U.S. patent application number 15/835738 was filed with the patent office on 2019-01-24 for compartmentalised combinatorial chemistry by microfluidic control.
This patent application is currently assigned to President and Fellows of Harvard College. The applicant listed for this patent is Medical Research Council, President and Fellows of Harvard College. Invention is credited to Keunho Ahn, Jerome Bibette, Andrew David Griffiths, Darren Roy Link, David A. Weitz.
Application Number | 20190024261 15/835738 |
Document ID | / |
Family ID | 35447882 |
Filed Date | 2019-01-24 |
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United States Patent
Application |
20190024261 |
Kind Code |
A1 |
Griffiths; Andrew David ; et
al. |
January 24, 2019 |
COMPARTMENTALISED COMBINATORIAL CHEMISTRY BY MICROFLUIDIC
CONTROL
Abstract
The invention describes a method for the synthesis of compounds
comprising the steps of: (a) compartmentalizing two or more sets of
primary compounds into microcapsules; such that a proportion of the
microcapsules contains two or more compounds; and (b) forming
secondary compounds in the microcapsules by chemical reaction
between primary compounds from different sets; wherein one or both
of steps (a) and (b) is performed under microfluidic control;
preferably electronic microfluidic control. The invention further
allows for the identification of compounds which bind to a target
component of a biochemical system or modulate the activity of the
target, and which is co-compartmentalized into the
microcapsules.
Inventors: |
Griffiths; Andrew David;
(Strasbourg, FR) ; Weitz; David A.; (Cambridge,
MA) ; Link; Darren Roy; (Lexington, MA) ; Ahn;
Keunho; (Boston, MA) ; Bibette; Jerome;
(Paris, FR) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
President and Fellows of Harvard College
Medical Research Council |
Cambridge
London |
MA |
US
GB |
|
|
Assignee: |
President and Fellows of Harvard
College
Cambridge
MA
Medical Research Council
London
|
Family ID: |
35447882 |
Appl. No.: |
15/835738 |
Filed: |
December 8, 2017 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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11665099 |
Dec 15, 2008 |
9839890 |
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PCT/GB2005/003927 |
Oct 12, 2005 |
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15835738 |
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10962952 |
Oct 12, 2004 |
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11665099 |
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PCT/GB04/01352 |
Mar 31, 2004 |
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10962952 |
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Current U.S.
Class: |
1/1 |
Current CPC
Class: |
B01J 2219/00853
20130101; B01L 2400/084 20130101; C12N 15/1096 20130101; C40B 40/08
20130101; B82Y 30/00 20130101; B01F 5/0647 20130101; B01J 2219/0086
20130101; B01L 3/50273 20130101; B01L 2300/0867 20130101; B01L
3/502784 20130101; B01J 2219/00725 20130101; G01N 2035/1034
20130101; B01J 2219/00889 20130101; B82Y 10/00 20130101; B01L
2200/0605 20130101; B01J 2219/00722 20130101; C40B 40/06 20130101;
B01F 13/0071 20130101; B01J 2219/00743 20130101; B01L 3/5027
20130101; B01J 2219/00599 20130101; B01L 2400/0406 20130101; C07K
1/047 20130101; B01L 3/5025 20130101; B01J 2219/00497 20130101;
B01F 3/0807 20130101; B01J 19/0046 20130101; H05K 999/99 20130101;
B01L 3/502761 20130101; C40B 40/10 20130101; B01J 2219/005
20130101; C12Q 2600/16 20130101; B01L 2300/0864 20130101; B01F
5/0646 20130101; B01F 13/0076 20130101; B01L 2400/0487 20130101;
B01F 5/0655 20130101; B01J 13/025 20130101; B01J 2219/00596
20130101; B01L 3/502746 20130101; B01J 2219/00576 20130101; C40B
50/08 20130101; B01J 2219/00585 20130101; B01J 2219/00707 20130101;
B01L 2400/0415 20130101; B01L 2200/0673 20130101 |
International
Class: |
C40B 40/08 20060101
C40B040/08; B01J 13/02 20060101 B01J013/02; B01L 3/00 20060101
B01L003/00; C40B 40/10 20060101 C40B040/10 |
Goverment Interests
STATEMENT OF GOVERNMENT SUPPORT
[0002] This invention was made with government support under
DMR-0213805 and DMR-0243715 awarded by the National Science
Foundation. The government has certain rights in the invention.
