U.S. patent application number 10/691038 was filed with the patent office on 2004-04-29 for methods of fabricating an addressable array of biopolymer probes.
Invention is credited to Bass, Jay K., Caren, Michael P., Schleifer, Kyle J., Webb, Peter G..
Application Number | 20040082059 10/691038 |
Document ID | / |
Family ID | 32107770 |
Filed Date | 2004-04-29 |
United States Patent
Application |
20040082059 |
Kind Code |
A1 |
Webb, Peter G. ; et
al. |
April 29, 2004 |
Methods of fabricating an addressable array of biopolymer
probes
Abstract
A method of fabricating an addressable array of biopolymer
probes on a substrate according to a target array pattern using a
deposition apparatus, and a deposition apparatus which can execute
the method and computer program products for the apparatus. The
deposition apparatus which, when operated according to a target
drive pattern based on nominal operating parameters of the
apparatus, provides the probes on the substrate in the target array
pattern. The method includes examining at least one operating
parameter for an error from a nominal value which error will result
in use of the target drive pattern producing a discrepancy between
the target array pattern and an actual array pattern deposited.
When an error is detected deriving, based on the error, a corrected
drive pattern different from the target drive pattern such that use
of the corrected drive pattern results in a reduced discrepancy
between the target and actual array patterns.
Inventors: |
Webb, Peter G.; (Menlo Park,
CA) ; Caren, Michael P.; (Palo Alto, CA) ;
Schleifer, Kyle J.; (Cupertino, CA) ; 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: |
32107770 |
Appl. No.: |
10/691038 |
Filed: |
October 21, 2003 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
|
10691038 |
Oct 21, 2003 |
|
|
|
09359527 |
Jul 22, 1999 |
|
|
|
Current U.S.
Class: |
435/287.2 ;
427/2.11 |
Current CPC
Class: |
B01J 2219/00637
20130101; G06T 7/0012 20130101; B01J 2219/00626 20130101; B82Y
30/00 20130101; B01J 2219/00315 20130101; B01J 2219/00527 20130101;
B01J 2219/00529 20130101; B01J 2219/00585 20130101; B01J 2219/00722
20130101; C40B 70/00 20130101; B01J 2219/00608 20130101; B01J
2219/00693 20130101; C40B 60/14 20130101; B01J 2219/00702 20130101;
B01J 2219/0036 20130101; B01J 2219/0061 20130101; B01J 19/0046
20130101; B01J 2219/00378 20130101; C40B 40/10 20130101; B01J
2219/00725 20130101; B01J 2219/0054 20130101; B01J 2219/00612
20130101; B01J 2219/00659 20130101; B01J 2219/00596 20130101; B01J
2219/00605 20130101; C40B 40/06 20130101; B01L 3/0241 20130101;
B01J 2219/00689 20130101; B01J 2219/00695 20130101; B01J 2219/00677
20130101 |
Class at
Publication: |
435/287.2 ;
427/002.11 |
International
Class: |
B05D 003/00; C12M
001/34 |
Claims
What is claimed is:
1. A method of fabricating an addressable array of biopolymer
probes on a substrate according to a target array pattern using a
deposition apparatus which, when operated according to a target
drive pattern based on nominal operating parameters of the
apparatus, provides the probes on the substrate in the target array
pattern, the method comprising: (a) examining at least one
operating parameter for an error from a nominal value which error
will result in use of the target drive pattern producing a
discrepancy between the target array pattern and an actual array
pattern deposited; (b) when an error is detected deriving, based on
the error, a corrected drive pattern different from the target
drive pattern such that use of the corrected drive pattern results
in a reduced discrepancy between the target and actual array
patterns.
2. A method according to claim 1, additionally comprising operating
the deposition apparatus according to the corrected drive
pattern.
3. A method according to claim 1 wherein the probes are DNA or RNA
probes.
4. A method according to claim 1 additionally comprising saving the
target drive pattern in a memory of the deposition apparatus.
5. A method according to claim 1 additionally comprising saving the
target drive pattern in a memory of the deposition apparatus, and
wherein the corrected drive pattern is saved in the memory.
6. A method according to claim 1 wherein the corrected drive
pattern is derived without obtaining a target drive pattern.
7. A method according to claim 4 wherein: the deposition apparatus
includes a dispensing head to dispense fluid droplets containing
the probes or probe precursors, and a transport system to move at
least one of the dispensing head and substrate relative to the
other as the droplets are dispensed from the head, so as to form
the array; and the drive pattern controls operation of the
transport system.
8. A method according to claim 1 wherein: the deposition apparatus
includes a dispensing head to dispense fluid droplets containing
the probes or probe precursors, and a transport system to move at
least one of the dispensing head and substrate relative to the
other as the droplets are dispensed from the head, so as to form
the array; the drive pattern controls operation of the transport
system; and the operating parameter is the position of the
substrate or dispensing head, which is examined by viewing the
substrate or dispensing head.
9. A method according to claim 8 wherein the operating parameter is
examined by viewing a fiducial mark on the dispensing head or
substrate
10. A method according to claim 1 wherein: the deposition apparatus
includes a dispensing head with multiple nozzles to dispense fluid
droplets containing the probes or probe precursors, and a transport
system to move at least one of the dispensing head and substrate
relative to the other as the droplets are dispensed from the head,
so as to form the array; the drive pattern controls operation of
the transport system; the operating parameter is the position of
the substrate or dispensing head, or orientation of a nozzle, and
is examined by viewing the substrate, dispensing head, or nozzle,
or a droplet pattern previously dispensed from the head.
11. A method according to claim 7 additionally comprising saving
the target drive pattern in a memory of the deposition apparatus,
and wherein the corrected drive pattern is saved in the memory,
prior to operating the dispensing head and transport system to form
the array.
12. A method according to claim 7 additionally comprising saving
the target drive pattern in a memory of the deposition apparatus,
and wherein the corrected drive pattern is derived by modifying,
based on the detected error, instructions to at least one
deposition apparatus component based on the target drive pattern
during operation of the dispensing head and transport system to
form the array.
