U.S. patent application number 10/933122 was filed with the patent office on 2005-04-28 for method of performing array-based hybridization assays using thermal inkjet deposition of sample fluids.
Invention is credited to Caren, Michael P., Luebke, Kevin J..
Application Number | 20050089903 10/933122 |
Document ID | / |
Family ID | 23159744 |
Filed Date | 2005-04-28 |
United States Patent
Application |
20050089903 |
Kind Code |
A1 |
Caren, Michael P. ; et
al. |
April 28, 2005 |
Method of performing array-based hybridization assays using thermal
inkjet deposition of sample fluids
Abstract
Methods are provided for depositing a quantity of fluid onto the
surface of an array. In the subject methods, a thermal inkjet head
loaded with the fluid is positioned in opposing relationship to,
e.g. over, the array surface. Actuation of the thermal ink-jet
results in the expulsion of a quantity of fluid onto the array
surface. The subject methods find particular use in array-based
binding assays in which an array of binding agents is employed for
the detection of an analyte(s), particularly array-based
hybridization assays.
Inventors: |
Caren, Michael P.; (Palo
Alto, CA) ; Luebke, Kevin J.; (Dallas, TX) |
Correspondence
Address: |
AGILENT TECHNOLOGIES, INC.
Legal Department, DL429
Intellectual Property Administration
P.O. Box 7599
Loveland
CO
80537-0599
US
|
Family ID: |
23159744 |
Appl. No.: |
10/933122 |
Filed: |
September 1, 2004 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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10933122 |
Sep 1, 2004 |
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09819923 |
Mar 26, 2001 |
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6797469 |
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09819923 |
Mar 26, 2001 |
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09300589 |
Apr 27, 1999 |
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6221653 |
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Current U.S.
Class: |
506/9 ; 347/1;
435/6.11; 435/7.1; 506/16; 506/18 |
Current CPC
Class: |
B01J 19/0046 20130101;
B01J 2219/00596 20130101; B01J 2219/00659 20130101; B01J 2219/0059
20130101; B01J 2219/00637 20130101; C40B 40/10 20130101; B01J
2219/00378 20130101; C40B 40/06 20130101; B01J 2219/00605 20130101;
C40B 60/14 20130101; B01J 2219/00585 20130101; B01J 2219/00527
20130101; B01J 2219/00722 20130101; B01J 2219/0074 20130101; B01J
2219/00619 20130101; B01J 2219/00608 20130101; B01J 2219/00621
20130101; B01J 2219/00725 20130101; B01J 2219/00612 20130101; B01J
2219/00707 20130101; B01J 2219/00529 20130101 |
Class at
Publication: |
435/006 ;
435/007.1; 347/001 |
International
Class: |
C12Q 001/68; G01N
033/53 |
Claims
1-21. (canceled)
22. A method for screening a fluid sample at least suspected of
containing an analyte, comprising: positioning an inkjet head
filled with a fluid in opposing relation to an array surface
comprising a plurality of binding agents stably associated
therewith; and actuating the inkjet head in a manner sufficient to
expel said fluid onto a location on the array substrate comprising
a binding agent; detecting a specific binding interaction between
the binding agent and an analyte in said fluid.
23. The method of claim 22 further comprising depositing a diluent
solution onto the array surface at the same location that the fluid
sample is deposited.
24. The method of claim 22, further comprising filling the inkjet
head with a wash fluid and depositing said wash fluid on said
surface.
25. The method of claim 22, wherein the fluid sample comprises a
biomolecule.
26. The method of claim 22, wherein the fluid sample comprises a
nucleic acid.
27. The method of claim 22, wherein the fluid sample comprises a
polypeptide.
28. The method of claim 22, wherein the fluid sample comprises a
cell.
29. The method of claim 22, wherein the fluid sample is heated
prior to being expelled.
30. The method according to claim 22, wherein said fluid sample
does not exceed 200 picoliters in volume.
31. The method of claim 22, wherein said positioning and actuating
steps are performed at each of a plurality of locations on the
array.
Description
CROSS REFERENCE TO RELATED APPLICATIONS
[0001] This application is a continuation of U.S. patent
application Ser. No. 09/819,923 filed Mar. 26, 2001, which is a
continuation of U.S. patent application Ser. No. 09/300,589 filed
Apr. 27, 1999, now issued U.S. Pat. No. 6,221,653 from which
priority is claimed under 35 U.S.C. 120. The entireties of these
applications are incorporated herein by reference.
INTRODUCTION
[0002] 1. Technical Field
[0003] The field of this invention is nucleic acid arrays.