Claims
1. A method for analyzing compounds, the method comprising: forming
a plurality of microcapsules, wherein each microcapsule comprises a
microbead and a cell, and wherein each microbead comprises one of a
plurality of compounds; performing a reaction within each
microcapsule, wherein the reaction involves the compound and a
molecule associated with the cell; pooling the plurality of
microcapsules into a common compartment; and identifying the
microbeads comprising a portion of the compounds that cause a
selectable change in a product of the reaction.
2. The method of claim 1, wherein each of the plurality of
microcapsules is surrounded by an immiscible fluid comprising a
surfactant.
3. The method of claim 1, wherein the plurality of microcapsules
are monodisperse.
4. The method of claim 1, wherein each of the plurality of
microcapsules comprises no more than one microbead.
5. The method of claim 1, wherein the plurality of compounds
comprise nucleic acids or proteins.
6. The method of claim 1, wherein the plurality of compounds are
labeled.
7. The method of claim 1, wherein each of the plurality of
compounds comprises a primer sequence for amplification.
8. The method of claim 1, wherein the reaction is an amplification
reaction.
9. The method of claim 1, wherein the reaction comprises a reverse
transcription reaction.
10. The method of claim 1, wherein the plurality of compounds
comprise primers for a polymerase chain reaction (PCR).
11. The method of claim 1, wherein reaction is performed in a fluid
channel.
12. The method of claim 1, wherein the molecule comprises a
gene.
13. The method of claim 12, further comprising expressing the gene
to form a gene product.
14. The method of claim 13, wherein the gene product is a protein
or a cDNA.
15. The method of claim 14, wherein the protein is an antibody.
16. The method of claim 15, wherein the protein is located within
the cell or outside of the cell.
17. The method of claim 1, wherein identifying comprises optically
identifying.
Description
RELATED APPLICATIONS
[0001] This application is a continuation of U.S. Ser. No.
11/665,099, filed Dec. 15, 2008, which is a 35 U.S.C. .sctn. 371
National Phase Application of PCT/GB2005/003927, filed Oct. 12,
2005, which is a continuation of U.S. Ser. No. 10/962,952, filed
Oct. 12, 2004, which is a continuation of PCT/GB2004/001352 filed
Mar. 31, 2004, each of which is incorporated herein by reference in
its entirety.
DESCRIPTION
[0003] The present invention relates to methods for use in the
synthesis and identification of molecules which bind to a target
component of a biochemical system or modulate the activity of a
target.
[0004] Over the past decade, high-throughput screening (HTS) of
compound libraries has become a cornerstone technology of
pharmaceutical research. Investment into HTS is substantial. A
current estimate is that biological screening and preclinical
pharmacological testing alone account for .about.14% of the total
research and development (R&D) expenditures of the
pharmaceutical industry (Handen, Summer 2002). HTS has seen
significant improvements in recent years, driven by a need to
reduce operating costs and increase the number of compounds and
targets that can be screened. Conventional 96-well plates have now
largely been replaced by 384-well, 1536-well and even 3456-well
formats. This, combined with commercially available plate-handling
robotics allows the screening of 100,000 assays per day, or more,
and significantly cuts costs per assay due to the miniaturisation
of the assays.
[0005] HTS is complemented by several other developments.
