U.S. patent application number 11/225590 was filed with the patent office on 2006-02-09 for arrays with elongated features.
Invention is credited to Jay K. Bass.
Application Number | 20060030034 11/225590 |
Document ID | / |
Family ID | 29249575 |
Filed Date | 2006-02-09 |
United States Patent
Application |
20060030034 |
Kind Code |
A1 |
Bass; Jay K. |
February 9, 2006 |
Arrays with elongated features
Abstract
Arrays having multiple biopolymer features on a substrate,
including elongated features which have a length/width ratio
greater than 1.3 or more. Such arrays may be oriented in various
directions and of shapes described, and fabricated using apparatus,
methods, or computer program products of the invention.
Inventors: |
Bass; Jay K.; (Mountain
View, CA) |
Correspondence
Address: |
AGILENT TECHNOLOGIES, INC.;Legal Department, DL429
Intellectual Property Administration
P.O. Box 7599
Loveland
CO
80537-0599
US
|
Family ID: |
29249575 |
Appl. No.: |
11/225590 |
Filed: |
September 12, 2005 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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10135944 |
Apr 29, 2002 |
6946285 |
|
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11225590 |
Sep 12, 2005 |
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Current U.S.
Class: |
435/287.2 ;
427/2.11 |
Current CPC
Class: |
B41J 3/407 20130101;
B01L 3/0241 20130101; B29C 41/36 20130101; B01J 2219/00722
20130101; C40B 40/06 20130101; B29C 41/20 20130101; C40B 60/14
20130101; B01J 2219/00608 20130101; B01J 2219/00596 20130101; B82Y
30/00 20130101; B01J 19/0046 20130101; B01J 2219/00554 20130101;
B01J 2219/00529 20130101; B01J 2219/00378 20130101; C40B 70/00
20130101; B41J 2/2114 20130101; B29C 31/045 20130101; B01J
2219/00677 20130101 |
Class at
Publication: |
435/287.2 ;
427/002.11 |
International
Class: |
G01N 1/28 20060101
G01N001/28; C12M 1/34 20060101 C12M001/34 |
Claims
1-12. (canceled)
13. A method of fabricating an array having biopolymer features on
a substrate, comprising: (a) for each of multiple features,
depositing multiple drops at least some of which carry the
biopolymer or a biopolymer precursor, onto the substrate from a
drop deposition head system while the head system is spaced from
the substrate; and (b) moving the head system with respect to the
substrate; so as to fabricate the array with elongated features
having a length width ratio greater than 1.3.
14. A method according to clam 13 wherein the lengths of at least
some of the elongated features arc oriented in different
directions.
15. A method according to claim 13 wherein the head system is
scanned in a raster fashion and wherein the lengths of at least
some of the elongated features are oriented in a direction other
than along the lines of the raster.
16. A method according to claim 13 wherein other of the drops
deposited in (a) do not carry the biopolymer or biopolymer
precursor, and wherein the elongated features arc not formed absent
the other of the drops.
17. A method according to claim 13 wherein the head system has
multiple pulse jets and multiple drops for a feature are deposited
from different pulse jets while the head system is moved with
respect to the substrate.
18. A method according to claim 17 wherein the at least some of the
drops deposited from different pulse jets arc of the same
composition.
19. A method according to claim 13 wherein the elongated features
have a narrower portion which is intermediate wider portions.
20. A method according to claim 13 wherein the head system has
multiple pulse jets and the multiple drops for a feature are
deposited from a same pulse jet while the head system is moved with
respect to the substrate.
21. A method according to claim 20 wherein multiple drops of a
liquid carrying a biopolymer precursor are deposited at each
feature.
22. A method according to claim 13 wherein the multiple drops of
liquid deposited for each feature include at least one drop of a
biopolymer precursor and at least one drop of an activator which
causes the biopolymer precursor to link to a moiety on the
substrate.
23. A method according to claim 22 additionally comprising
repeating one or more cycles of (a) and (h) for each of the
elongated features.
24. A method according to claim 20 wherein for each of multiple
elongated features the rate of deposition of the drops and the
velocity of the head system are such that the elongated features
have a length/width ratio of greater than 1.5.
25. A method according to claim 20 wherein for each of multiple
elongated features the rate of deposition of the drops and the
velocity of the head system are such that the elongated features
have a length/width ratio greater than 3.
26. A method comprising, following exposure of an array of claim 1
to a sample, reading the array.
27. A method comprising forwarding data representing a result of a
reading obtained by the method of claim 26.
28. A method according to claim 27 wherein the data is communicated
to a remote location.
29. A method comprising receiving data representing a result of a
reading obtained by the method of claim 26.
30. An apparatus for fabricating an array having multiple
biopolymer features on a substrate, comprising: a substrate holder
on which the substrate can be mounted; a deposition head system
which deposits drops onto a mounted substrate while being spaced
therefrom; a transporter system to move the deposition head system
with respect to a mounted substrate; a processor which controls the
deposition head system and transporter system so as to fabricate
the array with elongated features having lengths oriented in a
common direction and a length/width ratio greater than 1.3.
31. An apparatus according to claim 30 wherein the head system has
multiple pulse jets and the processor controls the deposition head
system and transporter system such that multiple drops for a
feature are deposited from different same pulse jets while the head
system is moved with respect to the substrate.
32. An apparatus according to claim 32 wherein the processor
controls the deposition head system and transporter system so that
the elongated features have a length/width ratio greater than
1.5.
33. An apparatus according to claim 31 wherein the processor
control the deposition head system and transporter system so that
the elongated features have a length/width ratio greater than
3.
34. A computer program product For use with an apparatus for
fabricating an array having multiple biopolymer features on a
substrate, the program product comprising a computer readable
storage medium having a computer program stored thereon which
controls the apparatus to performs the method of: (a) for each of
multiple features, depositing multiple drops at least some of which
carry the biopolymer or a biopolymer precursor, onto the substrate
from a drop deposition head system of the apparatus while the head
system is spaced from the substrate; and (b) moving the head system
with respect to the substrate; so as to fabricate the array with
elongated features having lengths oriented in a common direction
and a length/width ratio greater than 1.3.
35. A computer program product according to claim 34 wherein the
program controls the apparatus so as to fabricate the array with
the elongated features having a length/width ratio greater than
1.5.
36. A computer program product according to claim 34 wherein the
program controls the transporter system and multiple pulse jets of
a deposition head system such that multiple drops for a feature arc
deposited from different pulse jets while the head system is moved
with respect to the substrate.
Description
RELATED APPLICATION
[0001] This application claims priority to, and is a divisional of,
copending application Ser. No. 10/135,944, filed Apr. 29, 2002,
under 35 U.S.C. .sctn.120, the entirety of which is incorporated
herein by reference.
FIELD OF THE INVENTION
[0002] This invention relates to arrays, particularly biopolymer
arrays such as DNA or protein arrays, which are useful in
diagnostic, screening, gene expression analysis, and other
applications.