13. A method according to claim 1 wherein the at least one
parameter is the position of the substrate in the deposition
apparatus.
14. A method according to claim 7 wherein the at least one
parameter is a position of the dispensing head.
15. A method according to claim 7 wherein the deposition apparatus
further includes a position encoder to detect the position of the
dispensing head or the substrate, and wherein the at least one
parameter is the accuracy of the encoder.
16. A method according to claim 7 wherein the at least one
parameter is the accuracy in an ability of the transport system to
move the substrate to an expected location in response to a
command.
17. A method according to claim 7 wherein the dispensing head has
multiple droplet dispensing nozzles, and wherein the at least one
parameter is a position of a nozzle.
18. A method of fabricating an addressable array of biopolymer
probes on a substrate according to a target array pattern using a
deposition apparatus which, when operated according to a target
drive pattern based on nominal operating parameters of the
apparatus and which is stored in a memory of the deposition
apparatus, provides the probes on the substrate in the target array
pattern, the method comprising: when an error from a nominal value
exists in at least one operating parameter, which error will result
in use of the target drive pattern producing a discrepancy between
the target array pattern and an actual array pattern deposited then
deriving, based on the error, a corrected drive pattern from the
target drive pattern such that use of the corrected drive pattern
results in a reduced discrepancy between the target and actual
array patterns.
19. A method according to claim 18 wherein the corrected drive
pattern is saved in the memory.
20. A method of fabricating an addressable array of biopolymer
probes on a substrate carrying at least one fiducial mark, using a
fabrication apparatus which includes a dispensing head to dispense
fluid droplets containing the probes or probe precursors, the
method comprising observing the at least one fiducial mark and,
based upon the observation, rotating the substrate to a
predetermined angular relationship with respect to the dispensing
head.
21. An apparatus for fabricating an addressable array of biopolymer
probes on a substrate according to a target array pattern which
apparatus, when operated according to a target drive pattern based
on nominal operating parameters of the apparatus, provides the
probes on the substrate in the target array pattern, the apparatus
comprising: (a) a sensor which senses at least one operating
parameter for an error from a nominal value which error will result
in use of the target drive pattern producing a discrepancy between
the target array pattern and an actual array pattern deposited; (b)
a processor which, when an error is detected by the sensor derives,
based on the error, a corrected drive pattern different from the
target drive pattern such that use of the corrected drive pattern
results in a reduced discrepancy between the target and actual
array patterns.
22. An apparatus according to claim 21 additionally comprising: a
dispensing head to dispense fluid droplets containing the probes or
probe precursors, and a transport system to move at least one of
the dispensing head and substrate relative to the other as the
droplets are dispensed from the head, so as to form the array; and
wherein: the drive pattern controls operation of the transport
system; the operating parameter is the position of the substrate or
dispensing head; and the sensor views the substrate or dispensing
head to obtain its position.
23. An apparatus according to claim 22 wherein the sensor views a
fiducial mark on the dispensing head or substrate
24. An apparatus according to claim 21 additionally comprising: a
dispensing head with multiple nozzles to dispense fluid droplets
containing the probes or probe precursors, and a transport system
to move at least one of the dispensing head and substrate relative
to the other as the droplets are dispensed from the head, so as to
form the array; and wherein: the drive pattern controls operation
of the transport system; the operating parameter is the position of
the substrate or dispensing head, or orientation of a nozzle; and
the sensor views the substrate, dispensing head, or nozzle, or a
droplet pattern previously dispensed from the head.
25. An apparatus according to claim 21 additionally comprising a
memory accessible by the processor to save the target drive
pattern, and wherein the processor, when no error is detected,
causes the apparatus to operate in accordance with the target drive
pattern.
26. An apparatus according to claim 21 comprising a memory
accessible by the processor to save the target drive pattern, and
wherein the processor: when no error is detected, causes the
apparatus to operate in accordance with the target drive pattern;
and when an error is detected and a corrected drive pattern derived
by the processor, saves the corrected drive pattern is saved in the
memory.
27. An apparatus according to claim 21 wherein the processor
derives the corrected drive without obtaining a target drive
pattern.
28. An apparatus according to claim 21 additionally comprising: a
dispensing head to dispense fluid droplets containing the probes or
probe precursors; and a transport system to move at least one of
the dispensing head and substrate relative to the other as the
droplets are dispensed from the head, so as to form the array; and
wherein the processor controls operation of the transport system in
accordance with one of the drive patterns.
29. An apparatus according to claim 28 wherein the processor saves
the target drive pattern in the memory, and saves the corrected
drive pattern in the memory prior to operating the dispensing head
and transport system to form the array.
30. An apparatus according to claim 21 additionally comprising a
memory accessible by the processor, wherein the processor saves the
target drive pattern in a memory of the deposition apparatus; and
the processor derives the corrected drive pattern by modifying,
based on the detected error, instructions to at least one apparatus
component based on the target drive pattern during deposition of
the probes to form the array.
31. An apparatus according to claim 25 wherein the at least one
parameter is the position of the substrate in the deposition
apparatus.
32. An apparatus according to claim 28 wherein the at least one
parameter is a position of the dispensing head.
33. An apparatus according to claim 28 additionally comprising a
position encoder to detect the position of the dispensing head or
the substrate, and wherein the at least one parameter is the
accuracy of the encoder.
34. An apparatus according to claim 28 wherein the at least one
parameter is the accuracy in an ability of the transport system to
move the dispensing head or substrate to an expected location in
response to a command.
35. An apparatus according to claim 34 wherein the transporter
moves the dispensing head or substrate along a corresponding
nominal axis, and wherein the at least one parameter is the
deviation of actual movement from the corresponding nominal
axis.
36. An apparatus according to claim 28 wherein the dispensing head
has multiple droplet dispensing nozzles, and wherein the at least
one parameter is a position of a nozzle.