Combinatorial chemistry is a potent technology for creating large
numbers of structurally related compounds for HTS. Currently,
combinatorial synthesis mostly involves spatially resolved parallel
synthesis. The number of compounds that can be synthesised is
limited to hundreds or thousands but the compounds can be
synthesised on a scale of milligrams or tens of milligrams,
enabling full characterisation and even purification. Larger
libraries can be synthesised using split synthesis on beads to
generate one-bead-one compound libraries. This method is much less
widely adopted due to a series of limitations including: the need
for solid phase synthesis; difficulties characterising the final
products (due to the shear numbers and small scale); the small
amounts of compound on a bead being only sufficient for one or a
few assays; the difficulty in identifying the structure of a hit
compound, which often relies on tagging or encoding methods and
complicates both synthesis and analysis. Despite this split
synthesis and single bead analysis still has promise. Recently
there have been significant developments in miniaturised screening
and single bead analysis. For example, printing techniques allow
protein-binding assays to be performed on a slide containing 10,800
compound spots, each of 1 nl volume (Hergenrother et al., 2000).
Combichem has so far, however, generated only a limited number of
lead compounds. As of April 2000, only 10 compounds with a
combinatorial chemistry history had entered clinical development
and all but three of these are (oligo)nucleotides or peptides
(Adang and Hermkens, 2001). Indeed, despite enormous investments in
both HTS and combinatorial chemistry during the past decade the
number of new drugs introduced per year has remained constant at
best.
[0006] Dynamic combinatorial chemistry (DCC) can also be used to
create dynamic combinatorial libraries (DCLs) from a set of
reversibly interchanging components, however the sizes of libraries
created and screened to date are still fairly limited (<40,000)
(Ramstrom and Lehn, 2002).
[0007] Virtual screening (VS) (Lyne, 2002), in which large compound
bases are searched using computational approaches to identify a
subset of candidate molecules for testing may also be very useful
when integrated with HTS. However, there are to date few studies
that directly compare the performance of VS and HTS, and further
validation is required.
[0008] Microfluidic technology has been applied to high throughput
screening methods. For example, U.S. Pat. No. 6,508,988 describes
combinatorial synthesis systems which rely on microfluidic flow to
control the flow of reagents in a multichannel system. U.S. Pat.
No. 5,942,056, and continuations thereof, describes a microfluidic
test system for performing high throughput screening assays,
wherein test compounds can be flowed though a plurality of channels
to perform multiple reactions contemporaneously.
[0009] Despite all these developments, current screening throughput
is still far from adequate. Recent estimates of the number of
individual genes in the human genome (30,000) and the number of
unique chemical structures theoretically attainable using existing
chemistries suggests that an enormous number of assays would be
required to completely map the structure-activity space for all
potential therapeutic targets (Burbaum, 1998).
[0010] Hence, a method with the capability to both create and
screen vast numbers (>10.sup.10) of compounds quickly, using
reaction volumes of only a few femtolitres, and at very low cost
should be of enormous utility in the generation of novel drug
leads.
SUMMARY OF THE INVENTION
[0011] The present inventors have found that the powerful technique
of microfiuidic control of microcapsules, in particular the
electronic control of micro fluid based technology can be applied
to the compartmentalised microcapsule system described in Griffith
& Tawfik (1998) which is herein incorporated by reference. The
result is a novel method which is capable of creating and screening
vast quantities of compounds both quickly and efficiently.
[0012] Thus, the invention, in a first aspect, provides a method
for preparing a repertoire of compounds comprising the steps
of:
(a) compartmentalising two or more sets of primary compounds into
microcapsules; such that a proportion of the microcapsules contains
multiple copies of one or more compounds representative of each of
said sets, and wherein said one or more compounds represents a
subset of the set of primary compounds; and (b) forming secondary
compounds in the microcapsules by chemical reactions between
primary compounds from different sets; wherein either one or both
of steps (a) and (b) is performed under the microfiuidic control of
fluidic species.