BACKGROUND OF THE INVENTION
[0003] In the following discussion and throughout the present
application, no cited reference is admitted to be prior art to the
present application.
[0004] Biopolymer arrays, such as polynucleotide arrays and peptide
array, are known and may be used, for example, as diagnostic or
screening tools. Such arrays include regions (sometimes referenced
as spots or features) of usually different sequence polynucleotides
or peptides arranged in a predetermined configuration on a
substrate. The array is "addressable" in that different features
have different predetermined locations ("addresses") on a substrate
carrying the array.
[0005] Biopolymer arrays can be fabricated using in situ synthesis
methods or deposition of the previously obtained biopolymers. The
in situ fabrication methods include those described in U.S. Pat.
No. 5,449,754 for synthesizing peptide arrays, and in U.S. Pat. No.
6,180,351 and WO 98/41531 and the references cited therein for
synthesizing polynucleotide arrays. In situ methods also include
photolithographic techniques such as described, for example, in WO
91/07087, WO 92/10587, WO 92/10588, and U.S. Pat. No. 5,143,854.
The deposition methods basically involve depositing biopolymers at
predetermined locations on a substrate which are suitably activated
such that the biopolymers can link thereto. Biopolymers of
different sequence may be deposited at different feature locations
on the substrate to yield the completed array. Procedures known in
the art for deposition of biopolymers, particularly DNA such as
whole oligomers or cDNA, are described, for example, in U.S. Pat.
No. 5,807,522 (touching drop dispensers to a substrate), and in PCT
publications WO 95/25116 and WO 98/41531, and elsewhere (use of a
pulse jet in the form of a piezoelectric inkjet head).
[0006] The in situ method for fabricating a polynucleotide array
typically follows, at each of the multiple different addresses at
which features are to be formed, the same conventional iterative
sequence used in forming polynucleotides from nucleoside reagents
on a support by means of known chemistry. This iterative sequence
can be considered as multiple ones of the following attachment
cycle at each feature to be formed: (a) coupling an activated
selected nucleoside (a monomeric unit) through a phosphite linkage
to a functionalized support in the first iteration, or a nucleoside
bound to the substrate (i.e. the nucleoside-modified substrate) in
subsequent iterations; (b) optionally, blocking unreacted hydroxyl
groups on the substrate bound nucleoside (sometimes referenced as
"capping"); (c) oxidizing the phosphite linkage of step (a) to form
a phosphate linkage; and (d) removing the protecting group
("deprotection") from the now substrate bound nucleoside coupled in
step (a), to generate a reactive site for the next cycle of these
steps. The coupling can be performed by depositing drops of an
activator and phosphoramidite at the specific desired feature
locations for the array. Capping, oxidation and deprotection can be
accomplished by treating the entire substrate ("flooding") with a
layer of the appropriate reagent. The functionalized support (in
the first cycle) or deprotected coupled nucleoside (in subsequent
cycles) provides a substrate bound moiety with a linking group for
forming the phosphite linkage with a next nucleoside to be coupled
in step (a). Final deprotection of nucleoside bases can be
accomplished using alkaline conditions such as ammonium hydroxide,
in another flooding procedure in a known manner. Conventionally, a
single pulse jet or other dispenser is assigned to deposit a single
monomeric unit.
[0007] The foregoing chemistry of the synthesis of polynucleotides
is described in detail, for example, in Caruthers, Science 230:
281-285, 1985; Itakura et al., Ann. Rev. Biochem. 53: 323-356;
Hunkapillar et al., Nature 310: 105-110, 1984; and in "Synthesis of
Oligonucleotide Derivatives in Design and Targeted Reaction of
Oligonucleotide Derivatives", CRC Press, Boca Raton, Fla., pages
100 et seq., U.S. Pat. No. 4,458,066, U.S. Pat. No. 4,500,707, U.S.
Pat. No. 5,153,319, U.S. Pat. No. 5,869,643, EP 0294196, and
elsewhere The phosphoramidite and phosphite triester approaches are
most broadly used, but other approaches include the phosphodiester
approach, the phosphotriester approach and the H-phosphonate
approach. The substrates are typically functionalized to bond to
the first deposited monomer. Suitable techniques for
functionalizing substrates with such linking moieties are
described, for example, in Southern, E. M., Maskos, U. and Elder,
J. K., Genomics, 13, 1007-1017, 1992.
[0008] In the case of in situ array fabrication, different monomers
and an activator may be deposited at different addresses on the
substrate during any one cycle so that the different features of
the completed array will have different desired biopolymer
sequences. One or more intermediate further steps may be required
in each cycle, such as the conventional oxidation, capping and
washing steps in the case of in situ fabrication of polynucleotide
arrays (again, these steps may be performed in flooding
procedure).
[0009] Further details of large scale fabrication of biopolymer
arrays by depositing either previously obtained biopolymers or by
the in situ method, are disclosed in U.S. Pat. No. 6,242,266, U.S.
Pat. No. 6,232,072, U.S. Pat. No. 6,180,351, and U.S. Pat. No.
6,171,797.
[0010] In array fabrication, the quantities of DNA available for
the array are usually very small and expensive. Sample quantities
available for testing are usually also very small and it is
therefore desirable to simultaneously test the same sample against
a large number of different probes on an array. These conditions
require the manufacture and use of arrays with large numbers of
very small, closely spaced features. This then leads to arrays
which are time consuming and costly to manufacture.
[0011] The arrays, when exposed to a sample, will exhibit a binding
pattern. The array can be read by observing this binding pattern
by, for example, labeling all targets such as polynucleotide
targets (for example, DNA), in the sample with a suitable label
(such as a fluorescent compound), scanning an illuminating beam
across the array one pixel at a time and accurately detecting the
fluorescent signal from the different features of the array.
Techniques and apparatus for scanning chemical arrays are
described, for example, in U.S. Pat. No. 5,763,870 and U.S. Pat.
No. 5,945,679. Assuming that the different sequence polynucleotides
were correctly deposited in accordance with the predetermined
configuration, then the observed binding pattern will be indicative
of the presence and/or concentration of one or more polynucleotide
components in the sample. Peptide or arrays of other chemical
moieties can be used in a similar manner.
[0012] In interpreting the data from an array (a process which may
be referenced as "feature extraction") it is necessary to decide if
a signal for a given pixel should be counted as part of an array
feature and, if so, which feature, or whether the pixel represents
background signal (such as from areas on the substrate not carrying
any biopolymer probes. With thousands of features in an array, it
is usually best that an automated image analysis be performed to
first identify where a feature is located, then to identify its
boundary. Given that the pixel signal may decrease gradually over
several pixels near the boundary and not necessarily evenly around
it, this task may not be precise. This may be particularly true
when a feature produces only a weak signal. One way to facilitate
this task is to assume the feature has a conventional shape, for
example to assume that the features are circular. When arrays are
made by drop deposition processes, this is usually a good
assumption since drops deposited onto a surface will typically form
a circular shape.