37. An apparatus for fabricating an addressable array of biopolymer
probes on a substrate according to a target array pattern,
comprising (a) a memory to store a target drive pattern based on
nominal operating parameters of the apparatus to provide the probes
on the substrate in the target array pattern; (b) a processor to
receive an indication of an error from a nominal value in at least
one operating parameter, which error will result in use of the
target drive pattern producing a discrepancy between the target
array pattern and an actual array pattern deposited, and to derive
a corrected drive pattern from the target drive pattern such that
use of the corrected drive pattern results in a reduced discrepancy
between the target and actual array patterns.
38. An apparatus for fabricating an addressable array of biopolymer
probes on a substrate carrying at least one fiducial mark, the
apparatus comprising: a dispensing head to dispense fluid droplets
containing the probes or probe precursors; a sensor to sense the
position of the at least one fiducial mark on the substrate, and a
transporter which based on the position of the at least one
fiducial marked as sensed by the sensor, can rotate the substrate
to a predetermined angular relationship with respect to the
dispensing head.
39. An apparatus according to claim 37 wherein the corrected drive
pattern is saved in the memory.
40. A computer program product, for use on an apparatus for
fabricating an addressable array of biopolymer probes on a
substrate according to a target array pattern which apparatus, when
operated according to a target drive pattern based on nominal
operating parameters of the apparatus, provides the probes on the
substrate in the target array pattern; the program product
comprising: a computer readable storage medium having a computer
program stored thereon which, when loaded into a computer of the
apparatus performs the steps of: (a) receiving a signal from a
sensor which senses at least one operating parameter for an error
from a nominal value which error will result in use of the target
drive pattern producing a discrepancy between the target array
pattern and an actual array pattern deposited; and (b) when an
error is detected by the sensor, deriving, based on the error, a
corrected drive pattern different from the target drive pattern
such that use of the corrected drive pattern results in a reduced
discrepancy between the target and actual array patterns.
41. A computer program product according to claim 40, wherein the
program additionally performs the step of operating the apparatus
according to the corrected drive pattern.
42. A computer program product according to claim 41, wherein the
program additionally performs the steps of saving the target drive
pattern in a memory of the apparatus, and saving the corrected
drive pattern in the memory prior to operating the apparatus
according to the corrected drive pattern.
43. A computer program product according to claim 41 wherein the
program additionally performs the steps of: saving the target drive
pattern in a memory of the deposition apparatus; and deriving the
corrected drive pattern by modifying, based on the detected error,
instructions to at least one apparatus component based on the
target drive pattern, during deposition of the probes to form the
array.
44. A computer program product, for use on an apparatus for
fabricating an addressable array of biopolymer probes on a
substrate according to a target array pattern which apparatus, when
operated according to a target drive pattern based on nominal
operating parameters of the apparatus, provides the probes on the
substrate in the target array pattern the program product
comprising: a computer readable storage medium having a computer
program stored thereon which, when loaded into a computer of the
apparatus performs the steps of: (a) storing the target drive
pattern in a memory; (b) receiving an input signal indicating an
error from a nominal value in at least one operating parameter,
which error will result in use of the target drive pattern
producing a discrepancy between the target array pattern and an
actual array pattern deposited; and (c) deriving a corrected drive
pattern from the target drive pattern such that use of the
corrected drive pattern results in a reduced discrepancy between
the target and actual array patterns.
45. A computer program product according to claim 44, wherein the
program additionally performs the step of operating the apparatus
according to the corrected drive pattern.
Description
FIELD OF THE INVENTION
[0001] This invention relates to arrays, particularly
polynucleotide arrays such as DNA arrays, which are useful in
diagnostic, screening, gene expression analysis, and other
applications.
BACKGROUND OF THE INVENTION
[0002] Polynucleotide arrays (such as DNA or RNA arrays), are known
and are used, for example, as diagnostic or screening tools. Such
arrays include regions (sometimes referenced as features) of
usually different sequence polynucleotides arranged in a
predetermined configuration on a substrate. The arrays, when
exposed to a sample, will exhibit an observed binding pattern. This
binding pattern can be detected, for example, by labeling all
polynucleotide targets (for example, DNA) in the sample with a
suitable label (such as a fluorescent compound), and accurately
observing the fluorescence pattern on the array. 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 of the
sample.
[0003] Biopolymer arrays can be fabricated using either in situ
synthesis methods or deposition of the previously obtained
biopolymers. The in situ synthesis methods include those described
in U.S. Pat. No. 5,449,754 for synthesizing peptide arrays, as well
as WO 98/41531 and the references cited therein for synthesizing
polynucleotides (specifically, DNA). Such in situ synthesis methods
can be basically regarded as iterating the sequence of depositing
droplets of: (a) a protected monomer onto predetermined locations
on a substrate to link with either a suitably activated substrate
surface (or with a previously deposited deprotected monomer); (b)
deprotecting the deposited monomer so that it can now react with a
subsequently deposited protected monomer; and (c) depositing
another protected monomer for linking. Different monomers may be
deposited at different regions on the substrate during any one
iteration so that the different regions of the completed array will
have different desired biopolymer sequences. One or more
intermediate further steps may be required in each iteration, such
as oxidation and washing steps. 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 regions of the substrate to yield the
completed array. Washing or other additional steps may also be
used.
[0004] Typical procedures known in the art for deposition of
polynucleotides, particularly DNA such as whole oligomers or cDNA,
are to load a small volume of DNA in solution in one or more drop
dispensers such as the tip of a pin or in an open capillary and,
touch the pin or capillary to the surface of the substrate. Such a
procedure is described in U.S. Pat. No. 5,807,522. When the fluid
touches the surface, some of the fluid is transferred. The pin or
capillary must be washed prior to picking up the next type of DNA
for spotting onto the array. This process is repeated for many
different sequences and, eventually, the desired array is formed.
Alternatively, the DNA can be loaded into a drop dispenser in the
form of an inkjet head and fired onto the substrate. Such a
technique has been described, for example, in PCT publications WO
95/25116 and WO 98/41531, and elsewhere. This method has the
advantage of non-contact deposition. Still other methods include
pipetting and positive displacement pumps such as the Biodot
equipment (available from Bio-Dot Inc., Irvine Calif., USA).