[0013] A compound is "representative" of a set where is is member
of said set; advantageously, therefore, each microcapsule contains
compound(s) from each set. Although a microcapsule may contain more
than one different compound from each set, it contains only a
proportion of said set--i.e. a subset. The subset of a set
advantageously represents no more that 10% of the members of the
set; preferably, this figure is 9%, 8%, 7%, 6%, 5%, 4%, 3%, 2%, 1%
or less.
[0014] Most advantageously a microcapsule contains only a single
compound from each set of primary compounds.
[0015] The sets of primary compounds used in the method of the
invention can consist of any number of different compounds. At
least a first set comprises two or more compounds; but the other
set may be a single compound. Preferably, if a first set is a
single compound, at least one further set comprises a repertoire of
compounds. The larger this repertoire, the greater the number of
different secondary compounds that will be generated.
[0016] Preferably, at least one set of compounds comprises a
repertoire of different compounds. At least one set, however, may
consist of a single compound, such that secondary compounds are all
constructed based on or containing the single compound used in one
set. The greater the number of sets, and the greater the diversity
of each set, the greater the final diversity of the secondary
compounds generated.
[0017] Advantageously, in step (a) the number of different
compounds per compartment will be equivalent to the the number of
primary compounds forming the secondary compound in step (b).
[0018] In a second aspect, the invention provides a method for
identifying primary compounds which react together to form
secondary compounds capable of binding to or modulating the
activity of a target, comprising the steps of:
(a) compartmentalising two or more sets of primary compounds into
microcapsules; such that a proportion of the microcapsules contains
two or more compounds; (b) forming secondary compounds in the
microcapsules by chemical reactions between primary compounds from
different sets; and (c) identifying subsets of primary compounds
which react to form secondary compounds which bind to or modulate
the activity of the target; wherein one or more of steps (a), (b)
and (c) is performed under the micro fluidic control of fluidic
species.
[0019] In a third aspect, the invention provides a method for
synthesising compounds with enhanced ability to bind to or modulate
the activity of the target, comprising the steps of: (a)
compartmentalising into microcapsules subsets of primary compounds
identified in step (c) of the second aspect of the invention and,
optionally, compartmentalising additional sets of primary
compounds;
(b) forming secondary compounds in the microcapsules by chemical
reactions between primary compounds from different sets; and (c)
identifying subsets of primary compounds which react to form
secondary compounds which bind to or modulate the activity of the
target; wherein one or more of steps (a), (b) and (c) is performed
under the micro fluidic control of fluidic species.
[0020] Advantageously, steps (a) to (c) can be repeated, but after
the first cycle, step (a) comprises compartmentalising subsets of
primary compounds identified in step (c) into microcapsules and,
optionally, compartmentalising additional sets of compounds.
[0021] In a fourth aspect, the invention provides a method for
identifying individual compounds which bind to or modulate the
activity of the target, comprising the steps of:
(a) compartmentalising into microcapsules a primary compound
identified in step (c) of the second or third aspect of the
invention and additional sets of primary compounds; (b) forming
secondary compounds in the microcapsules by chemical reactions
between primary compounds from different sets; and (c) identifying
subsets of primary compounds which react to form secondary
compounds which bind to or modulate the activity of the target;
wherein one or more of steps (a), (b) and (c) is performed under
the microfluidic control of fluidic species.
[0022] If the secondary compound is formed by the chemical reaction
between more than two primary compounds it can be identified by
iteratively repeating steps (a) to (c), but after the first cycle,
step (c) comprises compartmentalising the primary compound
identified in step (c) of the second or third aspect of the
invention, a primary compound identified in step (c) of each of the
previous cycles (of the fourth aspect of the invention) and
additional sets of primary molecules.
[0023] Preferably, the desired activity is selected from the group
consisting of a binding activity and the modulation of the activity
of a target. Advantageously, the target is compartmentalised into
microcapsules together with the compounds.