[0004] 2. Background of the Invention
[0005] "Biochips" or arrays of binding agents, such as
oligonucleotides and peptides, have become an increasingly
important tool in the biotechnology industry and related fields.
These binding agent arrays, in which a plurality of binding agents
are deposited onto a solid support surface in the form of an array
or pattern, find use in a variety of applications, including gene
expression analysis, drug screening, nucleic acid sequencing,
mutation analysis, and the like.
[0006] In array-based assays in which an array of binding agents is
employed, the array is typically contacted with a fluid sample that
is suspected of containing the analyte(s) of interest. In currently
employed protocols, contact of the array with the sample fluid is
achieved in a number of different ways. Thus, a fluid sample may be
contacted with the surface of the array using a pipette. In other
embodiments, the sample may be flowed over the surface of an array
by injecting the sample through a septum. In yet other embodiments,
the sample may be flowed over the surface of the array using
surface tension, centrifugal force or pressure differentials.
[0007] Although effective, there are drawbacks associated with each
of the above techniques. First, each of the above techniques
requires the deposition of relatively large sample volumes, e.g.
greater than 2 .mu.l. Second, such techniques provide little or no
spatial resolution of sample presentation. Third, sample
pre-manipulation or pre-treatment, e.g. heating, dilution, etc., is
difficult.
[0008] As such, there is continued interest in the development of
new methods of depositing sample volumes onto array surfaces. Of
particular interest would be the development of a sample deposition
method capable of depositing relatively small quantities of sample
on the array surface in a manner in which the position of
deposition can be controlled.
[0009] Relevant Literature
[0010] U.S. Patents disclosing the use of inkjet devices to
dispense bio/chemical agents such as proteins and nucleic acids
include: U.S. Pat. Nos. 4,877,745; 5,338,688; 5,474,796; 5,449,754;
5,658,802; and 5,700,637.
SUMMARY OF THE INVENTION
[0011] Methods for depositing small quantities of a fluid sample
onto the surface of an array are provided. In the subject methods,
a thermal inkjet device is employed to expel a quantity of a fluid
sample onto the surface of an array. The subject methods find use
in array-based assays, particularly array-based analyte detection
assays, e.g. differential gene expression assays, gene
identification assays, nucleotide sequencing assays, and the
like.
BRIEF DESCRIPTION OF THE FIGURES
[0012] FIG. 1A provides a representation of the deposition profile
of a diluent solution onto two features (i.e. nucleotide spots) of
an array.
[0013] FIG. 1B provides a representation of the deposition profile
of four different sample solutions deposited onto the two features
of an array shown in FIG. 1A.
DEFINITIONS
[0014] The term "nucleic acid" as used herein means a polymer
composed of nucleotides, e.g. deoxyribonucleotides or
ribonucleotides.
[0015] The terms "ribonucleic acid" and "RNA" as used herein mean a
polymer composed of ribonucleotides.
[0016] The terms "deoxyribonucleic acid" and "DNA" as used herein
mean a polymer composed of deoxyribonucleotides.
[0017] The term "oligonucleotide" as used herein denotes single
stranded nucleotide multimers of from about 10 to up to about 100
nucleotides in length.
[0018] The term "polynucleotide" as used herein refers to a single
or double stranded polymer composed of nucleotide monomers of
generally greater than 100 nucleotides in length and up to about
8,000 or more nucleotides in length.
[0019] The term "cDNA" as used herein means a complementary DNA
molecule made as a copy of mRNA amplified using PCR for deposition
on arrays. cDNAs can range from about 100 bp to about 8,000 bp,
where average cDNAs are typically 1 to 2 kb in length.
[0020] The term "array" as used herein means an substrate having a
plurality of binding agents stably attached to its surface, where
the binding agents may be spatially located across the surface of
the substrate in any of a number of different patterns.
[0021] The term binding agent means any agent that is a member of a
specific binding pair, where such agents include: polypeptides,
e.g. proteins or fragments thereof; nucleic acids, e.g.
oligonucleotides, polynucleotides, and the like; etc.
DESCRIPTION OF THE SPECIFIC EMBODIMENTS
[0022] Methods are provided for depositing a quantity of a fluid
sample onto the surface of an array. In the subject methods, a
thermal inkjet head loaded with the fluid sample is positioned in
opposing relationship to, e.g. over, an array surface. The
temperature of the heating element of the inkjet head is then
raised such that a bubble is formed at the surface of the heating
element and a quantity of the fluid sample is expelled from the
head onto the array surface. The subject methods find use in
array-based analyte detection applications, particularly in
array-based hybridization assays.