[0005] 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 use of arrays with large numbers of very small, closely
spaced features. It is important in such arrays that features
actually be present, that they are put down accurately in the
desired pattern, are of the correct size, and that the DNA is
uniformly coated within the feature. Normally, in an automated
apparatus the features are deposited according to a target array
pattern. A target drive pattern is created from the target array
pattern, which target drive pattern contains the instructions for
driving the various components so as to provide the probes on the
substrate in the target array pattern. The target drive pattern is
created on the assumption that all components of the deposition
apparatus are in their expected or normal ("nominal") positions and
operating according to nominal parameters.
[0006] However, the present invention realizes that every component
in an array deposition apparatus is subject to variances in its
parameters within, or sometimes even outside of, normal tolerances
for such component. For example, a dispensing head used to dispense
fluid droplets to form the array, may have jets which vary slightly
in the size of the droplets dispensed, the orientation of the jets
with respect to one another, or the orientation of the head itself
in the apparatus may be slightly off from a nominal position. While
such variances can be reduced by constructing a dispensing
apparatus with components of higher tolerance (that is, less
variation), this can increase cost. Furthermore, the present
invention realizes that while a given set of parameters may exist
during manufacture of a given batch of arrays, these parameters may
change over time. For example, thermal expansion or of components
or slight displacement of them from their original positions over
long periods of operation, leads to variance in position
parameters. These effects result in use of the target drive pattern
not producing the target array on the substrate. That is, there is
a discrepancy between the target array pattern and the actual array
pattern deposited. Such discrepancy may include mislocation of
features, or features not being of the correct size. These
discrepancies can occur in each cycle of the in situ process, or
during deposition of presynthesized polynucleotides.
[0007] It would be useful then, to provide a means by which arrays
can be fabricated with an actual array pattern which is close to
the target array pattern. It would also be useful if such means was
relatively reliable and not overly costly.
SUMMARY OF THE INVENTION
[0008] The present invention then, provides in one aspect, a method
of fabricating an addressable array of biopolymer probes on a
substrate according to a target array pattern, using a deposition
apparatus. The deposition apparatus, when operated according to a
target drive pattern based on nominal operating parameters of the
apparatus, provides the probes on the substrate in the target array
pattern. The method includes examining at least one operating
parameter of the apparatus for an error from a nominal value which
error will result in use of the target drive pattern producing a
discrepancy between the target array pattern and an actual array
pattern deposited. When an error is detected, a corrected drive
pattern different from the target drive pattern is derived, based
on the error, such that use of the corrected drive pattern results
in a reduced discrepancy between the target and actual array
patterns.
[0009] The method may also include operating the deposition
apparatus according to the corrected drive pattern. Furthermore,
the present invention can be used to deposit different types of
biopolymers or even other different chemical moieties, including
peptides and polynucleotides such as DNA or RNA. Thus, various
additional embodiments of the invention can be described by
replacing biopolymer probes in the descriptions herein, with
moieties. The target drive pattern can initially be saved in a
memory of the deposition apparatus, and the corrected drive pattern
can also optionally be saved in the memory (for example, either
after or during its derivation). In one particular construction,
the deposition apparatus includes a dispensing head to dispense
fluid droplets containing the probes or probe precursors (for
example, monomers), and a transport system to move at least one of
the dispensing head and substrate relative to the other as the
droplets are dispensed from the head, so as to form the array. In
this case, the drive pattern controls operation of the transport
system. The saving of the corrected drive pattern may, for example,
be done prior to operating the dispensing apparatus. As an
alternative, the corrected drive pattern may be derived by
modifying, based on the detected error, instructions to at least
one deposition apparatus component based on the target drive
pattern during deposition of the probes to form the array. For
example, an instruction based on the target drive pattern may be
sent to the foregoing dispensing head but that instruction is
modified, before actually driving the head in some manner, based on
the detected error. In this arrangement then, the corrected drive
pattern is derived during apparatus operation.
[0010] The at least one operating parameter can be selected from
one or more of any parameter which would affect the actual array
pattern deposited. For example, these may include: a position of
the dispensing head or any other dispensing apparatus component;
the accuracy of an encoder used to detect the position of the
dispensing head or the substrate; the accuracy in an ability of the
transport system to move the substrate or head to an expected
location in response to a command (for example, deviation of actual
movement from a corresponding nominal axis of movement); or the
position of a position of a nozzle in a multiple nozzle dispensing
head. Note that "position" includes linear position as well as
orientation of one component with respect to the other, and may be
an absolute or relative quantity (for example, the position of a
dispensing jet in the head relative to another jet in that head, or
relative to the substrate). Parameters can be directly examined
(such as by examining movement of the transport system or nozzle),
or indirectly examined (such as by examining the actual results
from previous depositions of the apparatus and comparing with
expected results). Such examination can be made during formation of
a given array, or obtained during (or from) previous depositions
from the apparatus, for example either test depositions (sometimes
referenced as "test prints") or a previous array deposition (such
as an immediately preceding array deposition).
[0011] Another aspect of the method of the present invention, the
target drive pattern is stored in a memory of the deposition
apparatus, and when an error from a nominal value exists in at
least one operating parameter, a corrected drive pattern is derived
from the target drive pattern such that use of the corrected drive
pattern results in a reduced discrepancy between the target and
actual array patterns.
[0012] The present invention also provides an apparatus which, in
one or more aspects, may be of a type described in connection with
any of the above methods. Such an apparatus includes, in one
aspect, a sensor which senses at least one operating parameter for
an error from a nominal value which error will result in use of the
target drive pattern producing a discrepancy between the target
array pattern and an actual array pattern deposited. This apparatus
also includes a processor which, when an error is detected by the
sensor derives, based on the error, a corrected drive pattern
different from the target drive pattern such that use of the
corrected drive pattern results in a reduced discrepancy between
the target and actual array patterns.