[0024] Sets of compounds may be compartmentalised in different ways
to achieve encapsulation of multiple copies of two or more
compounds into microcapsules.
[0025] For example, small aliquots of an aqueous solution of each
compound can be deposited into an oil phase (advantageously
containing surfactants and/or other stabilising molecules) whilst
applying mechanical energy, thereby dispersing each compound into
multiple aqueous microcapsules, each of which contains (for the
most part) a single sort of compound but multiple copies thereof.
Advantageously, the compounds can be deposited into the oil phase
in the form of droplets generated using inkjet printing technology
(Calvert, 2001; de Gans et al., 2004), and more advantageously by
piezoelectric drop-on-demand (DOD) inkjet printing technology.
InkJet printing technology can be used to mix primary compounds
and, optionally, other reagents (e.g the target and reagents to
assay target activity) immediately prior to forming the emulsion.
Advantageously, multiple compounds can be mixed with multiple
targets in a combinatorial manner.
[0026] Thus, step (a) above can be modified such that it comprises
forming separate emulsion compartments containing two or more
compounds and mixing the emulsion compartments to form an
emulsified compound repertoire wherein a subset of the repertoire
is represented in multiple copies in any one microcapsule.
[0027] Moreover, compound libraries can be be compartmentalised in
highly monodisperse microcapsules produced using microfluidic
techniques. For example, aliquots of each compound can be
compartmentalised into one or more aqueous microcapsules (with less
than 1.5% polydispersity) in water-in-oil emulsions created by
droplet break off in a co-flowing stream of oil (Umbanhowar et al.,
2000). Advantageously, the aqueous microcapsules are then
transported by laminar-flow in a stream of oil in microfluidic
channels (Thorsen et al., 2001). The microcapsules containing
single compounds can, optionally, be split into two or more smaller
microcapsules using microfluidics (Link et al., 2004; Song et al.,
2003). Microcapsules containing primary compounds can be fused with
other microcapsules (Song et al., 2003) to form secondary
compounds.
[0028] Microcapsules containing compounds can also, optionally, be
fused with microcapsules containing a target. A single microcapsule
containing a target can, optionally, be split into two or more
smaller microcapsules which can subsequently be fused with
microcapsules containing different compounds, or compounds at
different concentrations. Advantageously, a compound and a target
can be mixed by microcapsule fusion prior to a second microcapsule
fusion which delivers the reagents necessary to assay the activity
of the target (e.g. the substrate for the target if the target is
an enzyme). This allows time for the compound to bind to the
target. The microcapsules can be analysed and, optionally, sorted
using micro fluidic devices (Fu et al., 2002).
[0029] In a further aspect, there is provided a method for
preparing a repertoire of compounds comprising the steps of:
(a) attaching two or more sets of primary compounds onto
microbeads; (b) compartmentalising the microbeads into
microcapsules such that a proportion of the microcapsules contains
two or more microbeads; (c) releasing at least one of the sets of
primary compounds from the microbeads; (d) forming secondary
compounds in the microcapsules by chemical reactions between
primary compounds from different sets; wherein one or more of steps
(a), (b), (c) and (d) is performed under the micro fluidic control
of fluidic species.
[0030] Advantageously, the compounds are cleavable from the beads.
Where more than two sets of compounds are used, all the sets with
the exception of one are cleavable; preferably, they are all
cleavable. The compounds may be attached to the microbeads by
photochemically cleavable linkers.
[0031] In a still further aspect, the invention provides a method
for identifying primary compounds which react together to form
secondary compounds capable of binding to or modulating the
activity of a target, comprising the steps of:
(a) attaching two or more sets of primary compounds onto
microbeads; (b) compartmentalising the microbeads into
microcapsules together with the target such that many compartments
contain two or more microbeads; (c) releasing the primary compounds
from the microbeads; (d) forming secondary compounds in the
microcapsules by chemical reactions between primary compounds from
different sets; and (e) identifying subsets of primary compounds
which react to form secondary compounds which bind to or modulate
the activity of the target; wherein one or more of steps (a), (b),
(c), (d) and (e) is performed under the microfluidic control of
fluidic species.
