U.S. patent application number 12/380291 was filed with the patent office on 2010-06-10 for systems and methods for rapidly changing the solution environment around sensors.
This patent application is currently assigned to Cellectricon AB. Invention is credited to Daniel Chiu, Kent Jardemark, Mattias Karlsson, Jessica Olofsson, Owe Orwar, Johan Pihl, Jon Sinclair.
Application Number | 20100143944 12/380291 |
Document ID | / |
Family ID | 27734640 |
Filed Date | 2010-06-10 |
United States Patent
Application |
20100143944 |
Kind Code |
A1 |
Orwar; Owe ; et al. |
June 10, 2010 |
Systems and methods for rapidly changing the solution environment
around sensors
Abstract
The invention provides microfluidic systems for altering the
solution environment around a nanoscopic or microscopic object,
such as a sensor, and methods for using the same. The invention can
be applied in any sensor technology in which the sensing element
needs to be exposed rapidly, sequentially, and controllably, to a
large number of different solution environments whose
characteristics may be known or unknown.
Inventors: |
Orwar; Owe; (Hovas, SE)
; Chiu; Daniel; (Seattle, WA) ; Pihl; Johan;
(Olofstorp, SE) ; Sinclair; Jon; (Goteborg,
SE) ; Olofsson; Jessica; (Goteborg, SE) ;
Karlsson; Mattias; (Onsala, SE) ; Jardemark;
Kent; (Tyreso, SE) |
Correspondence
Address: |
EDWARDS ANGELL PALMER & DODGE LLP
P.O. BOX 55874
BOSTON
MA
02205
US
|
Assignee: |
Cellectricon AB
Goteborg
SE
|
Family ID: |
27734640 |
Appl. No.: |
12/380291 |
Filed: |
February 25, 2009 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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10345107 |
Jan 15, 2003 |
7563614 |
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12380291 |
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60356377 |
Feb 12, 2002 |
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Current U.S.
Class: |
435/7.21 ;
435/353 |
Current CPC
Class: |
B01L 2300/14 20130101;
B82Y 5/00 20130101; B82Y 10/00 20130101; G01N 33/554 20130101; B01L
2300/0829 20130101; G01N 33/48728 20130101; G01N 33/54366 20130101;
G01N 33/5438 20130101; B01L 2300/0636 20130101; B01L 2300/0874
20130101; B01L 3/50273 20130101; B82Y 20/00 20130101; B01L 3/0293
20130101; B01L 2300/0867 20130101; B01L 2200/0636 20130101; B01L
2200/10 20130101; B01L 2300/0627 20130101; G01N 33/15 20130101;
B01L 2300/0645 20130101; B01L 2300/087 20130101; B01L 3/502715
20130101; B01L 2400/0487 20130101; B01L 3/5027 20130101; B01L
2300/0816 20130101; B01L 2200/027 20130101 |
Class at
Publication: |
435/7.21 ;
435/353 |
International
Class: |
G01N 33/567 20060101
G01N033/567; C12N 5/071 20100101 C12N005/071 |
Claims
1.-84. (canceled)
85. A method for generating an activated receptor, comprising a)
providing a substrate, the substrate comprising: a chamber
comprising a cell-based biosensor comprising a receptor which is
activated by an agonist; and a plurality of delivery channels
delivering agonist, antagonist, or both agonist and antagonist,
each channel comprising an outlet for delivering a substantially
separate aqueous stream into the chamber; and b) selectively
exposing the biosensor to a fluid stream from one or more
outlets.
86. The method of claim 85, wherein the chamber comprises a buffer,
at least one agonist, at least one antagonist, or a combination
thereof.
87. A method for detection of a modulator of a receptor, comprising
a) providing a substrate, the substrate comprising: a chamber
comprising a cell-based biosensor, the biosensor comprising the
receptor; and a plurality of channels, each channel comprising an
outlet for delivering a substantially separate fluid stream into
the chamber; and a scanning mechanism for selectively exposing the
biosensor to a fluid stream from one or more outlets, b) providing
a sample suspected of containing a modulator to at least one of the
channels; c) measuring the response of the biosensor as it is
selectively exposed to a fluid stream comprising the sample,
wherein a change in the response of the biosensor indicates the
presence of a modulator in the sample.
88. The method of claim 85 or 87, wherein the exposing step is
performed by moving the substrate or the sensor or both the
substrate and the sensor relative to at least one channel
outlet.
89. The method of claim 88, wherein both the substrate and sensor
are moved independently of each other.
90. The method of claim 85 or 87, wherein the exposing step further
comprises producing pressure drops across one or more channels.
91. The method of claim 87, wherein the same suspected modulator is
provided to a plurality of channels.
92. The method of claim 87, wherein different concentrations of the
modulator are provided to the plurality of channels.
93. The method of claim 87, wherein the modulator varies in
concentration in at least one channel, forming a gradient of
modulator in the at least one channel.
94. The method of claim 87, further comprising generating a
dose-response curve for the modulator.
95. The method of claim 87, comprising exposing the biosensor to
buffer delivered by at least one channel.
96. The method of claim 95, comprising selectively exposing the
biosensor to streams of buffer and sample.
97. The method of claim 96, comprising selectively exposing the
biosensor to alternating streams of buffer and sample.
98. The method of claim 85 or 87, wherein the cell-based biosensor
comprises a patch-clamped cell or patch-clamped cell membrane
fraction.
99. The method of claim 98, wherein the patch-clamped cell is
positioned relative to the outlets using a patch clamp pipette
coupled or connected to a positioner.
100. The method of claim 98, wherein the patch-clamped cell or
patch-clamped cell membrane fraction is positioned in a depression
in the base of the chamber.
101. The method of claim 87, wherein the receptor is activated by
an agonist which produces a measurable response by the biosensor
upon binding to the receptor, and wherein the modulator modulates
the activity of the agonist.
102. The method of claim 87, wherein the receptor is inactivated by
an antagonist which eliminates or reduces a measurable response by
the biosensor upon binding to the receptor, and wherein the
modulator modulates the activity of the antagonist.
103. The method of claim 87, wherein the modulator is an
agonist.
104. The method of claim 87, wherein the modulator is an
antagonist.
105. The method of 87, wherein the channels deliver a buffer, at
least one agonist; at least one antagonist; at least one agonist
and a buffer; at least one antagonist and a buffer; or at least one
antagonist, at least one agonist, and a buffer.
106. The method of claim 87 or 105, wherein the chamber comprises a
buffer, at least one agonist, or at least one antagonist.
107. The method of claim 85 or 87, wherein the cell-based biosensor
comprises an ion-channel.
108. The method of claim 85 or 87, wherein the receptor comprises a
G-protein coupled receptor.
109. The method of claim 85 or 87, wherein the cell-based biosensor
comprises a recombinantly expressed receptor.
110. The method of claim 109, wherein the recombinantly expressed
receptor is an orphan receptor.
111. The method of claim 87, wherein the response is determined by
measuring cell surface area.
112. The method of claim 87, wherein the response is determined by
measuring an electrical property of the cell-based biosensor.
113. The method of claim 87, wherein the modulator is a modulator
of neurotransmitter release.
114. The method of claim 87, wherein the response is determined by
measuring ion-channel permeability properties.
115.-170. (canceled)
Description
FIELD OF THE INVENTION
[0001] The invention relates to systems and methods for rapid and
programmable delivery of aqueous streams to a sensor, such as a
cell-based biosensor. In particular, the invention provides methods
and systems for high throughput patch clamp analysis.
BACKGROUND OF THE INVENTION
[0002] Ion-channels are important therapeutic targets. Neuronal
communication, heart function, and memory all critically rely upon
the function of ligand-gated and voltage-gated ion-channels. In
addition, a broad range of chronic and acute pathophysiological
states in many organs such as the heart, gastrointestinal tract,
and brain involve ion channels. Indeed, many existing drugs bind
receptors directly or indirectly connected to ion-channels. For
example, anti-psychotic drugs interact with receptors involved in
dopaminergic, serotonergic, cholinergic and glutamatergic
neurotransmission.
[0003] Because of the importance of ion-channels as drug targets,
there is a need for methods which enable high throughput screening
(HTS) of compounds acting on ligand-gated and voltage-gated
channels (see e.g., Sinclair et al., 2002, Anal. Chem. 74:
6133-6138). However, existing HTS drug discovery systems targeting
ion channels generally miss significant drug activity because they
employ indirect methods, such as raw binding assays or
fluorescence-based readouts. Although as many as ten thousand drug
leads can be identified from a screen of a million compounds,
identification of false positives and false negatives can still
result in a potential highly therapeutic blockbuster drug being
ignored, and in unnecessary and costly investments in false drug
leads.
[0004] Patch clamp methods are superior to any other technology for
measuring ion channel activity in cells, and can measure currents
across cell membranes in ranges as low as picoAmps (see, e.g.,
Neher and Sakmann, 1976, Nature 260: 799-802; Hamill, et al., 1981,
Pflugers Arch 391: 85-100; Sakmann and Neher, 1983, In
Single-Channel Recording pp. 37-52, Eds. B. Sakmann and E. Neher.
New York and London, Plenum Press, 1983). However, patch clamp
methods generally have not been the methods of choice for
developing HTS platforms.
SUMMARY OF THE INVENTION
[0005] The invention provides microfluidic systems for altering the
solution environment around a nanoscopic or microscopic object,
such as a sensor, and methods for using the same. The invention can
be applied in any sensor technology in which the sensing element
needs to be exposed rapidly, sequentially, and controllably, to a
large number of different solution environments (e.g., greater than
10 and preferably, greater than about 96 different environments)
whose characteristics may be known or unknown. In contrast to prior
art microfluidic systems, the interval between sample deliveries is
minimized, e.g., on the order of microseconds and seconds,
permitting rapid analysis of compounds (e.g., drugs).
[0006] In one aspect, the invention provides a system comprising a
substrate for changing the solution environment around a nanoscopic
or microscopic object, such as a sensor. The substrate comprises an
open-volume chamber for the sensor, and a plurality of channels.
Each channel comprises an outlet for delivering a substantially
separate aqueous stream into the chamber. In one aspect, the
outlets are substantially parallel, i.e., arrayed linearly in a
single plane. The dimensions of the outlets can vary; however, in
one aspect, where the sensor is a biological cell, the diameter of
each of the outlets is, preferably, at least about the diameter of
the cell. Preferably, a plurality, if not all, of the channels
programmably deliver a fluid stream into the chamber.
[0007] In a preferred aspect, each channel of the substrate
comprises at least one inlet for receiving solution from a
reservoir, conforming in geometry and placement on the substrate to
the geometry and placement of wells in a multi-well plate. For
example, the substrate can comprise 96-1024 reservoirs, each
connected to an independent channel on the substrate. Preferably,
the center-to-center distance of each reservoir corresponds to the
center-to-center distance of wells in an industry standard
microtiter or multi-well plate.
[0008] In a further aspect, the substrate comprises one or more
treatment chambers or microchambers for delivering a treatment to a
cell placed within the treatment chamber. The treatment can
comprise exposing the cell to a chemical or compound, (e.g. drugs
or dyes, such as calcium ion chelating fluorogenic dyes), exposing
the cell to an electrical current (e.g., electroporation,
electrofusion, and the like), or exposing the cell to light (e.g.,
exposure to a particular wavelength of light). A treatment chamber
can be used for multiple types of treatments which may be delivered
sequentially or simultaneously. For example, an electrically
treated cell also can be exposed to a chemical or compound and/or
exposed to light. Treatment can be continuous over a period of time
or intermittent (e.g., spaced over regular or irregular intervals).
The cell treatment chamber can comprise a channel with an outlet
for delivering a treated cell to the sensor chamber or directly to
a mechanism for holding the cell connected to a positioner (e.g., a
micropositioner or nanopositioner) for positioning the cell within
the chamber.
[0009] Preferably, the base of the sensor chamber is optically
transmissive and in one aspect, the system further comprises a
light source (e.g., such as a laser) in optical communication with
the open volume chamber. The light source can be used to
continuously or intermittently expose the sensor to light of the
same or different wavelengths. The sensor chamber and/or channels
additionally can be equipped with control devices. For example, the
sensor chamber and/or channels can comprise temperature sensors, pH
sensors, and the like, for providing signals relating to chamber
and/or channel conditions to a system processor.
[0010] The sensor chamber can be adapted for receiving a variety of
different sensors. In one aspect, the sensor comprises a cell or a
portion of a cell (e.g., a cell membrane fraction). In another
aspect, the cell or cell membrane fraction comprises an ion
channel, including, but not limited to, a presynaptically-expressed
ion channel, a ligand-gated channel, a voltage-gated channel, and
the like. In a further aspect, the cell comprises a receptor, such
as a G-Protein-Coupled Receptor (GPCR), or an orphan receptor for
which no ligand is known, or a receptor comprising a known
ligand.
[0011] A cultured cell can be used as a sensor and can be selected
from the group consisting of CHO cells, NIH-3T3 cells, and HEK-293
cells, and can be recombinantly engineered to express a sensing
molecule such as an ion channel or receptor. Many other different
cell types also can be used, which can be selected from the group
consisting of mammalian cells (e.g., including, but not limited to
human cells, primate cells, bovine cells, swine cells, other
domestic animals, and the like); bacterial cells; protist cells;
yeast cells; plant cells; invertebrate cells, including insect
cells; amphibian cells; avian cells; fish; and the like.
[0012] A cell membrane fraction can be isolated from any of the
cells described above, or can be generated by aggregating a
liposome or other lipid-based particle with a sensing molecule,
such as an ion channel or receptor, using methods routine in the
art.
[0013] The cell or portion of the cell can be positioned in the
chamber using a mechanism for holding the cell or cell portion,
such as a pipette (e.g., a patch clamp pipette) or a capillary
connected to a positioner (e.g., such as a micropositioner or
nanopositioner or micromanipulator), or an optical tweezer.
Preferably, the positioner moves the pipette at least in an x-, y-,
z-, direction. Alternatively or additionally, the positioner may
rotate the pipette. Also, preferably, the positioner is coupled to
a drive unit which communicates with a processor, allowing movement
of the pipette to be controlled by the processor.
[0014] In one aspect, the base of the chamber comprises one or more
depressions and the cell or portion of the cell is placed in a
depression which can be in communication with one or more
electrodes (e.g., the sensor can comprise a planar patch clamp
chip).
[0015] Non-cell-based sensors also can be used in the system.
Suitable non-cell based sensors include, but are not limited to: a
surface plasmon energy sensor; an FET sensor; an ISFET; an
electrochemical sensor; an optical sensor; an acoustic wave sensor;
a sensor comprising a sensing element associated with a Quantum Dot
particle; a polymer-based sensor; a single molecule or an array of
molecules (e.g., nucleic acids, peptides, polypeptides, small
molecules, and the like) immobilized on a substrate. The sensor
chamber also can comprise a plurality of different types of
sensors, non-cell based and/or cell-based. A sensor substrate can
be affixed to the base of the chamber or the substrate can simply
be placed on the base of the chamber. Alternatively, the base of
the chamber itself also can serve as the sensor substrate and one
or more sensing elements can be stably associated with the base
using methods routine in the art. In one aspect, sensing elements
are associated at known locations on a substrate or on the base of
the sensor chamber.
[0016] However, an object placed within a chamber need not be a
sensor. For example, the object can be a colloidal particle, beads,
nanotube, a non-sensing molecule, silicon wafer, or other small
elements.
[0017] The invention also provides a system comprising a substrate
which comprises at least one chamber for receiving a cell-based
biosensor, a plurality of channels, at least one cell storage
chamber and at least one cell treatment chamber. Preferably, each
channel comprises an outlet for delivering a fluid stream into the
chamber, and the cell treatment chamber is adapted for delivering
an electrical current to a cell placed within the cell treatment
chamber. In one aspect, the cell treatment chamber further
comprises a channel with an outlet for delivering a cell to the
sensor chamber for receiving the cell-based biosensor. The system
can be used to rapidly and programmably change the solution
environment around a cell which has been electroporated and/or
electrofused, and/or otherwise treated within the cell treatment
chamber. Alternatively, or additionally, the sensor chamber also
can be used as a treatment chamber and in one aspect, the sensor
chamber is in electrical communication with one or more electrodes
for continuously or intermittently exposing a sensor to an electric
field.
[0018] In one aspect, a system according to the invention further
comprises a scanning mechanism for scanning the position of a
sensor relative to the outlets of the channels. The scanning
mechanism can translate the substrate relative to a stationary
sensor, or can translate the sensor relative to a stationary
substrate, or can move both sensor and substrate at varying rates
and directions relative to each other. In one aspect, the sensor is
positioned relative to an outlet using a mechanism for holding the
sensor (e.g., such as a pipette or capillary) coupled to a
positioner (e.g., a micropositioner or nanopositioner or
micromanipulator). Thus, the positioner can be used to move the
sensor across a plurality of fluid streams exiting the outlets of
the channels by moving the mechanism for holding the sensor.
Alternatively, or additionally, scanning also can be regulated by
producing pressure drops sequentially across adjacent
microchannels.
[0019] Preferably, the scanning mechanism is in communication with
a processor and translation occurs in response to instructions from
the processor (e.g., programmed instructions or instructions
generated as a result of a feedback signal). In one aspect, the
processor controls one or more of: the rate of scanning, the
direction of scanning, acceleration of scanning, and number of
scans. Thus, the system can be used to move nanoscopic and
microscopic objects in a chamber to user-selected, or
system-selected coordinates, for specified (e.g., programmable)
lengths of time. Preferably, the system processor also can be used
to locate the position of one or more objects in the chamber, e.g.,
in response to previous scanning actions and/or in response to
optical signals from the objects detected by the system detector.
In one aspect, the system further comprises a user device in
communication with the processor which comprises a graphical user
display for interfacing with a user. For example, the display can
be used to display coordinates of object(s) within the chamber, or
optical data or other data obtained from the chamber.
[0020] The invention additionally provides a substrate comprising a
chamber for receiving a cell-based biosensor which comprises a
receptor or ion channel. In one aspect, the system sequentially
exposes a cell-based biosensor for short periods of time to one or
several ligands which binds to the receptor/ion channel and to
buffer without ligand for short periods of time through
interdigitated channels of the substrate. For example, selective
exposure of a cell biosensor to these different solution conditions
for short periods of time can be achieved by scanning the
cell-based biosensor across interdigitated channels which alternate
delivery of one or several ligands and buffer. The flow of buffer
and sample solution in each microfluidic channel is preferably a
steady state flow at constant velocity.
[0021] However, in another aspect, the system delivers pulses
(e.g., pulsatile on/off flow) of buffer to a receptor through a
superfusion capillary positioned in proximity to both the
cell-based biosensor or other type of sensor and to an outlet
through which a fluid is streaming. For example, the system can
comprise a mechanism for holding the sensor which is coupled to a
positioner (e.g., a micropositioner, nanopositioner,
micromanipulator, etc.) for positioning the c sensor in proximity
to the outlet and a capillary comprising an outlet in sufficient
proximity to the mechanism for holding the sensor to deliver a
buffer from the capillary to the sensor. A scanning mechanism can
be used to move both the capillary and sensor simultaneously, to
maintain the appropriate proximity of the capillary to the sensor.
The capillary also can be coupled to a pumping mechanism to provide
pulsatile delivery of buffer to the sensor. In another aspect, the
flow rate of buffer from the one or more superfusion capillaries in
proximity to one or more sensors can be higher or lower than the
flow rate of fluid from the channels.
[0022] The invention further provides a substrate which comprises a
circular chamber for receiving a sensor, comprising a cylindrical
wall and a base. In one aspect, the substrate comprises a plurality
of channels comprising outlets whose openings are radially disposed
about the circumference of the wall of the chamber (e.g., in a
spokes-wheel configuration), for delivering samples into the
chamber. Preferably, the substrate also comprises at least one
output channel for draining waste from the chamber. In one aspect,
at least one additional channel delivers buffer to the chamber.
Preferably, the angle between the at least one additional channel
for delivering buffer and the output channel is greater than
10.degree.. More preferably, the angle is greater than 90.degree..
The channel "spokes" may all lie in the same plane, or at least two
of the spokes may lie in different planes.
[0023] Rapid, programmed exchange of solutions in the chamber is
used to alter the solution environment around a sensor placed in
the chamber and multiple output channels can be provided in this
configuration. For example, there may be an output channel for each
channel for delivering sample/buffer. The number of channels for
delivering also can be varied, e.g., to render the substrate
suitable for interfacing with an industry standard microtiter
plate. For example, there may be 96 to 1024 channels for delivering
samples. In another aspect, there may be an additional, equal
number of channels for delivering buffer (e.g., to provide
interdigitating fluid streams of sample and buffer).