[0013] It would be desirable then, to manufacture biopolymer arrays
at low cost while permitting feature extraction to be readily
performed.
SUMMARY OF THE INVENTION
[0014] The present invention realizes that arrays can be fabricated
at a high speed by drop deposition processes if the features do not
have to be round. The present invention further realizes that
feature extraction techniques do not necessarily need circular
features such that high speed fabrication processes of the
foregoing type can be implemented.
[0015] The present invention then, provides an array having
multiple biopolymer features on a substrate, including elongated
features which have a length/width ratio which may be equal to or
greater than 1.2 or 1.3. Such a length/width ratio may be equal to
or greater than any one of 1.5, 1.6, 1.7, 1.8, 2, 2.2, 2.4, 2.6,
2.8, 3, or even equal to or greater than any of 3.2, 3.5, or 4 or
5. The majority of features on the array (that is, greater than
50%) may be such elongated features, or such feature may even make
up at least 60%, 70%, 80%, 90% or at least 98% (or all) of the
total number of features on the array. The lengths of the elongated
features (for example, at least 50%, 70%, or at least 90% of them,
or all of them) may be oriented in a common direction.
[0016] The present invention further provides a method of
fabricating arrays of the present invention. This method includes,
for each of multiple features, depositing multiple drops at least
some (and optionally, multiple ones) of which carry the biopolymer
or a biopolymer precursor, onto the substrate from a drop
deposition head system while the head system is spaced from the
substrate. The head system is moved with respect to the substrate.
This procedure is executed so as to fabricate the array with the
elongated features. The desired degree of elongation may can be
controlled, for example, by adjusting the rate of drop deposition
and head system movement velocity. In executing a method of the
present invention, a head system may be used which has multiple
pulse jets, and the multiple drops for a feature may be deposited
from a same pulse jet while the head system is moved with respect
to the substrate. In one aspect the multiple drops of liquid
deposited for each feature include at least one drop of a
biopolymer precursor and at least one drop of an activator which
causes the biopolymer precursor to link to a moiety on the
substrate. Each cycle of deposition and head system movement may be
repeated one or more times for each of the elongated features.
[0017] An apparatus for fabricating an array having multiple
biopolymer features on a substrate, is also provided by the present
invention. Such an apparatus may include a substrate holder on
which the substrate can be mounted. A deposition head system of the
apparatus is provided which deposits drops onto a mounted substrate
while being spaced from it. A transporter system moves the
deposition head system with respect to a mounted substrate. A
processor which controls the deposition head system and transporter
system so as to fabricate an array of the present invention, for
example by a method of the present invention.
[0018] A computer program product is also provided by the present
invention, which may be used with an apparatus for fabricating an
array of the present invention, such as an apparatus of the present
invention. The program product comprises a computer readable
storage medium having a computer program stored thereon which
controls the apparatus (such as a transporter system for the head
system, and multiple pulse jets of the deposition head system) to
perform a method of the present invention.
[0019] The various aspects of the present invention can provide any
one or more of the following and/or other useful benefits. For
example, the speed at which a drop deposition head moves relative
to the surface can be increased thereby increasing the speed of
array fabrication. Some features can be oriented in different
directions from other for easier identification. A deposition
system can be used with nozzles in rows parallel to the direction
of travel of the head which can also provide drops for the same
feature during a same cycle.
BRIEF DESCRIPTION OF THE DRAWINGS
[0020] FIG. 1 illustrates a substrate carrying multiple arrays,
such as may be fabricated by methods of the present invention;
[0021] FIG. 2 is an enlarged view of an array on FIG. 1 which has a
conventional feature shape;
[0022] FIG. 3 is an enlarged illustration of a portion of the array
in FIG. 2 or FIG. 4;
[0023] FIG. 4 is a view similar to FIG. 2 but showing an array of
the present invention with elongated features;
[0024] FIG. 5 illustrates movement of a drop deposition head system
and coordinated ejection of drops during one cycle to link a first
nucleotide on some features of the array of FIG. 3;
[0025] FIG. 6 schematically illustrates the sequence of drop
deposition during two cycles to link the first two nucleotides to
some of the features of the array of FIG. 3 using the procedure
illustrated in FIG. 5;
[0026] FIG. 7 is similar to FIG. 5 but using a method of the
present invention to link a first nucleotide on some features of
the array of FIG. 4;
[0027] FIGS. 8A-8C schematically illustrates the sequence of drop
deposition during one cycle to link the first nucleotide to some of
the features of the array of FIG. 4 using the procedure illustrated
in FIG. 7;
[0028] FIG. 9 schematically illustrates an apparatus of the present
invention; and
[0029] FIG. 10 is view similar to FIG. 4 of another array of the
present invention showing the elongated features oriented in
different directions.
[0030] To facilitate understanding, identical reference numerals
have been used, where practical, to designate identical elements
that are common to the figures.
DETAILED DESCRIPTION OF EMBODIMENTS OF THE INVENTION
[0031] In the present application, unless a contrary intention
appears, the following terms refer to the indicated
characteristics. A "biopolymer" is a polymer of one or more types
of repeating units. Biopolymers are typically found in biological
systems and particularly include polysaccharides (such as
carbohydrates), and peptides (which term is used to include
polypeptides and proteins) and polynucleotides as well as their
analogs such as those compounds composed of or containing amino
acid analogs or non-amino acid groups, or nucleotide analogs or
non-nucleotide groups. This includes polynucleotides in which the
conventional backbone has been replaced with a non-naturally
occurring or synthetic backbone, and nucleic acids (or synthetic or
naturally occurring analogs) in which one or more of the
conventional bases has been replaced with a group (natural or
synthetic) capable of participating in Watson-Crick type hydrogen
bonding interactions. Polynucleotides include single or multiple
stranded configurations, where one or more of the strands may or
may not be completely aligned with another. A "nucleotide" refers
to a sub-unit of a nucleic acid and has a phosphate group, a 5
carbon sugar and a nitrogen containing base, as well as functional
analogs (whether synthetic or naturally occurring) of such
sub-units which in the polymer form (as a polynucleotide) can
hybridize with naturally occurring polynucleotides in a sequence
specific manner analogous to that of two naturally occurring
polynucleotides. For example, a "biopolymer" includes DNA
(including cDNA), RNA, oligonucleotides, and PNA and other
polynucleotides as described in U.S. Pat. No. 5,948,902 and
references cited therein (all of which are incorporated herein by
reference), regardless of the source. An "oligonucleotide"
generally refers to a nucleotide multimer of about 10 to 100
nucleotides in length, while a "polynucleotide" includes a
nucleotide multimer having any number of nucleotides. A
"biomonomer" references a single unit, which can be linked with the
same or other biomonomers to form a biopolymer (for example, a
single amino acid or nucleotide with two linking groups one or both
of which may have removable protecting groups). A "biopolymer
precursor" is any sub-unit of the final biopolymer such that linked
biopolymer precursors can form the biopolymer, and includes a
biomonomer although it also includes a multimer. A biomonomer fluid
or biopolymer fluid reference a liquid containing either a
biomonomer or biopolymer, respectively (typically in solution).