[0013] The apparatus may also include a memory accessible by the
processor to save the target drive pattern, and wherein the
processor, when no error is detected, causes the apparatus to
operate in accordance with the target drive pattern. The processor
may further optionally save a corrected drive pattern in the
memory. Alternatively, the processor may derive the corrected drive
pattern during deposition of the probes to form the array, by
modifying, based on the detected error, instructions to at least
one apparatus component based on the target drive pattern, as
mentioned above. The apparatus may further include a dispensing
head and a transport system controlled by the processor, as already
described. Various parameters are also described above.
[0014] In another aspect, the apparatus includes a memory to store
a target drive pattern based on nominal operating parameters of the
apparatus to provide the probes on the substrate in the target
array pattern. This aspect of the apparatus also includes a
processor to receive an error indication of the type already
described, and to derive the corrected drive pattern.
[0015] The present invention further provides a computer program
product which can be used on one or more of the apparatus types
already described. This computer program product includes a
computer readable storage medium having a computer program stored
on it which, when loaded into a computer, instructs the processor
to execute the steps described above.
[0016] The present invention then, including methods, apparatus,
and computer program products thereof, can provide any one or more,
of a number of useful benefits. For example, arrays can be
fabricated with an actual array pattern which is close to the
target array pattern. Further, the invention is relatively reliable
and not overly costly.
BRIEF DESCRIPTION OF THE DRAWINGS
[0017] FIG. 1 is a perspective view of a substrate bearing multiple
arrays, as may be produced by a method and apparatus of the present
invention;
[0018] FIG. 2 is an enlarged view of a portion of FIG. 1 showing
some of the identifiable individual regions (or "features") of a
single array of FIG. 1;
[0019] FIG. 3 is an enlarged cross-section of a portion of FIG.
2;
[0020] FIG. 4 is a schematic view of apparatus of the present
invention;
[0021] FIG. 5 is a flowchart illustrating a method of the present
invention; and
[0022] FIGS. 6 through 8 are memory images illustrating the
operation of the present invention.
[0023] 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
[0024] 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 found in biological systems and
particularly include peptides or polynucleotides, as well as such
compounds composed of or containing amino acid 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 in
which one or more of the conventional bases has been replaced with
a synthetic base 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 subunit of a nucleic acid and has a phosphate group, a
5 carbon sugar and a nitrogen containing base, as well as analogs
of such subunits. Specifically, a "biopolymer" includes DNA
(including cDNA), RNA and oligonucleotides. 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 biomonomer fluid
or biopolymer fluid reference a liquid containing either a
biomonomer or biopolymer, respectively (typically in solution). An
"addressable array" includes any one or two dimensional arrangement
of discrete regions (or "features") bearing particular biopolymer
moieties (for example, different polynucleotide sequences)
associated with that region and positioned at a particular location
on the substrate (an "address"). These regions may or may not be
separated by intervening spaces. It will also be appreciated that
throughout the present application, words such as "upper", "lower"
and the like are used with reference to a particular orientation of
the apparatus with respect to gravity, but it will be understood
that other operating orientations of the apparatus or any of its
components, with respect to gravity, are possible. Reference to a
"droplet" being dispensed from a pulse jet herein, merely refers to
a discrete small quantity of fluid (usually less than about 1000
pL) being dispensed upon a single pulse of the pulse jet
(corresponding to a single activation of an ejector) and does not
require any particular shape of this discrete quantity. However, it
will be understood that a given feature may be formed from one or
multiple pulses from one or multiple nozzles. When a "spot" is
referred to, this may reference a dried spot on the substrate
resulting from drying of one or more dispensed droplets, or a wet
spot on the substrate resulting from one or more dispensed droplets
which have not yet dried, depending upon the context. The dried
spot will normally be the resulting feature in the case of
deposition of pre-synthesized biopolymer, but will not be the
resulting feature in the case of in situ formation synthesis of
biopolymers. Reference to "viewing" indicates observation by any
optical device, such as a camera. The head or substrate moving "as"
droplets are dispensed includes actual movement during and/or
between the dispensing of multiple droplets. "Fluid" is used herein
to reference a liquid. By one item being "remote" from another is
referenced that they are at least in different buildings, and may
be at least one, at least ten, or at least one hundred miles
apart.
[0025] Referring first to FIGS. 1-3, typically the present
invention will produce multiple identical arrays 12 (only some of
which are shown in FIG. 1) across the complete upper surface 11a of
a single substrate 10. However, the arrays 12 produced on a given
substrate need not be identical and some or all could be different.
Each array 12 will contain multiple spots or features 16. A typical
array 12 may contain from 100 to 100,000 features. All of the
features 16 may be different, or some or all could be the same.
Each feature carries a predetermined polynucleotide having a
particular sequence, or a predetermined mixture of polynucleotides.
This is illustrated schematically in FIG. 3 where different regions
16 are shown as carrying different polynucleotide sequences.
Substrate 10 also includes fiducial markings 18 on upper surface
11a, for purposes which will be described below. Fiducial markings
18 can be scratches, ink marks, metallized markings (for example,
chromium) markers, laser ablated grooves, or any other suitable
marking.
[0026] Referring to FIG. 4 the apparatus shown includes a substrate
station 20 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.
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.
[0027] A dispensing head 210 is retained by a head retainer 208.
Head 210 has fiducial markings 211, for purposes described below,
and can be positioned at any position facing substrate 10 by means
of a positioning system. The positioning 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 nominal 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 nominal axis 204. In this manner, head
210 can be scanned line by line, by scanning along a line over
substrate 10 in the direction of axis 204 using transporter 100,
while line by line movement of substrate 10 in a direction of axis
63 is provided by transporter 60. Head 210 may also optionally be
moved in a vertical direction 202, by another suitable transporter
(not shown). However, it will be appreciated that other scanning
configurations could be used. However, it will 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 refers to "positioning" 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. 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. Angular positioning of substrate station
20 is provided by a transporter 120, which can rotate substrate
station 20 about axis 202 under control of processor 140.
