U.S. patent application number 14/198417 was filed with the patent office on 2014-09-18 for chemical sensor with consistent sensor surface areas.
This patent application is currently assigned to LIFE TECHNOLOGIES CORPORATION. The applicant listed for this patent is LIFE TECHNOLOGIES CORPORATION. Invention is credited to James BUSTILLO, Keith G. FIFE, Shifeng LI, Jordan OWENS.
Application Number | 20140264472 14/198417 |
Document ID | / |
Family ID | 50349935 |
Filed Date | 2014-09-18 |
United States Patent
Application |
20140264472 |
Kind Code |
A1 |
FIFE; Keith G. ; et
al. |
September 18, 2014 |
CHEMICAL SENSOR WITH CONSISTENT SENSOR SURFACE AREAS
Abstract
In one embodiment, a chemical sensor is described. The chemical
sensor includes a chemically-sensitive field effect transistor
including a floating gate conductor having an upper surface. A
material defines an opening extending to the upper surface of the
floating gate conductor, the material comprising a first dielectric
underlying a second dielectric. A conductive element contacts the
upper surface of the floating gate conductor and extending a
distance along a sidewall of the opening.
Inventors: |
FIFE; Keith G.; (Palo Alto,
CA) ; OWENS; Jordan; (Austin, TX) ; LI;
Shifeng; (Fremont, CA) ; BUSTILLO; James;
(Castro Valley, CA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
LIFE TECHNOLOGIES CORPORATION |
Carlsbad |
CA |
US |
|
|
Assignee: |
LIFE TECHNOLOGIES
CORPORATION
Carlsbad
CA
|
Family ID: |
50349935 |
Appl. No.: |
14/198417 |
Filed: |
March 5, 2014 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
|
|
61900907 |
Nov 6, 2013 |
|
|
|
61790866 |
Mar 15, 2013 |
|
|
|
Current U.S.
Class: |
257/253 ;
438/49 |
Current CPC
Class: |
B01L 2300/0636 20130101;
B01L 2300/0877 20130101; H01L 29/40114 20190801; G01N 27/4145
20130101; B01L 3/502761 20130101; B01L 2200/0668 20130101; G01N
27/414 20130101; G01N 27/4148 20130101 |
Class at
Publication: |
257/253 ;
438/49 |
International
Class: |
G01N 27/414 20060101
G01N027/414 |
Claims
1. A chemical sensor comprising: a chemically-sensitive field
effect transistor including a floating gate conductor having an
upper surface; a material defining an opening extending to the
upper surface of the floating gate conductor, the material
comprising a first dielectric underlying a second dielectric; and a
conductive element contacting the upper surface of the floating
gate conductor and extending a distance along a sidewall of the
opening.
2. The chemical sensor of claim 1, wherein the opening includes a
lower portion within the first dielectric, and an upper portion
within the second dielectric.
3. The chemical sensor of claim 2, wherein a width of the lower
portion of the opening is substantially the same as a width of the
upper portion.
4. The chemical sensor of claim 2, wherein the conductive element
is conformal with a shape of the opening.
5. The chemical sensor of claim 1, wherein the conductive element
extends to an upper surface of the second dielectric.
6. The chemical sensor of claim 1, wherein the conductive element
includes an inner surface defining a lower portion of a reaction
region for the chemical sensor, and the second dielectric includes
an inner surface defining an upper portion of the opening.
7. The chemical sensor of claim 1, wherein the conductive element
comprises an electrically conductive material, and an inner surface
of the conductive element includes an oxide of the electrically
conductive material.
8. The chemical sensor of claim 1, wherein a sensing surface of the
chemical sensor includes an inner surface of the conductive
element.
9. The chemical sensor of claim 1, wherein the chemically-sensitive
field effect transistor generates a sensor signal in response to a
chemical reaction occurring proximate to the conductive
element.
10. The chemical sensor of claim 1, wherein the floating gate
conductor comprises a plurality of conductors electrically coupled
to one another and separated by dielectric layers, and the floating
gate conductor is an uppermost conductor in the plurality of
conductors.
11. A method for manufacturing a chemical sensor, the method
comprising: forming a chemically-sensitive field effect transistor
including a floating gate conductor having an upper surface;
forming a material defining an opening extending to the upper
surface of the floating gate conductor, the material comprising a
first dielectric underlying a second dielectric; and forming a
conductive element contacting the upper surface of the floating
gate conductor and extending a distance along a sidewall of the
opening.
12. The method of claim 11, wherein forming the material and
forming the conductive element include: forming the first
dielectric on the floating gate conductor, the first dielectric
defining a cavity extending to the upper surface of the floating
gate conductor; forming the second dielectric thereon; etching the
second dielectric to expose the conductive element, thereby
defining an opening; and forming the conductive element within the
opening.
13. The method of claim 12, wherein forming the conductive element
within the opening comprises: depositing a conductive material
within the opening and on an upper surface of the first dielectric;
and removing at least a portion of the conductive material from the
upper surface of the second dielectric.
14. The method of claim 13, wherein removing at least the portion
of the conductive material comprises: depositing a layer of
photoresist within the opening and; and removing at least a portion
of the conductive material together with the photoresist from the
upper surface of the second dielectric.
15. The method of claim 14, further comprising removing remaining
photoresist.
16. The method of claim 11, wherein the conductive material
comprises titanium.
17. The method of claim 11, wherein the opening is a nanowell.
18. The method of claim 11, wherein the forming a conductive
element includes depositing a conductive material conformally
within the opening.
19. The method of claim 11, wherein the conductive element includes
an inner surface defining a lower portion of a reaction region for
the chemical sensor, and the second dielectric includes an inner
surface defining an upper portion of the opening
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application claims priority to U.S. Provisional
Application No. 61/900,907 filed Nov. 6, 2013 and 61/790,866 filed
Mar. 15, 2013, the entire contents of which are incorporated by
reference herein in their entirety.
FIELD OF THE INVENTION
[0002] The present disclosure relates to sensors for chemical
analysis, and to methods for manufacturing such sensors.