[0023] Before the subject invention is described further, it is to
be understood that the invention is not limited to the particular
embodiments of the invention described below, as variations of the
particular embodiments may be made and still fall within the scope
of the appended claims. It is also to be understood that the
terminology employed is for the purpose of describing particular
embodiments, and is not intended to be limiting. Instead, the scope
of the present invention will be established by the appended
claims.
[0024] In this specification and the appended claims, the singular
forms "a," "an," and "the" include plural reference unless the
context clearly dictates otherwise. Unless defined otherwise, all
technical and scientific terms used herein have the same meaning as
commonly understood to one of ordinary skill in the art to which
this invention belongs.
[0025] The subject invention is a method of depositing a quantity
of a fluid sample onto the surface of an array. Specifically, the
subject invention provides a method of depositing an extremely
small quantity of a fluid sample, e.g. a pico liter volume of fluid
sample, onto the surface of an array. As the subject methods are
capable of depositing an extremely small volume of fluid onto an
array surface, the subject methods can be used to deposit a pico
liter quantity of fluid onto an array surface. By "pico liter
quantity" is meant a volume of fluid that is at least about 0.05
pl, usually at least about 0.1 pl and more usually at least about 1
pl, where the volume may be as high as 250 pl or higher, but
generally does not exceed about 1 .mu.l and usually does not exceed
about 1 nl.
[0026] In the broadest sense, the subject methods may be used to
deposit a volume of fluid sample onto any structure having at least
one binding agent stably associated with its surface. Generally,
the structures onto which the fluid sample is deposited in the
subject methods comprise a substrate surface having at least one
location thereon occupied by a composition made up of a single type
of binding agent, e.g. identical proteins, nucleic acids with the
same sequence, etc., where this homogenous composition is present
on the substrate surface in the form a spot or some other shape. In
many embodiments, the subject methods are employed to deposit a
volume of fluid sample onto the surface of an array. Arrays onto
which fluid sample is deposited in the subject methods are
compositions of matter having a plurality of distinct binding
agents, e.g. probes, stably associated with a substrate surface,
where the plurality of binding agents is generally known and
positioned across the surface of the array in a pattern. Each
distinct binding agent present on the array is generally a member
of a specific binding pair. Binding agents of interest are
generally biological molecules or biomolecules and include:
polypeptides, nucleic acids, carbohydrates, glycoproteins, etc. As
such, binding pairs in which one member thereof is stably
associated to the array surface include: ligands and receptors;
antibodies and antigens; complementary nucleic acids; etc. As
mentioned above, the plurality of binding agents are arranged
across the surface of a substrate in the arrays. Typically, the
arrays comprise a plurality of spots, where each spot contains a
different and distinct binding agent, i.e. the arrays comprise a
plurality of homogenous binding agent compositions, where each
composition is in the form of a spot on the substrate surface of
the array. The number of spots on a substrate surface in any given
array varies greatly, where the number of spots is at least about
1, usually at least about 10 and more usually at least about 100,
and may be as great as 100,000 or greater, but usually does not
exceed about 10.sup.7 and more usually does not exceed about
10.sup.6. The spots may range in size from about 0.1 .mu.m to 10
mm, usually from about 1 to 1000 .mu.m and more usually from about
10 to 100 .mu.m. The density of the spots may also vary, where the
density is generally at least about 1 spot/cm.sup.2, usually at
least about 100 spots/cm.sup.2 and more usually at least about 400
spots/cm.sup.2, where the density may be as high as 10.sup.6
spots/cm.sup.2 or higher, but generally does not exceed about
10.sup.5 spots/cm.sup.2 and usually does not exceed about 104
spots/cm.sup.2. A variety of arrays are known to those of skill in
the art, where representative arrays include those disclosed or
referenced in: U.S. Pat. Nos. 5,242,974; 5,384,261; 5,405,783;
5,412,087; 5,424,186; 5,429,807; 5,436,327; 5,445,934; 5,472,672;
5,527,681; 5,529,756; 5,545,531; 5,554,501; 5,556,752; 5,561,071;
5,624,711; 5,639,603; 5,658,734; as well as in WO 93/17126; WO
95/11995; WO 95/35505; EP 742 287; and EP 799 897; the disclosures
of which are herein incorporated by reference. Of particular
interest in many embodiments of the subject methods is the
deposition of a fluid sample onto arrays of nucleic acids,
including arrays of oligonucleotides and polynucleotides, e.g.
cDNAs.
[0027] In certain embodiments, the arrays employed in the subject
methods are those in which two or more distinct regions are present
on the surface of the array, where fluid communication between
regions is prevented by a barrier means. A variety of barrier means
may be present, including raised structures or walls arising from
the surface of the array, hydrophobic strips of material positioned
on the array surface in a manner sufficient to produce two or more
distinct regions, and the like. Such arrays are described in U.S.