[0032] A "drop" is a small amount of liquid traveling in a space,
and while often approximately spherical if no external forces are
acting upon it, may have other shapes depending upon those other
forces. In the present case, a drop which has contacted a substrate
is often referred to as a deposited drop, although sometimes it
will be simply referenced as a drop when it is understood that it
was previously deposited. Detecting a drop "at" a location,
includes the drop being detected while it is traveling between a
dispenser and that location, or after it has contacted that
location (and hence may no longer retain its original shape) such
as capturing an image of a drop on the substrate after it has
assumed an approximately circular shape of a deposited drop. A
"pulse jet" is a device which can dispense drops in the formation
of an array. Pulse jets operate by delivering a pulse of pressure
to liquid adjacent an outlet or orifice (such as by a piezoelectric
or thermoelectric element positioned near the orifice) such that a
drop will be dispensed therefrom.
[0033] A "set" of anything (such as a set of drops), may contain
only one, or only two, or three, or any number of multiple drops
(although where "drops" are referenced in relation to a set implies
the set in that case includes multiple drops).
[0034] An "array", unless a contrary intention appears, includes
any one-, two- or three-dimensional arrangement of addressable
regions bearing a particular chemical moiety or moieties (for
example, biopolymers such as polynucleotide sequences) associated
with those regions. An array is "addressable" in that it has
multiple regions of different moieties (for example, different
polynucleotide sequences) such that a region (also referenced as a
"feature" or "spot" of the array) at a particular predetermined
location (an "address") on the array will detect a particular
target or class of targets (although a feature may incidentally
detect non-targets of that feature). Note that the finite small
areas on the array which can be illuminated and from which any
resulting emitted light can be simultaneously (or shortly
thereafter) detected, define pixels which are typically
substantially smaller than a feature (typically having an area
about 1/10 to 1/100 the area of a feature). Array features are
typically, but need not be, separated by intervening spaces. In the
case of an array, the "target" will be referenced as a moiety in a
mobile phase (typically fluid), to be detected by probes ("target
probes") which are bound to the substrate at the various features.
However, either of the "target" or "target probes" may be the one
which is to be evaluated by the other (thus, either one could be an
unknown mixture of polynucleotides to be evaluated by binding with
the other). An "array layout" refers to one or more characteristics
of the features, such as feature positioning on the substrate, one
or more feature dimensions, and an indication of a moiety at a
given location. "Hybridizing" and "binding", with respect to
polynucleotides, are used interchangeably. During a "cycle" for
forming a given feature, typically at least 50% (and more typically
at least 70%, 80% or more preferably at least 90% or 95%) of
moieties bound to a substrate surface available to link with a
deposited monomeric unit or previously obtained complete moiety for
forming the desired feature, actually link to such deposited
monomeric unit or complete moiety.
[0035] When one item is indicated as being "remote" from another,
this is referenced that the two items are at least in different
buildings, and may be at least one mile, ten miles, or at least one
hundred miles apart. "Communicating" information references
transmitting the data representing that information as electrical
signals over a suitable communication channel (for example, a
private or public network). "Forwarding" an item refers to any
means of getting that item from one location to the next, whether
by physically transporting that item or otherwise (where that is
possible) and includes, at least in the case of data, physically
transporting a medium carrying the data or communicating the data.
It will also be appreciated that throughout the present
application, that words such as "front", "back", and the like are
used in a relative sense only.
[0036] A "processor" references any hardware and/or software
combination which will perform the functions required of it. For
example, any processor herein may be a programmable digital
microprocessor such as available in the form of a mainframe,
server, or personal computer (desktop or portable). Where the
processor is programmable, suitable programming can be communicated
from a remote location to the processor, or previously saved in a
computer program product (such as a portable or fixed computer
readable storage medium, whether magnetic, optical or solid state
device based). For example, a magnetic or optical disk may carry
the programming, and can be read by a suitable disk reader
communicating with each processor at its corresponding station.
Reference to a singular item, includes the possibility that there
are plural of the same items present. "May" means optionally.
Methods recited herein may be carried out in any order of the
recited events which is logically possible, as well as the recited
order of events. All patents and other references cited in this
application, are incorporated into this application by reference
except insofar as they may conflict with those of the present
application (in which case the present application prevails).
[0037] Referring first to FIGS. 1-3, these illustrate arrays of
conventional configuration. In these FIGS. a planar substrate 10
carries one or more arrays 12 disposed across a front surface 11a
of substrate 10 and separated by inter-array areas 13. A back side
11b of substrate 10 does not carry any arrays 12. The arrays on
substrate 10 can be designed for testing against any type of
sample, whether a trial sample, reference sample, a combination of
them, or a known mixture of polynucleotides (in which latter case
the arrays may be composed of features carrying unknown sequences
to be evaluated). While ten arrays 12 are shown in FIG. 1 on a
substrate 10, any number of arrays 12 may be present on substrate
10. Similarly, substrate 10 may be of any shape, and any apparatus
used with it adapted accordingly. Depending upon intended use, any
or all of arrays 12 may be the same or different from one another
and each will contain multiple spots or features 16 of biopolymers
in the form of polynucleotides. In the case where arrays 12 are
formed by the conventional in situ or deposition of previously
obtained moieties, as described above, by depositing for each
feature a droplet of reagent in each cycle such as by using a pulse
jet such as an inkjet type head, interfeature areas 17 will
typically (but not essentially) be present which do not carry any
polynucleotide. It will be appreciated though, that the
interfeature areas 17 could be of various sizes and configurations.
It will also be appreciated that there need not be any space
separating arrays 12 from one another. Each feature carries a
predetermined polynucleotide (which includes the possibility of
mixtures of polynucleotides). As per usual, A, C, G, T represent
the usual nucleotides. It will be understood that there is usually
a linker molecule (not shown) of any known types between the front
surface 11a and the first nucleotide.
[0038] FIG. 3 in particular illustrates the circular features 16 of
a conventional ideal array, with each feature 16 being uniform in
shape, size and composition, and the features being regularly
spaced. Note that features 16a, 16b, 16c have polynucleotides of
different sequences.