BACKGROUND
[0003] A variety of types of chemical sensors have been used in the
detection of chemical processes. One type is a chemically-sensitive
field effect transistor (chemFET). A chemFET includes a source and
a drain separated by a channel region, and a chemically sensitive
area coupled to the channel region. The operation of the chemFET is
based on the modulation of channel conductance, caused by changes
in charge at the sensitive area due to a chemical reaction
occurring nearby. The modulation of the channel conductance changes
the threshold voltage of the chemFET, which can be measured to
detect and/or determine characteristics of the chemical reaction.
The threshold voltage may for example be measured by applying
appropriate bias voltages to the source and drain, and measuring a
resulting current flowing through the chemFET. As another example,
the threshold voltage may be measured by driving a known current
through the chemFET, and measuring a resulting voltage at the
source or drain.
[0004] An ion-sensitive field effect transistor (ISFET) is a type
of chemFET that includes an ion-sensitive layer at the sensitive
area. The presence of ions in an analyte solution alters the
surface potential at the interface between the ion-sensitive layer
and the analyte solution, due to the protonation or deprotonation
of surface charge groups caused by the ions present in the analyte
solution. The change in surface potential at the sensitive area of
the ISFET affects the threshold voltage of the device, which can be
measured to indicate the presence and/or concentration of ions
within the solution. Arrays of ISFETs may be used for monitoring
chemical reactions, such as DNA sequencing reactions, based on the
detection of ions present, generated, or used during the reactions.
See, for example, Rothberg et al., U.S. patent application Ser. No.
12/002,291 (now U.S. Pat. No. 7,948,015), filed Dec. 14, 2009,
based on U.S. Prov. Pat. Appl. Nos. 60/956,324, filed Aug. 16,
2007, 60/968,748, filed Jul. 10, 2007, and 60/870,073, filed Dec.
14, 2006, which is incorporated by reference herein in its
entirety. More generally, large arrays of chemFETs or other types
of chemical sensors may be employed to detect and measure static
and/or dynamic amounts or concentrations of a variety of analytes
(e.g. hydrogen ions, other ions, compounds, etc.) in a variety of
processes. The processes may for example be biological or chemical
reactions, cell or tissue cultures or monitoring neural activity,
nucleic acid sequencing, etc.
[0005] An issue that arises in the operation of large scale
chemical sensor arrays is the susceptibility of the sensor output
signals to noise. Specifically, the noise affects the accuracy of
the downstream signal processing used to determine the
characteristics of the chemical and/or biological process being
detected by the sensors. In addition, chemical sensor performance
variation across the array results in undesirable differences in
the sensor output signals, which further complicates the downstream
signal processing. It is therefore desirable to provide devices
including low noise chemical sensors, and methods for manufacturing
such devices.
SUMMARY
[0006] In one embodiment, a chemical sensor is described. The
chemical sensor includes a chemically-sensitive field effect
transistor including a floating gate conductor having an upper
surface; a material defining an opening extending to the upper
surface of the floating gate conductor, the material comprising a
first dielectric underlying a second dielectric; and a conductive
element contacting the upper surface of the floating gate conductor
and extending a distance along a sidewall of the opening. In an
exemplary embodiment, the opening of the chemical sensor may
include a lower portion within the first dielectric, and an upper
portion within the second dielectric. In another embodiment, a
width of the lower portion of the opening is substantially the same
as a width of the upper portion. In yet another embodiment, the
conductive element is conformal with a shape of the opening. In one
embodiment, the conductive element extends to an upper surface of
the second dielectric. In an exemplary embodiment, the conductive
element includes an inner surface defining a lower portion of a
reaction region for the chemical sensor, and the second dielectric
includes an inner surface defining an upper portion of the opening.
In an exemplary embodiment, the conductive element comprises an
electrically conductive material, and an inner surface of the
conductive element includes an oxide of the electrically conductive
material. In another embodiment, a sensing surface of the chemical
sensor includes an inner surface of the conductive element. In yet
another embodiment, the chemically-sensitive field effect
transistor generates a sensor signal in response to a chemical
reaction occurring proximate to the conductive element.
[0007] In one embodiment, the floating gate conductor comprises a
plurality of conductors electrically coupled to one another and
separated by dielectric layers, and the floating gate conductor is
an uppermost conductor in the plurality of conductors.
[0008] In another embodiment, a method for manufacturing a chemical
sensor is described. The method includes forming a
chemically-sensitive field effect transistor including a floating
gate conductor having an upper surface; forming a material defining
an opening extending to the upper surface of the floating gate
conductor, the material comprising a first dielectric underlying a
second dielectric; and forming a conductive element contacting the
upper surface of the floating gate conductor and extending a
distance along a sidewall of the opening. In an exemplary
embodiment, forming the material and forming the conductive element
may include forming the first dielectric on the floating gate
conductor, the first dielectric defining a cavity extending to the
upper surface of the floating gate conductor; forming the second
dielectric thereon; etching the second dielectric to expose the
conductive element, thereby defining an opening; and forming the
conductive element within the opening. According to another
embodiment, forming the conductive element within the opening may
include depositing a conductive material within the opening and on
an upper surface of the first dielectric; and removing at least a
portion of the conductive material from the upper surface of the
second dielectric. In yet another embodiment, removing at least the
portion of the conductive material may comprises depositing a layer
of photoresist within the opening; and removing at least a portion
of the conductive material together with the photoresist from the
upper surface of the second dielectric. In one embodiment, the
conductive material comprises titanium. In an exemplary embodiment,
the opening is a nanowell. In an exemplary embodiment, the forming
a conductive element includes depositing a conductive material
conformally within the opening. In another embodiment, the
conductive element includes an inner surface defining a lower
portion of a reaction region for the chemical sensor, and the
second dielectric includes an inner surface defining an upper
portion of the opening.
[0009] Particular aspects of one embodiment of the subject matter
described in this specification are set forth in the drawings and
the description below. Other features, aspects, and advantages of
the subject matter will become apparent from the description, the
drawings, and the claims.
BRIEF DESCRIPTION OF THE DRAWINGS
[0010] FIG. 1 illustrates a block diagram of components of a system
for nucleic acid sequencing according to an exemplary
embodiment.