Pat. Nos. 5,545,531 and 5,807,522, the disclosures of which are
herein incorporated by reference.
[0028] The fluid sample that is deposited on the array according to
the subject invention is a fluid sample that is suspected of
containing an analyte of interest. In other words, the fluid sample
may or may not actually contain the analyte of interest, where the
purpose of the array-based assays in which the methods of the
subject invention find use is to determine whether or not the
sample has the analyte of interest. The analyte of interest, e.g.
target, is generally a biomolecule, where by biomolecule is meant a
molecule that is a naturally occurring molecule associated with an
agent that is capable of replication, either by itself or with the
use of other organisms, e.g. viruses, single-celled organisms and
multi-celled organisms; including animals and plants. Biomolecules
therefore include polypeptides, polysaccharides, nucleic acids and
the like, as well as derivatives thereof, where of particular
interest in many embodiments are nucleic acids, including
oligonucleotides and polynucleotides, e.g cDNA.
[0029] The fluid sample is generally derived from a physiological
fluid, e.g. naturally occurring fluids, such as plasma, tears,
urine, etc., derivatives of cells or tissues, e.g. cell lysates,
etc., where the fluid may or may not be pre-treated to produce the
sample. Examples of pre-treatments to which the original fluid may
be subjected in order to produce the sample include dilution,
concentration, labeling, denaturation, etc., where such protocols
are well known to those of skill in the art. Generally, the fluid
sample is an aqueous fluid sample, where the fluid sample may or
may not include one or more additional agents, such as co-solvents,
buffering salts, surfactants, ions, denaturants, enzymes etc.
[0030] In many embodiments, the fluid sample deposited on the array
surface in the subject methods is a nucleic acid fluid sample. By
nucleic acid fluid sample is meant a fluid sample that contains a
nucleic acid, usually a plurality of distinct nucleic acids, where
the nucleic acids may be oligonucleotides, polynucleotides, e.g.
mRNAs, cDNAs, etc. In many preferred embodiments, the nucleic acid
fluid sample contains a plurality of distinct labeled derivatives
of mRNAs from a physiological sample, e.g. cell or tissue of
interest, where labeled derivatives include cDNA, a RNA, etc.
[0031] Critical to the subject method is the use of a thermal
inkjet head to deposit a quantity of the fluid sample onto the
array surface. Thermal inkjet heads are well known in the art of
conventional printing and document production. As is known to those
of skill in the art, thermal inkjet heads typically have at least
the following components: (a) an orifice; (b) a firing chamber; and
(c) a heating element. Thermal inkjet heads and methods for their
manufacture and use are described in a number of different U.S.
Patents, including: U.S. Pat. Nos. 5,772,829; 5,745,128; 5,736,998;
5,736,995; 5,726,690; 5,714,989; 5,682,188; 5,677,577; 5,642,142;
5,636,441; 5,635,968; 5,635,966; 5,595,785; 5,477,255; 5,434,606;
5,426,458; 5,350,616; 5,341,160; 5,300,958; 5,229,785; 5,187,500;
5,167,776; 5,159,353; 5,122,812; and 4,791,435; the disclosures of
which are herein incorporated by reference.
[0032] Thermal inkjet heads finding use in the subject methods will
generally have the following characteristics. The size of the
orifice is sufficient to produce a spot of suitable dimensions on
the substrate surface (described in greater detail infra), where
the orifice generally has a diameter (or exit diagonal depending on
the specific format of the ink jet head) ranging from about 1 to
1000 .mu.m, usually from about 5 to 100 .mu.m and more usually from
about 10 to 60 .mu.m. The firing chamber has a volume ranging from
about 1 pl to 10 nl, usually from about 10 pl to 5 nl and more
usually from about 50 pl to 1.5 nl. The heating element will
preferably be made out of a material that can deliver a quick
energy pulse, where suitable materials include: TaAl and the like.
The thermal element is capable of achieving temperatures sufficient
to vaporize a sufficient volume of the nucleic acid composition in
the firing chamber to produce a bubble of suitable dimensions upon
actuation of the head. Generally, the heating element is capable of
attaining temperatures of at least about 100.degree. C., usually at
least about 400.degree. C. and more usually at least about
700.degree. C., where the temperature achievable by the heating
element may be as high as 1000.degree. C. or higher. The device may
also have one or more reservoirs. In other words, the device may be
a single reservoir device or a multi-reservoir device. When
present, the reservoir will typically have a volume ranging from
about 1 pl to 1 l, usually from about 0.5 .mu.l to 10 .mu.l and
more usually from about 1 .mu.l to 5 .mu.l. A variety of thermal
inkjet heads are available commercially, where such devices
include: the HP92261A thermal inkjet head (available from
Hewlett-Packard Co., Palo Alto Calif.), the HP 51645A thermal
inkjet head (available from Hewlett-Packard Co. Palo Alto Calif.),
the inkjet produced by (Cannon Kabushiki Kaisha, Tokyo, Japan) and
the like. Specific inkjet heads of interest are disclosed in U.S.