[0024] The invention also provides a multi-layered substrate for
changing the solution environment around a sensor, comprising: a
first substrate comprising channels for delivering fluid to a
sensor; a filter layer for retaining one or more sensors which is
in proximity to the first substrate; and a second substrate
comprising a waste reservoir for receiving fluid from the filter
layer. One or more sensors can be provided between the first
substrate and the filter layer. In one aspect, at least one of the
sensors is a cell. Preferably, the system further comprises a
mechanism for creating a pressure differential between the first
and second substrate to force fluid flowing from channels in the
first substrate through the filter and into the waste reservoir,
i.e., providing rapid fluid exchange through the filter (i.e.,
sensor) layer.
[0025] The invention additionally provides a substrate which
comprises a chamber for receiving a sensor, a first channel
comprising an outlet intersecting with the chamber, and a plurality
of sample delivery channels intersecting with the first channel.
The first channel also is connected to a buffer reservoir (e.g.,
through a connecting channel). In one aspect, the longitudinal axes
of the sample delivery channels are parallel with respect to each
other, but are angled with respect to the longitudinal axis of the
first channel (e.g., providing a "fish bone" shape). Rapid flow of
solution through the first channel and/or sample channels can be
achieved through a positive pressure mechanism in communication
with the buffer reservoir and/or sample channels. Passive one-way
valves can be provided at the junction between sample delivery
channels and the first channel to further regulate flow rates. In
one aspect, at least one of the sample reservoirs is sealed by a
septum which can comprise a needle or tube inserted therein.
[0026] The invention further provides a substrate which comprises a
chamber for receiving a sensor, a plurality of delivery channels
comprising outlets for feeding sample or buffer into the chamber,
and a plurality of drain channels comprising inlets opposite the
outlets of the delivery channels. The longitudinal axes of the
delivery channels can be in the same, or a different plane, from
the longitudinal axes of the drain channels. In one aspect, the
plurality of drain channels is on top of the plurality of inlet
channels (i.e., the substrate is three-dimensional).
[0027] Any of the systems described above can further comprise a
pressure control device for controlling positive and negative
pressure applied to at least one microchannel of the substrate. In
systems where substrates comprise both delivery channels as well as
output channel(s), the system preferably further comprises a
mechanism for applying a positive pressure to at least one delivery
channel while applying a negative pressure to at least one output
channel. Preferably, hydrostatic pressure at least one of the
channels can be changed in response to a feedback signal received
by the processor.
[0028] The system can thus regulate when, and through which
channel, a fluid stream is withdrawn from the chamber. For example,
after a defined period of time, a fluid stream can be withdrawn
from the chamber through the same channel through which it entered
the system or through a different channel. When a drain channel is
adjacent to a delivery channel, the system can generate a U-shaped
fluid stream which can efficiently recycle compounds delivered
through delivery channels.
[0029] As described above, multiple delivery channel configurations
can be provided: straight, angled, branched, fish-bone shaped, and
the like. In one aspect, each delivery channel comprises one or
more intersecting channels whose longitudinal axes are
perpendicular to the longitudinal axis of the delivery channels. In
another aspect, each delivery channel comprises one or more
intersecting channels whose longitudinal axes are at an angle with
respect to the delivery channel.
[0030] In general, any of the channel configurations described
above are interfaceable with containers for delivering samples to
the reservoirs or sample inlets (e.g., through capillaries or
tubings connecting the containers with the reservoirs/inlets). In
one aspect, at least one channel is branched, comprising multiple
inlets. Preferably, the multiple inlets interface with a single
container. However, multiple inlets also may interface with several
different containers.
[0031] Further, any of the substrates described above can be
interfaced to a multi-well plate (e.g., a microtiter plate) through
one or more external tubings or capillaries. The one or more
tubings or capillaries can comprise one or more external valves to
control fluid flow through the tubings or capillaries. In one
aspect, a plurality of the wells of the multi-well plates comprise
known solutions. The system also can be interfaced with a plurality
of microtiter plates; e.g., the plates can be stacked, one on top
of the other. Preferably, the system further comprises a micropump
for pumping fluids from the wells of a microtiter plate or other
suitable container(s) into the reservoirs of the substrate. More
preferably, the system programmably delivers fluids to selected
channels of the substrate through the reservoirs.
[0032] In one aspect, a system according to the invention further
comprises a detector in communication with a sensor chamber for
detecting sensor responses. For example, the detector can be used
to detect a change in one or more of: an electrical, optical, or
chemical property of the sensor. In one aspect, in response to a
signal from the detector, the processor alters one or more of: the
rate of scanning, the direction of scanning, acceleration of
scanning, number of scans, and pressure on one or more
channels.
[0033] The invention also provides a method for changing an aqueous
solution environment locally around a nanoscopic or microscopic
object (e.g., such as a sensor). The method comprises providing a
substrate which comprises an open volume chamber comprising a
nanoscopic or microscopic object and an aqueous fluid. The
substrate further comprises a plurality of channels, each channel
comprising an outlet intersecting with the open volume chamber.
Substantially separate aqueous streams of fluid are delivered into
the open volume chamber, at least two of which comprise different
fluids.
[0034] Preferably, fluid streams exiting from the at least two
adjacent channels are collimated and laminar within the open
volume. However, the system can comprise sets of channels (at least
two adjacent channels) wherein at least one set delivers collimated
laminar streams, while at least one other set delivers
non-collimated, non-laminar streams. In one aspect, the streams
flow at different velocities. Fluid can be delivered from the
channels to the chamber by a number of different methods, including
by electrophoresis and/or by electroosmosis and/or by pumping.
[0035] In one aspect, the longitudinal axes of the channels are
substantially parallel. The channels can be arranged in a linear
array, in a two-dimensional array, or in a three-dimensional array,
can comprise treatment chambers, sensor chambers, reservoirs,
and/or waste channels, and can be interfaced with container(s) or
multi-well plate(s) as described above. In one aspect, output
channels can overly input channels (i.e., in a three-dimensional
configuration). Preferably, the longitudinal axis of at least one
output or drain channel is parallel, but lying in a different
plane, relative to the longitudinal axis of at least one input
channel. By applying a positive pressure to an input channel at the
same time that a negative pressure is applied to an adjacent output
or drain channel, a U-shaped fluid stream can be generated within
the chamber. In this way, an object within the chamber can be
exposed to a compound in a fluid stream from an inlet channel which
can, for example, be recycled by being withdrawn from the chamber
through the adjacent output or drain channel. The U-shaped fluid
streams can, preferably, be used to create local well-defined
regions of fluid streams with specific composition in a
large-volume reservoir or open volume.
[0036] Preferably, the object is scanned sequentially across the at
least two aqueous fluid streams, thereby altering the aqueous
solution environment around the object. Scanning can be performed
by moving the substrate and/or the object, or, can be mediated by
pressure drops applied to the channels.
[0037] The open volume chamber can comprise a plurality of objects;
preferably, each object is scanned across at least two streams.
Scanning can be performed by a scanning mechanism controlled by a
processor as described above. The open volume can, additionally
have inlets and outlets for adding and withdrawal of solution. For
example, fresh buffer solution can be added to the recording
chamber by using a peristaltic pump.
[0038] In one aspect, the method further comprises modifying one or
more scanning parameters, such as the rate of scanning, the
direction of scanning, acceleration of scanning, number of scans,
and pressure across one or more channels. Scanning parameters can
be modified in response to a feedback signal, such as a signal
relating to the response of an object to one or more of aqueous
streams. Scanning also can be coordinated with other system
operations. For example, in a system comprising a cell-based
biosensor, scanning can be coordinated with exposure of the
biosensor to an electrical current, i.e., inducing pore formation
in a cell membrane of the biosensor, as the biosensor is scanned
past one or more sample outlets.
[0039] Hydrostatic pressure at one or more channels also can be
varied by the processor according to programmed instructions and/or
in response to a feedback signal. In one aspect, hydrostatic
pressure at each of the plurality of channels is different.
[0040] In another aspect, the viscosity of fluids in at least two
of the channels is different. In yet another aspect, fluid within
at least two of the channels are at a different temperature. In a
further aspect, the osmolarity of fluid within at least two of the
channels is different. In a still further aspect, the ionic
strength of fluid within at least two of the channels is different.
Fluid in at least one of the channels also can comprise an organic
solvent. By changing these parameters at different outlets, sensor
responses can be optimized to maximize sensitivity of detection and
minimize background. In some aspects, parameters also can be varied
to optimize certain cell treatments being provided (e.g., such as
electroporation or electrofusion).
[0041] The invention also provides a method for rapidly changing
the solution environment around a nanoscopic or microscopic object
which comprises rapidly exchanging fluid in a sensor chamber
comprising the nanoscopic or microscopic object. In one aspect,
fluid exchange in the chamber occurs within less than about 1
minute, preferably, with less than about 30 seconds, less than
about 20 seconds, less than about 10 seconds, less than about 5
seconds, or less than about 1 second. In another aspect, fluid
exchange occurs within milliseconds. In another aspect fluid
exchange occurs within nanoseconds.
[0042] In one aspect, the method comprises providing a chamber
comprising the object (which may be a sensor or even a single
molecule), wherein the chamber comprises a plurality of inlet
channels for delivering a fluid into the chamber and a plurality of
outlet channels for draining fluid from the chamber. Preferably,
the longitudinal axes of the drain channels are at an angle with
respect to the longitudinal axes of the delivery channels. In one
aspect, the longitudinal axis of at least one drain channel is
.gtoreq.90.degree. with respect to the longitudinal axis of a
delivery channel. Preferably, the angle is about 180.degree.. Fluid
entering the chamber is withdrawn from the chamber after a
predetermined period of time or in response to a feedback signal.
By controlling the velocity of fluid flow through the inlet
channels and the output or drain channels, complete exchange of
fluid in the chamber can occur in less than about 30 seconds, and
preferably, in milliseconds.
[0043] Preferably, the velocity of fluids in the channels at an
angle with respect to each other is different. In one aspect, the
hydrostatic pressure of fluids in the channels at an angle with
respect to each other is different. In another aspect, the
viscosity of fluids in the channels at an angle with respect to
each other is different. In still another aspect, the osmolarity of
fluids in the channels at an angle with respect to each other is
different. In a further aspect, the ionic strength of fluids in the
channels at an angle with respect to each other is different. In
yet a further aspect, the channels at an angle with respect to each
other comprise different organic solvents.
[0044] The chamber can be circular, comprising a cylindrical wall
and a base and the outlets can be radially disposed around the
circumference of the wall, i.e., in a two-dimensional or
three-dimensional spokes-wheel configuration. Other configurations
are also possible. For example, each delivery channel can comprise
an intersecting inlet channel whose longitudinal axis is
perpendicular to the delivery channel.
[0045] The method can generally be used to measure responses of a
cell or portion thereof to a condition in an aqueous environment,
by providing a cell or portion thereof in the chamber of any of the
substrates described above, exposing the cell or portion thereof to
one or more aqueous streams for creating the condition, and
detecting and/or measuring the response of the cell or portion
thereof to the condition. For example, the condition may be a
chemical or a compound to which the cell or portion thereof is
exposed and/or can be the osmolarity and/or ionic strength and/or
temperature and/or viscosity of a solution in which the cell or
portion thereof is bathed.
[0046] The composition of the bulk solution in the sensor chamber
in any of the substrates described above can be controlled, e.g.,
to vary the ionic composition of the sensor chamber or to provide
chemicals or compounds to the solution. For example, by providing a
superfusion system in proximity to the sensor chamber, a chemical
or a compound, such as a drug, can be added to the sensor chamber
during the course of an experiment.
[0047] In one aspect, exposure of the cell or portion thereof to
the condition occurs in the sensor chamber. However, alternatively,
or additionally, exposure of the cell or portion thereof to the
condition can occur in a microchamber which connects to the sensor
chamber via one or more channels. The cell or portion thereof can
be transferred to the sensor chamber in order to measure a response
induced by changing the conditions around the cell.
[0048] In one aspect, the invention also provides a method for
generating an activated receptor or ion channel in order to detect
or screen for antagonists. The method comprises delivering a
constant stream of an agonist to a cell-based biosensor in a sensor
chamber through a plurality of microchannels feeding into the
sensor chamber (e.g., using any of the substrates described above).
Preferably, the cell-based biosensor expresses receptor/ion channel
complexes which do not desensitize or which desensitize very
slowly. Exposure of the biosensor to the agonist produces a
measurable response, such that the receptor is activated each time
it passes a microchannel delivering agonist. Preferably, a
plurality of the agonist delivering microchannels also comprise
antagonist whose presence can be correlated with a decrease in the
measurable response (e.g., antagonism) when the cell-based
biosensor passes by these microchannels. In one aspect, a plurality
of microchannels comprises equal amounts of agonist but different
concentrations of antagonist. Inhibition of the measurable response
can thus be correlated with the presence of a particular dose of
antagonist. In another aspect, a plurality of microchannels
comprise equal amounts of agonist, but one or more, and preferably
all of the plurality of microchannels, comprises different kinds of
antagonists. In this way the activity of particular types of
antagonists (or compounds suspected of being antagonists) can be
monitored.
[0049] In one aspect, a periodically resensitized receptor is
provided using the superfusion system described above to deliver
pulses of buffer to the cell-based biosensor, to thereby remove any
bound agonist or modulator desensitizing the receptor, before the
receptor is exposed to the next channel outlet containing agonists
or receptor modulators. In detection of antagonists, the pulsated
superfusion system can also periodically remove the constantly
applied agonist. A transient peak response (which is desensitized
to a steady state response) is generated when the resensitized
biosensor is exposed to the agonist. The generation of this peak
response can provide a better signal-to-noise ratio in detection of
antagonists.
[0050] In another aspect, ion-channels in a cell-based biosensor
are continuously activated or periodically activated by changing
the potential across the cell-membrane. This provides a sensor for
detection of compounds or drugs modulating voltage-dependent
ion-channels.
[0051] Responses measured by the systems or methods will vary with
the type of sensor used. When a cell-based biosensor is used, the
agonist-, antagonist-, or modulator-induced changes of the
following parameters or cell properties can be measured: cell
surface area, cell membrane stretching, ion-channel permeability,
release of internal vesicles from a cell, retrieval of vesicles
from a cell membrane, levels of intracellular calcium, ion-channel
induced electrical properties (e.g., current, voltage, membrane
capacitance, and the like), optical properties, or viability.
[0052] In one aspect, the sensor comprises at least one
patch-clamped cell. For example, the method can be performed by
combining the system with a traditional patch clamp set-up. Thus, a
cell or cell membrane fraction can be positioned appropriately
relative to channel outlets using a patch clamp pipette connected
to a positioner such as a micropositioner or nanopositioner.
[0053] Alternatively, a patch-clamped cell or patch-clamped cell
membrane fraction can be positioned in a depression in the base of
the chamber which is in communication with one or more electrodes
(e.g., providing a patch clamp chip).
[0054] The systems and methods according to the invention can be
used to perform high throughput screening for ion channel ligands
and for drugs or ligands which act directly or indirectly on ion
channels. However, more generally, the systems and methods can be
used to screen for compounds/conditions which affect any
extracellular, intracellular, or membrane-bound target(s). Thus,
the systems and methods can be used to characterize, for example,
the effects of drugs on cell. Examples of data that can be obtained
for such purposes according to the present invention includes but
is not limited to: dose response curves, IC.sub.50 and EC.sub.50
values, voltage-current curves, on/off rates, kinetic information,
thermodynamic information, etc.
[0055] Thus, the system can, for example, be used to characterize
if an ion channel or receptor antagonists is a competitive or
non-competitive inhibitor. The systems and methods according to the
invention also can be used for toxicology screens, e.g., by
monitoring cell viability in response to varying kinds or doses of
compound, or in diagnostic screens. The method can also be used to
internalize drugs, in the cell cytoplasm, for example, using
electroporation to see if a drug effect is from interaction with a
cell membrane bound outer surface receptor or target or through an
intracellular receptor or target. It should be obvious to those of
skill in the art that the systems according to the invention can be
used in any method in which an object would benefit from a change
in solution environment, and that such methods are encompassed
within the scope of the instant invention.
BRIEF DESCRIPTION OF THE FIGURES
[0056] The objects and features of the invention can be better
understood with reference to the following detailed description and
accompanying drawings. The Figures are not to scale.
[0057] FIGS. 1A and 1B show a schematic of a system according to
one aspect of the invention showing integration of a microfluidic
chip with patch clamp recordings of ion channel activity. FIG. 1A
is a perspective view of a microfluidic chip in which a cell is
positioned in proximity to microchannel outlets of the chip using a
patch clamp micropipette connected to a positioner. FIG. 1B is a
side view, partially in section, of FIG. 1A. FIG. 1C is a side
view, partially in section, of a chip-based patch clamp system. In
operation, the chip is preferably covered.
[0058] FIGS. 2A-C show top views of different embodiments of
microfluidic chips according to aspects of the invention
illustrating exemplary placements of reservoirs for interfacing
with 96-well plates. FIG. 2A shows a chip comprising ligand
reservoirs (e.g., the reservoirs receive samples of ligands from a
96-well plate). FIG. 2B shows a chip comprising alternating or
interdigitating ligand and buffer reservoirs (e.g., every other
reservoir receives samples of ligands from one 96-well plate, while
the remaining reservoirs receive samples of buffer from another
96-well plate). As shown in FIG. 2C, additional reservoirs can be
placed on chip for the storage and transfer of cells or other
samples of interest.
[0059] FIG. 3 is a perspective view of a kit in accordance with one
aspect of the invention illustrating a process for dispensing
fluids from 96-well plates onto a microfluidic chip comprising
interdigitating reservoirs using automated array pipettors and cell
delivery using a pipette.
[0060] FIGS. 4A-C comprise a top view of a microfluidic chip
structure for HTS of drugs according to one aspect of the
invention, for scanning a sensor such as a patch-clamped cell or
cells across interdigitated ligand and buffer streams. FIG. 4A
depicts the overall chip structure for both a 2D and 3D
microfluidic system. FIG. 4B shows an enlarged view of the
reservoirs of the chip and their individual connecting channels.
FIG. 4C shows an enlarged view of interdigitating microchannel
whose outlets intersect with the sensor chamber of the chip.
[0061] FIG. 5A schematically depicts a top view of the
interdigitating channels of a microfluidic chip, with a
patch-clamped cell being moved past the outlets of the channels.
FIGS. 5B and 5C depict side views of alternate embodiments of the
outlets and microchannels. FIGS. 5B and 5C are side views showing a
2D and 3D microfluidic chip design, respectively. FIG. 5D is a
perspective view of a 3D chip design according to one aspect of the
invention, in which the chip comprises a bottom set and top set of
channels. FIG. 5E is a side view of FIG. 5D, showing fluid flow can
be controlled through pressure differentials so that fluid flowing
out of a channel in the bottom set will make a "U-turn" into an
overlying channel. FIG. 5F is a top view of FIG. 5D and shows cell
scanning across the "U-turn" fluid streams.
[0062] FIG. 6A is a perspective view showing a 3D array of
microchannel outlet arrangements for increased throughput in HTS
applications. FIG. 6B depicts the use of a microchannel array as
depicted in FIG. 6A, but with a plurality of patch-clamped cells.
The arrows in the Figures indicate directions in which the
patch-clamped cell(s) can be scanned.
[0063] FIGS. 7A-N are schematics showing chip designs for carrying
out cell scanning across ligand streams using buffer superfusion to
provide a periodically resensitized sensor. FIG. 7A is a
perspective view of the overall chip design and microfluidic
system. FIGS. 7B-G show enlarged views of the outlets of
microchannels and their positions with respect to a superfusion
capillary and a patch clamp pipette, as well as a procedure for
carrying out cell superfusion while scanning a patch-clamped cell
across different fluid streams. "P" indicates a source of pressure
on fluid in a microchannel or capillary. Bold arrows indicate
direction of movement. FIGS. 7H-7N show a different embodiment for
superfusing cells. As shown in the perspective view in FIG. 7H,
instead of providing capillaries for delivering buffer, a number of
small microchannels placed at each of the outlets of the ligand
delivery channels are used for buffer delivery. As a patch-clamped
cell is moved to a ligand channel and the system detects a
response, a pulse of buffer can be delivered via the small
microchannels onto the cell for superfusion. The advantage to using
this system is that the exposure time of the patch-clamped cell to
a ligand can be precisely controlled by varying the delay time
between signal detection and buffer superfusion. FIG. 7I is a
cross-section through the side of a microfluidic system used in
this way showing proximity of a patch-clamped cell to both ligand
and buffer outlets. FIG. 7J is a cross section, front view of the
system, showing flow of buffer streams. FIG. 7K is a cross-section
through a top view of the device showing flow of ligand streams and
placement of the buffer microchannels. FIGS. 7L-7M show use of
pressure applied to a ligand and/or buffer channel to expose a
patch clamped cell to ligand and then buffer.