[0011] FIG. 2 illustrates a cross-sectional view of a portion of
the integrated circuit device and flow cell according to an
exemplary embodiment.
[0012] FIG. 3 illustrates a cross-sectional view of two
representative chemical sensors and their corresponding reaction
regions according to a first embodiment.
[0013] FIGS. 4 to 12 illustrate stages in a manufacturing process
for forming an array of chemical sensors and corresponding reaction
regions according to a first embodiment.
[0014] FIGS. 13 to 25 illustrate stages in a manufacturing process
for forming an array of chemical sensors and corresponding reaction
regions according to a second embodiment.
DETAILED DESCRIPTION
[0015] A chemical detection device is described that includes low
noise chemical sensors, such as chemically-sensitive field effect
transistors (chemFETs), for detecting chemical reactions within
overlying, operationally associated reaction regions. Reducing the
plan or top view area (or footprint) of individual chemical sensors
and the overlying reaction regions allows for higher density
devices. However, as the dimensions of the chemical sensors are
reduced, Applicants have found that a corresponding reduction in
the sensing surface area of the sensors can significantly impact
performance. For example, for chemical sensors having sensing
surfaces defined at the bottom of the reaction regions, reducing
the plan view dimensions (e.g. the width or diameter) of the
reaction regions results in a similar reduction in the sensing
surface areas. Applicants have found that as the sensing surface
area is reduced to technology limits, fluidic noise due to the
random fluctuation of charge on the sensing surface contributes to
an increasing proportion of the total variation in sensing surface
potential. This can significantly reduce the signal-to-noise ratio
(SNR) of the sensor output signal, which affects the accuracy of
the downstream signal processing used to determine the
characteristics of the chemical and/or biological process being
detected by the sensor.
[0016] Chemical sensors described herein have sensing surface areas
which are not limited to a two-dimensional area at the bottom of
the reaction regions. In embodiments described herein, the sensing
surface of the chemical sensor includes a generally horizontal
portion along the bottom surface of the reaction region, as well as
a generally vertical portion extending along a sidewall of an
opening containing the reaction region. The distance that the
generally vertical portion extends along the sidewall is defined by
the thickness of a dielectric material that forms a lower portion
of the opening. The dielectric material can be deposited using a
process (e.g. thin film deposition) which results in very small
thickness variation across the array. In doing so, the sensor
surface areas of the chemical sensors can be very well controlled,
resulting in uniform chemical sensor performance across the array
and thus simplifying the downstream signal processing. By extending
the sensing surface in the generally vertical direction, the
chemical sensor can have a small footprint, while also having a
sufficiently large sensing surface area to avoid the noise issues
associated with small sensing surfaces. The footprint of a chemical
sensor is determined in part by the width (e.g. diameter) of the
overlying reaction region and can be made small, allowing for a
high density array. In addition, because the sensing surface
extends a controlled distance up the sidewall, the sensing surface
area can be relatively large. As a result, low noise chemical
sensors can be provided in a high density array, such that the
characteristics of reactions can be accurately detected.
[0017] FIG. 1 illustrates a block diagram of components of a system
for nucleic acid sequencing according to an exemplary embodiment.
The components include a flow cell 101 on an integrated circuit
device 100, a reference electrode 108, a plurality of reagents 114
for sequencing, a valve block 116, a wash solution 110, a valve
112, a fluidics controller 118, lines 120/122/126, passages
104/109/111, a waste container 106, an array controller 124, and a
user interface 128. The integrated circuit device 100 includes a
microwell array 107 overlying a sensor array that includes chemical
sensors as described herein. The flow cell 101 includes an inlet
102, an outlet 103, and a flow chamber 105 defining a flow path for
the reagents 114 over the microwell array 107. The reference
electrode 108 may be of any suitable type or shape, including a
concentric cylinder with a fluid passage or a wire inserted into a
lumen of passage 111. The reagents 114 may be driven through the
fluid pathways, valves, and flow cell 101 by pumps, gas pressure,
vacuum, or other suitable methods, and may be discarded into the
waste container 106 after exiting the outlet 103 of the flow cell
101. The fluidics controller 118 may control driving forces for the
reagents 114 and the operation of valve 112 and valve block 116
with suitable software.
[0018] The microwell array 107 includes reaction regions, also
referred to herein as microwells, which are operationally
associated with corresponding chemical sensors in the sensor array.
For example, each reaction region may be coupled to a chemical
sensor suitable for detecting an analyte or reaction property of
interest within that reaction region. The microwell array 107 may
be integrated in the integrated circuit device 100, so that the
microwell array 107 and the sensor array are part of a single
device or chip. The flow cell 101 may have a variety of
configurations for controlling the path and flow rate of reagents
114 over the microwell array 107. The array controller 124 provides
bias voltages and timing and control signals to the integrated
circuit device 100 for reading the chemical sensors of the sensor
array. The array controller 124 also provides a reference bias
voltage to the reference electrode 108 to bias the reagents 114
flowing over the microwell array 107.
[0019] During an experiment, the array controller 124 collects and
processes output signals from the chemical sensors of the sensor
array through output ports on the integrated circuit device 100 via
bus 127. The array controller 124 may be a computer or other
computing means. The array controller 124 may include memory for
storage of data and software applications, a processor for
accessing data and executing applications, and components that
facilitate communication with the various components of the system
in FIG. 1. In the illustrated embodiment, the array controller 124
is external to the integrated circuit device 100. In some
alternative embodiments, some or all of the functions performed by
the array controller 124 are carried out by a controller or other
data processor on the integrated circuit device 100. The values of
the output signals from the chemical sensors indicate physical
and/or chemical parameters of one or more reactions taking place in
the corresponding reaction regions in the microwell array 107. For
example, in an exemplary embodiment, the values of the output
signals may be processed using the techniques disclosed in Rearick
et al., U.S. patent application Ser. No. 13/339,846, filed Dec. 29,
2011, based on U.S. Prov. Pat. Appl. Nos. 61/428,743, filed Dec.