[0032] Advantageously, in step (b) the modal number of microbeads
per compartment will be equivalent to the number of primary
compounds forming the secondary compound in step (d).
[0033] Li a further aspect, the invention provides a method for
synthesising compounds with enhanced ability to bind to or modulate
the activity of the target, comprising the steps of:
(a) attaching onto microbeads subsets of primary compounds
identified in step (e) of the second aspect of the invention and,
optionally, attaching additional sets of primary compounds; (b)
compartmentalising the microbeads into microcapsules together with
the target such that many compartments contain two or more
microbeads; (c) releasing the primary compounds from the
microbeads; (d) forming secondary compounds in the microcapsules by
chemical reactions between primary compounds from different sets;
and (e) identifying subsets of primary compounds which react to
form secondary compounds which bind to or modulate the activity of
the target; wherein one or more of steps (a), (b), (c), (d) and (e)
is performed under the microfluidic control of fluidic species.
[0034] Advantageously, steps (a) to (e) can be repeated, but after
the first cycle, step (a) comprises attaching onto microbeads
subsets of primary compounds identified in step (e) and,
optionally, attaching additional sets of compounds.
[0035] In a further aspect, the invention provides a method for
identifying individual compounds which bind to or modulate the
activity of the target, comprising the steps of:
(a) attaching onto microbeads a primary compound identified in step
(e) of the second or third aspect of the invention and additional
sets of primary compounds; (b) compartmentalising the microbeads
into microcapsules together with the target such that many
compartments contain two or more microbeads; (c) releasing the
primary compounds from the microbeads; (d) forming secondary
compounds in the microcapsules by chemical reactions between
primary compounds from different sets; and (e) identifying subsets
of primary compounds which react to form secondary compounds which
bind to or modulate the activity of the target; wherein one or more
of steps (a), (b), (c), (d) and (e) is performed under the
microfluidic control of fluidic species.
[0036] If the secondary compound is formed by the chemical reaction
between more than two primary compounds it can be identified by
iteratively repeating steps (a) to (e), but after the first cycle,
step (a) comprises attaching onto microbeads the primary compound
identified in step (e) of the second or third aspect of the
invention, a primary compound identified in step (e) of each of the
previous cycles (of the fourth aspect of the invention) and
additional sets of primary molecules.
[0037] Preferably, the desired activity is selected from the group
consisting of a binding activity and the modulation of the activity
of a target. Advantageously, the target is compartmentalised into
microcapsules together with the microbeads.
[0038] According to a preferred implementation of the present
invention, the compounds may be screened according to an activity
of the compound or derivative thereof which makes the microcapsule
detectable as a whole. Accordingly, the invention provides a method
wherein a compound with the desired activity induces a change in
the microcapsule, or a modification of one or more molecules within
the microcapsule, which enables the microcapsule containing the
compound and, optionally, the microbead carrying it to be
identified. In this embodiment, therefore, the microcapsules are
either: (a) physically sorted from each other according to the
activity of the compound(s) contained therein, by for example,
placing an electric chrage on the microcapsule and `steering` the
microcapsule using an electric field, and the contents of the
sorted microcapsules analysed to determine the identity of the
compound(s) which they contain; or (b) analysed directly without
sorting to determine the identity of the compound(s) which the
microcapsules contain.
[0039] According to a preferred embodiment of the present
invention, the screening of compounds may be performed by, for
example:
(I) In a first embodiment, the microcapsules are screened according
to an activity of the compound or derivative thereof which makes
the microcapsule detectable as a whole.