[0064] FIGS. 8A-I are top views of microchannel outlets in
relationship to a patch-clamped cell, collectively showing
different methods by which a patch-clamped cell can be moved in
relation to the fluid streams. FIGS. 8A-C show mechanical scanning
of the patched cell across stationary microchannel outlets. FIGS.
8D-F show mechanical scanning of microchannel outlets relative to a
stationary patch-clamped cell. FIGS. 8G-I show a method for
sweeping fluid streams across an immobilized patched cell by
controlled variation of the pressure across, and flow rates
through, each individual microchannel.
[0065] FIGS. 9A-C are top views of one design of a microfluidic
chip for carrying out cycles of rapid delivery and withdrawal of
compounds into and from a cell chamber for housing a patch-clamped
cell. FIG. 9A shows the overall arrangements of the microchannels
feeding the cell chamber. FIG. 9B is an expanded view of reservoirs
and the individual channels through which they are accessed. FIG.
9C shows an enlarged view of microchannel outlets which feed into
the cell chamber.
[0066] FIG. 10 is an enlarged top view of the cell chamber of FIG.
9A, depicting the arrangement of microchannels around a cell
chamber comprising a patch-clamped cell.
[0067] FIGS. 11A-C are top views showing a microfluidic chip for
carrying out rapid and sequential exchange of fluids around a
patch-clamped cell. FIG. 11A shows the overall arrangement of
channels feeding into, and draining from, a cell chamber. The drain
channels feed into a plurality of reservoirs such that the pressure
drops across each channel can be independently controlled. FIG. 11B
shows an enlarged view of reservoirs and their connecting channels.
FIG. 11C shows an enlarged view of microchannel outlets which feed
into the cell chamber.
[0068] FIG. 12 is an enlarged illustration of FIG. 11A, depicting
the arrangement of and flow directions of fluids in microchannels
around a cell chamber with a patch-clamped cell in a planar 2D
microfluidic system according to one aspect of the invention.
[0069] FIG. 13 is an enlarged perspective view of the system of
FIG. 11A depicting the arrangement of microchannels, and flow
directions in a 3D microfluidic system according to one aspect of
the invention.
[0070] FIGS. 14A-C are top views depicting the chip structure of a
fishbone design for carrying out rapid and sequential exchange of
fluids around a patch-clamped cell (not shown) according to one
aspect of the invention. In the example shown in FIG. 14A, a single
drain channel is provided which feeds into a single waste
reservoir. FIG. 14B shows an enlarged view of reservoirs for
providing sample to the microchannels. FIG. 14C shows an enlarged
view of a plurality of inlet channels intersecting with a central
"spine" channel which feeds sample into the sensor chamber. In this
enlarged view, intersecting channels are perpendicular to the spine
channel rather than slanted; either configuration is possible.
[0071] FIG. 15 is a schematic illustration of an enlarged view of
FIG. 14A depicting arrangements of, and flow directions in,
microchannels, and a patch-clamped cell in a chip according to one
aspect of the invention, as well as the presence of passive one-way
valves, which are schematically depicted as crosses.
[0072] FIGS. 16A and B are microphotographs showing flow profiles
at the outlet of a single microchannel (FIG. 16A) and an array of
microchannels (FIG. 16B). Fluid flow was imaged under fluorescence
using a fluorescent dye (fluorescein) as a flow tracer. The
channels were 100-.mu.m wide, 50 .mu.m thick, with an inter-channel
spacing of 25 .mu.m; the flow rate was 4 mm/s.
[0073] FIG. 17 is a schematic illustrating the arrangement of the
outlets of an interdigitating array of microchannels in which
varying dilutions of a sample (e.g., a drug) are provided in every
other microchannel. By scanning a patch-clamped cell across the
outlets of the channels, dose-response measurements can be
obtained.
[0074] FIGS. 18A-I show schematics of systems for obtaining
dose-response measurements based on high-frequency superfusion and
re-sensitization of a patch-clamped cell. Superfusion can be
achieved through a capillary co-axially placed with respect to a
patch-clamp pipette, or through any capillary placed adjacent to
the patch pipette which is suitable for superfusion, while
translating the patch-clamped cell across a concentration gradient
created by streams exiting microchannel outlets. FIGS. 18A-C show a
concentration gradient generated by diffusion broadening of a
ligand plug in a microchannel. FIGS. 18D-F show lateral diffusion
spreading of a ligand stream as it exits a microchannel. FIG. 18G-H
show the use of networks of microchannels. "P" indicates a source
of pressure applied at one or more microchannels of the
systems.
[0075] FIGS. 19A-C show scanning electron micrographs of
microchannels fabricated in silicon. FIG. 19A shows simple
microchannel arrangements in which the patch-clamped cell or cells
can be scanned across interdigitated ligand and buffer streams.
FIG. 19B shows a simple planar radial spokes-wheel structure for
carrying out cycles of rapid delivery and withdrawal of compounds
into and from a cell chamber housing a patch-clamped cell. FIG. 19C
shows a simple fishbone arrangement of microchannel outlets for
carrying out rapid and sequential exchange of fluids around a
patch-clamped cell.
[0076] FIG. 20 shows whole cell patch clamp recordings of
transmembrane current responses elicited by manual repeated
scanning of a cell across the channel outlet where it was
superfused by buffer into an open reservoir containing
acetylcholine (1 mM). A train of peaks are produced by repeated
manual scanning of the patched cell across the
superfusion-generated gradient. The cell was scanned back and forth
at an average scan rate of 100 .mu.m/s and at a maximum rate of up
to 150 .mu.m/s across the entire outlet of the microchannel
depicted in the inset.
[0077] FIGS. 21A-D show patch clamp current responses of a whole
cell to 1 mM acetylcholine as the patch-clamped cell is scanned
across the outlets of a parallel 7-channel structure (same
structure as that shown in FIG. 16B). Channels 1, 3, 5 and 7 were
filled with PBS buffer, while channels 2, 4 and 6 were filled with
acetylcholine. The channel flow rate was 6.8 mm/s and the cell
scanning speeds in the Figures were A) 0.61 mm/s, B) 1.22 mm/s, C)
2 mm/s and in D) 4 mm/s
[0078] FIG. 22 shows patch clamp current responses of a whole cell
to 1 mM acetylcholine as the patch-clamped cell was scanned across
the outlets of a 7-channel structure (same structure as that shown
in FIG. 16B). Channels 1, 3, 5 and 7 were filled with PBS buffer;
channels 2, 4 and 6 with acetylcholine. The channel flow rate was
2.7 mm/s and the cell scanning speed was 6.25 .mu.m/s.
[0079] FIG. 23 shows concentration-dependent patch clamp current
responses of whole cells to 1 .mu.M, 12 .mu.M and 200 .mu.M
nicotine as the patch-clamped cell was scanned across the outlets
of a 7-channel structure (same structure as that shown in FIG.
16B); channels 1, 3, 5 and 7 were filled with PBS buffer; channel 2
with 1 .mu.M, 4 with 12 .mu.M and 6 with 200 .mu.M nicotine
respectively. The flow rate was 3.24 mm/s and the cell scanning
speed was 250 .mu.m/s.
[0080] FIGS. 24A-C show agonist screening according to one method
of the invention using a microfluidic chip comprising 26 outlets
feeding into a sensor chamber. As shown in FIG. 24A, the screen is
performed linearly from channel outlet position 1 to 26. The scans
can be repeated until a sufficient number of scans are performed. A
simulated trace and score sheet are shown in FIGS. 24B and C for a
single forward scan across microfluidic channel outlets. From this
analysis, .alpha. 6 is the agonist with highest potency, followed
by .alpha. 2.
[0081] FIGS. 25A-C show a method for antagonist screening according
to one aspect of the invention using a microfluidic chip comprising
26 outlets feeding into a sensor chamber. As shown in FIG. 25A, the
screen is performed linearly from position 1-to-26. The scans can
be repeated until a sufficient number of scans are performed. As
shown in the simulated trace and score sheet, FIGS. 25B and C,
respectively, for a single forward scan across microfluidic channel
outlets, .zeta. 3 is the antagonist with highest potency followed
by .zeta. 5.
[0082] FIGS. 26A-C show a method for dose-response screening using
a microfluidic chip comprising 28 outlets feeding into a sensor
chamber. As shown in FIG. 24A, the screen is performed linearly
from channel outlet position 1 to 28. The scans can be repeated
until a sufficient number of scans are performed. A simulated trace
and score sheet are shown in FIGS. 26B and C for a single forward
scan across microfluidic channel outlets. From these data, a
dose-response curve can be created for the unknown agonist
.alpha..
[0083] FIGS. 27A-C show a method for agonist screening using a
microfluidic chip comprising 14 outlets feeding into a sensor
chamber and high repetition rate buffer superfusion using a fluidic
channel placed close to a patch-clamped cell. As shown in FIG. 27A,
the screen is performed linearly from channel outlet position 1 to
-14. The scans can be repeated until a sufficient number of scans
are performed. A simulated trace for a single forward scan across
microfluidic channel outlets and score sheet are shown in FIGS.
27B-C. A plurality of peak responses are obtained per single
microchannel outlet. From this analysis, .alpha. 3 is the agonist
with highest potency, followed by .alpha. 5.
DETAILED DESCRIPTION OF THE INVENTION
[0084] The invention provides a system and method for rapidly and
programmably altering the local solution environment around a
sensor, such as a cell-based biosensor. The invention further
provides a system and method for interfacing microfluidics with
patch-clamp detection.
DEFINITIONS
[0085] The following definitions are provided for specific terms
which are used in the following written description.
[0086] As used herein, a "microchannel" refers to a groove in a
substrate comprising two walls, a base, at least one inlet and at
least one outlet. In one aspect, a microchannel also has a roof.
The term "micro" does not imply a lower limit on size, and the term
"microchannel" is generally used interchangeably with "channel".
Preferably, a microchannel ranges in size from about 0.1 .mu.m to
about 500 .mu.m, and more preferably ranges from, 1 .mu.m to about
150 .mu.m.
[0087] As used herein, a "positioner" refers to a mechanism or
instrument that is capable of moving an object or device (e.g., a
substrate, a sensor, a cell, a mechanism for holding a sensor,
etc.) to which it is coupled. Preferably, the positioner can
control movement of an object over distances such as nanometers
(e.g., the petitioner is a nanopositioner), micrometers (e.g., the
positioner is a micropositioner) and/or millimeters. Suitable
positioners move at least in an x-, y-, or z-direction. In one
aspect, positioners according to the invention also rotate about
any pivot point defined by a user. In a preferred aspect, the
positioner is coupled to a drive unit that communicates with a
processor, allowing movement of the object to be controlled by the
processor through programmed instructions, use of joysticks or
other similar instruments, or a combination thereof.
[0088] As used herein, "a mechanism for holding a sensor" refers to
a device for receiving at least a portion of a sensor to keep the
sensor in a relatively stationary position relative to the
mechanism. In one aspect, the mechanism comprises an opening for
receiving at least a portion of a sensor. For example, such
mechanisms include, but are not limited to: a patch clamp pipette,
a capillary, a hollow electrode, and the like.
[0089] As used herein, the term "moving a sensor" refers to moving
the sensor directly or through the use of a mechanism for holding
the sensor which is itself moved.
[0090] As used herein, a "chamber" refers to an area formed by
walls (which may or may not have openings) surrounding a base. A
chamber may be "open volume" (e.g., uncovered) or "closed volume"
(e.g., covered by a coverslip, for example). A "sensor chamber" is
one which receives one or more sensors and comprises outlets in one
or more walls from at least two microchannels. However, a sensor
chamber according to the invention generally can receive one or
more nanoscopic or microscopic objects, without limitation as to
their purpose. A sensor chamber can comprise multiple walls in
different, not necessarily parallel planes, or can comprise a
single wall which is generally cylindrical (e.g., when the chamber
is "disc-shaped"). It is not intended that the geometry of the
sensor chamber be a limiting aspect of the invention. One or more
of the wall(s) and/or base can be optically transmissive.
Generally, a sensor chamber ranges in size but is at least about 1
.mu.m. In one aspect, the dimensions of the chamber are at least
large enough to receive at least a single cell, such as a mammalian
cell. The sensor chamber also can be a separate entity from the
substrate comprising the microchannels. For example, in one aspect,
the sensor chamber is a petrie dish and the microchannels extend to
a surface of the substrate opening into the petrie dish so as to
enable fluid communication between the microchannels and the petrie
dish.
[0091] As used herein, a "sensor" refers to a device comprising one
or more molecules capable of producing a measurable response upon
interacting with a condition in an aqueous environment to which the
molecule is exposed (e.g., such as the presence of a compound which
binds to the one or more molecules). In one aspect, the molecule(s)
are immobilized on a substrate, while in another aspect, the
molecule(s) are part of a cell (e.g., the sensor is a "cell-based
biosensor").
[0092] As used herein, "a nanoscopic or microscopic object" is an
object whose dimensions are in the nm to mm range.
[0093] As used herein, the term, "a cell-based biosensor" refers to
an intact cell or a part of an intact cell (e.g., such as a
membrane patch) which is capable of providing a detectable
physiological response upon sensing a condition in an aqueous
environment in which the cell (or part thereof) is placed. In one
aspect, a cell-based biosensor is a whole cell or part of a cell
membrane in electrical communication with an electrically
conductive element, such as a patch clamp electrode or an
electrolyte solution.
[0094] As used herein, the term "receptor" refers to a
macromolecule capable of specifically interacting with a ligand
molecule. Receptors may be associated with lipid bilayer membranes,
such as cellular, golgi, or nuclear membranes, or may be present as
free or associated molecules in a cell's cytoplasm or may be
immobilized on a substrate. A cell-based biosensor comprising a
receptor can comprise a receptor normally expressed by the cell or
can comprise a receptor which is non-native or recombinantly
expressed (e.g., such as in transfected cells or oocytes).
[0095] As used herein, "periodically resensitized" or "periodically
responsive" refers to an ion-channel which is maintained in a
closed (i.e., ligand responsive) position when it is scanned across
microchannel outlets providing samples suspected or known to
comprise a ligand. For example, in one aspect, an receptor or
ion-channel is periodically resensitized by scanning it across a
plurality of interdigitating channels providing alternating streams
of sample and buffer. The rate at which the receptor/ion channel is
scanned across the interdigitating channels is used to maintain the
receptor/ion-channel in a ligand-responsive state when it is
exposed to a fluid stream comprising sample. Additionally, or
alternatively, the receptor/ion channel can be maintained in a
periodically resensitized state by providing pulses of buffer,
e.g., using one or more superfusion capillaries, to the ion
channel, or by providing rapid exchange of solutions in a sensor
chamber comprising the ion channel.
[0096] As used herein, a "substantially separate fluid stream"
refers to a flowing fluid in a volume of fluid (e.g., such as
within a chamber) that is physically continuous with fluid outside
the stream within the volume, or other streams within the volume,
but which has at least one bulk property which differs from and is
in non-equilibrium from a bulk property of the fluid outside of the
stream or other streams within the volume of fluid. A "bulk
property" as used herein refers to the average value of a
particular property of a component (e.g., such as an agent, solute,
substance, or a buffer molecule) in the stream over a cross-section
of the stream, taken perpendicular to the direction of flow of the
stream. A "property" can be a chemical or physical property such as
a concentration of the component, temperature, pH, ionic strength,
or velocity, for example.
[0097] As used herein, the term "in communication with" refers to
the ability of a system or component of a system to receive input
data from another system or component of a system and to provide an
output response in response to the input data. "Output" may be in
the form of data, or may be in the form of an action taken by the
system or component of the system. For example, a processor "in
communication with a scanning mechanism" sends program instructions
in the form of signals to the scanning mechanism to control various
scanning parameters as described above. A "detector in
communication with a sensor chamber" refers to a detector in
sufficient optical proximity to the sensor chamber to receive
optical signals (e.g., light) from the sensor chamber. A "light
source in optical communication" with a chamber refers to a light
source in sufficient proximity to the chamber to create a light
path from the chamber to a system detector so that optical
properties of the chamber or objects contained therein can be
detected by the detector.
[0098] As used herein, "a measurable response" refers to a response
which differs significantly from background as determined using
controls appropriate for a given technique.
[0099] As used herein, an outlet "intersecting with" a chamber or
microchamber refers to an outlet that opens or feeds into a wall or
base or top of the chamber or microchamber or into a fluid volume
contained by the chamber or microchamber.
[0100] As used herein, "superfuse" refers to washing the external
surface of an object or sensor (e.g., such as a cell).
The System
[0101] In one aspect, the system provides a substrate comprising a
plurality of microchannels fabricated thereon whose outlets
intersect with, or feed into, a sensor chamber comprising one or
more sensors. The system further comprises a scanning mechanism for
programmably altering the position of the microchannels relative to
the one or more sensors and a detector for monitoring the response
of the sensor to exposure to solutions from the different channels.
In a preferred aspect, the sensor chamber comprises a cell-based
biosensor in electrical communication with an electrode and the
detector detects changes in electrical properties of the cell-based
biosensor.
[0102] The system preferably also comprises a processor for
implementing system operations including, but not limited to:
controlling the rate of scanning by the scanning mechanism (e.g.,
mechanically or through programmable pressure drops across
microchannels), controlling fluid flow through one or more channels
of the substrate, controlling the operation of valves and switches
that are present for directing fluid flow, recording sensor
responses detected by the detector, and evaluating and displaying
data relating to sensor responses. Preferably, the system also
comprises a user device in communication with the system processor
which comprises a graphical interface for displaying operations of
the system and for altering system parameters.
[0103] The Substrate
[0104] In a preferred aspect, the system comprises a substrate that
delivers solutions to one or more sensors at least partially
contained within a sensor chamber. The substrate can be configured
as a two-dimensional (2D) or three-dimensional (3D) structure, as
described further below. The substrate, whether 2D or 3D, generally
comprises a plurality of microchannels whose outlets intersect with
a sensor chamber that receives the one or more sensors. The base of
the sensor chamber can be optically transmissive to enable
collection of optical data from the one or more sensors placed in
the sensor chamber. When the top of the sensor chamber is covered,
e.g., by a coverslip or overlying substrate, the top of the chamber
is preferably optically transmissive.
[0105] Each microchannel comprises at least one inlet (e.g., for
receiving a sample or a buffer). Preferably, the inlets receive
solution from reservoirs (e.g., shown as circles in FIGS. 2A and B)
that conform in geometry and placement on the substrate to the
geometry and placement of wells in an industry-standard microtiter
plate. The substrate is a removable component of the system and
therefore, in one aspect, the invention provides kits comprising
one or more substrates for use in the system, providing a user with
the option of choosing among different channel geometries.
[0106] Non-limiting examples of different substrate materials
include crystalline semiconductor materials (e.g., silicon, silicon
nitride, Ge, GaAs), metals (e.g., Al, Ni), glass, quartz,
crystalline insulators, ceramics, plastics or elastomeric materials
(e.g., silicone, EPDM and Hostaflon), other polymers (e.g., a
fluoropolymer, such as Teflon.RTM., polymethylmethacrylate,
polydimethylsiloxane, polyethylene, polypropylene, polybutylene,
polymethylpentene, polystyrene, polyurethane, polyvinyl chloride,
polyarylate, polyarylsulfone, polycaprolactone, polyestercarbonate,
polyimide, polyketone, polyphenylsulfone, polyphthalamide,
polysulfone, polyamide, polyester, epoxy polymers, thermoplastics,
and the like), other organic and inorganic materials, and
combinations thereof.
[0107] Microchannels can be fabricated on these substrates using
methods routine in the art, such as deep reactive ion etching
(described further below in Example 1). Channel width can vary
depending upon the application, as described further below, and
generally ranges from about 0.1 .mu.m to about 10 mm, preferably,
from about 1 .mu.m to about 150 .mu.m, while the dimensions of the
sensor chamber generally will vary depending on the arrangement of
channel outlets feeding into the chamber. For example, where the
outlets are substantially parallel to one another (e.g., as in
FIGS. 2A-C), the length of the longitudinal axis of the chamber is
at least the sum of the widths of the outlets which feed into the
chamber. In one aspect, where a whole cell biosensor is used as a
sensor in the sensor chamber, the width of one or more outlets of
the microchannels is at least about the diameter of the cell.
Preferably, the width of each of the outlets is at least about the
diameter of the cell.
[0108] In one aspect, a cover layer of an optically transmissive
material, such as glass, can be bonded to a substrate, using
methods routine in the art, preferably leaving openings over the
reservoirs and over the sensor chamber when interfaced with a
traditional micropipette-based patch clamp detection system.
Preferably, the base of the sensor chamber also is optically
transmissive, to facilitate the collection of optical data from the
sensor.