30, 2010, and 61/429,328, filed Jan. 3, 2011, and in Hubbell, U.S.
patent application Ser. No. 13/339,753, filed Dec. 29, 2011, based
on U.S. Prov. Pat. Appl. No. 61/428,097, filed Dec. 29, 2010, each
of which are incorporated by reference herein. The user interface
128 may display information about the flow cell 101 and the output
signals received from chemical sensors in the sensor array on the
integrated circuit device 100. The user interface 128 may also
display instrument settings and controls, and allow a user to enter
or set instrument settings and controls.
[0020] The fluidics controller 118 may control delivery of the
individual reagents 114 to the flow cell 101 and integrated circuit
device 100 in a predetermined sequence, for predetermined
durations, at predetermined flow rates. The array controller 124
can then collect and analyze the output signals of the chemical
sensors indicating chemical reactions occurring in response to the
delivery of the reagents 114. During the experiment, the system may
also monitor and control the temperature of the integrated circuit
device 100, so that reactions take place and measurements are made
at a known predetermined temperature.
[0021] The system may be configured to let a single fluid or
reagent contact the reference electrode 108 throughout an entire
multi-step reaction during operation. The valve 112 may be shut to
prevent any wash solution 110 from flowing into passage 109 as the
reagents 114 are flowing. Although the flow of wash solution may be
stopped, there may still be uninterrupted fluid and electrical
communication between the reference electrode 108, passage 109, and
the microwell array 107. The distance between the reference
electrode 108 and the junction between passages 109 and 111 may be
selected so that little or no amount of the reagents flowing in
passage 109 (and possibly diffusing into passage 111) reach the
reference electrode 108. In an exemplary embodiment, the wash
solution 110 may be selected as being in continuous contact with
the reference electrode 108, which may be especially useful for
multi-step reactions using frequent wash steps.
[0022] FIG. 2 illustrates cross-sectional and expanded views of a
portion of the integrated circuit device 100 and flow cell 101. The
integrated circuit device 100 includes the microwell array 107 of
reaction regions operationally associated with sensor array 205.
During operation, the flow chamber 105 of the flow cell 101
confines a reagent flow 208 of delivered reagents across open ends
of the reaction regions in the microwell array 107. The volume,
shape, aspect ratio (such as base width-to-well depth ratio), and
other dimensional characteristics of the reaction regions may be
selected based on the nature of the reaction taking place, as well
as the reagents, byproducts, or labeling techniques (if any) that
are employed. The chemical sensors of the sensor array 205 are
responsive to (and generate output signals related to) chemical
reactions within associated reaction regions in the microwell array
107 to detect an analyte or reaction property of interest. The
chemical sensors of the sensor array 205 may for example be
chemically sensitive field-effect transistors (chemFETs), such as
ion-sensitive field effect transistors (ISFETs). Examples of
chemical sensors and array configurations that may be used in
embodiments are described in Schultz et al., U.S. patent
application Ser. No. 12/785,667 (now U.S. Pat. No. 8,546,128),
filed May 24, 2010, titled "Fluidics System for Sequential Delivery
of Reagents"; Rotherberg et al., U.S. patent application Ser. No.
12/721,458 (now U.S. Pat. No. 8,306,757), filed Mar. 10, 2010,
titled "Methods and Apparatus for Measuring Analytes Using Large
Scale FET Arrays"; Rotherberg et al., U.S. patent application Ser.
No. 12/475,311, filed May 29, 2009, titled "Methods and Apparatus
for Measuring Analytes"; Rotherberg et al., U.S. patent application
Ser. No. 12/474,897, filed May 29, 2009, titled "Methods and
Apparatus for Measuring Analytes"; Rotherberg et al., U.S. patent
application Ser. No. 12/002,781, filed Dec. 17, 2007, titled
"Methods and Apparatus for Measuring Analytes Using Large Scale FET
Arrays"; and U.S. patent application Ser. No. 12/474,897 (now U.S.
Pat. No. 7,575,865) filed Aug. 1, 2005, titled "Methods of
Amplifying and Sequencing Nucleic Acids", each of which are
incorporated by reference herein in their entirety.
[0023] FIG. 3 illustrates a cross-sectional view of two
representative chemical sensors and their corresponding reaction
regions according to a first embodiment. In FIG. 3, two chemical
sensors 350, 351 are shown, representing a small portion of a
sensor array that can include millions of chemical sensors.
Chemical sensor 350 is coupled to corresponding reaction region
301, and chemical sensor 351 is coupled to corresponding reaction
region 302. Chemical sensor 350 is representative of the chemical
sensors in the sensor array. In the illustrated example, the
chemical sensor 350 is a chemically-sensitive field effect
transistor (chemFET), more specifically an ion-sensitive field
effect transistor (ISFET) in this example. The chemical sensor 350
includes a floating gate structure 318 having a sensor plate 320
coupled to the reaction region 301 by an electrically conductive
element 370. As can be seen in FIG. 3, the sensor plate 320 is the
uppermost floating gate conductor in the floating gate structure
318. In the illustrated example, the floating gate structure 318
includes multiple patterned layers of conductive material within
layers of dielectric material 319.
[0024] The chemical sensor 350 also includes a source region 321
and a drain region 322 within a semiconductor substrate 354. The
source region 321 and the drain region 322 comprise doped
semiconductor material have a conductivity type different from the
conductivity type of the substrate 354. For example, the source
region 321 and the drain region 322 may comprise doped P-type
semiconductor material, and the substrate may comprise doped N-type
semiconductor material. Channel region 323 separates the source
region 321 and the drain region 322. The floating gate structure
318 overlies the channel region 323, and is separated from the
substrate 354 by a gate dielectric 352. The gate dielectric 352 may
be for example silicon dioxide. Alternatively, other dielectrics
may be used for the gate dielectric 352.
[0025] As shown in FIG. 3, the reaction region 301 is within an
opening having a sidewall 303 extending through dielectric
materials 310, 308 to the upper surface of the sensor plate 320.