[0039] Arrays of the present invention may have any characteristics
of the arrays illustrated in FIGS. 1-3 except the features 160 are
elongated as shown in FIG. 4. That is, they have a length 162 which
is greater than a width 164. For example, the length to width ratio
may be greater than 1.3, 1.4, 1.5, 1.6, 1.8, 2, 2.2, 2.4, 2.6, 2.8,
3, 3.2, 3.5, 4, or 4.5, or even greater than 5. By "length" in this
context is referenced the longest linear dimension of a feature 160
and which will be taken to define one axis, while the "width" will
be a maximum linear dimension along another axis orthogonal to the
one axis along which length is measured. It will also be seen in
FIG. 4 that due to the speed of a deposition head and frequency at
which drops are deposited from it, features 160 have two narrower
portion 166 each of which is intermediate two wider portions. In
this context the "narrow" and "wider" portion dimensions are
measured perpendicular to the length of the features. Such arrays
of the present invention may contain at least ten features 160, or
at least one hundred features, at least one thousand, five
thousand, or even at least ten thousand such features 160. All of
the features 16 may be of different composition, or some could be
the same (for example, when any repeats of each feature composition
are excluded the remaining features may account for at least 5%,
10%, 20%, or 50% of the total number of features). Each features
160 carries probes in the form of a one moiety or a mixture of
moieties, which in the case of each feature 160 is a polynucleotide
having a particular sequence. Interfeature areas 17 do not carry
any moieties of a type the same as the features 16 (for example, no
polynucleotides in the case of features 160 carrying
polynucleotides). Features 160 may have lengths of less than 1 cm,
less than 1 mm, less than 200 .mu.m, or even less than 100 .mu.m.
The area of each feature 160 may be at least 15 or 75 .mu.m.sup.2,
and less than 2.0 cm.sup.2. In embodiments where very small spot
sizes or feature sizes are desired, each of the features 160 may
have areas of at least 1.0 .mu.m.sup.2 and less than 1.0 mm.sup.2,
usually less than 0.2 mm.sup.2, and more usually less than 0.05
mm.sup.2. The probes of features 160 are typically linked to
substrate 10 through a suitable linker, not shown, in a similar
manner as those of FIG. 3.
[0040] While substrate 10 in FIG. 4 is planar and rectangular in
form, other shapes (for example, circular) could be used with
housing 34 being adjusted accordingly. In many embodiments,
substrate 10 will be shaped generally as a planar, rectangular
solid, having a length in the range about 4 mm to 200 mm, usually
about 4 mm to 150 mm, more usually about 4 mm to 125 mm; a width in
the range about 4 mm to 200 mm, usually about 4 mm to 120 mm and
more usually about 4 mm to 80 mm; and a thickness in the range
about 0.01 mm to 5.0 mm, usually from about 0.1 mm to 2 mm and more
usually from about 0.2 to 1 mm. However, larger substrates can be
used. Substrate 10 could also have a three-dimensional shape with
irregularities in first surface 11a. Substrates of other
configurations and equivalent areas can be chosen. The
configuration of the array may be selected according to
manufacturing, handling, and use considerations. Typical non-porous
substrates 10 include glass, silica, and rigid and flexible
plastics. However, other materials can be used which provide
physical support for the deposited material and endure the
conditions of the deposition process and of any subsequent
treatment or handling, or processing that may be encountered in the
use of the particular array. Ideally, any material used should
exhibit a low level of non-specific binding during hybridization
events and, for situations where the array is read by detecting
fluorescence in response to an interrogating light, should also
ideally exhibit low intrinsic fluorescence and be transparent to
visible and/or UV light.
[0041] A method of fabricating an array of the present invention
will now be described with reference to FIGS. 7 and 8A-8C, versus a
method of fabricating a conventional array shown in FIGS. 5 and 6.
For the purposes of the discussions below, it will be assumed
(unless the contrary is indicated) that the array being formed in
any case is a polynucleotide array formed by the in situ method
using pulse jet dispensers. However, the applicability of the
method to arrays of other polymers or chemical moieties generally,
whether formed by multiple cycle in situ methods or deposition of
previously obtained moieties (this latter can be considered
essentially as a one cycle process), or using other procedures or
types of dispensers, will be understood from these discussions. In
the discussion below, a, c, g, t or A, C, G, T by themselves or as
number suffixes, represent adenosine, cytidine, guanosine, and
thymidine, phosphoramidite aqueous solutions which nucleoside
phosphoramidites will only become attached to a location at which
it is deposited, upon activation by a suitable activator
(represented by b or B). Suitable activators and related chemistry
are described in those references cited above relating to
polynucleotide synthesis, as well as in U.S. Pat. No. 6,306,599.
While for simplicity the FIGS. show a head system having a single
head 210 which single head has only six nozzles 220, it will be
understood that in practice head 210 will usually have many more
nozzles (such as more than ten, twenty, fifty, or even more than
one hundred). It will also be understood that the head system can
include two, three or more such heads 210 which are mounted on a
same holder for movement in unison with one another (or may be
mounted for independent movement).
[0042] Turning first to FIG. 5 this illustrates the co-ordination
of movement and nozzle firing of a head 210 having multiple drop
dispensing nozzles 220b, 220g, 220t, 220c over the first cycle of
fabrication of the polynucleotides at the multiple features 160a,
160b, 160c illustrated in FIG. 4. Nozzles 220 are the outlets of
pulse jets from which drops are ejected. In this situation head 210
moves in a straight line along direction 204a and ejects one drop
from nozzle 220t at region 240T when that nozzle reaches an upper
end 238t of a trajectory 236t. This is followed (or preceded) by a
drop of activator solution from a nozzle 220b when it reaches upper
end 238t. Similarly, a drop is ejected at region 240G from nozzle
220g when it reaches upper end 238g of trajectory 236g, followed
(or preceded) by a drop of activator solution from a nozzle 220b.
The same occurs as a nozzle 240a and 240b reach upper end 238a of
trajectory 236a. When multiple cycles of an in situ synthesis are
repeated in this manner, the result will be the circular features
16a, 16b, 16c as shown in FIG. 2.
[0043] FIG. 6 schematically illustrates a deposited drop pattern on
substrate 10 over two cycles using the procedure of FIG. 5, for
fabrication of the first two nucleotides of the polynucleotides at
the multiple locations of features 16a, 16b, 16c to be formed as
illustrated in FIG. 2. While only locations of features 16a, 16b,
16c will be discussed for simplicity, it will be understood that
drops are deposited during each cycle at further feature locations
in an analogous manner. Specifically, in the first cycle in FIG. 5
orifices on a drop deposition head 210 deposit respective single
drops 240T, 240G, 240A of phosphoramidite monomer solution at
locations 16a, 16b, 16c, respectively on substrate 10. Note that in
FIG. 5 deposited drops 240 of a drop set for any given one of the
features are shown as only somewhat overlapping for clarity,
whereas in conventional practice the aim is has been to have all
drops at a feature location completely overlap each other. This is
followed, or preceded, by dispensing of a drop 240B of activator
solution in the same cycle. As a result, a T, G, or A monomer
becomes attached to locations 16a, 16b, or 16c, respectively, as
seen in FIG. 3. All locations on substrate 10 may then be exposed
simultaneously (by flowing across the surface) to reagents for
phosphite oxidation, deblocking, and optionally capping, in a known
manner. The same movement and drop dispensing is repeated in a
second cycle in FIG. 5 except that a single drop 240G, 240C, 240T
of corresponding phosphoramidite containing monomer is deposited at
locations 16a, 16b, 16c, respectively. This is followed, or
preceded, by dispensing of a drop of activator solution from an
orifice 220B, in the second cycle. Further cycles are performed as
required at all feature locations for the array 12 until array 12
is fabricated.
