"'"'s fingers to grasp opposite sides of the enclosed and protected slide at a position between the guides.

103. A holder for a transparent slide having front and rear surfaces, and carrying moieties on at least a portion of the rear surface which is opposite a first portion on the front surface, comprising:

. (a) a body having side portions and a channel intermediate the side portions and extending in a direction between ends of the body;

(b) front and rear clamp member sets with members disposed about the channel, one set of which is fixed to the body side portions while the other set is movable to an open position away from the fixed set so as to receive the slide between the sets and urge the enclosed and protected slide against the fixed set to retain the slide between the sets with the rear surface facing, and spaced apart from, a bottom surface of the channel, wherein both clamp sets are out of contact with the moieties and the first portion of the enclosed and protected slide.

104. A holder according to claim 103, wherein the clamp sets are resiliently urged toward one another.

105. A holder according to claim 103 additionally comprising a control member set positioned on the holder outside the channel and connected to move the movable clamp set to the open position.

106. A holder according to claim 105, wherein the control member set is on a front side of the holder.

107. A holder according to claim 106, wherein the front clamp member set is fixed to the body side portions and the rear clamp member set is movable.

108. A holder according to claim 107, wherein rearward movement of the control member moves the rear clamp member set to the open position.

109. A holder according to claim 103, wherein members of each of the front and rear clamp member sets are disposed on opposite sides of the channel such that when the sets are in the open position the slide can be slid in an endways direction of the channel between the members and into the enclosed and protected position.

110. A holder according to claim 109, additionally comprising two spaced apart guides extending from the body adjacent respective sides of the channel so as to guide the sliding of the slide into the enclosed and protected environment while allowing a users fingers to grasp opposite sides of the enclosed and protected slide at a position between the guides.

111. A holder according to claim 110, wherein the channel is no wider than 10 cm.

112. A transparent slide having opposed front and rear surfaces, the slide carrying an array of biopolymers on a rear surface and an identification code on a front surface.

113. A transparent slide according to claim 112, wherein the identification code is carried on an opaque medium attached to the front surface.

114. A method comprising reading the array through the front side and reading the identification code from the front side.

115. A method according to claim 114, wherein the identification code is a bar code.