Pat. Nos. 5,736,998 and 4,668,052, the disclosures of which are
herein incorporated by reference.
[0033] In practicing the subject methods, the thermal inkjet device
is loaded with a fluid sample, e.g. a nucleic acid fluid sample.
The fluid may be loaded into the firing chamber and fluid reservoir
using any convenient means. Thus, conventional methods of
introducing ink into thermal inkjet heads may be employed. Where
such methods are employed, following loading of the fluid sample
into the inkjet head, it is often desirable to "prime" the device
prior to use. One means of priming the device is to apply
sufficient pressure to the fluid in the reservoir (or conversely
negative pressure to the orifice) such that a volume of fluid is
forced out of the orifice. Such priming methods are currently
employed in the printing industry and thus are well known to those
of skill in the art.
[0034] Alternatively, where minimal waste of the fluid sample
desired, e.g. where the fluid is an expensive or rare cDNA sample,
the following method of loading the fluid sample into the firing
chamber and reservoir may be employed. In this method of fluid
sample loading, the orifice is contacted with the fluid under
conditions sufficient for fluid to flow through the orifice and
into the firing chamber of the head, where fluid flow is due, at
least in part, to capillary forces. To assist in the flow of fluid
into the orifice, back pressure in the form of suction (i.e.
negative pressure) may be applied to the firing chamber (and
reservoir, if present) of the head, where the back pressure will
typically be at least about 5, and may be at least about 10 and
even as great as about 100 inches of H.sub.2O or more.
[0035] To deposit fluid onto the surface of an array according to
the subject methods, the fluid sample loaded thermal inkjet head is
positioned in opposing relationship relative to the surface of the
array (e.g. with an XYZ translational means), where the orifice is
in opposition to the position on the array surface at which
deposition of the nucleic acid is desired (e.g. opposite a binding
agent spot on the array). The distance between the orifice and the
array surface will not be so great that the volume of nucleic acid
fluid cannot reach the array surface and produce a spot in a
reproducible manner. As such, the distance between the orifice and
the array surface will generally range from about 10 .mu.M to 10
mm, usually from about 100 .mu.m to 2 mm and more usually from
about 200 .mu.m to 1 mm.
[0036] After the head is placed into position relative to the array
surface, the temperature of the heating element or resistor of the
head is raised to a temperature sufficient to vaporize a portion of
the fluid immediately adjacent to the resistor and produce a
bubble. In raising the temperature of the heating element, the
temperature of the heating element is raised to at least about
100.degree. C., usually at least about 400.degree. C. and more
usually at least about 700.degree. C., where the temperature may be
raised as high as 1000.degree. C. or higher, but will usually be
raised to a temperature that does not exceed about 2000.degree. C.
and more usually does not exceed about 1500.degree. C. As such, a
sufficient amount of energy will be delivered to the resistor to
produce the requisite temperature rise, where the amount of energy
will generally range from about 1.0 to 100 .mu.J, usually from
about 1.5 to 15 .mu.J. The portion of fluid in the firing chamber
that is vaporized will be sufficient to produce a bubble in the
firing chamber of sufficient volume to force an amount of liquid
out of the orifice.
[0037] The formation of the bubble in the firing chamber traps a
portion or volume of the fluid present in the firing chamber
between the heating element and the orifice and forces an amount or
volume of fluid out of the orifice at high speed. The amount or
volume of fluid that is forced out of the firing chamber can be
controlled depending on the specific amount of fluid that is
desired to be deposited on the substrate. As is known in the art,
the amount of fluid that is expelled can be controlled by changing
one or more of a number of different parameters of the ink jet
head, including: the orifice diameter, the orifice length (depth),
the size of the firing chamber, the size of the heating element,
and the like. Such variations are well known to those of skill in
the art. As such, the amount or volume of fluid that is forced out
or expelled from the firing chamber may range from about 0.1 to
2000 pl, usually from about 0.5 to 500 pl and more usually from
about 1.0 to 250 pl. The speed at which the fluid is expelled from
the firing chamber is at least about 1 m/s, usually at least about
10 m/s and may be as great as about 20 m/s or greater.