[0109] The Sensor
[0110] Cell-Based Biosensors
[0111] The system can be used in conjunction with a cell-based
biosensor to monitor a variety of cellular responses. The biosensor
can comprise a whole cell or a portion thereof (e.g., a cell
membrane patch) which is positioned in the sensor chamber using a
mechanism for holding a sensor (which may be stationary or movable)
such as a pipette, capillary, or column connected to a positioner,
such as a micropositioner, a nanopositioner or a micromanipulator,
or an optical tweezer, or by controlling flow or surface tension,
thereby exposing the cell-based biosensor to solution in the
chamber. The biosensor can be scanned across the various channels
of the substrate by moving the substrate, i.e., changing the
position of the channels relative to the biosensor, or by moving
the cell (e.g., by scanning the micropositioner or by changing flow
and/or surface tension).
[0112] In one aspect, the cell-based biosensor comprises an ion
channel and the system is used to monitor ion channel activity.
Suitable ion channels include ion channels gated by voltage,
ligands, internal calcium, other proteins, membrane stretching
(e.g., lateral membrane tension) and phosphorylation (see e.g., as
described in Hille B., In Ion Channels of Excitable Membranes 1992,
Sinauer, Sunderland, Mass., USA). In another aspect, the ion-gated
channel is a voltage-gated channel. Voltage-gated channels open in
response to a threshold transmembrane voltage. Voltage-gated
sodium, potassium, and calcium channels are all essential for
conducting an action potential (or a nerve pulse) down an axon and
to another nerve cell (or neuron). These ion channels typically
comprise a transmembrane sequence with a lysine and/or
arginine-rich S4 consensus sequence. The positive amino acids
within the S4 sequence are thought to "sense" voltage across a cell
membrane; causing an ion channel containing the sequence to either
open or close under different voltage conditions.
[0113] In another aspect, the ion channel in the cell-based
biosensor is a ligand-gated channel. Ligand-gated channels gate
(open or close) in response to ligand binding. There are two types
of ligand-gated channels, those gated when bound by ligands inside
the cell and those gated by ligands outside the cell. Ion channels
gated by ligands from outside of the cell are very important in
chemical synaptic transmission. These types of ion channels are
gated by neurotransmitters, which are the small molecules that
actually carry the signal between two nerve cells. Ion channels
gated from the inside of the cell are generally controlled by
second messengers, which are small signaling molecules inside the
cell. Intracellular calcium ions, cAMP and cGMP are examples of
second messengers. The most common calcium-gated channel is the
calcium-gated potassium channel. This ion channel can generate
oscillatory behavior (e.g., for frequency tuning of hair cells in
the ear) upon changes in membrane voltage when placed in a positive
feedback environment.
[0114] In yet another aspect, the ion channel is gated by another
protein. Certain signaling proteins have been found to directly
gate ion channels. One example of this is a potassium channel gated
by the beta-gamma subunit of the G protein, which is a common
signaling protein activated by certain membrane receptors.
[0115] In a further aspect, the ion channel is gated by
phosphorylation. Phosphorylation can be mediated by a protein
kinase (e.g., a serine, threonine, or tyrosine kinase), e.g., as
part of a signal transduction cascade.
[0116] In still a further aspect, the cell-based biosensor
comprises a mechanotransduction channel that can be directly gated
by a mechanical trigger. For example, the cell-based biosensor can
comprise the cation channel of an inner ear hair cell, which is
directly gated by a mechanical vibration such as sound. Bending of
the hair bundle in a particular direction will affect the
probability of channel gating, and therefore, the amplitude of a
depolarizing receptor current.
[0117] In another aspect, the cell-based biosensor comprises a
receptor, preferably, a receptor involved in a signal transduction
pathway. For example, the cell-based biosensor can comprise a G
Protein Coupled Receptor or GPCR, glutamate receptor, a
metabotropic receptor, a hematopoietic receptor, or a tyrosine
kinase receptor. Biosensors expressing recombinant receptors also
can be designed to be sensitive to drugs which may inhibit or
modulate the development of a disease.
[0118] Suitable cells which comprise biosensors include, but are
not limited to: neurons; lymphocytes; macrophages; microglia;
cardiac cells; liver cells; smooth muscle cells; and skeletal
muscle cells. In one aspect, mammalian cells are used; these can
include cultured cells such as Chinese Hamster Ovary Cells (CHO)
cells, NIH-3T3, and HEK-293 cells and can express recombinant
molecules (e.g., recombinant receptors and/or ion channels).
However, bacterial cells (E. coli, Bacillus sp., Staphylococcus
aureus, and the like), protist cells, yeast cells, plant cells,
insect and other invertebrate cells, avian cells, amphibian cells,
and oocytes, also can be used, as these are well suited to the
expression of recombinant molecules. Cells generally are prepared
using cell culture techniques as are know in the art, from cell
culture lines, or from dissected tissues after one or more rounds
of purification (e.g., by flow cytometry, panning, magnetic
sorting, and the like).
[0119] Non-Cellular Sensors
[0120] In one aspect, the sensor comprises a sensing element,
preferably, a molecule which is cellular target (e.g., an
intracellular receptor, enzyme, signalling protein, an extra
cellular protein, a membrane protein, a nucleic acid, a lipid
molecule, etc.), which is immobilized on a substrate. The substrate
can be the base of the sensor chamber itself, or can be a substrate
placed on the base of the chamber, or can be a substrate which is
stably positioned in the chamber (e.g., via a micropositioner) and
which is moveable or stationary.
[0121] The sensor may consist of one or several layers that can
include any combination of: a solid substrate; one or more
attachment layers that bind to the substrate, and a sensing
molecule for sensing compounds introduced into the sensor chamber
from one or more channel outlets. Suitable sensors according to the
invention, include, but are not limited to, immunosensors, affinity
sensors and ligand binding sensors, each of which can respond to
the presence of binding partners by generating a measurable
response, such as a specific mass change, an electrochemical
reaction, or the generation of an optical signal (e.g.,
fluorescence, or a change in the optical spectrum of the sensing
molecule). Such sensors are described in U.S. Pat. No. 6,331,244,
for example, the entirety of which is incorporated by reference
herein.
[0122] In one aspect, the sensor comprises a microelectrode which
is modified with a molecule which transports electrons. In response
to a chemical reaction caused by contact with one or more compounds
in an aqueous stream from one of the microchannels, the molecule
will produce a change in an electrical property at the electrode
surface. For example, the molecule can comprise an
electron-transporting enzyme or a molecule which transduces signals
by reduction or oxidation of molecules with which it interacts
(see, e.g., as described in, Gregg, et al., J. Phys. Chem. 95:
5970-5975, 1991; Heller, Acc. Chem. Res. 23(5): 128-134, 1990; In
Diagnostic Biosensor Polymers. ACS Symposium Series. 556; Usmani, A
M, N; eds. American Chemical Society; Washington, D.C.; pp. 47-70,
1994; U.S. Pat. No. 5,262,035). Enzymatic reactions also can be
performed using field-effect-transistors (FETs) or ion-sensitive
field effect transistors (ISFETs).
[0123] In another aspect, the sensor comprises a sensing molecule
immobilized on a solid substrate such as a quartz chip in
communication with an electronic component. The electronic
component can be selected to measure changes in any of: voltage,
current, light, sound, temperature, or mass, as a measure of
interaction between the sensing element and one or more compounds
delivered to the sensor chamber (see, as described in, Hall, Int.
J. Biochem. 20(4): 357-62, 1988; U.S. Pat. No. 4,721,677; U.S. Pat.
No. 4,680,268; U.S. Pat. No. 4,614,714; U.S. Pat. No. 6,879,11).
For example, in one aspect, the sensor comprises an acoustic wave
biosensor or a quartz crystal microbalance, on which a sensor
element is bound. In this embodiment, the system detects changes in
the resonant properties of the sensor upon binding of compounds in
aqueous streams delivered from the microchannels to the sensor
element.
[0124] In another aspect, the sensor comprises an optical
biosensor. Optical biosensors can rely on detection principles such
as surface plasmon resonance, total internal reflection
fluorescence (TIRF), critical angle refractometry, Brewster Angle
microscopy, optical waveguide lightmode spectroscopy (OWLS),
surface charge measurements, and evanescent wave ellipsometry, and
are known in the art (see, for example, U.S. Pat. No. 5,313,264;
EP-A1-0 067 921; EP-A1-0 278 577; Kronick, et al., 1975, J.
Immunol. Meth. 8: 235-240).
[0125] For example, for a sensor employing evanescent wave
ellipsometry, the optical response related to the binding of a
compound to a sensing molecule is measured as a change in the state
of polarization of elliptically polarized light upon reflection.
The state of polarization is related to the refractive index,
thickness, and surface concentration of a bound sample at the
sensing surface (e.g., the substrate comprising the sensing
element). In TIRF, the intensity and wavelength of radiation
emitted from either natively fluorescent or fluorescence-labelled
sample molecules at a sensor is measured. Evanescent wave
excitation scattered light techniques rely on measuring the
intensity of radiation scattered at a sensor surface due to the
interaction of light with sensing molecules (with or without bound
compounds). Surface plasmon resonance (SPR) measures changes in the
refractive index of a layer of sensor molecules close to a thin
metal film substrate (see, e.g., Liedberg, et al., 1983, Sensors
and Actuators 4: 299; GB 2 197 068). Each of these sensing schemes
can be used to provide useful sensors according to the
invention.
[0126] In yet another aspect, the sensor comprises a sensing
molecule associated with a fluorescent semiconductor nanocrystal or
a Quantum Dot.TM. particle. The Quantum Dot particle has a
characteristic spectral emission which relates to its composition
and particle size. Binding of a compound to the sensing element can
be detected by monitoring the emission of the Quantum Dot particle
(e.g., spectroscopically) (see, e.g., U.S. Pat. No. 6,306,610).
[0127] The sensor further can comprise a polymer-based biosensor
whose physical properties change when a compound binds to a sensing
element on the polymer. For example, binding can be manifested as a
change in volume (such as swelling or shrinkage), a change in
electric properties (such as a change in voltage or current or
resonance) or in optical properties (such as modulation of
transmission efficiency or a change in fluorescence intensity).
[0128] It should be obvious to those of skill in the art that a
variety of different types of sensors may be adapted for use in
present invention, and the examples above are intended to be
non-limiting.
[0129] In general, the measurement outputs of one or more sensors
are connected to a control and evaluating device which is in
electrical communication with a detection device and/or system
processor. The control and evaluating device can be integrated with
the substrate of the sensor and/or with the base of the sensing
chamber. The control and evaluating device can comprise various
electronic components such as microprocessors, multiplexers, IO
units, etc. (see, e.g., as described in U.S. Pat. No.
6,280,586).
Microfluidics
[0130] In a preferred aspect, the substrates according to the
invention are adapted for microfluidic transport of sample and/or
buffer to a sensor chamber.
[0131] Interfacing Microfluidic Structures with Well Plates
[0132] Samples (i.e., drugs, etc.) contained in sample-well plates
(e.g., industry-standard microtiter plates such as 96-well plates)
are manipulated and transferred, preferably, using robotic
automated array pipettors as are known in the art (see, e.g.,
Beckman's Biomek 1000 & 2000 automated workstations, available
from Beckman Coulter, Inc., Fullerton, Calif.).
[0133] To be able to leverage the same sample transfer platform
used to array a sample in a well plate, one important design
parameter is to ensure the reservoir arrangements in the chip
described above are compatible for use with such array pipettors.
For example, preferably, the reservoirs in the microfluidic chip
are arranged such that the center-to-center distance between each
reservoir is identical to the center-to-center distance between
each well of the well plate to which the chip interfaced.
Preferably, each reservoir has a diameter suitable for receiving a
fluid stream from an array pipetter without significantly impeding
the flow of fluid from the array pipettor.
[0134] In addition to array pipettors, there are other suitable
automated devices for transferring samples from well plates onto
chips, such as robotic sequential pipettors. It is important to
note that the use of these other devices may permit more flexible
placement of reservoirs and microchannels on the chip, providing
more flexibility in the design of channel parameters. Although a
substrate suitable for interfacing between 96-well array pipettors
is described in more detail below owing to the widespread use of
these pipettors, it should be obvious to those of skill in the art
that the general design of the chip and placement of reservoirs can
be modified for interfacing with any desirable sample transfer
platform, as such platforms evolve. In general, reference to
96-well plates is not intended to be limiting.
[0135] FIGS. 2A and 2B show examples of microfluidic chips
according to the invention that are suitable for interfacing with a
96-well plate. FIG. 2A illustrates reservoir arrangements for which
no buffer reservoirs are required. FIG. 2B illustrates reservoir
arrangements for applications in which alternating (i.e.,
interdigitating) streams of buffer and sample are provided to a
sensor. In this arrangement, the center-to-center distances for
both the ligand and buffer reservoirs are identical to the
center-to-center distance of the wells of a 96-well plate. To
compensate for doubling the number of reservoirs on chip, the
diameter of all reservoirs are decreased by half.
[0136] FIG. 3 illustrates how sample solutions can be transferred
from the wells of a 96-well plate into reservoirs on a chip
according to one aspect of the invention using traditional robotic
automated array pipettors. For a microchip with interdigitated
ligand and buffer reservoirs (e.g., as shown in FIG. 2B), buffer
solution can be transferred from a bath, where only one buffer is
needed, or from a 96-well plate, with wells comprising the same or
different buffers.
[0137] In addition to the reservoirs needed for interfacing with
sources of sample and/or buffer (e.g., such as well plates), there
may be additional reservoirs placed on the chip for storing and
transferring cells or other samples of interest. FIG. 2C
illustrates the possible placement of additional reservoirs and
microchannels for storing and transporting cells into reservoirs or
the sensor chamber of the chip, according to one aspect of the
invention.
[0138] The cell chambers can be adapted for performing on-chip
manipulation of cells. In one aspect, the chip provides one or more
cell treatment chambers for performing one or more of:
electroporation, electroinjection, and/or electrofusion. Chemicals
and/or molecules can be introduced into a cell within a chamber
which is in electrical communication with a source of current. For
example, one or more electrodes may be placed in proximity to the
chamber, or the chamber can be configured to receive an electrolyte
solution through which current can be transmitted, for example,
from an electrode/capillary array as described in WO 99/24110, the
entirety of which is incorporated by reference herein.
[0139] Suitable molecules which can be introduced into a cell in
the cell treatment chamber include, but are not limited to: nucleic
acids (including gene fragments, cDNAs, antisense molecules,
ribozymes, and aptamers); antibodies; proteins; polypeptides;
peptides; analogs; drugs; and modified forms thereof. In a
preferred aspect, the system processor controls both the delivery
of molecules to the one or more cell treatment chambers (e.g., via
capillary arrays as described above) and incubation conditions
(e.g., time, temperature, etc.). For example, a cell can be
incubated for suitable periods of times until a desired biological
activity is manifested, such as transcription of an mRNA;
expression of a protein; inactivation of a gene, mRNA, and/or
protein; chemical tagging of a nucleic acid or protein;
modification or processing of a nucleic acid or protein;
inactivation of a pathway or toxin; and/or expression of a
phenotype (e.g., such as a change in morphology).
[0140] The treated cells can be used to deliver molecules of
interest to the sensor in the sensor chamber, e.g., exposing the
sensor to secreted molecules or molecules expressed on the surface
of the cells. In this aspect, the system can be programmed to
release a cell from a cell treatment chamber into a channel of the
system intersecting with the sensor chamber, thereby exposing a
sensor in the sensor chamber to the molecule of interest.
[0141] Alternatively, or additionally, when the system is used in
conjunction with a cell-based biosensor, the cell treatment chamber
can be used to prepare the biosensor itself. In one aspect, a cell
is delivered from the treatment chamber to a channel whose outlet
intersects with the sensor chamber. In one aspect, the scanning
mechanism of the system is used to place a micropositioner in
proximity to the outlet so that the micropositioner can position
the cell within the sensor chamber. In another aspect, fluid flow
or surface tension is used to position a cell in a suitable
position. For example, the system can be used to deliver the cell
to the opening of a pipette which is part of a patch clamp
system.
[0142] In another aspect, a cell can be delivered to the sensor
chamber to periodically replace a cell-based biosensor in the
sensor chamber. In this aspect, the cell can be untreated, e.g.,
providing a substantially genetically and pharmacologically
identical cell (i.e., within the range of normal biological
variance) as the previous sensor cell. Alternatively, the
replacement cell can be biochemically or genetically manipulated to
be different from the previous sensor cell, to enable the system to
monitor and correlate differences in biochemical and/or genetic
characteristics of the cells with differences in sensor responses.
The biochemical or genetic difference can be known or unknown.
[0143] The system can be programmed to deliver cells from the cell
treatment chamber at selected time periods based on control
experiments monitoring uptake of chemicals and molecules by cells.
Alternatively, the system can monitor the phenotype of cells and
deliver cells when a certain phenotype is expressed. For example,
in one aspect, the cell treatment chamber is in communication with
an optical sensor which provides information relating to optical
properties of the cell to the system processor, and in response to
optical parameters indicating expression of a particular phenotype,
the system can trigger release of the cell from the cell treatment
chamber. Optical parameters can include the uptake of a fluorescent
reporter molecule or optical parameters identified in control
experiments.
[0144] The combination of on-chip electroporation with
microfluidics and patch clamp (or other methods for monitoring cell
responses) facilitates screening for molecules (e.g., ligands or
drugs) which modulate the activity of intracellular targets. In one
aspect, the system is used to deliver a cell-impermeant molecule
into the interior of a cell by transiently electroporating the
cell. In this way, the molecule can be introduced to intracellular
receptors, intracellular proteins, transcriptional regulators, and
other intracellular targets. The cell can be delivered to the
sensor chamber and the response of the cell can be monitored (e.g.,
by patch clamp or by fluorescence, if the molecule is tagged with a
fluorescent label). Alternatively, the sensor chamber can be
modified to perform both treatment and response detection.
[0145] In a further aspect, the system can be modified to perform
electroporation by scanning. For example, a cell can be repeatedly
electroporated as it is being translated or scanned across a
plurality of different fluid streams containing different
compounds. In one aspect, pores are introduced into one or more
cells as they come into contact with a sample stream, enabling
compounds in the sample stream to be taken up by the cell.
[0146] Rapid Alterations of the Solution Environment Around a
Sensor
[0147] Central to the present invention is the use of
two-dimensional (2D) and three-dimensional (3D) networks of
microfabricated channels for the complex manipulation of compounds
or reagents contained in the fluid in a way that permits repeated
and rapid delivery of different solutions to the sensor in the
sensor chamber. For example, the microfluidics used with the system
enables the system to programmably deliver a ligand to a cell-based
biosensor comprising a receptor. This enables the system to be used
for HTS screening of samples (e.g., such as compound libraries) to
monitor the effects of compounds on the responses of the biosensor.
In one aspect, electrical properties of a cell-based biosensor are
monitored using voltage clamp or patch clamp techniques.
[0148] Because the system provides a scanning mechanism for
changing the position of channels relative to a sensor, the system
can be used to flush a cell-based biosensor with buffer after
exposure to a sample compound, enabling a receptor or ion channel
that is part of the biosensor to be resensitized prior to exposure
to the next compound. Thus, the system can provide a periodically
resensitized receptor for exposure to potential modulators of
receptor function (e.g., such as agonists or antagonists). For
receptors that do not desensitize, the system is still advantageous
for providing pulsed delivery of buffer to a receptor, e.g., to
remove unbound ligand from the receptor, to enhance the specificity
and/or decrease background of a response.
[0149] The geometry of different network structures of
microchannels is designed to exploit the unique characteristic of
fluid behavior in micro-dimensions. Three exemplary designs are
described below.
[0150] The first design relies on the system's ability to transport
one or more sensors, rapidly across different streams of fluid
flowing from channel outlets by translating the sensors across the
channels or by translating the substrate comprising the channels
relative to the one or more sensors. The system also can sweep
different fluid streams across a stationary sensor by varying
pressure drops across individual channels of the substrate. This
design is derived from the discovery of a new and unique fluidic
behavior; i.e., that lateral interactions and couplings between
neighbouring fluid streams as they exit from a set of closely
spaced microchannels into an open volume can extend dramatically
the distance over which these streams remain collimated. The second
design exploits the reversibility of fluid behavior at low
Reynold's numbers while the third design is based on the ability to
rapidly exchange fluids in microchannels and chambers.
[0151] The theme that runs through these designs is a
microfluidic-based approach for rapidly and efficiently altering
the local solution microenvironment in which one or more biosensors
reside, providing complete or near-complete solution exchange. The
system requires small sample volumes (nLs to .mu.Ls) and can be
easily automated and programmed for HTS applications.
[0152] (1) The Rapid Transport of Sensors Across Different Streams
of Fluids
[0153] Adjacent fluid streams exiting the plurality of
microchannels of a substrate according to the invention have a low
Reynold's number and undergo minimal mixing by diffusion. For
example, a small molecule with a diffusion coefficient of about
5.times.10.sup.-6 cm.sup.2/s would take approximately 0.1 seconds
to diffuse 10 .mu.m, but 10 s to diffuse 100 .mu.m, owing to the
square dependence of distance on diffusion time (x.sup.2=2Dt, where
D is the diffusion coefficient). Similarly, for typical proteins
having D.about.10.sup.-6 cm.sup.2/s, it will take 0.5 second to
diffuse 10 .mu.m and 50 seconds for 100 .mu.m.