[0044] The result of the conventional practice of FIGS. 5 and 6
will be to produce circular features 16a, 16b, 16c and the like as
shown in FIG. 2. Even if multiple drops of a same reagent were to
be ejected from a same nozzle during a same cycle instead of the
single drop described, if such multiple drops are all ejected too
close to the same position 238 of each trajectory 236 the result
will still be features which are circular, or close to circular, in
shape. However, a method of the present invention produces
elongated features as will now be described in connection with
FIGS. 7 and 8A-8C.
[0045] In particular, FIG. 7 shows a method of the present
invention over a single cycle. This method is similar to that of
FIGS. 5 and 6 except that in this method multiple drops of a same
phosphoramidite reagent are deposited from a same nozzle while head
210 is moving along a same straight line with respect to substrate
10. Head 210 is again moved in a line in direction 204a (one of the
lines in the raster formed by scanning head 210 along axis 204 as
discussed below). In particular when a nozzle 220t is aligned with
each of the three upper ends 224t of trajectory 226t it ejects a
drop of T phosphoramidite reagent along each of those three
trajectories onto the location of feature 160a (that is, a set of
three T phosphoramite drops are ejected onto the feature 160a to be
formed). When a nozzle 220b is aligned with each of the three upper
ends 224t of trajectory 226t it ejects a drop of activator reagent
along each of those trajectories onto the location of feature 160a
(that is, a set of three activator drops are ejected onto the
feature 160a to be formed). The deposition of activator may occur
before or after the deposition of any phosphoramidite reagent.
Similarly, when a nozzle 220g is aligned with each of the three
upper ends 224g of trajectory 226g it ejects s a drop of G
phosphoramidite reagent along each of those trajectories onto the
location of feature 160b. When a nozzle 220b is aligned with each
of the three upper ends 224g of trajectory 226g it ejects a drop of
activator reagent along each of those trajectories onto the
location of feature 160b. When a nozzle 220a is aligned with each
of the three upper ends 224a of trajectory 226a it ejects a drop of
A phosphoramidite reagent along each of those trajectories onto the
location of feature 160c. When a nozzle 220b is aligned with each
of the three upper ends 224a of trajectory 226a it ejects a drop of
activator reagent along each of those trajectories onto the
location of feature 160c.
[0046] The result of the foregoing sequence will first be three
overlapping deposited drops illustrated as 227T, 227G, and 227A at
a corresponding feature 160a, 160b, 160c, in a manner illustrated
in FIG. 8A. These deposited overlapping drops will coalesce to
yield the elongated deposited regions 228T, 228G, and 228A as shown
in FIG. 8B. The deposition of the three overlapping drops 226B of
activator at each feature 160a, 160b, 160c during the same cycle is
illustrated in FIG. 8c. However, note that drops 226B are shown as
only somewhat overlapping regions 228 whereas in practice they will
almost completely coincide or overlap them. Therefore, when this
procedure is repeated over multiple cycles the result will be
elongated features of the shape illustrate in FIG. 4. Furthermore,
while in the above description multiple drops of a same composition
are deposited from a same pulse jet, it is possible to deposit at
least some of the drops of same composition from different pulse
jets in a manner as described in allowed U.S. patent application
Ser. No. 09/491,692 titled "Multiple Pass Deposition For Chemical
Array Fabrication " by Jay Bass and filed Jan. 26, 2000,
incorporated herein by reference. Note also that the multiple drops
for a feature which are deposited from different pulse jets may
include the activator containing drops which do not carry any
biopolymer or biopolymer precursor (for example, they do not carry
any biomonomer). For example, the multiple drops for a feature may
have only one or two drops of biopolymer or biopolymer precursor
containing drops, or such other number such that the elongated
features are not formed absent the other of the drops which do not
contain the biopolymer or biopolymer precursor.
[0047] It will be appreciated though that in order for the three
same drops of a set to be overlapping and coalesce in the manner
illustrated in FIGS. 8A and 8B in particular, the drop size and
velocity of head 210 in direction 204a should be controlled. For a
given distance of head 210 from front surface 11a, and a given size
of drop ejected (which is controllable by the power pulse to each
jet), an appropriate rate of deposition of the drops (firing
frequency) can be determined for a given velocity of head 210 by
depositing drops as the head is moved over a substrate and varying
the firing frequency for a set of the same drops from a jet. The
resulting deposited drops can be examined with a camera having
suitable resolution, to determine the length to width ratio as a
function of firing frequency. A graph or look-up table can then be
constructed. This procedure can be repeated for any one or more of
the following as may be desired: other head 210 velocities; drop
sizes ejected; and distance of head 210 from front surface 11a.
Thus, the head velocity and frequency of firing of each pulse jet,
can be controlled to yield the desired length/width ratio since the
other parameters will usually not be varied significantly during
fabrication of a same array.
[0048] Note that in FIGS. 4, 7, and 8 all features 160 have their
length oriented in a same direction of travel 204a of head 210.
This results from the multiple same overlapping droplets within
each drop set deposited at a feature during a same cycle being all
deposited in sequence from the same nozzle during a same straight
line of travel of head 210. This can be useful in that the head
velocity can be increased allowing formation of such features 160
with the foregoing orientation. However, it will be appreciated
that if, for example, some of the overlapping drops in a set
deposited at a feature during a same cycle are deposited from a
nozzle on a line of travel parallel to a line of travel along which
other of the overlapping drops in the set are deposited, elongated
features can be obtained with any other orientation. This drop
deposition of different drops of an overlapping set can be obtained
from different nozzles of head 210 which eject the same reagent and
travel simultaneously along parallel lines, or by the same nozzle
after it has shifted along axis 63 to travel on a parallel line. In
this configuration, even drops of different reagent from different
nozzles (for example, one or more drops of a polymer precursor such
as a phosphoramidite, plus one or more drops of an activator) can
be used to obtain the elongated features as long as there is only
partial overlap of drops in a set for a feature during a same cycle
and the drops of different reagent are able to mix (for example,
the activator drops are deposited before the drops containing the
polymer precursor have evaporated). The result can be an array such
as illustrated in FIG. 10, in which features 160d, 160e have their
lengths 162 oriented in different directions from the other
features 160, which directions are other than along the lines of
the raster in which head 210 is scanned (note that the lines of the
scanned raster lie along axis 204 as discussed below). Elongated
features which are oriented in a direction different from most of
the remainder of the features on an array can be used to identify
locations in an array to aid in feature extraction (for example, a
corner feature which is oriented differently can be readily
identified during feature extraction as a location of a corner of
the array).