Each of the dielectric materials 310, 308 may comprise one or more
layers of material, such as silicon dioxide or silicon nitride. The
opening includes a lower portion 314 within dielectric material 308
and proximate to the sensor plate 320. The opening also includes an
upper portion 315 within the dielectric material 310 and extending
from the lower portion 314 to the upper surface of the dielectric
material 310. In the illustrated embodiment, the width of the upper
portion 315 of the opening is substantially the same as the width
of the lower portion 314 of the opening. However, depending on the
material(s) and/or etch process used to create the opening, the
width of the upper portion 315 of the opening may be greater than
the width of the lower portion 314 of the opening, or vice versa.
The opening may for example have a circular cross-section.
Alternatively, the opening may be non-circular. For example, the
cross-section may be square, rectangular, hexagonal, or irregularly
shaped. The dimensions of the openings, and their pitch, can vary
from embodiment to embodiment. In some embodiments, the openings
can have a characteristic diameter, defined as the square root of 4
times the plan view cross-sectional area (A) divided by Pi (e.g.,
sqrt(4*A/.pi.)), of not greater than 5 micrometers, such as not
greater than 3.5 micrometers, not greater than 2.0 micrometers, not
greater than 1.6 micrometers, not greater than 1.0 micrometers, not
greater than 0.8 micrometers, not greater than 0.6 micrometers, not
greater than 0.4 micrometers, not greater than 0.2 micrometers or
even not greater than 0.1 micrometers.
[0026] The lower portion 314 of the opening includes the
electrically conductive element 370 on the sidewall 303 of the
dielectric material 310. In the illustrated embodiment, the inner
surface 371 of the electrically conductive element 370 defines a
lower segment of the reaction region 301. That is, there is no
intervening deposited material layer between the inner surface 371
of the electrically conductive element 370 and the reaction region
301 for the chemical sensor 350. As a result of this structure, the
inner surface 371 of the electrically conductive element 370 is
conformal to the opening and acts as the sensing surface for the
chemical sensor 350. It should be understood by those skilled in
the art that precise shape and dimension of the electrically
conductive element 370, as with all other materials illustrated in
the figures, is process dependant.
[0027] In the illustrated embodiment, the electrically conductive
element 370 is a conformal layer of material within the lower
portion 314 of the opening, such that the electrically conductive
element 370 extends across the upper surface of the sensor plate
320. In the illustrated embodiment, the electrically conductive
element 370 extends beyond the lower portion 314 of the opening and
into the upper portion 315 of the opening. The inner surface of the
dielectric material 310 defines an upper segment of the reaction
region 301. The conductive element 370 may for example extend along
at least 5% of the sidewall 303, at least 10%, at least 25%, at
least 50%, at least 75%, or at least 85% of the sidewall 303, or
even extend along 99% of the sidewall 303. The conformal inner
surface 371 of the electrically conductive element 370 allows the
chemical sensor 350 to have a small plan view area, while also
having a sufficiently large surface area to avoid the noise issues
associated with small sensing surfaces. The plan view area of the
chemical sensor 350 is determined in part by the width (or
diameter) of the reaction region 301 and can be made small,
allowing for a high density array. In addition, because the sensing
surface extends up the sidewall 303, the sensing surface area
depends upon the distance of this extension and the circumference
of the reaction region 301, and can be relatively large. As a
result, low noise chemical sensors 350, 351 can be provided in a
high density array, such that the characteristics of reactions can
be accurately detected.
[0028] During manufacturing and/or operation of the device, a thin
oxide of the material of the electrically conductive element 370
may be grown which acts as a sensing material (e.g. an
ion-sensitive sensing material) for the chemical sensor 350.
Whether an oxide is formed depends on the conductive material, the
manufacturing processes performed, and the conditions under which
the device is operated. For example, in one embodiment the
electrically conductive element 370 may be titanium nitride, and
titanium oxide or titanium oxynitride may be grown on the inner
surface 371 of the conductive element 370 during manufacturing
and/or during exposure to solutions during use. In the illustrated
example, the electrically conductive element 370 is shown as a
single layer of material. More generally, the electrically
conductive element 370 may comprise one or more layers of a variety
of electrically conductive materials, such as metals or ceramics,
depending upon the embodiment. The conductive material can be for
example a metallic material or alloy thereof, or can be a ceramic
material, or a combination thereof. An exemplary metallic material
includes one of aluminum, copper, nickel, titanium, silver, gold,
platinum, hafnium, lanthanum, tantalum, tungsten, iridium,
zirconium, palladium, or a combination thereof. An exemplary
ceramic material includes one of titanium nitride, titanium
aluminum nitride, titanium oxynitride, tantalum nitride or a
combination thereof. In some alternative embodiments, an additional
conformal sensing material (not shown) is deposited on the
conductive element 370 and within the openings. The sensing
material may comprise one or more of a variety of different
materials to facilitate sensitivity to particular ions. For
example, silicon nitride or silicon oxynitride, as well as metal
oxides such as silicon oxide, aluminum or tantalum oxides,
generally provide sensitivity to hydrogen ions, whereas sensing
materials comprising polyvinyl chloride containing valinomycin
provide sensitivity to potassium ions. Materials sensitive to other
ions such as sodium, silver, iron, bromine, iodine, calcium, and
nitrate may also be used, depending upon the embodiment.
[0029] In operation, reactants, wash solutions, and other reagents
may move in and out of the reaction region 301 by a diffusion
mechanism 340. The chemical sensor 350 is responsive to (and
generates an output signal related to) the amount of charge 324
proximate to the conductive element 370. The presence of charge 324
in an analyte solution alters the surface potential at the
interface between the conductive element 370 and the analyte
solution within the reaction region 301. Changes in the charge 324
cause changes in the voltage on the floating gate structure 318,
which in turn changes in the threshold voltage of the transistor.