Typically, substrate station 20 (and hence a mounted substrate) is
rotated by transporter 120 under control of processor 140 in
response to an observed angular position of substrate 10 as
determined by processor 140 through viewing one or more fiducial
marks on substrate 10 (particularly fiducial marks 18) with camera
304. This rotation will continue until substrate 10 has reached a
predetermined angular relationship with respect to dispensing head
210. In the case of a square or rectangular substrate, the mounted
substrate 10 will typically be rotated to align one edge (length or
width) with the scan direction of head 210 along axis 204.
[0028] Head 210 may be of a type commonly used in an ink jet type
of printer and may, for example, have one hundred fifty drop
dispensing orifices in each of two parallel rows, six chambers for
holding polynucleotide solution communicating with the three
hundred orifices, and three hundred ejectors which are positioned
in the chambers opposite a corresponding orifice. 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 with the orifice acting as a nozzle. Thus, there are three
hundred pulse jets in this configuration, although 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). In this manner, application of a single
electric pulse to an ejector causes a droplet to be dispensed from
a corresponding orifice. In the foregoing configuration, typically
about twenty orifices in each group of six reservoirs (many of the
orifices are unused and are plugged with glue), will be dispensing
the same fluid. 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. The
foregoing head 210 and other suitable dispensing head designs are
described in more detail in U.S. patent application entitled "A
MULTIPLE RESERVOIR INK JET DEVICE FOR THE FABRICATION OF
BIOMOLECULAR ARRAYS" Ser. No. 09/150,507 filed Sep. 9, 1998.
However, other head configurations can be used, for example a head
with thirty reservoirs, and even multiple heads can also be used as
desired.
[0029] 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 will be appreciated, if the
orifice is in motion with respect to the receiving 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 in a line-of-sight relation to the orifice, but will be
a location that is predictable for the given distances and
velocities.
[0030] The sizes of the features can have widths (that is,
diameter, for a round spot) in the range from a minimum of about 10
.mu.m to a maximum of about 1.0 cm. In embodiments where very small
spot sizes or feature sizes are desired, material can be deposited
according to the invention in small spots whose width is in the
range about 1.0 .mu.m to 1.0 mm, usually about 5.0 .mu.m to 500
.mu.m, and more usually about 10 .mu.m to 200 .mu.m. Spot sizes can
be adjusted as desired, by using one or a desired number of pulses
from a pulse jet to provide the desired final spot size.
[0031] The apparatus further includes a sensor in the form of a
first camera 300 located to view fiducial markings on head 210
and/or the positions of the nozzles on head 210. Typical fiducial
markings are shown as fiducial markings 211 on the side of head 210
for visibility, although in practice fiducial marks viewed by first
camera 300 may be on the underside of head 210. A second sensor in
the form of a second camera 304, is located to observe the
positions of fiducial markings 18 on substrate. Cameras 300 and 304
communicate with processor 140, and each should have a resolution
that provides a pixel size of about 1 to 100 micrometers and more
typically about 4 to 20 micrometers or even 1 to 5 micrometers. Any
suitable analog or digital image capture device (including a line
by line scanner) can be used for such camera, although if an analog
camera is used processor 140 should include a suitable
analog/digital converter. Further, other numbers of cameras may be
used. For example, a single camera with the correct orientation and
parameters, could be used in place of cameras 300 and 304. A
display 310, speaker 314, and operator input device 312, are
further provided. 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 positioning system,
operation of each jet in print head 210, capture of images from the
cameras, and operation 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 fucntions required of it as
described below. It will be appreciated though, that when a
"processor" such as processor 140 is referenced throughout this
application, that such includes any hardware and/or software
combination which will perform the required functions. For example,
for errors in the transport system, a corrected drive pattern can
be produced by programming a device such as the Programmable Error
Correction PKE 80, available form RSF Electronik, Rancho Cordova,
Calif., USA, with measured error data obtained from examining the
transport system of the deposition apparatus apparatus. A
microprocessor which provides the target drive pattern, together
with the foregoing programmed device, then operates as a
"processor" of the present invention. The programming can be
provided remotely to processor 140, 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 324 may carry the programming, and can
be read by disk reader 326.
[0032] Operation of the apparatus of FIG. 4 in accordance with a
method of the present invention, will now be described with
reference to that FIG. and FIG. 5. First, it will be assumed that
memory 141 holds a target drive pattern. This target drive pattern
is the instructions for driving the apparatus components as
required to form the target array (which includes target locations
and dimension for each spot) on substrate 10 and includes, for
example, movement commands to transporters 60 and 100 as well as
firing commands for each of the pulse jets in head 210 coordinated
with the movement of head 210 and substrate 10, as well as
instructions for which polynucleotide solution (or precursor) is to
be loaded in each pulse jet (that is, the "loading pattern"). This
target drive pattern is based upon the target array pattern and can
have either been input from an appropriate source (such as input
device 312, a portable magnetic or optical medium, or from a remote
server, any of which communicate with processor 140), or may have
been determined (402) by processor 140 based upon an input target
array pattern (using any of the appropriate sources previously
mentioned) and the previously known nominal operating parameters of
the apparatus (400). Further, it will be assumed that drops of
different biomonomer or biopolymer containing fluids (or other
fluids) have been placed at respective regions of a loading station
(not shown). Operation of the following sequences are controlled by
processor 140, following initial operator activation, unless a
contrary indication appears.
[0033] For any given substrate 10, the operation is basically
follows: (i) determine (402) target drive pattern (if not already
provided) to obtain target array pattern, based on nominal
operating parameters and target polynucleotide array pattern; (ii)
examine (406) operating parameter data (404) from sensors 300, 304
for an error from a nominal value, which error will result in use
of the target drive pattern producing a discrepancy between the
target array pattern and an actual array pattern which would be
deposited if the target drive pattern was used; (iii) if there is
no error in one or more operating parameters (406) then the
apparatus is operated according to the target drive pattern; (iv)
if there is an error in one or more operating parameters (406) then
processor 140 derives, based on the error, a corrected drive
pattern from the target pattern such that use of the corrected
drive pattern results in a reduced discrepancy between the target
and actual array patterns than would have occurred if the target
drive pattern had been used.