[0154] However, flow rates in microchannels can vary dramatically
from many meters per second to micrometers per second. The flow
rate in the present system is limited to the maximum flow rate that
can be used without disturbing the activity of the sensor. For
example, when using a patch clamp sensor, flow rate is typically on
the order of hundreds of .mu.m/s to mm/s for a patch-clamped cell
(see below for discussion), in order to prevent dislodgement of the
patch-clamped cell from the pipette which positions it at a channel
opening.
[0155] Flow Profiles of Multiple Fluid Streams Exiting into the
Sensor Chamber
[0156] When a plurality of microchannels is used, an understanding
of the flow profile of the multiple streams of fluid at the
interface between the outlets of the microchannels and the
open-volume reservoir is essential. FIGS. 16A and 16B show
photomicrographs of flow profiles of a fluid comprising 500 .mu.M
of a fluorescent dye (fluorescein) from a single channel (FIG. 16A)
and multiple channels (FIG. 16B). Excitation of the fluorescent
tracer was carried out using the 488-nm line of an Argon Ion laser
in an epi-illumination configuration and fluorescence of the tracer
was collected and imaged using a CCD camera. As shown in FIG. 16A,
in the absence of adjacent microchannels and fluid streams, the
fluid exits the single channel and disperses at the channel outlet
in a semicircular fashion. FIG. 16B shows a flow profile of
interdigitated buffer and fluorescein fluid streams exiting from a
plurality of channel outlets. The dimensions of microchannels were
100 .mu.m wide, 50 .mu.m thick, with an interchannel interval of 25
.mu.m. The flow rate in the microchannels in both FIGS. 16A and 16B
was 4 mm/s.
[0157] As shown in FIG. 16B, the fluid stream exiting multiple
microchannels into an open volume is collimated for at least a
distance that is about 4-5 times the width of the microchannels
(e.g., about several hundred micrometers) at a flow rate of about 4
mm/s. In this range of low flow rates (i.e., mm/s), the rate of
fluid flow is still much faster than diffusion. For example, at a
flow rate of mm/s, channel width of 10 .mu.m, and channel intervals
(the space between channels) of 10 .mu.m, different streams of
fluid containing small molecules (D=5.times.10.sup.-6 cm.sup.2/s)
exiting different channel outlets will not be fully mixed until at
a distance of at least about 0.4 mm downstream of the channel
outlets. This is more than sufficient for making measurements of a
typical mammalian cell having a diameter of about 10 to 20 .mu.m
which is placed 10 to 20 .mu.m outside the outlet of a channel.
Since diffusion time varies with the square of the distance,
doubling the width and spacing of microchannels to 20 .mu.m extends
the downstream distance at which the cell can be placed to at least
about 1.6 mm. The average linear velocity of the flow will vary
depending on the exact application, with typical flow rates ranging
from about 100 .mu.m/s to about 10 mm/s for a 10 .mu.m cell. Thus,
a sensor can be scanned across substantially distinct and separate
aqueous streams of fluid which exit from the microchannel
outlets.
[0158] At the preferred flow rates for use with patch clamp
measurements and at a cell-to-outlet distance of about 20 .mu.m or
less, the different fluid streams are essentially distinct and
separate and are undisturbed by the presence of a patch-clamped
cell. Even at much lower flow rates (e.g., <100 .mu.m/s) that
may be used with patch clamp measurements, different fluid streams
are still well separated. This observed behaviour (e.g.,
collimation of fluid streams) of fluid flow at the exits of
microchannels into an open volume sensor chamber facilitates HTS
applications which require relatively rapid translation of patched
cells with respect to different fluid streams. Spacing between
microchannel outlets can be optimised to optimise separation
between fluid streams, as can flow rate. For example, the more
rapid the flow rate, the less mixing is observed. Preferably, flow
rate and interchannel spacing are optimised to minimize the width
of a boundary zone (i.e., an area of mixing). Preferably, a
boundary zone is less than about 50% of the width of a fluid
stream, or less than about 40%, less than about 30%, less than
about 20%, less than about 10%, less than about 5%, or less than
about 1% of the width of the stream. In one aspect, the boundary
zone is about 2-3 microns. Optimal fluid flow rates and
interchannel spacings can be devised readily using one or more
tracer dyes as described above.
[0159] To exploit the unique behaviour of fluid flow into open
volumes, the pressure applied to each of a plurality of
microchannels can be individually varied for precise manipulation
of each flow stream. For example, in the extreme case in which
positive pressure is applied to one channel and negative pressure
is applied to an adjacent channel, the fluid stream can be made to
make a "U-turn", going from the channel with positive pressure to
the one with negative pressure while drawing in a sheath of buffer
into the channel with negative pressure. Therefore, the position,
width, collimation, direction, and rate of flow, as well as the
composition of the fluid streams, can be controlled by varying the
relative pressure applied to each channel.
[0160] As shown in FIG. 5D-F, this can be used to create a U-shaped
fluid stream which has the advantage that sample delivered onto a
cell from a channel experiencing positive pressure can be withdrawn
into a waste channel experiencing negative pressure. This minimizes
the accumulation of ligands in the open volume where the
patch-clamped cell resides. In situations where a sample (e.g., a
drug, ligand, and the like) is in low concentration and/or is
expensive, the system further can be used to recycle ligand and/or
to feed ligand back into the system (i.e., the U-shaped stream can
be turned into a closed loop).
[0161] By controlling pressure, the system can control the velocity
(both amplitude and direction) of fluid streams. Velocity control
also may be exercised by controlling the resistance of each channel
without changing the pressure or by changing both resistance and
pressure. Fluid shear also can be varied by using solutions of
different viscosity (e.g., adding different amounts of a sugar such
as sucrose to a fluid stream) in both the microchannels and sensor
chamber. Thus, by varying a number of different parameters, the
flow profile of different fluid streams can be precisely tuned.
[0162] Patch Clamp Under Fluid Flow
[0163] The ability to rapidly scan patch-clamped cells across
interdigitated streams of receptor modulators (agonists or
antagonists) and buffer depends on the mechanical stability of the
patched cell under the required flow conditions as well as scan
speeds. Here, the stability of the "giga seal" and ion-channel
activities of patch-clamped cells under a range of flow conditions
is described.
[0164] The effects of liquid flow on a patch-clamped cell arise
from the force (Stokes drag) exerted by the flow on the cell. This
Stokes drag can be calculated from the following equation:
Force=(frictional coefficient).times.(velocity of the flow)
Where the frictional coefficient (f) can be calculated from:
f=6.pi.r.mu.
where r is the radius of the cell and .mu. is the viscosity of the
solution. This relationship is valid for low Reynold's number flow
and for particles that are spherical. Both conditions are
adequately met in the methods and devices utilized in connection
with the present invention.
[0165] For water at room temperature, .mu. is .about.1 centipoise
(1 centipoise=0.01 g/[cm s]) and for a typical mammalian cell, r=5
.mu.m. Using these values and for flow rates of 1 mm/s,
Force=9.4.times.10.sup.-11 N or 94 picoNewtons. Since force is
linearly proportional to the flow rate, at 0.1 mm/s, Force is 9.4
picoN. To put this number in perspective, micropipettes can
routinely exert nano- and micro-Newtons on a small particle such as
a cell. In addition to the force that arises owing to the drag on
the cell from fluid flow, the scanning of the cell at a certain
velocity exerts a similar drag force in the direction of cell
translation, which is typically orthogonal to the direction of
fluid flow. Scanning of a cell at 1 mm/s under no flow typically
has the same effect as keeping the cell stationary while flowing
the fluid at the same rate.
[0166] For applications that require extremely high flow rates in
which cell dislodgement may become an issue, patch-clamped cell(s)
may be put into a recessed region or well in the sensor chamber
that matches the dimension of the cell. This design will permit the
use of high flow rates while preventing cell dislodgement because
the flow profile in a channel or chamber is parabolic, owing to
no-slip boundary conditions at the interface of a fluid and a solid
surface (i.e., the velocity at the interface of the fluid and the
solid surface is zero). By placing cell(s) in well(s) having
similar dimensions as the cell, the cell is essentially "shielded"
from the high velocity flow region that is located away from the
well and the solid surface. Therefore, although the average flow
rate and the flow velocity away from the solid surface can be
extremely high, the flow velocity near the well in which the
patched cell is placed can be very small. By using this strategy,
very high average flow rates can be used.
[0167] As discussed above, fluid flow also can be used to maximize
the sensitivity of patch clamp. As shown in FIG. 5D-F, a U-shaped
fluid stream created by two parallel channels can be used to create
an optimal seal between a cell and a patch clamp micropipette.
[0168] Scanning Mechanisms
[0169] Scanning can be mediated mechanically (by moving the
substrate while the sensor is stationary or by moving the sensor
while the substrate is stationary or by moving both the substrate
and sensor at different speeds and/or in different directions) or
by pressure drops across different microchannels. FIGS. 8A-I
schematically depict how each of these methods may be carried out.
The mechanical movement and scanning of a sensor can be readily
accomplished by translating a micropositioner positioning the
sensor. For example, a cell-based biosensor can be physically
attached to a micropipette by suction, which in turn is attached to
a micromanipulator. Most micromanipulators can be controlled
manually as well as actuated electronically, so preprogrammed
movement can be easily achieved. A number of parameters that can be
programmed, include, but are not limited to, the linear velocity
for constant velocity scans; accelerations for variable velocity
scans; trajectories of the scan, both in two dimensions and three
dimensions; and the number of repeated scans. For scans based on
real-time signal feedback from one or more sensors in the sensor
chamber, programmable parameters include, but are not limited to,
the time delay between signal detection and the change of scan
settings. A variety of signal processing and computational
functions can be performed to determine correct feedback parameters
to output for the scan.
[0170] The mechanical movement and scanning of a platform on which
the substrate (e.g., a chip) is resting also can be readily
achieved, thereby moving the substrate relative to a stationary
biosensor. For example, computer-controlled microscope stages with
different designs (e.g., ones based on piezo-electric crystals, or
electronically actuated thread screws) and having the needed
specifications are commercially available (for example, from Prior
Scientific Inc., 80 Reservoir Park Drive, Rockland, Mass.).
Suitable scanning parameters can be programmed using the system
processor which is in communication with the platform, e.g., in
response to user directions or feedback signals from one or more
sensors in the sensor chamber, as described above.
[0171] In one aspect, one or more sensors are moved rapidly over
the distance between the outlets of closely spaced channels in the
sensor chamber, exposing the one or more biosensors in the chamber
to different streams of fluid exiting the outlets. For example, the
sensor can be a cell or a membrane patch attached to a micropipette
which is programmed to move across the outlets of the channels. In
another aspect, one or more stationary cells are immobilized in the
sensor chamber (e.g., in a planar-patch clamp format) and different
streams of fluid are made to sweep over the stationary cell(s),
e.g., by adjusting pressures and flow rates at each individual
channel through which the different streams exit. Alternatively,
channel outlets can be moved physically past a stationary cell as
described above.
[0172] Because the aqueous solutions flowing through the channels
are non-compressible (unlike air), the width and placement of each
fluid stream depends on the relative flow rate through each
microchannel. Therefore, fluid streams from the microchannels also
can be made to move and translate by varying the flow rate through
each channel. This is most easily achieved by controlling the
pressure drops across each channel or by changing the resistance of
each channel. The ability to move fluid streams by pressure
variations (or other means) is particular useful in applications in
which the sensor(s) are cell-based and are immobilized on the chip,
such that such that mechanical movements of the cell(s) relative to
the chip are not possible. As with mechanical scanning, the
pressure and resistances of each channel can be programmed, using
the system processor. Parameters which can be programmed include,
but are not limited to, linear changes in the pressure and
resistance of each channel, stepwise or constantly variable changes
in the pressure and resistance of each channel, and the sequence of
changes among the different channels. In addition, pressure and
resistance changes can be based on real-time feedback signals, and
these signals may be processed and computed prior to outputting new
pressure and resistance parameters.
[0173] Scanning speed can be adjusted depending on the application.
For example, when the sensor comprises a receptor which is
desensitized upon continued exposure to an agonist, the sensor can
be moved from a sample-containing stream to a buffer-containing
stream to allow the receptor to resensitize. By sequentially
sweeping a sensor across sample streams and buffer streams
(mechanically or through pressure differentials), pulsed delivery
of agonist and buffer can be provided, thereby generating a
periodically resensitized receptor.
[0174] Scanning speed can be adjusted in this scenario to
accommodate the amount of time necessary for resensitization,
which, in the case of an ion channel, is often on the order of
milliseconds (depending on ligand-ion channel pair). In general,
the exposure time of the sensor to solution can be controlled and
can range from microseconds to hours. For drug-receptor pairs
having long equilibration times, however, throughput may be limited
by the length of equilibration time. Similarly, the responses of a
cell-based biosensor may depend on transduction of a signal through
a biochemical pathway, which can require from milliseconds to
longer intervals (e.g., minutes). Scan rates therefore will be
adjusted to accommodate the type of sensor being used and can be
determined readily from control experiments, such as time course
experiments.
[0175] Preferably, therefore, the scanning mechanism (whether it
moves the sensor, or the chip, or acts by controlling pressure
drops across channels) is controlled by the system processor to
move the position of the sensor relative to the chip, at a
user-selected or system-selected rate. For example, a user can
implement a system program which alters translation parameters of
the scanning mechanism, e.g., by selecting an action button on a
graphical interface displayed on a computer in communication with
the system processor. Alternatively, scanning rates can be modified
by the system processor in response to a feedback signal (e.g.,
such as a patch clamp recording of a cell indicating
desensitization). The scanning mechanism can be programmed for
linear or stepwise scanning (e.g., moving a sensor to a channel
outlet which is not adjacent to the previous outlet to which the
sensor was exposed).
[0176] A sensor may comprise a receptor/ion channel which does not
desensitize, eliminating the need to resensitize the receptor.
However, the system may still be used to provide pulsed delivery of
buffer, for example, to wash a cell free of unbound compounds. In
this scenario, the scan rate can be adjusted based on "noise"
observed in the response. For example, the scan rate can be
adjusted to achieve a linear dose-response over certain
concentrations of sample compound.
[0177] A ligand also may irreversibly block a sensor, rendering it
unresponsive to other ligands in other fluid streams. In this case,
pulsing with buffer will have no effect. It is straightforward to
ascertain whether the cell is inactivated by introducing compounds
of known effect periodically to the cell and verifying whether an
appropriate response is obtained. Preferably, the system is able to
sense a lack of response by a sensor as it is scanned past a
selected number of sample fluid streams. For example, the system
can provide a feedback signal when no response is observed in patch
clamp recordings over as a sensor is scanned past a selected number
of consecutive fluid streams.
[0178] Alternatively, or additionally, devices can be provided in
the sensor chamber to monitor sensor function. In one aspect, an
optical sensor is provided in communication with the sensor chamber
for monitoring the viability of a cell-based biosensor. For
example, spectroscopic changes associated with cell death (e.g.,
such as from chromatin condensation) may be observed, or the uptake
of a dye by a dead or dying cell can be monitored.
[0179] In one aspect, the system executes certain program
instructions when a selected number of scanning intervals in which
no sensor signal has been received have gone by. For example, the
system can vary pressure at particular channels to stop flow in
those channels, thereby minimizing sample waste. In another aspect,
in response to an absence of a response signal from a sensor over a
threshold period, one or more replacement biosensors are delivered
to the sensor chamber (e.g., from the cell treatment chambers
described above).
[0180] If a sensor is translated at a constant speed compared to
flow rate from channel outlets (e.g., mm/s), then the screening
rate (e.g., compounds screened per second) for channels having a
width and spacing of about 10 .mu.m will be approximately 25 Hz.
Using about 100 .mu.m wide channels with channel intervals of about
10 .mu.m, the screening rate will be about 4.5 Hz. If the
translation speed is increased, the scan range may be in the range
of hundreds of Hz. For some applications, e.g., where the sensors
comprise rapidly desensitizing ion channels, fluidic channels with
narrow outlets are preferred as these can provide sharp
concentration profile over short periods of time. Preferably, such
channels range from about 1 .mu.m to about 100 .mu.m in width.
[0181] Scanning rates can be uniform or non-uniform. For example,
scanning rates across channels providing sample streams (e.g.,
providing agonists) can differ from scanning rates across channels
providing buffer streams. Variable scanning rates can be based on
preprogramming or on feedback signals from the sensor measurements,
e.g., such as from patch clamp measurements. The actual scan rate
will vary depending on the exact screening system, but a typical
linear scan rate will range from between about 100 .mu.m/s to
hundreds of mm/s for a sensor comprising a mammalian cell having a
diameter of about 10 .mu.m.
[0182] A two-dimensional microfluidic system is shown in FIGS. 4A
and 5A. The system comprises a substrate comprising a plurality of
microchannels corresponding in number to the number of wells in an
industry-standard microtiter plate to which the microchannels will
be interfaced, e.g., 96 channels. When the system is used to
provide alternating streams of sample and buffer to a sensor, at
least 96 sample and 96 buffer microchannels (for a total of at
least 192 channels) are provided. Wells of a microtiter plate, or
of another suitable container, are coupled to reservoirs which feed
sample or buffer to channels, e.g., for the system described
previously, the substrate comprises 192 reservoirs, each reservoir
connecting to a different channel. Additional reservoirs can be
provided for cell storage and delivery, e.g., to provide cells for
patch clamp recordings.
[0183] In the embodiment shown in FIGS. 4A and 5A, microchannels
are substantially parallel, having widths of about 100 .mu.M and
thicknesses of about 50 .mu.m. The exact thickness of channels may
be varied over a wide range, but preferably is comparable to, or
greater than, the diameter of the sensor, e.g., the diameter of a
patched cell. In the Figure, inter-channel spacings of about 10
.mu.m are provided.
[0184] Pressure can be applied simultaneously to all microchannels
such that a steady state flow of solutions is made to flow through
all microchannels at the same rate into the open volume that houses
the sensor. In this way, steady state concentrations of different
solutions containing ligands or pure buffer can be established at
the immediate outlet of each of the microchannels. The width of
each microchannel may be adjusted to achieve the desired flow rate
in each microchannel.
[0185] Although the fluid streams exiting from the parallel
channels enter an open volume sensor chamber in the embodiment
discussed above, it may be more convenient and desirable to provide
a set of parallel drain channels opposite the set of sample and
buffer channels. A groove having an appropriate width (e.g., about
50 .mu.m) can be placed in between, and orthogonal to, the two sets
of channels (i.e., the delivery and drain channels) to accommodate
scanning of a sensor in the sensor chamber. To establish an
appropriate flow profile, a negative pressure may be applied to all
the drain channels while simultaneously applying a positive
pressure to the delivery channels. This induces fluid exiting the
delivery channels to enter the set of drain channels.
[0186] FIG. 5C shows a three-dimensional microfluidic system. The
main difference between this 3D structure and the planar structure
shown in FIG. 5B is the displacement along the z axis of fluid
flowing between the outlet of the parallel array channels (e.g.,
interdigitated sample and buffer channels) and the inlet of the
waste channels. In this embodiment, a positive pressure is applied
to all sample and buffer channels while a negative pressure is
simultaneously applied to all waste channels. Consequently, a
steady state flow is established between the outlets of the
sample/buffer channels and the inlets of the waste channels. In
this configuration, a sensor, such as a patch-clamped cell, is
scanned across the z-direction flow of fluid, preferably close to
the outlet of the sample/buffer microchannels.
[0187] Although the fabrication of this 3D structure is more
complex than the planar structure, the presence of z-direction flow
in many cases will provide better flow profiles (e.g., sharper
concentration gradients) across which to scan a sensor, such as a
patch-clamped cell. The length over which z-direction flow is
established should be significantly greater than the
diameter/length of a sensor used. For example, the length of
z-direction flow of a cell-based biosensor, such as a patch-clamp
cell, should preferably range from about 10 .mu.m to hundreds of
.mu.m.
[0188] Another strategy for providing alternating sample streams
and buffer streams, in addition to scanning, is shown in FIGS.
7A-N. In this embodiment, rather than providing interdigitating
outlets which feed sample and buffer, respectively, into the sensor
chamber, all outlet streams are sample streams. Buffer superfusion
is carried out through one or more capillaries placed in proximity
to one or more sensors. In FIG. 7A, the sensor shown is a
patch-clamped cell positioned in proximity to an outlet using a
patch clamp pipette connected to a positioner, such as a
micropositioner or a nanopositioner or micromanipulator. A
capillary is placed adjacent to the patch clamp pipette and can be
used for superfusion, e.g., to resensitize a desensitized cell. By
this means, a cell-based biosensor comprising an ion channel can be
maintained in a periodically responsive state, i.e., toggled
between a ligand non-responsive state (e.g. bound to an agonist
when exposed to drugs) and an ligand responsive state (e.g. ligand
responsive after superfusion by buffer).