This change in threshold voltage can be measured by measuring the
current in the channel region 323 between the source region 321 and
a drain region 322. As a result, the chemical sensor 350 can be
used directly to provide a current-based output signal on an array
line connected to the source region 321 or drain region 322, or
indirectly with additional circuitry to provide a voltage-based
output signal. Because the charge 324 may be more highly
concentrated near the bottom of the reaction region 301, the
distance that the conductive element 370 extends up the sidewall
303 of the opening is a tradeoff between the amplitude of the
desired signal detected in response to the charge 324, and the
fluidic noise due to random fluctuation of charge between the
conductive element 370 and the analyte solution. Increasing the
distance that the conductive element 370 extends up the sidewall
303 increases the fluidic interface area for the chemical sensor
350, which acts to reduce the fluidic noise. However, due to the
diffusion of charge 324 out of the reaction region 301, the
concentration of charge 324 decreases with distance from the bottom
of the reaction region 301. As a result, upper sidewall segments of
the conductive element 370 detect portions of the signal from areas
having lower charge concentration, which can reduce the overall
amplitude of the desired signal detected by the sensor 350. In
contrast, decreasing the distance the conductive element 370
extends up the sidewall 303 reduces the sensing surface area and
thus increases the fluidic noise, but also increases the overall
amplitude of the desired signal detected by the sensor 350.
[0030] For a very small sensing surface area, Applicants have found
that the fluidic noise changes as a function of the sensing surface
area differently than the amplitude of the desired signal. Because
the SNR of the sensor output signal is the ratio of these two
quantities, there is an optimal distance the conductive element 370
extends along the sidewall 303 at which SNR is maximum. The optimal
distance can vary from embodiment to embodiment depending on the
material characteristics of the conductive element 370 and the
dielectric material 310, the volume, shape, aspect ratio (such as
base width-to-well depth ratio), and other dimensional
characteristics of the reaction regions, the nature of the reaction
taking place, as well as the reagents, byproducts, or labeling
techniques (if any) that are employed. The optimal distance may for
example be determined empirically.
[0031] As described in more detail below with respect to FIGS. 4 to
12, the distance the conductive element 370 extends along the
sidewall 303 is defined by the etch time of the deposited layer,
for example. The dielectric material 310 and electrically
conductive element 370 can be etched using a timed etch process,
for example, which results in selectivity of distance 309 (e.g. the
distance dielectric material 310 extends beyond electrically
conductive element 370). In doing so, the sensor surface areas of
the chemical sensors can be controlled, resulting in uniform
chemical sensor performance across the array and simplifying the
downstream signal processing.
[0032] In an embodiment, reactions carried out in the reaction
region 301 can be analytical reactions to identify or determine
characteristics or properties of an analyte of interest. Such
reactions can generate directly or indirectly byproducts that
affect the amount of charge adjacent to the electrically conductive
element 370. If such byproducts are produced in small amounts or
rapidly decay or react with other constituents, multiple copies of
the same analyte may be analyzed in the reaction region 301 at the
same time in order to increase the output signal generated. In an
embodiment, multiple copies of an analyte may be attached to a
solid phase support 312, as shown in FIG. 3, either before or after
deposition into the reaction region 301. The solid phase support
312 may be microparticles, nanoparticles, beads, solid or porous
gels, or the like. For simplicity and ease of explanation, solid
phase support 312 is also referred herein as a particle. For a
nucleic acid analyte, multiple, connected copies may be made by
rolling circle amplification (RCA), exponential RCA, Recombinase
Polymerase Amplification (RPA), Polymerase Chain Reaction
amplification (PCR), emulsion PCR amplification, or like
techniques, to produce an amplicon without the need of a solid
support.
[0033] In various exemplary embodiments, the methods, systems, and
computer readable media described herein may advantageously be used
to process and/or analyze data and signals obtained from electronic
or charged-based nucleic acid sequencing. In electronic or
charged-based sequencing (such as, pH-based sequencing), a
nucleotide incorporation event may be determined by detecting ions
(e.g., hydrogen ions) that are generated as natural by-products of
polymerase-catalyzed nucleotide extension reactions. This may be
used to sequence a sample or template nucleic acid, which may be a
fragment of a nucleic acid sequence of interest, for example, and
which may be directly or indirectly attached as a clonal population
to a solid support, such as a particle, microparticle, bead, etc.
The sample or template nucleic acid may be operably associated to a
primer and polymerase and may be subjected to repeated cycles or
"flows" of deoxynucleoside triphosphate ("dNTP") addition (which
may be referred to herein as "nucleotide flows" from which
nucleotide incorporations may result) and washing. The primer may
be annealed to the sample or template so that the primer's 3' end
can be extended by a polymerase whenever dNTPs complementary to the
next base in the template are added. Then, based on the known
sequence of nucleotide flows and on measured output signals of the
chemical sensors indicative of ion concentration during each
nucleotide flow, the identity of the type, sequence and number of
nucleotide(s) associated with a sample nucleic acid present in a
reaction region coupled to a chemical sensor can be determined.
[0034] FIGS. 4 to 12 illustrate stages in a manufacturing process
for forming an array of chemical sensors and corresponding reaction
regions according to a first embodiment. FIG. 4 illustrates a
structure 400 formed in a first stage. The structure 400 includes
the floating gate structures (e.g. floating gate structure 318) for
the chemical sensors 350, 351. The structure 400 can be formed by
depositing a layer of gate dielectric material on the semiconductor
substrate 354, and depositing a layer of polysilicon (or other
electrically conductive material) on the layer of gate dielectric
material. The layer of polysilicon and the layer gate dielectric
material can then be etched using an etch mask to form the gate
dielectric elements (e.g. gate dielectric 352) and the lowermost
conductive material element of the floating gate structures.
Following formation of an ion-implantation mask, ion implantation
can then be performed to form the source and drain regions (e.g.
source region 321 and a drain region 322) of the chemical sensors.
A first layer of the dielectric material 319 can then be deposited
over the lowermost conductive material elements. Conductive plugs
can then be formed within vias etched in the first layer of
dielectric material 319 to contact the lowermost conductive
material elements of the floating gate structures. A layer of
conductive material can then be deposited on the first layer of the
dielectric material 319 and patterned to form second conductive
material elements electrically connected to the conductive plugs.
This process can then be repeated multiple times to form the
completed floating gate structure 318 shown in FIG. 4.