[0038] Upon actuation of the thermal inkjet head, as described
above, fluid is expelled from the orifice and travels to the array
surface. Upon contact with the array surface, the fluid interacts
with the binding agent(s) located at the position of the array on
which the fluid is deposited. The deposited fluid typically forms a
spot on the array surface. As mentioned above, by varying the
design parameters of the thermal inkjet head, the spot dimensions
can be controlled such that spots of various sizes can be produced.
With the subjects methods, one can produce spot sizes which have
diameters ranging from a minimum of about 10 .mu.m to a maximum of
about 1.0 cm. In those embodiments where very small spot sizes are
desired, one can produce small spots that have a diameter ranging
from about 1.0 .mu.m to 1.0 mm, usually from about 5.0 .mu.m to 500
.mu.m and more usually from about 10 .mu.m to 200 .mu.m. In many
embodiments, the spot sizes range from about 30 to 100 .mu.m.
[0039] An important feature of the subject invention is that the
deposition process does not adversely affect the binding
capabilities of the analyte (if present) in the sample with its
respective binding pair member present on the array. For example,
where the analyte is a nucleic acid, the deposited nucleic acid is
capable of hybridizing to complementary nucleic acids present on
the array. In other words, the deposition process does not
adversely affect the nucleic acid of the sample, e.g. does not
physically alter the nature of the nucleic acid such that it cannot
subsequently participate in Watson-Crick type hydrogen bonding
interactions.
[0040] The subject methods of depositing a volume of fluid sample
onto the surface of a array find use in a variety of different
array-based applications. Array-based applications in which the
subject invention finds use include: differential expression
analysis, gene discovery, and the like. A variety of array-based
applications are described in: U.S. Pat. Nos. 5,242,974; 5,384,261;
5,405,783; 5,412,087; 5,424,186; 5,429,807; 5,436,327; 5,445,934;
5,472,672; 5,527,681; 5,529,756; 5,545,531; 5,554,501; 5,556,752;
5,561,071; 5,624,711; 5,639,603; 5,658,734; as well as WO 93/17126;
WO 95/11995; WO 95/35505; EP 742 287; and EP 799 897; the
disclosures of which are herein incorporated by reference.
[0041] Although the exact steps in any given array-based
application in which the subject methods find use will vary
depending on the particular assay being performed, the following
steps are generally present. First, the thermal inkjet head
comprising the fluid sample is positioned and fired so as to
deposit a volume of fluid sample onto the array surface at a
desired location, as described supra. Following deposition of the
fluid sample onto the array surface, the deposited fluid is
maintained on the array surface for a sufficient period of time for
specific binding interactions to occur between specific binding
pair members, e.g. complementary nucleic acids. This incubation
period typically lasts at least about 1 min, usually at least about
1 hr and more usually at least about 3 hr, where the incubation
period may last as long as 24 hr or longer, but generally will not
be longer than 20 hr and usually will not be longer than 16 hr. In
certain embodiments, because of the small sample volumes that are
deposited, the incubation time may be very short, ranging from
about 1 to 30 min, usually from about 10 to 30 min.
[0042] In many embodiments, any unbound binding agents present on
the array surface are removed following incubation. Unbound binding
agents may be removed using any convenient washing protocol, where
a wash fluid, e.g. a wash solution, is contacted with the array
surface and removed. Washing protocols that may be employed
include: immersing the array in a wash solution, flowing a wash
solution over the service of the array, etc. In certain
embodiments, the wash fluid is deposited on the array using a
thermal inkjet head in a manner analogous to that employed for
deposition of the sample volume.
[0043] Depending on the particular assay being performed, the
particular protocol may include one or more of the following
additional steps. In certain embodiments, the fluid sample present
in the inkjet head is pre-heated prior to deposition. Where the
fluid sample is pre-heated, the fluid sample is heated to a
temperature of at least about 25, usually at least about 37 and
more usually at least about 50.degree. C., where the fluid sample
may be heated to a temperature as high as 100.degree. C. or higher,
but is generally not heated to a temperature that exceeds about the
boiling temperature of the solution, and is usually not heated to a
temperature that exceeds about 95.degree. C. The fluid sample is
conveniently heated by administering short bursts of energy to the
heating element of the inkjet head. The short bursts of energy are
sufficient to heat the fluid sample to the desired temperature, but
insufficient to result in the formation of a vapor bubble in the
inkjet head of sufficient to volume to expel a quantity of fluid
from the inkjet head. As such, the short bursts of energy are
sufficient to raise the temperature of the solution to 25 to 100,
usually to 30 to 90 and more usually to 37 to 50.degree. C. To
achieve this heating, a plurality of bursts of energy are delivered
to the heating element.