[0049] Referring now to FIG. 9, an apparatus of the present
invention which can execute a method of the present invention, will
now be described. The apparatus shown includes a substrate station
20 (sometimes referenced as a "substrate holder") on which can be
mounted a substrate 10. Pins or similar means (not shown) can be
provided on substrate station 20 by which to approximately align
substrate 10 to a nominal position thereon (with alignment marks 18
on substrate 10 being used for more refined alignment). Substrate
station 20 can include a vacuum chuck connected to a suitable
vacuum source (not shown) to retain a substrate 10 without exerting
too much pressure thereon, since substrate 10 is often made of
glass. A flood station 68 is provided which can expose the entire
surface of substrate 10, when positioned at station 68 as
illustrated in broken lines in FIG. 9, to a fluid typically used in
the in situ process, and to which all features must be exposed
during each cycle (for example, oxidizer, deprotection agent, and
wash buffer). In the case of deposition of a previously obtained
polynucleotide, flood station 68 need not be present.
[0050] A dispensing head 210 is retained by a head retainer 208. As
mentioned above though, the head system can include more than one
head 210 retained by the same head retainer 208 so that such
retained heads move in unison together. The transporter system
includes a carriage 62 connected to a first transporter 60
controlled by processor 140 through line 66, and a second
transporter 100 controlled by processor 140 through line 106.
Transporter 60 and carriage 62 are used execute one axis
positioning of station 20 (and hence mounted substrate 10) facing
the dispensing head 210, by moving it in the direction of axis 63,
while transporter 100 is used to provide adjustment of the position
of head retainer 208 (and hence head 210) in a direction of axis
204 (and therefore move head 210 in the direction of travel 204a
which is one direction on axis 204). In this manner, head 210 can
be scanned line by line along parallel lines in a raster fashion,
by scanning along a line over substrate 10 in the direction of axis
204 using transporter 100, while line to line transitioning
movement of substrate 10 in a direction of axis 63 is provided by
transporter 60. Transporter 60 can also move substrate holder 20 to
position substrate 10 in flood station 68 (as illustrated by the
substrate 10 shown in broken lines in FIG. 9). Head 210 may also
optionally be moved in a vertical direction 202, by another
suitable transporter (not shown) and its angle of rotation with
respect to head 210 also adjusted. It will be appreciated that
other scanning configurations could be used during array
fabrication. It will also be appreciated that both transporters 60
and 100, or either one of them, with suitable construction, could
be used to perform the foregoing scanning of head 210 with respect
to substrate 10. Thus, when the present application recites
"positioning", "moving", or similar, one element (such as head 210)
in relation to another element (such as one of the stations 20 or
substrate 10) it will be understood that any required moving can be
accomplished by moving either element or a combination of both of
them. The head 210, the transporter system, and processor 140
together act as the deposition system of the apparatus. An encoder
30 communicates with processor 140 to provide data on the exact
location of substrate station 20 (and hence substrate 10 if
positioned correctly on substrate station 20), while encoder 34
provides data on the exact location of holder 208 (and hence head
210 if positioned correctly on holder 208). Any suitable encoder,
such as an optical encoder, may be used which provides data on
linear position.
[0051] Processor 140 also has access through a communication module
144 to a communication channel 180 to communicate with a remote
station. Communication channel 180 may, for example, be a Wide Area
Network ("WAN"), telephone network, satellite network, or any other
suitable communication channel.
[0052] Each of one or more heads 210 which may be present in the
head system, may be of a type commonly used in an ink jet type of
printer and may, for example, include five or more chambers (at
least one for each of four nucleoside phosphoramidite monomers plus
at least one for an activator solution) each communicating with a
corresponding set of multiple drop dispensing orifices and multiple
ejectors which are positioned in the chambers opposite respective
orifices. Each ejector is in the form of an electrical resistor
operating as a heating element under control of processor 140
(although piezoelectric elements could be used instead). Each
orifice with its associated ejector and portion of the chamber,
defines a corresponding pulse jet. It will be appreciated that head
210 could, for example, have more or less pulse jets as desired
(for example, at least ten or at least one hundred pulse jets, with
their nozzles organized in rows and columns). Application of a
single electric pulse to an ejector will cause a droplet to be
dispensed from a corresponding orifice. Certain elements of the
head 210 can be adapted from parts of a commercially available
thermal inkjet print head device available from Hewlett-Packard Co.
as part no. HP51645A. A suitable head construction is described in
U.S. patent application Ser. No. 09/150,507 filed Sep. 9, 1998 by
Caren et al. for "Method And Multiple Reservoir Apparatus For
Fabrication Of Biomolecular Arrays", incorporated herein by
reference. Alternatively, multiple heads could be used instead of a
single head 210, each being similar in construction to head 210 and
being movable in unison by the same transporter or being provided
with respective transporters under control of processor 140 for
independent movement. In this alternate configuration, each head
may dispense a corresponding biomonomer (for example, one of four
nucleoside phosphoramidites) or an activator solution.
[0053] As is well known in the ink jet print art, the amount of
fluid that is expelled in a single activation event of a pulse jet,
can be controlled by changing one or more of a number of
parameters, including the orifice diameter, the orifice length
(thickness of the orifice member at the orifice), the size of the
deposition chamber, and the size of the heating element, among
others. The amount of fluid that is expelled during a single
activation event is generally in the range about 0.1 to 1000 pL,
usually about 0.5 to 500 pL and more usually about 1.0 to 250 pL. A
typical velocity at which the fluid is expelled from the chamber is
more than about 1 m/s, usually more than about 10 m/s, and may be
as great as about 20 m/s or greater. As discussed above, when the
orifice is in motion with respect to the substrate surface at the
time an ejector is activated, the actual site of deposition of the
material will not be the location that is at the moment of
activation perpendicularly aligned with an orifice. However, the
actual deposited location will be predictable for the given
distances and velocities.
[0054] The apparatus further includes a display 310, speaker 314,
and operator input device 312. Operator input device 312 may, for
example, be a keyboard, mouse, or the like. Processor 140 has
access to a memory 141, and controls print head 210 (specifically,
the activation of the ejectors therein), operation of the
transporter system, operation of each jet in print head 210, and
operation of display 310 and speaker 314. Memory 141 may be any
suitable device in which processor 140 can store and retrieve data,
such as magnetic, optical, or solid state storage devices
(including magnetic or optical disks or tape or RAM, or any other
suitable device, either fixed or portable). Processor 140 may
include a general purpose digital microprocessor suitably
programmed from a computer readable medium carrying necessary
program code, to execute all of the steps required by the present
invention, or any hardware or software combination which will
perform those or equivalent steps. The programming can be provided
remotely to processor 141 through communication channel 180, or
previously saved in a computer program product such as memory 141
or some other portable or fixed computer readable storage medium
using any of those devices mentioned below in connection with
memory 141. For example, a magnetic or optical disk 324a may carry
the programming, and can be read by disk writer/reader 326. A
cutter 152 is provided to cut substrate 10 into individual array
units 15 each carrying a corresponding array 12.