[0189] Programmed delivery of buffer through this co-axial or
side-capillary arrangement can be pre-set or based on the feedback
signal from the sensor (e.g., after signal detection, buffer
superfusion can be triggered in response to instructions from the
system processor to wash off all bound ligands), providing pulsed
delivery of buffer to the sensor. In one aspect, the longitudinal
axis of the capillary is at a 90.degree. angle with respect to the
longitudinal axis of a patch clamp micropipette, while in another
aspect, the longitudinal axis, is less than 90.degree..
[0190] Microchannel outlets themselves also may be arranged in a 3D
array (e.g., as shown in FIGS. 6A-B). A 3D arrangement of outlets
can increase throughput (e.g., increasing the number of samples
that can be screened) and therefore increase the amount of
biological information that the sensor can evaluate. In one aspect,
the microfluidic system is used to obtain pharmacological
information relating to cellular targets, such as ion channels.
[0191] There are several advantages to performing HTS in this
format over the scanning format described in the preceding
paragraphs: (1) ligand exposure time is determined by the
inter-superfusion period (e.g., time between pulses of buffer)
rather than by the scan speed and width of the ligand streams; (2)
buffer superfusion and resensitization time also is determined by
the duration of the superfusion pulse rather than by residence time
in the buffer stream; (3) higher packing density of the number of
ligand streams can be provided, thus resulting in the ability to
scan a large number of ligands per experiment.
[0192] (2) Cycles of Rapid Delivery
[0193] Another feature of the system according to the invention is
that fluid can be rapidly delivered through the channels into the
sensor chamber, enabling compounds to be introduced into the
microenvironment of a sensor and withdrawn from that
microenvironment rapidly.
[0194] Fluid flows inside micron-sized channels are laminar and
reversible, a property that can be gauged by a dimensionless
number, called the Reynold's number (Re): For example, typically,
fluid flow having a low Re number is reversible, while at high Re
numbers, fluid flow becomes turbulent and irreversible. The
transition between laminar reversible flow and turbulent flow
appears to occur at a Re number of about 2000, an estimation based
on flow through a smooth circular channel (e.g., approximating flow
through a microchannel). Even at high flow rates (m/s), Re for
channels measuring a few microns in width is .about.<10. This
means that fluid flow in micron-sized channels fall well within the
laminar reversible regime. The key feature of fluidic behaviour
exploited herein is the reversibility of fluid flow.
[0195] In one aspect, positive pressure is applied at a
microchannel to introduce a compound or drug into the sensor
chamber housing the biosensor, preferably a patch-clamped cell.
After a suitable incubation time to allow interaction between the
compound/drug and the biosensor, a negative pressure is applied to
withdraw the compound/drug from the chamber. Because fluid flow is
completely reversible and also because diffusion is negligible
under conditions used (e.g., relatively fast flow), the drug is
completely withdrawn from the chamber back into the microchannel
from which it came. In this way, each compound delivered onto the
cell to screen for potential interactions, can be subsequently
withdrawn from the cell so the cell is again bathed in buffer,
re-sensitized, and ready for interaction with the next compound
delivered via a different microchannel.
[0196] This scheme is particularly useful because of the small
channel and chamber dimensions used in particular aspects of the
invention. A number of channel geometries can be suitable to
implement this scenario, particularly, the spokes-wheel
configuration described above and shown in FIGS. 9A-C and 10. As
can be seen from the Figures, an array of microchannels is arranged
in a spokes-wheel format in which the microchannels converge in a
circular sensor chamber at the center. The number of microchannels
used depends on the number of sample wells in the sample-well plate
to which the microchannels are to be interfaced. For example, a 96
sample-well plate will require at least 96 microchannels. The
center sensor chamber can house one or more sensors, such as a
patch-clamped cell, which can be patch-clamped using a micropipette
or patch-clamped on a chip. FIGS. 9A-C show the layout of the
overall chip structure for interfacing with a 96 sample-well plate,
in which solutions from 96-well plates can be pipetted directly
from a sample-well plate onto the corresponding reservoirs of the
chip using standard array pipettors.
[0197] FIG. 10 schematically depicts the enlarged region around the
central chamber. The dimension of the chamber may vary depending on
the exact application (e.g., whether the sensor comprises a cell or
is another type of sensor), with typical diameters ranging from
about 10 to hundreds of .mu.m. The width of the microchannels will
also vary depending on the diameter of the center chamber, with
typical widths ranging from about 1 to about 20 .mu.m. The
thickness of the microchannels is less critical and will in most
cases be range from about 1 to about 50 microns. Flow rates also
can vary, with typical flow rates inside microchannels ranging from
mm/s to cm/s and with corresponding flow rates in the open chamber
across the sensor ranging from .mu.m/s to mm/s. Positive and
negative pressure applied to each of the microchannels can be
controlled individually by the system processor such that positive
pressure applied to one microchannel will cause its solution
content to perfuse over the sensor while negative pressure will
cause the withdrawal of this solution back to its respective
microchannel, thereby leaving the biosensor bathed in its original
buffer solution.
[0198] (3) Rapid Exchange of Fluids
[0199] This design relies on the fact that solutions contained in
the microchannels and sensor chamber (and/or cell treatment
chambers) can be rapidly and efficiently replaced and exchanged.
Rapid solution exchange can be achieved using a variety of
different microchannel network geometries. In one aspect, a
plurality of microchannels converge or feed into the sensor
chamber, while in another aspect, a plurality of microchannels
converge into a single channel which itself converges into the
sensor chamber. The plurality of microchannels can comprise
interdigitating channels for sample and buffer delivery
respectively. In a preferred aspect, the design is integrated with
a patch clamp system. Three exemplary constructions are described
below.
[0200] i) Planar Radial Spokes-Wheel Format
[0201] In this construction, a large number (e.g. 96-1024) of
microchannels are arranged as radial spokes which converge into a
chamber with dimensions ranging from about 10 .mu.m to about 10 mm
which houses the sensor. The number of microchannels used are
selected to accommodate the number of sample wells in an
industry-standard microtiter plate, e.g., 96 to 1024 wells. In
addition to the number of microchannels that matches the number of
inputs from the well plates, there are preferably, at least two
additional microchannels, one for the delivery of buffer for
superfusion/re-sensitization and the other for waste removal. For
patch clamp using micropipettes, this construction also contains an
open volume region for accessing the cell(s); however, for
chip-based patch clamp measurements (such as described in WO
99/31503 and WO 01/25769), there will preferably not be any open
volume regions. To prevent cell(s) from being dislodged by fluid
flow from the microchannels, it is preferable that the cell(s) be
placed in a recessed region or well that matches the dimensions of
the cell(s). For membrane patches having dimensions much smaller
than that of a cell, dislodging of patch by fluid flow is not an
issue because the force exerted by Stokes drag is inversely
proportional to the dimension of the object (i.e., patch).
[0202] In order to provide for efficient replacement of fluids
contained in the chamber by incoming fluids from the channels, the
angle between the input channel and waste channel is optimized.
Fluid mixing and replacement is optimal when this angle is about
180.degree. and gets progressively worse as this angle decreases
towards 0 degrees. For high flow rates (cm/s to m/s), the effect of
this angle becomes progressively more important, while for low flow
rates, the angle between the input channel and waste channel is
less important.
[0203] To maximize efficient replacement of fluids at high flow
rates, the number of radial channels can be increased such that
each input channel will have a corresponding waste channel, rather
than having all input channels share a common waste channel. In
this format, all angles between input and output channels are about
180 degrees, ensuring optimal fluid replacement. A second strategy
is to construct a three-dimensional radial spokes-wheel channel
network, while a third strategy involves the use of branched
channel geometries. These strategies are described further
below.
[0204] One preferred embodiment of a 2D radial spokes-wheel format
for rapid solution exchange is shown in FIGS. 11A-C and FIG. 12. In
this embodiment, an array of microchannels is arranged in a
spokes-wheel format and converges in a circular sensor chamber at
the center. The number of microchannels used will depend on the
number of wells in the well plate to which the microchannels are to
be interfaced. For example, a 96 sample-well plate will require at
least 96 microchannels for ligand delivery and an additional 96
microchannels for waste, with each waste microchannel oriented at
about 180.degree. with respect to its corresponding sample delivery
microchannel. In addition to these 192 microchannels, there is one
pair of microchannels used for buffer superfusion and buffer waste,
which brings the total number of channels to 194 for interfacing to
96 sample-well plates. A sensor, such as a patch-clamped cell is
housed in the center chamber, which may be open volume, if
interfaced with a traditional micropipette-based patch clamp
system, or which may be closed volume, if interfaced with a
chip-based patch clamp system. FIGS. 11A-C show the structure of
this microfluidic system, which again is designed to be compatible
for interfacing with a 96-well plate. Several spokes-wheel
microfluidic arrangements, each having a patch-clamped detector
cell, can be used on the same chip structure to obtain parallel
measurements.
[0205] FIG. 12 shows an enlarged view of the sensor chamber. The
dimensions of this center chamber may vary depending on the exact
application, with typical diameters ranging from about 10-100
.mu.m. The width of the microchannels will also vary, depending on
the diameter of the center chamber, with typical widths ranging
from about 1-10 .mu.m. The thickness of the microchannels is less
critical and will in most cases ranges from about 1-10 .mu.m. The
flow rates also can vary, with typical flow rates inside
microchannels ranging from .mu.m/s to cm/s, with corresponding flow
rates in the center chamber ranging from .mu.m/s to mm/s.
[0206] ii). Three-Dimensional Radial Spokes-Wheel Format
[0207] A three-dimensional radial spokes-wheel arrangement also can
be used to efficiently replace fluids entering the sensor chamber.
In this construction, one or more sensors (e.g., such as cells) are
placed on a filter membrane sandwiched between a substrate
comprising radial channels and a substrate comprising a waste
reservoir. In this format, fluids are forced to flow down from the
top layer where the radial channels reside (e.g., through input
channels which feed into the radial channels), past the sensor(s),
then through the filters and into the waste channel. The filter
thus permits the sensor(s) to be superfused with fast fluid flow
while supporting the sensors (e.g., such as cells), so they are not
carried away or dislodged by the flow. In addition, the fluids are
forced to flow past the sensors and to replace all the fluids that
surround the sensors.
[0208] There are a number of advantages offered by this 3D design:
(1) fluids around the cells are completely, efficiently, and
rapidly exchanged; (2) sensors, such as cells, are firmly placed on
the filter and will not be dislodged by fluid flow even at
extremely high flow speed, because in the axial or z-direction, the
flow pushes the cells against the filter; and (3) a minimal number
of radial channels is required in comparison with the planar radial
design described above. The main disadvantage of this design in
comparison with other planar designs is increased complexity in the
micro-fabrication.
[0209] One preferred embodiment of the 3D radial spokes-wheel
format is shown in FIG. 13. The main difference between this 3D
structure and the planar structure shown in FIG. 12 is the presence
of z-direction flow of fluids from the outlets of the microchannels
to the inlet of the waste microchannel. Another difference is the
presence of a porous membrane on which the sensor(s) (e.g., cells)
are placed, which provides mechanical support for the sensors as
the z-direction flow pushes the cell against the membrane. In this
embodiment, the arrangements and dimensions of the microchannels
are comparable to that of the 2D planar format (FIG. 12). Although
the fabrication of this 3D structure is more complex than the
planar structure, the presence of the z-direction flow in many
cases provides better flow profiles, especially for open volume
reservoirs. Because the sensors are placed immediately outside
(i.e., on top) of the inlet of the waste channels, both ligand
streams and superfusion streams are forced to flow past the
sensor(s), which result in more efficient and complete dosing of
the sensor(s) by the different fluid streams. Also, the presence of
the porous membrane support permits the use of higher flow rates
and thus higher throughput.
[0210] iii) Branched Channel Format
[0211] In this design, preferably only two channels are placed
directly adjacent to one or more sensors (e.g., such as
patch-clamped cells), one for the delivery of compounds and the
other for waste. Rather than separating all the input channels and
converging the outlets of each input channel so they feed into a
center sensor chamber, channels are arranged in a branched
geometry. To interface with 96-1024 well plates, the single
delivery channel adjacent to the sensor(s) is connected to a
multitude of input microchannels, each input channels receiving
input from a different well of the 96-1024 well plate. This format
has the advantage that the channel delivering compounds and the
waste channel can be placed in very close proximity to the
sensor(s), thereby ensuring a rapid response from the system. The
delivery of the large number of compounds onto the sensor(s) in
rapid succession is achieved by the controlled and multiplexed
delivery of fluids containing compounds into the single channel
feeding directly into the sensor chamber.
[0212] One preferred embodiment of this design is shown in FIGS.
14A-C and 15. In this embodiment, a "fish-bone" structure is
fabricated with each "bone" corresponding to a sample (e.g., a
ligand) delivery microchannel which intersects with a main "spine"
microchannel which is connected to a buffer reservoir. The rapid
and sequential delivery of sample and buffer onto one or more
sensors in a sensor chamber is achieved by first applying a
positive pressure to one of the sample delivery microchannels, thus
introducing a plug of sample (e.g., such as a ligand) from that
microchannel into the main microchannel containing the buffer. This
plug is introduced onto the cell by applying positive pressure to
the buffer reservoir, which carries the plug onto the sensor, and
then washes the sensor (e.g., resensitizing it) with the buffer
solution. This cycle of delivery of sample and buffer superfusion
is repeated with different samples contained in different
microchannels. The layout of this chip design is shown in FIGS.
14A-C. In the embodiment shown in the Figures, the chip can be
interfaced with a 96-well plate.
[0213] FIG. 15 is an enlarged view of the area around the main
buffer channel and the sensor chamber. The dimensions (width and
thickness) of the microchannel (for both sample delivery and buffer
delivery) can be highly variable, with typical dimensions ranging
from about 1-100 .mu.m, and preferably from about 10-90 .mu.m. Flow
rate also may be varied with preferred flow rates ranging from
.mu.m/s to cm/s.
[0214] Pressure is isotropic, therefore, upon application of a
positive or negative pressure, fluids will flow along any pressure
drop without preference to any particular direction. Therefore,
preferably, passive one-way valves are integrated at the junction
between sample delivery microchannels and the main buffer channel.
The purpose of these integrated one-way valves is to prevent any
flow from the main buffer channel into each of the sample delivery
microchannels upon application of a positive pressure to the buffer
reservoir, while allowing flow from each of the sample delivery
microchannels into the main buffer channels when positive pressure
is applied to reservoirs providing sample to these microchannels.
There are numerous suitable designs for microfluidic valves as well
as pumping mechanisms.
[0215] Although the discussion below emphasizes pressure driven
flow owing to its simplicity of implementation, a number of
appropriate means can be designed for transporting liquids in
microchannels, including but not limited to, pressure-driven flow,
electro-osmotic flow, surface-tension driven flow, moving-wall
driven flow, thermo-gradient driven flow, ultrasound-induced flow,
and shear-driven flow. These techniques are known in the art.
[0216] Valving and Pumping
[0217] Scheme 1: Using Septums to Address Individual
Microchannels
[0218] In this scheme, the reservoirs that connect to each of the
microchannels are sealed by a septum, for example, using
polydimethyl siloxane (PDMS) for sealing or another suitable
material as is known in the art. Because the septum forms an
airtight seal, application of a positive pressure (e.g., with air
or nitrogen) via a needle or a tube inserted through the septum
will cause fluid to flow down the microchannel onto one or more
sensors in a sensor chamber (e.g., to the center of a spokes-wheel
where radial microchannels converge). Application of a negative
pressure with a small suction through the needle or tubing inserted
through the septum will cause fluid to be withdrawn in the opposite
direction (e.g., from the chamber at the center of the spokes-wheel
to the reservoir feeding into the microchannel).
[0219] An array of such needle-septum arrangements allows each
reservoir to be individually addressed, and therefore, each
microchannel. The use of this scheme permits the simultaneous and
sequential pumping and valving of the fluids contained within each
of the microchannels. By exercising precise control over positive
and negative pressure applied to each of the microchannels,
controlled fluid flow and compound delivery onto the one or more
sensors can be achieved. For designs that do not require individual
addressing of the microchannels (e.g., design 1--the rapid
transport of patched cells across different streams of fluids), a
single or a few septa with a single or a few pressure control
devices will suffice.
[0220] Scheme 2: Controlling Fluidic Resistance by Varying Channel
Dimensions
[0221] Although the above design using individual septa offers
great flexibility and control, for certain applications in which
the sequence of compound delivery and fluid flow is predetermined,
a simpler design offers simplicity and ease of implementation. In
this scheme, equal positive pressure is applied to all reservoirs,
for example, by using pressurized air applied homogeneously to all
reservoirs via a single septum, or through the use of gravity flow
caused by the difference in height between inlet and outlet
reservoirs. The rapid sequential delivery of compounds from each
microchannel onto one or more sensors is accomplished by varying
the fluidic resistance of each microchannel, which is easily
achieved by varying the width and length of the each
microchannel.
[0222] Fluidic resistance increases linearly with length and to the
fourth power of the diameter for a circular capillary. By gradually
and systematically varying the dimension of each microchannel, the
time delay among the microchannels in their delivery of compounds
onto one or more sensors in a sensor chamber can be controlled.
This scheme is especially pertinent to high-throughput drug
screening applications in which a large number of compounds are to
be delivered sequentially and rapidly onto patched cell/cells with
pre-determined time delays.
[0223] Scheme 3: Control of Fluid Flow with External Valves
[0224] In this configuration, compounds from each of the wells of
an array well plate are introduced through external tubings or
capillaries which are connected to corresponding microchannels.
External valves attached to these external tubings or capillaries
can be used to control fluid flow. A number of suitable external
valves exist, including ones actuated manually, mechanically,
electronically, pneumatically, magnetically, fluidically, or by
chemical means (e.g., hydrogels).
[0225] Scheme 4: Control of Fluid Flow with Internal Valves
[0226] Rather than controlling fluid flow with external valves,
there are also a number of chip-based valves that can be used.
These chip-based valves can be based on some of the same principles
used for the external valves, or can be completely different, such
as ball valves, bubble valves, electrokinetic valves, diaphragm
valves, and one-shot valves. The advantage of using chip-based
valves is that they are inherently suited for integration with
microfluidic systems. Of particular relevance are passive one-way
valves, which are preferred for implementing some of the designs
mentioned in above (e.g., such as the branched channel format).
[0227] Other suitable geometries may be integrated with any of the
above systems. In one aspect, at least one channel of a
microfluidic system described above is a mixing channel which
receives two or more separate streams of fluid from two or more
other channels. The mixing channel can be used to combine the
separate streams in a single channel. Such a configuration can be
used to establish a concentration gradient of a substance provided
in different concentrations in the two or more separate streams as
is described in WO 02/22264.
Interfacing Patch Clamp Detection with Microfluidics
[0228] The system can be used to monitor cellular responses by
measuring changes in electrical properties of cells. In one aspect,
the sensor chamber of the chip comprises a cell-based biosensor and
the system comprises a detector for monitoring the response of the
biosensor to solution flow from the channels. One response which
can be monitored is a change in an electrical property of the
biosensor in response to gating of an ion channel. For example, a
change in current flowing across the membrane of the biosensor can
be measured using a voltage clamp technique. Currents can be in the
range of a few picoampere (pA) (e.g., for single ion-channel
openings) to several .mu.A (for cell membranes of larger cells such
as Xenopus oocytes).
[0229] Among voltage clamp techniques, patch clamp is most suitable
for measuring currents in the pA range (see e.g. Neher and Sakmann,
1976, supra; Hamill, et al., 1981, supra, Sakmann and Neher, 1983,
supra). The low noise property of patch clamp is achieved by
tightly sealing a glass microelectrode or patch clamp pipette onto
the plasma membrane of an intact cell thereby producing an isolated
patch. The resistance between the pipette and the plasma membrane
is critical to minimize background noise and should be in excess of
10.sup.9 ohm to form a "giga seal". The exact mechanism behind the
formation of the "giga seal" is debated, but it has been suggested
that various interactions such as salt-bridges, electrostatic
interactions, and van der Waal forces mediate the interaction
between the glass surface of the pipette and the hydrophilic heads
in the lipid layer of the cell membrane (see, e.g., Corey and
Stevens, 1983, In Single-Channel Recording, pp. 53-68, Eds. B.
Sakmann and E. Neher. New York and London, Plenum Press).
Variations of patch clamp techniques can be utilized such as
whole-cell recording, inside-out recording, outside-out recording;
and perforated patch recording as are known in the art.