[0044] In certain embodiments, it is desirable to deposit a
quantity of a diluent solution, e.g. water, buffer solution, etc.,
onto the array surface at the same location that the fluid sample
is deposited. The diluent may be deposited before and/or after the
deposition of the fluid sample. Deposition of the diluent solution
may serve a number of different purposes, including; dilution of
the fluid sample to achieve a desired concentration; introduction
of additional fluid to provide for an optimal binding environment
during incubation; mixing of the deposited sample (e.g. by drop
impact mixing, etc) and the like. The diluent may be deposited from
a thermal inkjet head according to the subject methods, where the
diluent may be present in a single reservoir head or a
multi-reservoir head that also includes the fluid sample.
[0045] As described above, the array onto which the fluid sample is
deposited comprises a plurality of binding agents located at
distinct positions, e.g. spots, on the substrate surface of the
array. Depending on the particular protocol being performed and the
size of each binding agent location or spot on the array, the ratio
of fluid sample depositions per binding agent location, i.e. drops
per spot, may be 1, greater than 1 or less than 1. For example,
where the array has spots of 500 .mu.m diameter on the surface, one
can deposit a single fluid sample drop on each spot. This
particular embodiment is depicted in FIGS. 1A and B, which show a
plurality of sample depositions into a single spot. The ability to
deposit a plurality of distinct sample drops onto a single spot
comes is a result of the precise manner in which the subject
invention is capable of depositing small volumes of fluid sample.
Alternatively, one could deposit a plurality of drops onto each
spot, where plurality means 2 or more, but usually does not exceed
about 100,000 and more usually does not exceed about 1000.
Alternatively, in high density arrays where the spots are small,
e.g. ranging in diameter from about 1 .mu.m to 200 .mu.m, a single
fluid sample drop may be deposited such that a plurality of spots
are covered by the deposited drop of fluid sample.
[0046] In certain embodiments, it may be desirable to prevent
evaporation of the fluid sample following deposition. Evaporation
may be prevented in a number of different ways. The subject methods
may be carried out in a high humidity environment. By "high
humidity" is meant an environment in which the humidity is at least
about 86% relative humidity, usually at least about 95% relative
humidity and more usually at least about 99% relative humidity.
Alternatively, one may apply an evaporation retarding agent, e.g.
mineral oil, glycerol solution, polyethylene glycol, etc., over the
surface of the deposited sample, e.g. by using a thermal inkjet as
described above.
[0047] In the course of practicing the subject methods, fluid
contacted arrays are produced in which each deposited fluid volume
occupies a small area, i.e. spot, on the array surface. By small is
meant that each fluid sample spot on the array has a diameter that
is at least about 1 .mu.m, usually at least about 5 .mu.m and more
usually at least about 10 .mu.m and does not exceed about 10 mm,
usually does not exceed about 1000 .mu.m and more usually does not
exceed about 200 .mu.m.
[0048] Also provided by the subject invention are automated devices
for depositing fluid samples on an array surface, e.g. for carrying
out array-based assays. The automated devices of the subject
invention are analogous to conventional thermal inkjet printing
devices, with the exception that the thermal inkjet head of the
device is filled with a fluid sample as described above, instead of
ink. Such automatic devices comprise at least a means for precisely
controlling the position of the head with respect to an array
surface (an XYZ translational mechanism) and for firing the head.
Such automated devices are well known to those of skill in the
printing and document production art, and are disclosed in U.S.
Pat. Nos. 5,772,829; 5,745,128; 5,736,998; 5,736,995; 5,726,690;
5,714,989; 5,682,188; 5,677,577; 5,642,142; 5,636,441; 5,635,968;
5,635,966; 5,595,785; 5,477,255; 5,434,606; 5,426,458; 5,350,616;
5,341,160; 5,300,958; 5,229,785; 5,187,500; 5,167,776; 5,159,353;
5,122,812; and 4,791,435; the disclosures of which are herein
incorporated by reference.
[0049] Also provided by the subject invention are kits for use in
depositing a fluid sample on a substrate according to the subject
methods. The subject kits include at least a thermal inkjet head
and instructions for practicing the subject invention, where the
instructions may be present as a package insert or on the packaging
of the device. The subject kits may further include various
reagents for preparing the fluid sample. In some embodiments, the
kits may also comprise the array onto which the fluid sample is to
be deposited.
[0050] The following examples are offered by way of illustration
and not by way of limitation.
EXPERIMENTAL
Example I
[0051] The following experiment is performed to profile the
expression levels of both very rare and abundant transcripts in
four different cellular states relative to a fifth reference state
with an array-based hybridization assay using a single array.