[0055] The operation of the fabrication station will now be
described. It will be assumed that a substrate 10 on which arrays
12 are to be fabricated, is in position on station 20 and that
processor 140 is programmed with the necessary layout information
to fabricate target arrays 12. Using information such as the
foregoing target layout and the number and location of drop
dispensers in head 210, processor 140 can then determine a reagent
drop deposition pattern. Alternatively, such a pattern could have
been determined by another processor (such as a remote processor)
and communicated to memory 141 through communication channel 180 or
by forwarding a portable storage medium carrying such pattern data
for reading by reader/writer 326. Processor 140 controls
fabrication, in accordance with the deposition pattern, to generate
the one or more arrays 12 on substrate 10 by depositing for each
target feature during each cycle, a reagent drop set as previously
described. Drops are deposited from the head while moving along
each line of the raster during scanning. No drops are dispensed for
features or otherwise during line transitioning. Processor 140 also
sends substrate 10 to flood station 68 for cycle intervening or
final steps as required, all in accordance with the conventional in
situ polynucleotide array fabrication process described above. The
substrate 10 is then sent to a cutter 152 wherein portions of
substrate 10 carrying one ore more arrays 12 are separated from the
remainder of substrate 10, to provide multiple array units 15 each
with one or more arrays 12. One or more array units 15 may then be
forwarded to one or more remote users. Processor 140 also causes
deposition of drops from all multi-dispenser drop groups to be
deposited at separate test locations, such as at a test pattern 250
which may be separate from arrays 12 as already described above.
The foregoing array fabrication sequence can be repeated at the
fabrication station as desired for multiple substrates 10 in
turn.
[0056] During array fabrication errors can be monitored and used in
any of the manners described in U.S. Patent Application
"Polynucleotide Array Fabrication" by Caren et al., Ser. No.
09/302,898 filed Apr. 30, 1999, and U.S. Pat. No. 6,232,072.
Optionally characteristics of the fabricated arrays can be included
in a code applied to the array substrate or a housing, or a file
linkable to such code, in a manner as described in the foregoing
patent application and U.S. Pat. No. 6,180,351. As mentioned above,
these references are incorporated herein by reference.
[0057] Following receipt by a user of an array according to the
present invention, it will typically be exposed to a contiguous
layer of a same sample (for example, a fluorescently labeled
polynucleotide or protein containing sample) and the array then
read. Reading of the array may be accomplished by illuminating the
array and reading the location and intensity of resulting
fluorescence at each feature of the array. For example, a scanner
may be used for this purpose which is similar to the AGILENT
MICROARRAY SCANNER manufactured by Agilent Technologies, Palo Alto,
Calif. Other suitable apparatus and methods are described in U.S.
patent applications: Ser. No. 09/846,125 "Reading Multi-Featured
Arrays" by Dorsel et al.; and allowed application Ser. No.
09/430,214 "Interrogating Multi-Featured Arrays" by Dorsel et al.
However, arrays may be read by any other method or apparatus than
the foregoing, with other reading methods including other optical
techniques (for example, detecting chemiluminescent or
electroluminescent labels) or electrical techniques (where each
feature is provided with an electrode to detect hybridization at
that feature in a manner disclosed in U.S. Pat. No. 6,251,685, U.S.
Pat. No. 6,221,583 and elsewhere). Feature extraction (in which
features and their corresponding signals are identified in an image
of a read array) can be performed using procedures such as
described in U.S. patent applications Ser. Nos. 09/589046,
09/659415 and 10/086839, all under the title "Method And System For
Extracting Data From Surface Array Deposited Features". Results
from the reading may be raw results (such as fluorescence intensity
readings for each feature in one or more color channels) or may be
processed results such as obtained by rejecting a reading for a
feature which is below a predetermined threshold and/or forming
conclusions based on the pattern read from the array (such as
whether or not a particular target sequence may have been present
in the sample, or whether or not a pattern indicates a particular
condition of an organism from which the sample came). The results
of the reading (processed or not) may be forwarded (such as by
communication) to a remote location if desired, and received there
for further use (such as further processing).
[0058] In a variation of the above, it is possible that each unit
15 may be contained with a suitable housing. Such a housing may
include a closed chamber accessible through one or more ports
normally closed by septa, which carries the substrate 10.
[0059] Modifications in the particular embodiments described above
are, of course, possible. For example, each unit 15 may be
contained with a suitable housing. Such a housing may include a
closed chamber accessible through one or more ports normally closed
by septa, which carries the substrate 10. Where a pattern of arrays
is desired, any of a variety of geometries may be constructed other
than the organized rows and columns of arrays 12 of FIG. 1. For
example, arrays 12 can be arranged in a series of curvilinear rows
across the substrate surface (for example, a series of concentric
circles or semi-circles of spots), and the like. The length of the
elongated features could be oriented along these or the linear rows
described above, or at any angle thereto as described above in
connection with linear rows of features. Similarly, as mentioned,
the pattern of features 16 may be varied from the organized rows
and columns of spots in FIG. 2 to include, for example, a series of
curvilinear rows across the substrate surface(for example, a series
of concentric circles or semi-circles of spots), and the like.
[0060] The substrate surface onto which the polynucleotide
compositions or other moieties is deposited may be porous or
non-porous, smooth or substantially planar, or have irregularities,
such as depressions or elevations. The surface may be modified with
one or more different layers of compounds that serve to modify the
properties of the surface in a desirable manner. Such modification
layers, when present, will generally range in thickness from a
monomolecular thickness to about 1 mm, usually from a monomolecular
thickness to about 0.1 mm and more usually from a monomolecular
thickness to about 0.001 mm. Modification layers of interest
include: inorganic and organic layers such as metals, metal oxides,
polymers, small organic molecules and the like. Polymeric layers of
interest include layers of: peptides, proteins, polynucleic acids
or mimetics thereof (for example, peptide nucleic acids and the
like); polysaccharides, phospholipids, polyurethanes, polyesters,
polycarbonates, polyureas, polyamides, polyethyleneamines,
polyarylene sulfides, polysiloxanes, polyimides, polyacetates, and
the like, where the polymers may be hetero- or homopolymeric, and
may or may not have separate functional moieties attached thereto
(for example, conjugated).
[0061] Various further modifications to the particular embodiments
described above are, of course, possible. Accordingly, the present
invention is not limited to the particular embodiments described in
detail above.
* * * * *