[0230] In whole-cell recording, the cell membrane covering the
electrode tip is ruptured by suction in order to establish an
electrical connection (and a chemical pathway) between the cell
interior and the electrode solution. Because electrode solution is
in great excess compared to the amount of cytosol in the cell
(about 10 .mu.l vs. about 1 pl), changing ionic species in the
electrode solution will create concentration gradients across the
cell membrane, providing a means to control the direction and
magnitude of the transmembrane ionic flow for a given
receptor/ion-channel complex.
[0231] In inside-out and outside-out patch clamp configurations,
the cytosolic environment is lost by excision of a membrane patch
from the entire cell (see, e.g., Neher and Sakmann, 1976, supra;
Sakmann and Neher, 1983, supra). To obtain an excision of a patch
in both the inside-out and the outside-out configurations, the
cells are preferably attached to the bottom of the sensor chamber.
In the case of acutely isolated cells, for example, poly-L-lysine
can be used to fix the cells to the bottom of the chamber.
[0232] The inside-out configuration allows exposure of the
cytosolic side of the membrane to solution in the chamber. It is
therefore a method of choice for studying gating properties of
second-messenger activated ion-channels at the single-channel
level. Thus, the effects of cytosolic signaling molecules or
enzymatic activity on ion-channel function can be studied by means
of this configuration. The outside out configuration, on the other
hand, allows exposure of the extracellular side of the patch. It
can therefore be used to monitor the activity of ligand-gated or
receptor-operated ion-channels.
[0233] Low noise levels provide better signal-to-noise ratios where
modulators (e.g., such as agonists or antagonists). Under optimal
conditions, single-channel currents in the higher femto-ampere
(10.sup.-15 A) range can be resolved. Strategies to decrease noise
(e.g., such as caused by a bad seal between the electrode and the
cell) to facilitate formation of G.OMEGA.-seals include, but are
not limited to, fire polishing of the glass electrode or treating
the surface the glass electrode using agents such as sigmacote.
Dielectric noise and capacitive-resistive charging noise also can
be decreased by selecting an expedient electrode/pipette geometry,
using quartz glass, and by coating of the glass surface of the
pipette with Sylgard.RTM. (silicone, PDMS) in order to insulate the
pipette tip as much as possible.
[0234] One frequently used modification of the whole-cell
configuration, the perforated patch mode, also can be used (see,
e.g., as described in Pusch and Neher, 1988, supra). In this
technique, holes are selectively made in the cell membrane using a
pore-building protein, such as amphotericin or nystatin (see, e.g.,
Akaike et al., 1994, Jpn. J. Physiol. 44: 433-473; Falke, et al.,
1989, FEBS Lett. 251: 167; Bolard, et al., 1991, Biochemistry 30:
5707-5715) to create increased conductivity across the patched cell
membrane without the loss of intracellular signalling
molecules.
[0235] In addition to measuring ion currents across ion channels at
constant membrane potential, the patch clamp technique can be used
to measure membrane voltage at a known constant or time-varying
current. This patch clamp configuration, referred to as "current
clamp", measures the change in membrane potential caused by
activation of ligand-gated ion-channels or by voltage-gated ion
channels and is particularly suited for creating a biosensor which
can be used to monitor the effects of agents (e.g., drugs) on
action potentials (i.e., frequency, duration, and amplitude). This
technique also can be used to study the effect of an agent to study
an agent's impact on the excitability of a nerve cell. Therefore,
in one aspect, the system is used to monitor the modulation of the
voltage threshold (e.g., hyperpolarizing or depolarizing) of a
cell-based biosensor in a current clamp mode when an action
potential is triggered.
[0236] In another aspect, the system is used to monitor capacitance
changes in cell membranes by providing a cell-based biosensor in
the open volume reservoir and measuring impedance of the membrane
across the membrane of the biosensor in an AC mode. For example,
the system can be used to monitor the effect of agents on the
release of vesicles from a cell (i.e., exocytosis) and/or on the
uptake of vesicles by a cell (i.e., endocytosis).
[0237] One preferred embodiment for interfacing microfluidic
systems with electrophysiological patch clamp recordings is shown
in FIG. 1A. In FIG. 1A, a single patch-clamped cell is shown;
however, several patch-clamped cells can be used simultaneously.
External pumps and fluid control equipments are placed adjacent to
a standard microscope. The entire integrated system preferably is
computer-controlled and automated. The different components of the
system (i.e. microfluidics, scanning mechanism, patch clamp, and
the like) may be controlled separately using separate controllers
and separate software, but most preferably these components are all
controlled by a single system processor as described above.
[0238] The system can be readily adapted for use with a
conventional patch clamp pipette or micropipette. In one aspect, a
cell or a fraction of a cell (e.g., a cell membrane) is positioned
at the opening of a patch clamp micropipette. Patch clamp
micropipettes are known in the art and are available, for example,
from World Precision Instruments, Inc. (Sarasota, Fla. 34240 USA;
at
http://www.wpiinc.com/WPI_Web/Glass-Holders/Patch_Clamp_Glas.html).
Suction is applied to the patch clamp micropipette until a
giga-seal (giga-ohms) is created between the end of the
micropipette and the membranes of the cell. Preferably, a change in
one or more electrical properties of the cell is monitored as a
means of determining the presence of a ligand or other compound in
a fluid stream coming into contact with the cell. For example, an
electrical signal can be detected by an electrode in the
micropipette and transmitted, preferably with amplification, to the
system processor. A reference electrode, which contacts solution in
the sensor chamber, also is required.
[0239] Various supporting solutions can be adapted for use in
sensor chamber. The type of solution will depend on the sensor and
compounds being evaluated. For example, a sensor solution can be a
recording solution used for traditional patch clamp analysis of an
ion channel. In general, the exact composition of a solution for
patch clamp recording will vary depending on the type of channel
being evaluated (see, e.g., U.S. Pat. No. 6,333,337, for potassium
channels; U.S. Pat. No. 6,323,191, for Cl.sup.- channels, and
PCT/US99/02008, for sodium channels); such solutions are well known
in the art.
[0240] In one aspect of the invention, patch clamp recording is
automated and controlled by the system processor. For example, the
system processor may direct the movement of one or more
micropipettes to pre-programmed locations. In another aspect, the
system processor directs the movement of the one or more
micropipettes in response to image analyses of cells in the sensor
chamber (e.g., the system monitors the delivery of cells to the
micropipette(s) from one or more treatment chambers). In a
preferred aspect, acquisition and analysis of patch clamp data,
followed by a feedback control to vary microfluidic settings (e.g.,
pressure, valves and switches) and to control scanning parameters
(e.g., speed and trajectory of scanning, pressure drops across
channels), is implemented by the system processor.
[0241] In addition to integrating with traditional patch clamp
systems, the microfluidics platform according to the invention also
is ideally suited for interfacing with chip-based patch clamp, as
described, for example, in WO 99/31503; WO 01/25769; WO 01/59447;
and WO 99/66329. This embodiment is shown in FIG. 1C and can
eliminate such system components as a microscope, micropipette,
micromanipulators, and the like. Chip-based patch clamp integrate
readily with the substrates of the invention. Chip-based patch
clamp systems also provide the ability to patch clamp several cells
together on a single substrate.
Methods of Using the System
[0242] The invention exploits the potential for using microfluidic
systems to control the delivery of a large number of different
biologically active molecules and compounds (e.g., candidate drugs)
to a sensor comprising a target molecule. Suitable
molecules/compounds which can be evaluated include, but are not
limited to, drugs; irritants; toxins; proteins; polypeptides;
peptides; amino acids; analogs and modified forms of proteins;
polypeptides, peptides, and amino acids; antibodies and analogs
thereof; immunological agents (e.g., such as antigens and analogs
thereof, haptens, pyrogens, and the like); cells (e.g., such as
eukaryotic cells, prokaryotic cells, infected cells, transfected
cells, recombinant cells, bacteria, yeast, gametes) and portions
thereof (e.g., cell nuclei, organelles, secretagogues; portions of
cell membranes); viruses; receptors; modulators of receptors (e.g.,
agonists, antagonists, and the like); enzymes; enzyme modulators
(e.g., such as inhibitors, cofactors, and the like); enzyme
substrates; hormones; metabolites and analogs thereof; nucleic
acids (e.g., such as oligonucleotides; polynucleotides;
fibrinotides; genes or fragments, including regulatory sequences,
and/or introns, and/or coding regions; allelic variants; RNA;
antisense molecules, ribozymes, nucleotides, aptamers), including
analogs and modified forms thereof; chemical and biological warfare
agents; metal clusters; and inorganic ions.
[0243] Combinations of two or more of any of these molecules also
can be delivered, sequentially or simultaneously, to one or more
sensors in the sensor chamber. Compounds also can be obtained from
synthetic libraries from drug companies and other commercially
available sources known in the art (e.g., including, but not
limited, to the LeadQuest.RTM. library comprising greater than
80,000 compounds, available through
http://www.tripos.com/compounds/; ChemRx Diversity Library,
comprising 1000 to 5000 compounds per scaffold, available through
http://www.chemrx.com; the Nanosyn Pharma library, available
through Nanoscale Combinatorial Synthesis Inc., Menlo Park, Calif.,
and the like) or can be generated through combinatorial synthesis
using methods well known in the art. In aspects in which molecules
are delivered to cells, any of the molecules described above may be
taken up by cells by transiently exposing the cells to an electric
field (e.g., in a cell treatment chamber or in a sensor chamber
which is adapted for electroporation) as described above.
[0244] Providing Periodically Resensitized Ion Channel Sensors
[0245] Binding a compound (such as an agonist or modulator or drug)
to a broad range of ion channels not only evokes conformational
changes in these channels, allowing a flux of ions across a cell
membrane, but also causes the ion channel to desensitize, i.e., to
reside in a long-lasting, ligand-bound, yet shut-off and
non-conducting state (see, e.g., Jones and Westbrook, 1996, GL
Trends Neurosci. 19: 96-101). Desensitization of many types of
ion-channels usually occurs within a few milliseconds and is
thought to be one of the mechanisms by which synaptic information
in the central nervous system is processed and modified.
Densitization also may serve as a negative feedback mechanism that
prevents excitotoxic processes caused by excessive activation of
ion channels by neurotransmitters or other neuromodulators (see,
e.g., Nahum-Levy, et al., 2000, Biophys J. 80: 2152-2166; Swope, et
al., 1999, Adv. Second Messenger Phosphoprotein. Res. 33:
49-78).
[0246] In one aspect, to achieve high screening rates in, for
example, HTS applications, patch-clamped cell(s) in the sensor
chamber are moved from the outlet of one microchannel to the next
in rapid succession. To achieve rapid resensitizaton of ion
channels and receptors, microchannels delivering samples comprising
suspected modulators, agonists, or drugs of receptor/ion channels
are interdigitated with microchannels delivering buffer for
resensitization of the receptor/ion channels (e.g., buffer free of
any agonist). In addition to resensitizing ion channels and
receptors, this delivery of buffer onto cells between ligand and
drug exposure serves to wash out ligands and drugs previously
administered to the cell. Thus, in this aspect, the system is used
to screen for an agonist or modulator or drug of a specific
ion-channel by providing a periodically responsive ion channel
sensor. For example, by providing pulsed or steady-state flow
delivery of buffer to the sensor, the system provides a cell that
is resensitized when exposed to a channel outlet delivering a
candidate agonist or modulator or drug. FIGS. 24A-C show simulated
screenings of unknown agonists according to one method using a
microfluidic chip comprising 26 outlets feeding into a sensor
chamber. The contents of each channel are shown in FIG. 24A.
Agonists with known pharmacological action (e.g., known efficacy,
or potency) have been included in certain channels to serving as
internal controls or standards. The score sheet for this
experiment, i.e., the patch clamp response obtained for each
microchannel is shown in FIG. 24 C.
[0247] In another embodiment, an additional superfusion pipette
proximal to the patch-clamped cell, e.g., in an arrangement that is
adjacent to or coaxial with respect to the patch pipette (as
detailed below), is used to continuously resensitize/wash
receptors/ion channels on the cell surface. This enables cells to
be extremely rapidly resensitized and washed (e.g., within ms) and
enables several different readings/registrations of ion channel
activation to be made as a cell moves across a channel outlet.
FIGS. 27A-C show a simulated method of rapid resensitization used
for screening of agonists which combines the use of a microfluidic
chip comprising 14 outlets feeding into a sensor chamber with
pulsed superfusion of agonist-free buffer solution using a fluidic
channel (or micropipet) placed coaxial or orthogonal or otherwise
in close proximity to a patched-clamped cell. The contents of each
microfluidic channel are shown in FIG. 27A. Agonists with known
pharmacological action (e.g., known efficacy, or potency) have been
included in certain channels to serve as internal standards or test
compounds.
[0248] The simulated trace, shown in FIG. 27B, for a linear,
single, forward scan of a cell-based biosensor across microfluidic
channel outlets, show a plurality of peak responses obtained per
single microchannel outlet. The score sheet for this experiment,
i.e., the patch clamp response obtained for each microchannel is
shown in FIG. 27C. In this case, a Gaussian-distributed response is
obtained because it was modeled that the ligands exiting
microchannels into the open volume had a gaussian distribution.
Many other types of distributions can be obtained depending on
substrate geometry and experimental parameters, such as level of
collimation of flows. However, this type of repeated superfusion of
cells during their passage across a single microchannel outlet
allows dose-response information and high signal-to-noise ratios to
be obtained for receptors/channels that rapidly desensitize.
[0249] To obtain desired data, variable scan rates of cell(s)
across individual streams of sample and buffer and variable
pressure drops across each microchannel can be implemented by the
system, either from pre-programmed instructions or in response to
feed-back signals from a detector in electrical communication with
the patch clamp electrode (e.g., based on a detected signal or in
real-time).
[0250] The system thus can be used to change microenvironments
rapidly around a cell comprising a receptor/ion-channel. For
example, the system can provide a periodically responsive ion
channel. Because of the small dimensions of the substrates and
microchannels used herein, which allows for rapid mass transport,
the system enables a user to screen for drugs, in some instances,
at the rate of hundreds per second (i.e., millions per hour) using
one patch clamp sensor, provided drugs and resensitization
solutions are delivered sequentially at a comparable rate to the
sensor. As discussed above, scanning rates can be modified to
account for the physiological responses of a cell-based sensor,
e.g., providing slower scanning rates for receptors that
equilibrate slowly.
[0251] Generating Dose-Response Curves and Analyzing Ion-Channel
Pharmacology
[0252] Dose-response curves provide valuable information regarding
the actions and potencies of drugs. Obtaining dose-response curves
using traditional methods involving micropipettes often can be time
consuming and tedious. The present invention, which uses
microfluidics for the rapid and controlled manipulation of the
microenvironemnt around cell(s), is uniquely suited for
dose-response measurements. Dose-response relationships most often
follow a sigmoidal curve in a lin-log plot, and can be described by
the Hill logistic functions:
I=I.sub.max/[1+(EC.sub.50/C).sup.n]
Where I is the whole-cell current, C is the concentration of
ligands, I.sub.max is the maximal current (i.e., when all channels
are in the open state), EC.sub.50 is the half-maximal value (i.e.,
when half of the receptor population is activated, and often equals
K.sub.D, the dissociation constant of the ligand), and n is the
Hill coefficient that reflects the stoichiometry of ligand binding
to the receptor.
[0253] In one aspect, to achieve dose-response information for
agonists, patch-clamped cell(s) in the sensor chamber are moved
from the outlet of one microchannel to the next in rapid
succession. Microchannels delivering agonists at different
concentration are interdigitated with microchannels delivering
buffer free of agonist (e.g., to resensitize receptors/ion channels
and/or to wash out compounds previously administered to the cell,
as described above). Preferably, the serially or sequentially
diluted agonists are loaded into different channels. FIG. 26A is an
example of such a loading scheme in a 56-channel substrate. Agonist
is present at highest concentration in channel 52 and then is
serially diluted at each subsequent channel until channel 6.
Agonists with known pharmacological action (e.g., known efficacy,
or potency) have been included in certain channels to serve as
internal standards. Preferably, the agonist concentration from the
channel with the highest concentration to the channel with the
lowest concentration covers many orders of magnitude. FIG. 26B show
simulated patch clamp recordings of agonists at different
concentration as described above. From the score sheet for this
simulated experiment, i.e., the patch clamp response obtained for
each microchannel as shown in FIG. 26 C, a dose-response curve can
be constructed.
[0254] Similarly, with some modifications, dose-response curves can
be obtained for antagonists as well using the system which is
described in more detail below. Furthermore, as described above,
the combination of microfluidics with patch clamp can provide a
wide range of information about the actions of modulators on
ion-channels, e.g., such as the association and dissociation
constants of a ligand for its receptor, and whether a modulator is
an agonist or an antagonist of a receptor. It is also possible,
however, to obtain dose-response information from accumulated
responses of ligands without washing or resensitizing the receptors
with interdigitated flows of buffer. In this aspect, the
microchannels need only contain ligand solutions at different
concentrations.
[0255] (i) Detection and Characterization of Agonists
[0256] Partial Agonists
[0257] The ability of a drug molecule to activate a
receptor-mediated response is a graded property, rather than an
all-or-nothing property. If a series of chemically related agonists
acting on the same receptor are tested on a cell, the maximal
response (i.e., the largest response that can be produced by an
agonist in high concentration) generally differs from one agonist
to another. Some compounds (known as "full agonists") can produce a
maximal response whereas others, referred to "partial agonists",
can only produce a submaximal response. An "partial agonist" can
therefore act as a "weak antagonist" by hampering a full agonist
from binding a receptor. Thus, by using a defined ion-channel
together with a known agonist that produces a maximal response, the
grade of an agonist's activity can be monitored (see, e.g., FIG.
24).
[0258] (ii) Detection and Characterization of Antagonists
[0259] In one aspect, the system is used to screen for antagonists
of ion-channel activity. Suitable ion-channels which can be
evaluated include: (i) ion channels that do not de-sensitize; (ii)
ion-channels that desensitize (iii) ion-channels that desensitize
but which mediate large current fluctuations when activated; and
(iv) ion-channels whose desensitizing property is blocked by
irreversible binding of an allosteric modulator (e.g., such as a
lectin). To detect antagonists, the ion-channels or receptors
expressed by a biosensor need to be activated or "tested" by an
agonist during, before, or after, application of the antagonist.
For example, different antagonists can be applied together with a
well-defined agonist with known pharmacological properties.
Antagonists at different concentrations also can be loaded into
microchannels together with agonists at a constant
concentration.
[0260] To achieve rapid resensitizaton of ion channels and
receptors, microchannels containing agonist and antagonist (e.g.,
such as ligands and drugs) can be interdigitated with microchannels
delivering buffer free of any agonist or antagonist (e.g., buffer
for resensitization of the receptor/ion channels). In addition to
resensitizing ion channels and receptors, exposure of cells to
buffer between periods of exposure to ligands and drugs serves to
wash out ligands and drugs previously administered to the cell.
Thus, in this aspect, the system is used to provide a periodically
responsive ion channel sensor. Antagonists are detected in this
system by their inhibition of the agonist-induced response.
[0261] In another aspect, the system is used to screen for
antagonists which can be detected through attenuation in the signal
mediated by constantly pre-activated receptors/ion-channels. In
this particular setup, different channels are loaded with different
antagonists, or with the same antagonist at different
concentrations, or a combination of both, while each channel
comprising antagonist comprises agonist at a constant
concentration. To achieve continuous activation of receptors and
ion channels, microchannels containing agonist and antagonist are
interdigitated with microchannels delivering buffer and agonist at
the same concentration as in the channels supplemented with
antagonist. This delivery of buffer supplemented with agonist onto
cells between ligand and drug exposure serves to wash out ligands
and drugs previously administered to the cell and also can serve to
resensitize a receptor/ion channel.
[0262] A simulation of such an experiment is shown in FIGS. 25A-C.
The contents of each channel is shown in FIG. 25A. Antagonists with
known pharmacological action (blocking potency) have been included
in certain channels to serve as internal standards. The simulated
trace shown in FIG. 25 B represents a linear single forward scan of
a cell-based biosensor across microfluidic channel outlets. As
shown in the Figure, a plurality of peak responses are obtained per
single microchannel outlet. The score sheet for this experiment,
i.e., the patch clamp response obtained for each microchannel, is
shown in FIG. 25C, from which the antagonist with the highest
blocking potency can be identified.
[0263] Competitive Antagonism
[0264] This type of antagonism refers to competition between
agonists and antagonists at the same binding site on the receptor.
Reversible competitive antagonism is characterized by a shift in
the slope of a dose response curve to higher concentrations while
maintaining the same maximum response and the slope of the curve.
In irreversible competitive antagonism, no change in antagonist
occupancy is observed when the cell is exposed to agonist.