[0052] A. Experimental Setup
[0053] Each of four samples contains a population of nucleic acids
representing the transcript profile of the reference state and a
population of nucleic acids representing the transcript profile of
one of the four alternative states, such as cells grown under four
different conditions, isolated from four different patients, or
treated with four different drug candidates. The representatives
from the reference state are labeled with one fluorophore and the
representatives from each of the other states are labeled with a
second different fluorophore. The samples are highly concentrated,
each in 2 .mu.l of hybridization buffer solution containing 1.0 M
NaCl, 10 mM Tris-HCl (pH 7.6), 0.005% Triton X-100 and 0.1 mg/ml
unlabeled, sonicated herring sperm DNA. In addition, 10%
polyethylene glycol is added to slow evaporation. A diluent
solution is also used that is identical in composition to the
sample solutions but lacks the fluorescently labeled nucleic acid.
Analysis of the samples is to be done by hybridization to an array
of nucleic acid receptors specific for individual transcripts of
interest. The receptors are arrayed in 400 micron features or spots
on a coated glass slide with a total of 4,800 different features.
The array is held on a surface of controlled temperature to
regulate the temperature of the glass. The samples and diluent are
delivered to the array using a multi-reservoir thermal inkjet head
attached to an XYZ positioning system. The head utilized, HP 51645A
(available from Hewlett-Packard Co. Palo Alto, Calif.), fires 35 pl
drops which cover 3800 micron.sup.2 on the surface.
[0054] B. Experimental Procedure
[0055] The four sample solutions and the diluent are manually
applied in separate locations to a transfer surface. The inkjet
head is moved over the solutions and loads them through the orifice
plate into the firing chamber. The head is then scanned across the
array and 9 firings of diluent solution (d in FIG. 1A) are
deposited into each of four spots within each of the features or
spots, 10 and 20. After the diluent is deposited, the sample
solutions are warmed to 95.degree. C. by applying short pulses of
energy to the firing resistors. The head then deposits one firing
of each sample solution into its own spot of diluent in each
feature, 10 or 20, as well as one firing of each sample solution
into a discrete spot without dilution (FIG. 1B). Thus, within each
feature, 10 or 20, there are eight separate regions covered with
liquid. Each region contains a single sample solution at one of two
concentrations, the initial concentration or ten percent of the
initial concentration. FIGS. 1A and 1B show one possible
arrangement of firings; others are possible.
[0056] After incubation at 37.degree. C. for one hour, the array is
washed with hybridization buffer at 37.degree. C. for one hour,
followed by washing with a solution containing 0.07 M NaCl, 5 mM
H.sub.2PO.sub.4, 0.5 mM EDTA, and 0.005% Triton X-100 at 50.degree.
C. for 15 minutes. Finally, the array is analyzed by laser
epifluorescent microscopy, and the signal within each sample region
of each feature is quantified for the two fluorescent labels. In
the concentrated solutions, which afford the highest signal from
rare transcripts, the labeled representatives of abundant
transcripts saturate their respective surface-bound receptors,
limiting the quantitative information that can be derived for those
transcripts. In the diluted solutions, the rarest transcripts
detectable in the concentrated solutions are not detectable, but
more quantitative information is available for the abundant
transcripts--labeled representatives which no longer saturate their
surface-bound receptors.
[0057] It is evident from the above results and discussion that a
simple and efficient way to deposit fluid samples onto arrays
during array-based assays is provided by the subject invention. By
using the subject methods, very small volumes of fluid can be
deposited quickly on an array surface, which is especially useful
where small or valuable samples are being employed. Furthermore,
the subject invention is a non-contact process such that the
potential contamination and surface disruption that could arise
from contact of an applicator with the substrate surface is
eliminated. Yet another advantage of the subject invention is that
the fluid sample can be precisely placed on the array. In addition,
deposition of the fluid sample using the subject methods can result
in very rapid reaction times and therefore short incubation times,
thereby speeding up the overall time required for performing an
array-based assay. As such, the subject invention is a significant
contribution to the art.
[0058] All publications and patent applications cited in this
specification are herein incorporated by reference as if each
individual publication or patent application were specifically and
individually indicated to be incorporated by reference. The
citation of any publication is for its disclosure prior to the
filing date and should not be construed as an admission that the
present invention is not entitled to antedate such publication by
virtue of prior invention.
[0059] Although the foregoing invention has been described in some
detail by way of illustration and example for purposes of clarity
of understanding, it is readily apparent to those of ordinary skill
in the art in light of the teachings of this invention that certain
changes and modifications may be made thereto without departing
from the spirit or scope of the appended claims.
* * * * *