Alternatively, other and/or additional techniques may be performed
to form the structure. Forming the structure 400 in FIG. 4 can also
include forming additional elements such as array lines (e.g. row
lines, column lines, etc.) for accessing the chemical sensors,
additional doped regions in the substrate 354, and other circuitry
(e.g. select switches, access circuitry, bias circuitry etc.) used
to operate the chemical sensors, depending upon the device and
array configuration in which the chemical sensors described herein
are implemented. In some embodiments, the elements of the structure
may for example be manufactured using techniques described in
Schultz et al., U.S. patent application Ser. No. 12/785,667 (now
U.S. Pat. No. 8,546,128), filed May 24, 2010, titled "Fluidics
System for Sequential Delivery of Reagents"; Rotherberg et al.,
U.S. patent application Ser. No. 12/721,458 (now U.S. Pat. No.
8,306,757), filed Mar. 10, 2010, titled "Methods and Apparatus for
Measuring Analytes Using Large Scale FET Arrays"; Rotherberg et
al., U.S. patent application Ser. No. 12/475,311, filed May 29,
2009, titled "Methods and Apparatus for Measuring Analytes";
Rotherberg et al., U.S. patent application Ser. No. 12/474,897,
filed May 29, 2009, titled "Methods and Apparatus for Measuring
Analytes"; Rotherberg et al., U.S. patent application Ser. No.
12/002,781, filed Dec. 17, 2007, titled "Methods and Apparatus for
Measuring Analytes Using Large Scale FET Arrays"; and U.S. patent
application Ser. No. 12/474,897 (now U.S. Pat. No. 7,575,865) filed
Aug. 1, 2005, titled "Methods of Amplifying and Sequencing Nucleic
Acids", which were incorporated by reference in their entirety
above.
[0035] Next, dielectric material 308 having a given thickness is
deposited on the structure 400 illustrated in FIG. 4, resulting in
the structure illustrated in FIG. 5. The dielectric material 308
comprises one or more dielectric layers of dielectric. The
dielectric material 308 may be deposited using a process which
results in very small variation in the thickness across the array.
For example, the dielectric material 308 may comprise silicon oxide
and be deposited using high density plasma (HDP) deposition.
Various other techniques may be used, such as sputtering, reactive
sputtering, atomic layer deposition (ALD), low pressure chemical
vapor deposition (LPCVD), plasma enhanced chemical vapor deposition
(PECVD), metal organic chemical vapor deposition (MOCVD), etc.
Next, the dielectric material 308 of the structure in FIG. 5 is
etched to form cavities 600, 602 extending to the upper surfaces of
the floating gate structures of the chemical sensors 350, 351,
resulting in the structure illustrated in FIG. 6. The cavities 600,
602 may for example be formed by using a lithographic process to
pattern a layer of photoresist on the dielectric material 308 to
define the locations of the cavities 600, 602, and then
anisotropically etching the dielectric material 308 using the
patterned photoreist as an etch mask. The anisotropic etching of
the dielectric material 308 may for example be a dry etch process,
such as a fluorine based Reactive Ion Etching (RIE) process. Next,
dielectric material 310 is formed on the structure illustrated in
FIG. 6, resulting in the structure illustrated in FIG. 7. The
dielectric material 310 may comprise one or more layers of
deposited dielectric material, such as silicon dioxide or silicon
nitride.
[0036] Next, dielectric material 310 is etched to form openings
defining reaction regions 301, 302 extending to the sensor plate
320, resulting in the structure illustrated in FIG. 8. Next, a
conformal layer of conductive material 900 is deposited on the
structure illustrated in FIG. 8, resulting in the structure
illustrated in FIG. 9. The conductive material 900 comprises one or
more layers of electrically conductive material. For example, the
conductive material 900 may be a layer of titanium nitride, or a
layer of titanium. Alternatively, other and/or additional
conductive materials may be used, such as those described above
with reference to the conductive element 370. In addition, more
than one layer of conductive material may be deposited. The
conductive material 900 may be deposited using various techniques,
such as sputtering, reactive sputtering, atomic layer deposition
(ALD), low pressure chemical vapor deposition (LPCVD), plasma
enhanced chemical vapor deposition (PECVD), metal organic chemical
vapor deposition (MOCVD), etc. In contemplated embodiments,
conductive element 370 may be formed to take various shapes and
thicknesses that may be determined based on material and techniques
described above. For example, instead of the depiction of
conductive element 370 as illustrated in FIG. 3, one may imagine
conductive element 370 is formed such that it is conformal with the
solid support (rounded to follow the shape of solid support
312).
[0037] Next, material 1000 is formed on the structure illustrated
in FIG. 9, resulting in the structure illustrated in FIG. 10. The
material 1000 may comprise one or more layers of deposited
dielectric material, such as silicon dioxide or silicon nitride.
Alternatively, material 1000 may comprise photoresist. In one
embodiment, where the material 1000 comprises photoresist, a
partial etch of material 1000 and conductive material 900 is
performed such that distance 309 of dielectric material 310 is
revealed (that is, distance 309 of sidewall 303 is exposed),
resulting in the structure illustrated in FIG. 11. Material 1000
and electrically conductive material 900 may be etched together or
separately depending on the process and/or material(s) used. For
example, a partial etch may be performed using at least one of an
O2 resist etch, Ar sputter breakthrough etch, and Hydrogen Bromide
Titanium etch. Next, material 1000 is etched to form openings
defining reaction regions 301, 302 extending to the conductive
element 370, 900, resulting in the structure illustrated in FIG.
12. In one embodiment, residual photoresist may need to be cleaned
from the opening using techniques known to those skilled in the
art, for example, O2 plasma ash.
[0038] FIG. 13 illustrates a cross-sectional view of two
representative chemical sensors and their corresponding reaction
regions according to a second embodiment. The structure of the two
representative chemical sensors illustrated in FIG. 13 differs in
one aspect from the two representative chemical sensors illustrated
in FIG. 3 in that FIG. 13 includes vias over sensor plates 320 on
top of which the microwells/nanowells are built. Accordingly,
fabrication for the structure in FIG. 3 is different from
fabrication of FIG. 13, as is explained in greater detail
below.