[0034] It will be appreciated that any discrepancy between a
nominal parameter and an actual sensed parameter, may optionally
only be classified as an "error" in an operating parameter, if it
meets or exceeds a predetermined threshold value. Particular
examples of operating parameter errors which may occur in the
apparatus of FIG. 4 include any one or more of the following:
[0035] 1. Substrate 10 may be incorrectly positioned with respect
to encoder 30 or encoder 34.
[0036] 2. Head 210 may be incorrectly positioned with respect to
encoder 34 or, where there are multiple heads 210 in the apparatus,
one or more of them may be incorrectly positioned with respect to
each other.
[0037] 3. Head 210 may be skewed (orientation error), and thus its
nozzles vary from their desired positions and/or orientations with
respect to encoder 34.
[0038] 4. Either encoder 30, 34 may have intrinsic errors, due to
which it will report an incorrect position.
[0039] 5. Either substrate 10 or either encoder 30, 34 may suffer
from thermal expansion.
[0040] 6. The transporter 60 and carriage 62 used to move the
substrate in the direction of nominal axis 63 (orthogonal to the
direction 204of scanning of head 210) may also have intrinsic
errors, suffer from thermal expansion, or operate at a deviation to
nominal axis 63 (a non-straight deviation in the direction of axis
204 and/or a non-flat deviation in the direction of axis 202). In
addition, component imperfections may cause the transport to suffer
from Abbe errors.
[0041] 7. The nozzles of head 210 may fire at an angle to that
intended. The above operating parameter errors can be sensed and
used by processor 140 to derive an actual drive map as follows:
[0042] 1. The actual position of substrate 10 can be determined by
observation of fiducial marks 18 by camera 304. If different
substrates are repeatedly placed on substrate station 20, this
error can be determined each time it is placed.
[0043] 2. The position of head 210 can be determined by observation
of fiducial marks 211 and/or the nozzles themselves by camera 300.
In a preferred embodiment, the same camera is used for this
observation and observation of substrate fiducials 18, this scheme
having the advantage that no inter-camera calibration is
required.
[0044] 3. Same as in 2.
[0045] 4. Laser-interferometer mapping of the errors in the
encoders is a method well established in the art, and will provide
a measurement of the relative error at many points along the
encoder.
[0046] 5. Thermal expansion can be measured by repeated observation
of substrate fiducial marks 18 by camera 304, and by repeated
observation of head fiducial marks 211 after movement by camera 300
or optionally by two cameras. Alternatively, a thermistor could be
used and an expected thermal expansion calculated.
[0047] 6. Errors in operation of transporter 60 and carriage 62 can
be mapped by means of camera 304, and thermal expansion mapped by
observation of fiducial marks on carriage 62 by a camera (or
optionally two cameras). Non-straightness and or flatness can be
determined by laser interferometry. Laser interferometry mapping of
Abbe errors in a transport system generally, is a known
technique.
[0048] 7. Test-print patterns can be observed with a camera (such
as camera 304) to observe drop placement. Suitable observations
techniques are described, for example, in co-pending U.S. patent
application Ser. No. 09/302,898 filed Apr. 30, 1999 by Caren et
al., assigned to the same assignee as the present application,
incorporated herein by reference.
[0049] The apparatus is then operated (410) as follows: (a) load
head 210 with a first set of polynucleotide containing solutions or
their precursors (for example, a given head may be able to hold n
different members); (b) dispense droplets from head 210 onto
substrate 10 or a set of substrates in accordance with the target
or corrected drive patterns to provide the target array pattern for
the first set on each of multiple arrays 12; and (c) repeat the
foregoing sequence starting at step (i) with a second set and
subsequent sets of polynucleotide containing solutions or their
precursors, until all required solutions have been dispensed onto
substrate 10 (for example, if each array has m.multidot.n members,
and presynthesized polynucleotides are being dispensed, then the
sequence will be repeated m times). Optionally, as another means of
providing operating parameter data, the deposited arrays can be
inspected by capturing one or more images such as from camera 304
and comparing the deposited array pattern with the target array
pattern. Differences in the foregoing may indicate particular types
of errors (for example, a single nozzle of head 210 is oriented
incorrectly with respect to other nozzles of head 210). For
example, an inspection could be performed on after step (b) in each
cycle. Preferably, all arrays on a given substrate 10 have been
inspected before shipping to an end user. The foregoing steps are
discussed in more detail below.
[0050] The manner of correction provided by processor 140 can be
more readily understood by reference to FIGS. 6 through 8. In
particular, FIG. 6 represents an image in memory 141 of a portion
of the target drive pattern. It will be assumed that this pattern
is created by a dispensing head with a three by two matrix of
dispensing jets (oriented with three jets in the vertical direction
of FIGS. 6-8 and two in the horizontal direction), thus requiring a
firing of all jets, followed by head displacement and another
firing of all jets. Hence FIG. 6 corresponds to the appearance of
the target array pattern if all relevant components of the
deposition apparatus are operating according to their normal
parameters ("operating" in this context includes correct
positioning, whether static or dynamic). However, from observations
of previous test prints by camera 300, processor 140 determines
there is an error in relative orientation of the nozzle of head 210
which produces spots 16a. Similarly, an error is determined in
fluid volumes deposited by the nozzle of head 210 which produces
spots 16b. Processor 140 then derives a corrected drive pattern,
the image in memory of the corrected drive pattern being
illustrated in FIG. 6. This corrected drive pattern incorporates an
inverse of the determined errors. That is, in order to correct for
displacement (in the upward direction as viewed in FIG. 7) of spots
16a, the actual drive image will contain an instruction to move the
head lower (as viewed in FIG. 8) than the nominal position of FIG.
6 to compensate for the displacement in FIG. 7. Similarly, to
correct for the below expected volume (that is, the nominal volume)
produced by the jets producing features 16b, the actual drive image
will contain an instruction for that jet to fire multiple spots or
with more energy (this appearing as enlarged features 16b in FIG.