[0265] Non-Competitive Antagonism
[0266] Non-competitive antagonism describes the situation where the
antagonist blocks, at some point, the chain of events that leads to
the production of a response by the agonist. In this type of
antagonism, the agonist and antagonist either bind to different
sites on the receptor/ion channel or the antagonists simply block
the ion channel pore. The net effect is to reduce the slope and
maximum of the agonist's dose-response curve.
[0267] Isosteric Inhibition
[0268] This type of antagonism refers to the self-inhibition of
agonists above a certain concentrations; that is, an agonist will
start to antagonize its own action at a sufficiently high
concentration. A bell-shaped dose-response curve often signals the
presence of this kind of antagonism.
[0269] Detection of Modulators of Presynaptically Expressed
Ion-Channels
[0270] In another aspect, the system is used to detect a modulator
of a presynaptically expressed ion-channel. Strategies for studying
presynaptically localized ion-channels often include patch clamp
recordings of synaptosomes (i.e., pinched-off nerve terminals
produced by homogenizing brain tissue) inserted in proteoliposomes
or planar phospholipid bilayers (see, as described in Farley and
Rudy, 1988, Biophys. J. 53: 919-934; Hirashima and Kirino, 1988,
Biochim Biophys Acta 946: 209-214, for example). The method of
Hirashima and Kirino, 1988, supra, is particularly preferred, as it
is a simple and rapid technique for generating giant
proteoliposomes comprising presynaptically expressed ion-channels
which can be used as biosensors for patch clamp analysis in the
system according to the invention.
[0271] Detection of Ligands Acting on Orphan
Receptors/Ion-Channels
[0272] Conventional drug discovery approaches often are initiated
by the discovery of ligand's biological activity which is
subsequently used to characterize its tissue pharmacology and
physiological role. Typically, after the ligand is characterized,
the corresponding receptor is identified as target for drug
screening in HTS applications. A relatively novel strategy for
characterizing orphan receptors (i.e., receptors with an undefined
biological activity) is often referred to as a "reverse
pharmacology" approach.
[0273] The reverse approach starts with an orphan receptor of
unknown function that is used as target for detection of its
ligand. The ligand is then used to explore the biological and
pathophysiological role of the receptor. High-throughput screening
is initiated on the receptor at the same time that the ligand is
being biologically characterized in order to develop antagonists
that will help determine the therapeutic value of the receptor.
[0274] The present invention is particularly useful for a reverse
pharmacological approach. In one aspect, the system comprises a
cell-based biosensor which is a non-native cell line which
expresses an exogenous orphan receptor (e.g., such as an ion
channel). Suitable native cell lines, include, but are not limited
to, HEK-293, CHO-KI, and COS-7.
[0275] There are several benefits coupled to screening ion channels
in a non-native cell background. First, a transfected cell line
containing a null background (e.g., which does not ordinarily
express the orphan receptor) allows one to be certain of the
molecular identity of the gene responsible for the observed signal.
Second, the orphan receptor can be over-expressed, thus improving
the signal-to-noise of the screening read-out. Third, host cells
with low background conductances can be chosen to allow very
sensitive assays of certain types of ion channels. Finally, these
cell lines are relatively easy to culture and are robust enough to
be handled by automated screening systems.
[0276] Detection of Modulators of Neurotransmitter Vesicular
Release
[0277] Patch-clamp techniques to measure membrane capacitance,
developed over ten years ago (see, e.g., Neher and Marty, 1982,
Proc. Natl. Acad. Sci. USA 79: 6712-6716), provide a powerful tool
to study the underlying mechanism and control of exocytosis.
[0278] The surface area of a cell depends on the balance between
exocytosis and endocytosis. Exocytosis results in the discharge of
vesicle contents (i.e., such as neurotransmitters) into the
extracellular space and the incorporation of vesicle membrane into
the plasma membrane, leading to an increase in cell surface area.
During endocytosis, parts of the plasma membrane are retrieved,
resulting in a decrease in the surface area. Changes in net
exocytotic and endocytotic activity thus can be monitored by
measuring changes in cell surface area.
[0279] Membrane capacitance is an electrical parameter of the cell
that is proportional to the plasma membrane area. Thus, providing
the specific capacitance remains constant, changes in plasma
membrane area resulting from drug-induced modulation of exocytotic
and endocytotic activity through presynaptically located
ion-channels, can be monitored by measuring membrane capacitance by
means of patch clamp in the open sensor chamber of the system.
[0280] Determining Permeability Properties of a Cell
[0281] When a cell used in a screening procedure expresses a broad
range of ion-channel types, characterizing the ion permeability
properties of the cell's activated ion-channels can be used to
characterize a drug's interaction with the cell. Information about
permeability properties of an ion-channel can be determined by
monitoring reversal potential which can be determined by evaluating
current-to-voltage relationships, created from measurements of
agonist-evoked currents at different holding potentials. By
employing the reversal potential and knowledge about intra- and
extra-cellular ion concentrations, the relative ion-channel
permeability properties are determined from different models.
[0282] Noise Analysis of Current Traces
[0283] Analysis of current-traces from ion-channels activated by
agonists can be performed on both an ensemble- and single-channel
level for further characterization of an agonist-ion-channel
interaction. The Fourier transformation of the autocorrelation
function obtained for the total current recorded with whole-cell
patch clamp yields power spectra that can be fitted by single or
double Lorentzian functions. These fits provide information about
mean single-channel conductances and ion-channel kinetics (e.g.,
mean single channel open time) through analysis of the frequency
dependence of the current response (i.e., corner frequency). In
principle, although a more difficult and tedious technique,
recordings obtained from outside-out patch-clamp configurations
also can be analysed to measure single-channel opening intervals
and different conductance levels mediated by the same receptor-ion
channel complex.
EXAMPLES
[0284] The invention will now be further illustrated with reference
to the following examples. It will be appreciated that what follows
is by way of example only and that modifications to detail may be
made while still falling within the scope of the invention.
Example 1
Microfabrication of a Substrate
[0285] FIG. 19 shows examples of microchannels fabricated in
silicon by deep reactive ion etching in SF.sub.6. Masks for
photolithography were produced using standard e-beam writing on a
JEOL JBX-5DII electron beam lithography system (medium reflective
4'' chrome masks and Shipley UV5 resists, 50 keV acc. voltage, dose
15 .mu.C/cm.sup.-2, exposure current 5 nA). The resist was spin
coated at 2000 rpm for 60 s giving 250 nm of resist and soft baked
for 10 minutes at 130.degree. C. on a hotplate before exposure. The
pattern was post exposure baked for 20 minutes in an oven at
130.degree. C. and developed for 60 s in Shipley MF24-A, rinsed in
DI water and etched in a reactive ion etcher (Plasmatherm RIE m-95,
30 s, 50 W, 250 mTorr, 10 ccm O.sub.2). The chrome was etched for
1-2 minutes in Balzers chrome etch #4, the mask was stripped of the
remaining resist using Shipley 1165 remover and rinsed in acetone,
isopropanol and DI water. A 3'', [100], two sides polished, low
N-doped Silicon wafers with 700 nm of thermally grown silicon
dioxide and a total thickness of 380 .mu.m was cleaned in a
reactive ion etcher Plasmatherm RIE m-95 (30 s, 50 W, 250 mTorr, 10
ccm O.sub.2), spin coated with Shipley S-1813 photoresist at 4000
rpm, giving 1.3 .mu.m of resist, and exposed for a dose of
[0286] 110 mJ/cm.sup.-2 at 400 nm wavelength on a Carl Suss MA6
mask aligner. The wafer was developed for 45 s in Shipley MF319
rinsed in DI water and ashed in a reactive ion etcher (Plasmatherm
RIE m-95, 30 s, 50 W, 250 mTorr, 10 ccm O.sub.2). The wafer was
hard baked for 10 minutes at 130.degree. C., the silicon dioxide
was etched with SioTech buffered oxide etch and rinsed in DI water.
The wafer was stripped of the remaining resist with acetone, rinsed
in isopropanol and DI water. The other side of the wafer was spin
coated with Shipley AZ4562 photoresist at 3000 rpm for 30 seconds
giving approximately 8 .mu.m of resist, soft baked for 3 minutes at
100.degree. C. on a hotplate and exposed for a dose of 480
mJ/cm.sup.-2 at 400 nm wavelength on a Carl Suss MA6 mask aligner.
The pattern was developed for 200 seconds in Shipley MF312 and DI
water in 50:50 mix, rinsed in DI water, and ashed in a reactive ion
etcher (Plasmatherm RIE m-95, 30 seconds, 50 W, 250 mTorr, 10 ccm
O.sub.2).
[0287] The pattern defined in the photoresist AZ4562, the recording
chamber and the combined access holes and sample wells was etched
in a STS Multiplex deep reactive ion etcher using SF.sub.6 as
etching gas and C.sub.4F.sub.8 as passivation gas at 600 W of RF
power and 30 W of platen power. The system was operating at a
constant APC angle of 74% and the etching time was 12 seconds with
an overrun time of 1 second, and the passivation time 8 seconds
with an overrun time of 1 second. The etching rate was
approximately 4.9 .mu.m/minute and the etching time 60 minutes
resulting in a depth of approximately 300 .mu.m. The wafer was
stripped of the remaining resist in acetone, rinsed in isopropanol
and DI water.
[0288] The pattern in silicon dioxide defining the microchannels
was etched with the same system as before but with 800 W of RF
power, at a constant APC angle of 68% and the etching time was 7 s
with an overrun time of 0.5 s, and the passivation time 4 second
with an overrun time of 1 second. The etching rate was
approximately 3.3 .mu.m/min and the etching time 30 minutes
resulting in a depth of 100 .mu.m. The wells and the recording
chamber were completely etched through resulting in holes in the
wafer at these points. The channels were sealed to a 3'', 1000
.mu.m thick wafer of Corning #7740 borosilicate glass using anodic
bonding at a temperature of 450.degree. C. and a voltage of 1000 V.
The maximum current during bonding was typically 500 .mu.A.
Example 2
Re-Sensitization of Patch-Clamped Cells Using Microfluidic-Based
Buffer Superfusion and Cell Scanning
[0289] Microchannels were molded in a polymer, polydimethylsiloxane
(PDMS), which were then sealed irreversibly onto a glass coverslip
to form an enclosed channel having four walls.
[0290] The procedure used is the following:
[0291] (1) A silicon master used for molding PDMS was fabricated by
first cleaning the wafer to ensure good adhesion to the
photoresist, followed by spin coating a layer (.about.50 .mu.m) of
negative photoresist (SU 8-50) onto the wafer. This layer of
negative photoresist was then soft baked to evaporate the solvents
contained in the photoresist. Photolithography with a mask aligner
was carried out using a photomask having the appropriate patterns
that were prepared using e-beam writing. The exposed wafer was then
baked and developed by washing away the unexposed photoresist in an
appropriate developer (e.g. propylene glycol methyl ether
acetate).
[0292] (2) This developed wafer (master) was surface passivated by
silanizing in vacuo with a few hundred microliters of
tridecafluoro-1,1,2,2-tetrahydrooctyl-1-trichlorosilane for a few
hours.
[0293] (3) Degassed PDMS prepolymer was poured on top of the
silicon master and left in an oven to cure at 60.degree. C. for two
hours, (4) The cured PDMS mold containing the microchannel features
was then sealed irreversibly to a glass substrate after oxidization
in an oxygen plasma for .about.1 min. Channel dimensions we used in
this example were approximately 100 .mu.m wide and 50 .mu.m
deep.
[0294] The experiments described here used a simple single-channel
structure. This microchannel was interfaced to a polyethylene
tubing by first punching a smooth hole through the PDMS with a
sharp hole-puncher having the appropriate dimensions. Polyethylene
tubing having an outer diameter slightly greater the punched hole
was inserted into the hole, and the tubing formed a pressure seal
owing to the elastomeric nature of PDMS. The polyethylene tubing
was connected to a syringe needle having the appropriate size
(gauge), which was connected to a syringe. Controlled pressure for
driving fluid flow was accomplished with a high precision syringe
pump (CMA/100, Microinjection pump, Carnegei Medicin).
[0295] Patch clamp experiments were carried out in the whole-cell
configuration. The pipettes for whole-cell recording were
fabricated from thick-walled borosilicate glass capillaries having
an outer diameter of 1.5 mm and an inner diameter of 0.86 mm
(Harvard Apparatus LTD Edenbridge, Kent, UK). The diameters and the
resistances of the tips were .about.2.5 .mu.M and 5-15 M.OMEGA.,
respectively. The estimated series resistance was always <50
M.OMEGA. and holding potentials were corrected for voltage errors
due to series resistance. The patch clamp electrode solution
contained 100-mM KCl, 2-mM MgCl.sub.2, 1-mM CaCl.sub.2, 11-mM EGTA,
and 10-mM HEPES; pH was adjusted to 7.2 with KOH. All experiments
were performed at room temperature (18-22.degree. C.).
[0296] Signals were recorded with an Axopatch 200 A (Axon inc.
California, U.S.A) patch-clamp amplifier, at a holding potential of
-70 mV, and were digitized and stored on the computer hard drive
(sample frequency 10 kHz, filter frequency 200 Hz using a 8 pole
Bessel filter) and analyzed using a PC and Clampfit 8.1 software
(Axon inc.). The experimental chamber containing the microchannel
structure was mounted on an inverted microscope stage equipped with
40.times. and 10.times. objectives (Nikon, Japan). Mounted to the
microscope was a CCD camera (Hamamatsu) connected to a video for
recording of the scan rates, the sampling rate for the video was 25
Hz. This equipment together with micromanipulators (Narishigi,
Japan) was placed on a vibration-isolated table inside a Faraday
cage. The patch clamp amplifier, the Digidata board, filters, the
video and PCs, were kept outside the cage to minimize interference
from line frequency.
[0297] Adherent PC-12 cells were cultivated on circular cover slips
in Petrie dishes for 2-6 days (DMEM/F12 medium supplemented with
antibiotics and antimyocotin (0.2%), fetal calf serum (10%), and
L-glutamine). Before the patch clamp experiments, cells were washed
and detached in a HEPES-saline buffer, containing (in mM): 10
HEPES, 140 NaCl, 5 KCl, 1 CaCl.sub.2, 1 MgCl.sub.2, 10 D-glucose
(pH 7.4), and placed in the open buffer reservoir at the outlet of
the microchannel.
[0298] The strength of the seals was tested with cells that were
patched-clamped without entering into a whole-cell configuration. A
membrane holding potential of -70 mV was applied and the cell was
positioned 10 .mu.m away from the channel outlet. Different flow
rates, which varied between 0.3-21 mm/s, were applied while the
seal was continuously monitored. The patched seal was stable (no
shift in the current trace) for flow rates up to 6.7 mm/s, in this
particular experiment.
[0299] For the re-sensitization experiment, agonist was added to
the open reservoir where the cell was patched while buffer was
delivered from the syringe into the microchannel and exits the
microchannel into the open reservoir. The patch-clamped cell was
placed .about.10 .mu.m away from the outlet of the microchannel.
The reservoir in which the patch-clamped cell resides was filled
with 1 mM acetylcholine (agonists). Buffer was delivered by the
syringe pump into the microchannel and was continuously flown
through the microchannel at .about.3 mm/s.
[0300] No current was observed while the giga Ohm seal was stable
(5-20 Gohm) as the cell was moved, in a direction parallel to the
microchannel, from .about.10 .mu.m to .about.80 .mu.m from the
outlet of the microchannel. This fact means the patch-clamped cell
was superfused by the buffer exiting from the microchannel and thus
was not in contact with the agonists in the open reservoir. At
.about.80 .mu.m from the outlet of the microchannel, the patched
cell was scanned repeatedly at .about.100 .mu.m/s, in a direction
perpendicular to the microchannel, between the reservoir containing
agonists and the microchannel outlet (FIG. 20).
[0301] De-sensitization of the current response could be observed
after exposure to the agonist for longer periods of time (>5 s)
as a decrease of the mean whole-cell current. No de-sensitization
of the cells was seen for the shorter exposure times (<5 s) to
the agonist nor for repeatedly short exposures as long as the
patched cell was resensitized in agonist free buffer between each
exposure.
Example 3
Rapid Scanning of a Patch-Clamped Cell Across Interdigitated
Streams of Ligands and Buffer for HTS Applications
[0302] One preferred embodiment for implementing HTS using the
current invention is to scan a patch-clamped cell rapidly across
interdigitated streams of buffer and ligands, with each ligand
stream corresponding to a different drug. In these applications, as
discussed above, both the flow rate of the fluids exiting the
microchannels and the scan rate of the patch clamped cell are
important. FIGS. 21A-D show the response of patch-clamped whole
cells after being scanned across the outlets of a 7-channel
structure. The width of each channel is 100 .mu.m, the thickness is
50 .mu.m, and the interchannel spacing is 25 .mu.m. This 7-channel
structure is identical to that shown in FIG. 16B. The procedure
used for fabricating the microchannels and for patch clamping are
identical to that described in Example 2 (see above). The patch
clamped cell used was a PC-12 cell, which was placed between 10 to
20 micrometers away from the outlets of the microchannels. Channels
1, 3, 5 and 7 were filled with PBS buffer, while channels 2, 4 and
6 were filled with acetylcholine. The flow rate of the fluid
streams was 6.8 mm/s.
[0303] In FIGS. 21A-D, a patch-clamped cell was scanned across
interdigitated streams at four different scan rates: A, 0.61 mm/s;
B, 1.22 mm/s; C, 2 mm/s; and D, 4 mm/s. The difference in the scan
rate is reflected in the width of the whole cell current response
peaks, the wider the width, the longer the transit time and the
wider the peak width. In addition, for slow scan rates (e.g., FIG.
21A), the maximal response for each peak decreases as the
patch-clamped cell is scanned from one acetylcholine stream to the
next. This decrease in the peak response is caused by
desensitisation of the patch-clamped cell as a result of the slow
scan rate that led to a longer residence time for the cell in the
acetylcholine stream.
[0304] From FIG. 21A, it can seen the decrease in height from the
second to third peak is greater when compared to the decrease from
the first to second peak. This is consistent with the fact that the
longer residence time (i.e., larger peak width) of the
patch-clamped cell in the second stream causes more
desensitisation. As the scan rate increases (FIGS. 21C and 21D),
the residence time in the acetylcholine stream decreases and
desensitisation is no longer an issue. For fast scan rates (e.g.,
tens of ms) as shown, for example, in FIG. 21D, no desensitisation
can be detected. FIG. 22 shows the opposite scenario in which the
scan rate is slow (seconds), and desensitisation is pronounced as
the patch-clamped cell is scanned across the width of the
acetylcholine stream.
[0305] From these experiments, it is clear that controlling the
scan rate is critical for achieving optimal performance of the
system for HTS applications. Scanning rates can be controlled by
any of the mechanisms described above or by other methods known in
the art.
[0306] Data obtained by the system relating to the dynamics of
desensitisation and resensitization can be exploited to provide
useful information in elucidating ion-channel pharmacology,
kinetics and identity.
Example 4
Dose-Response Measurements by Rapid Scanning of a Patch-Clamped
Cell Across Interdigitated Streams of Buffer and Ligands Having
Different Concentrations
[0307] The channel structure and experimental setup used in Example
3 can be used to carry out dose-response measurements, in which the
concentrations of the ligands in each of the ligand streams differ
by predetermined amounts. FIG. 23 shows the result of one such
experiment, in which three different concentrations (1 .mu.M, 12
and 200 .mu.M) of nicotine were applied to a patch-clamped cell. In
this 7-channel structure, channels 1, 3, 5 and 7 were filled with
PBS buffer, whereas channels 2, 4, and 6 were filled with 1 .mu.M,
12 .mu.M, and 200 .mu.M nicotine, respectively. The flow rate used
was 3.24 mm/s and the cell-scanning speed was 250 .mu.m/s. The
patch-clamped cell was placed between 10 to 20 .mu.m away from the
outlet of the microchannel.
[0308] At 1-.mu.M concentration of nicotine, the whole-cell current
response was barely discernible in the patch-clamp trace. The
current peak for 12 .mu.M was detected with good signal-to-noise
ratio, and the peak that corresponds to 200 .mu.M was approximately
15 to 20 times that of the peak for 12-.mu.M. With these
measurements, a dose-response curve can be generated that provides
valuable information about drug action and ion-channel
pharmacology. It should be emphasized that a number of on-chip
techniques for gradient generation as well as off-chip methods for
preparing different concentrations of ligands can be used (see,
e.g., Dertinger, et al., 2001, Analytical Chemistry 73: 1240-1246).
In addition, the number of different concentrations used for
constructing dose-response curves will in most cases be greater
than that used in this example, and will depend on the required
concentration resolution and range desired for a particular
application.
[0309] Variations, modifications, and other implementations of what
is described herein will occur to those of ordinary skill in the
art without departing from the spirit and scope of the invention.
The publications, patents, applications and other references cited
herein are all incorporated by reference in their entirety
herein.
* * * * *
References