[0039] FIGS. 14-25 illustrate stages in a manufacturing process for
forming an array of chemical devices and corresponding well
structures according to an exemplary embodiment. FIG. 14
illustrates a structure 1400 including the floating gate structures
(e.g. floating gate structure 318) for the chemical devices 350,
351. The structure 1400 can be formed in accordance with the
structure 400 described in detail above with reference to FIG. 4.
As illustrated in the structure 1500 illustrated in FIG. 15, a
dielectric material 1503 may be formed on the sensor plate 320 of
the field effect transistor of the chemical device 350. Next, as
illustrated in FIG. 16, the dielectric material 1503 of the
structure 1500 in FIG. 15 is etched to form openings 1618, 1620
(for vias) extending to the upper surfaces of the floating gate
structures of the chemical devices 350, 351, resulting in the
structure 1600 illustrated in FIG. 16. The openings 1618, 1620 may,
for example, be formed by using a lithographic process to pattern a
layer of photoresist on the dielectric material 1503 to define the
locations of the openings 1618, 1620, and then anisotropically
etching the dielectric material 1503 using the patterned photoreist
as an etch mask. The anisotropic etching of the dielectric material
1503 may, for example, be a dry etch process, such as a fluorine
based Reactive Ion Etching (RIE) process. In the illustrated
embodiment, the openings 1618, 1620 are separated by a distance
1630 and the openings 1618, 1620 are of a suitable dimension for a
via. For example, the separation distance 1630 may be a minimum
feature size for the process (e.g. a lithographic process) used to
form the openings 1618, 1620. In such a case, the distance 1630 may
be significantly more than the width 1620. Next, a layer of
conductive material 1704 is deposited on the structure 1600
illustrated in FIG. 16, resulting in the structure 1700 illustrated
in FIG. 17. Conductive material 1704 may be referred to as a
conductive liner. The conductive material 1704 may comprise one or
more layers of electrically conductive material. For example, the
conductive material 1704 may be a layer of titanium nitride, or a
layer of titanium. Alternatively, other and/or additional
conductive materials may be used, such as those described above
with reference to the electrically conductive element. In addition,
more than one layer of conductive material may be deposited. The
conductive material 1704 may be deposited using various techniques,
such as sputtering, reactive sputtering, atomic layer deposition
(ALD), low pressure chemical vapor deposition (LPCVD), plasma
enhanced chemical vapor deposition (PECVD), metal organic chemical
vapor deposition (MOCVD), etc.
[0040] Next, a layer of conductive material 1805 such as tungsten,
for example, is deposited on the structure 1700 illustrated in FIG.
17, resulting in the structure 1800 illustrated in FIG. 18. The
conductive material 1805 may be deposited using various techniques,
such as sputtering, reactive sputtering, atomic layer deposition
(ALD), low pressure chemical vapor deposition (LPCVD), plasma
enhanced chemical vapor deposition (PECVD), metal organic chemical
vapor deposition (MOCVD), etc. or any other suitable techniques.
Next, conductive material 1704 and conductive material 1805 are
planarized using a Chemical Mechanical Planarization (CMP) process,
for example, resulting in the structure 1900 illustrated in FIG.
19. As an optional, additional step, a via barrier liner (not
shown) may be formed on the planarized conductive material 1704 and
conductive material 1805. For example, the via barrier liner may
comprise titanium nitride.
[0041] Next, dielectric material 2006 is formed on the structure
illustrated in FIG. 19, resulting in the structure illustrated in
FIG. 20. The dielectric material 2006 may comprise one or more
layers of deposited dielectric material, such as silicon dioxide or
silicon nitride. Next, dielectric material 2006 is etched to form
openings extending to planarized conductive material 1704 and
conductive material 1805 and dielectric material 1503, resulting in
the structure illustrated in FIG. 21. Dielectric material 1503 may
be partially etched when the openings are formed such that
conductive material 1704 and conductive material 1805 are raised
above dielectric material 1503 and protrude into the opening, as
seen in the illustrated embodiment. Next, a conformal layer of
conductive material 2200 is deposited on the structure illustrated
in FIG. 21, resulting in the structure illustrated in FIG. 22. The
conductive material 2200 comprises one or more layers of
electrically conductive material. For example, the conductive
material 2200 may be a layer of titanium nitride, or a layer of
titanium. Alternatively, other and/or additional conductive
materials may be used, such as those described above with reference
to the conductive element 370. In addition, more than one layer of
conductive material may be deposited. The conductive material 2200
may be deposited using various techniques, such as sputtering,
reactive sputtering, atomic layer deposition (ALD), low pressure
chemical vapor deposition (LPCVD), plasma enhanced chemical vapor
deposition (PECVD), metal organic chemical vapor deposition
(MOCVD), etc.
[0042] Next, material 2300 is formed on the structure illustrated
in FIG. 22, resulting in the structure illustrated in FIG. 23. The
material 2300 may comprise one or more layers of deposited
dielectric material, such as silicon dioxide or silicon nitride.
Alternatively, material 2300 may comprise photoresist. In one
embodiment, where the material 2300 comprises photoresist, a
partial etch of material 2300 and conductive material 2200 is
performed such that distance 1309 of dielectric material 310 is
revealed (that is, distance 309 of sidewall 1303 is exposed),
resulting in the structure illustrated in FIG. 24. Material 2300
and conductive material 2200 may be etched together or separately
depending on the process and/or material(s) used. For example, a
partial etch may be performed using at least one of an O2 resist
etch, Ar sputter breakthrough etch, and Hydrogen Bromide Titanium
etch. Next, material 2300 is etched to form openings defining
reaction regions 301, 302 extending to the conductive elements 370,
2200, resulting in the structure illustrated in FIG. 25. In one
embodiment, residual photoresist may need to be cleaned from the
opening using techniques known to those skilled in the art, for
example, O2 plasma ash.
[0043] While the present invention is disclosed by reference to the
preferred embodiments and examples detailed above, it is to be
understood that these examples are intended in an illustrative
rather than in a limiting sense. It is contemplated that
modifications and combinations will readily occur to those skilled
in the art, which modifications and combinations will be within the
spirit of the invention and the scope of the following claims.
* * * * *