8) to compensate for the low volume error. Alternatively, the
actual drive image can be an instruction to switch to a different
jet in the head when a deviation from nominal volume is encountered
which may be more than a predetermined tolerance, and to compensate
for the different position of the different jet accordingly. While
the illustrated errors in FIG. 7 relate to individual spots, other
errors can be general in that they relate to all spots. For
example, an error in the position of substrate 10 on substrate
station 20 is a general error, and the corrected drive pattern
could be the same as the target drive pattern but with the addition
of a set of offset instructions to the positioning system, such as
a single instruction to one or any combination of transporters 60,
100, 120, to offset the position system from nominal to compensate
for this error.
[0051] A loading sequence for head 210 is more completely described
in co-pending patent applications "FABRICATING BIOPOLYMER ARRAYS",
by Caren et al., Ser. No. 09/302,922, and "PREPARATION OF
BIOPOLYMER ARRAYS" by A. Schleifer et al., Ser. No. 09/302,899,
both filed Apr. 30, 1999 and both assigned to the same assignee as
the present application, and the references cited therein,
including the possibility of using a flexible microtitre plate as
described in U.S. patent application "Method and Apparatus for
Liquid Transfer", Ser. No. 09/183,604. Those references and all
other references cited in the present application, are incorporated
into this application by reference. Processor 140 can control
pressure within head 210 to load each polynucleotide solution into
the chambers in the head by drawing it through the orifices.
[0052] Substrate 10 is loaded onto substrate station 20 either
manually by an operator, or optionally by a suitable automated
driver (not shown) controlled, for example, by processor 140.
[0053] The deposition sequence is then initiated to deposit the
desired arrays of polynucleotide containing fluid droplets on the
substrate to provide dried drops on the substrate according to the
target pattern each with respective feature locations and
dimensions. As already mentioned, in this sequence processor 140
will operate the apparatus according to the target or corrected
drive pattern, by causing the positioning system to position head
210 facing substrate station 20, and particularly the mounted
substrate 10, and with head 210 at an appropriate distance from
substrate 10. Processor 140 then causes the positioning system to
scan head 210 across substrate 10 line by line (or in some other
desired pattern), while co-ordinating activation of the ejectors in
head 210 so as to dispense droplets in accordance with the target
pattern. If necessary or desired, processor 140 can repeat the load
and dispensing sequences one or more times until head 210 has
dispensed droplets in accordance with the target or corrected drive
pattern for all arrays 12 to be formed on substrate 10. The number
of spots in any one array 12 can, for example, be at least ten, at
least one hundred, at least one thousand, or even at least one
hundred thousand.
[0054] At this point the droplet dispensing sequence is
complete.
[0055] In an alternative to the above described embodiment the
corrected drive pattern, instead of being derived prior to
beginning deposition of droplets, may be created "on the fly". In
one way of accomplishing this, the corrected drive pattern is
created by modifying, based on the detected error, instructions to
at least one deposition apparatus component which were based on the
target drive pattern. This is done during the deposition of the
probes or probe precursors. For example, the encoders 34 may be of
a type which simply sends a pulse to the head at a certain spatial
frequency; on each such pulse, the image file instructs the drive
electronics which nozzles should be fired. Instead of deriving a
corrected drive pattern in memory 141 so that the encoder pulses
will cause accurate printing, the encoder signals may be processed
by processor 140 to cause a non-distorted image to print
accurately.
[0056] It is preferable in an apparatus, method, or computer
program of the present invention, to not actually derive a target
drive pattern from a target array pattern, but instead to simply
derive a corrected drive pattern from the target pattern, nominal
conditions and detected error, when an error is detected. This can
be done before fabrication of a given array has started at least
when the error is detected before such fabrication has started (for
example, as a result of examining an operating parameter by
examining a previously fabricated array), or during such
fabrication. Again, the target drive pattern may be saved in memory
or just derived during the actual array fabrication and sent as
instructions directly to the apparatus components.
[0057] The present methods and apparatus may be used to deposit
biopolymers or other moieties on surfaces of any of a variety of
different substrates, including both flexible and rigid substrates.
Preferred materials 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. The array substrate
may take any of a variety of configurations ranging from simple to
complex. Thus, the substrate could have generally planar form, as
for example a slide or plate configuration, such as a rectangular
or square or disc. In many embodiments, the substrate will be
shaped generally as a rectangular solid, having a length in the
range about 4 mm to 1 m, usually about 4 mm to 600 mm, more usually
about 4 mm to 400 mm; a width in the range about 4 mm to 1 m,
usually about 4 mm to 500 mm and more usually about 4 mm to 400 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, particularly when such are
cut after fabrication into smaller size substrates carrying a
smaller total number of arrays 12.
[0058] In the present invention, any of a variety of geometries of
arrays on a substrate 10 may be fabricated 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. Similarly, the pattern of
regions 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. Even
irregular arrangements of the arrays or the regions within them can
be used, at least when some means is provided such that during
their use the locations of regions of particular characteristics
can be determined (for example, a map of the regions is provided to
the end user with the array). The configuration of the arrays and
their features may be selected according to manufacturing,
handling, and use considerations.
[0059] The substrates may be fabricated from any of a variety of
materials. In certain embodiments, such as for example where
production of binding pair arrays for use in research and related
applications is desired, the materials from which the substrate may
be fabricated should ideally exhibit a low level of non-specific
binding during hybridization events. In many situations, it will
also be preferable to employ a material that is transparent to
visible and/or UV light. For flexible substrates, materials of
interest include: nylon, both modified and unmodified,
nitrocellulose, polypropylene, and the like, where a nylon
membrane, as well as derivatives thereof, may be particularly
useful in this embodiment. For rigid substrates, specific materials
of interest include: glass; plastics (for example,
polytetrafluoroethylene, polypropylene, polystyrene, polycarbonate,
and blends thereof, and the like); metals (for example, gold,
platinum, and the like).
[0060] The substrate surface onto which the polynucleotide
compositions or other moieties is deposited may be 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), Various modifications to the embodiments
of the particular embodiments described above are, of course,
possible. Accordingly, the present invention is not limited to the
particular embodiments described in detail above.
* * * * *