[0040] Accordingly, the invention provides a method wherein a
compound with the desired activity induces a change in the
microcapsule, or a modification of one or more molecules within the
microcapsule, which enables the microcapsule containing the
compound and the microbead carrying it to be identified. hi this
embodiment, therefore, the microcapsules are either: (a) physically
sorted from each other according to the activity of the compound(s)
contained therein, the contents of the sorted microcapsules
optionally pooled into one or more common compartments, and the
microcapsule contents analysed to determine the identity of the
compound(s); or (b) analysed directly without sorting to determine
the identity of the compound(s) which the microcapsules contained.
Where the microcapsule contains microbeads, the microbeads can be
analysed to determine the compounds with which they are coated.
(II) In a second embodiment, microbeads are analysed following
pooling of the microcapsules into one or more common compartments.
In this embodiment, a compound having the desired activity modifies
the microbead which carried it (and which resides in the same
microcapsule) in such a way as to make it identifiable in a
subsequent step. The reactions are stopped and the microcapsules
are then broken so that all the contents of the individual
microcapsules are pooled. Modified microbeads are identified and
either: (a) physically sorted from each other according to the
activity of the compound(s) coated on the microbeads, and the
sorted microbeads analysed to determine the identity of the
compound(s) with which they are/were coated; or (b) analysed
directly without sorting to determine the identity of the
compound(s) with which the microbeads are/were coated. It is to be
understood, of course, that modification of the niicrobead may be
direct, in that it is caused by the direct action of the compound,
or indirect, in which a series of reactions, one or more of which
involve the compound having the desired activity, leads to
modification of the microbead. Advantageously, the target is bound
to the microbead and is a ligand and the compound within the
microcapsule binds, directly or indirectly, to said ligand to
enable the isolation of the microbead. In another configuration, a
substrate for the target is and is bound to the microbead, and the
activity of the compound within the microcapsule results, directly
or indirectly, in the conversion of said substrate into a product
which remains part of the microbead and enables its isolation.
Alternatively, the activity of the compound may prevent or inhibit
the conversion of said substrate into product. Moreover, the
product of the activity of the compound within the microcapsule can
result, directly or indirectly, in the generation of a product
which is subsequently complexed with the microbead and enables its
identification. (III) In a third embodiment, the microbeads are
analysed following pooling of the microcapsules into one or more
common compartments. In this embodiment, a compound with a desired
activity induces a change in the microcapsule containing the
compound and the microbead which carries it. This change, when
detected, triggers the modification of the microbead within the
compartment. The reactions are stopped and the microcapsules are
then broken so that all the contents of the individual
microcapsules are pooled. Modified microbeads are identified and
either: (a) physically sorted from each other according to the
activity of the compound(s) coated on the microbeads, and the
sorted microbeads analysed to determine the identity of the
compound(s) with which they are/were coated; or (b) analysed
directly without sorting to determine the identity of the
compound(s) with which the microbeads are/were coated.
[0041] The microcapsules or microbeads may be modified by the
action of the compound(s) such as to change their optical
properties and/or electrical charge properties. For example, the
modification of the microbead can enable it to be further modified
outside the microcapsule so as to induce a change in its optical
and/or electrical charge properties.
[0042] In another embodiment, the change in optical and/or
electrical charge properties of the microcapsules or microbeads is
due to binding of a compound with distinctive optical and/or
electrical charge properties respectively to the target.
[0043] Moreover, the change in optical and/or electrical charge
properties of the microcapsules or microbeads can be due to binding
of a target with distinctive optical and/or electrical charge
properties respectively by the compound.
[0044] The change in the optical and/or electrical charge
properties of the microcapsule may be due to modulation of the
activity of the target by the compound. The compound may activate
or inhibit the activity of the target. For example, if the target
is an enzyme, the substrate and the product of the reaction
catalysed by the target can have different optical and/or
electrical charge properties. Advantageously, the substrate and
product have different fluorescence properties. In the case where
the microcapsules contain microbeads, both the substrate and the
product can have similar optical and/or electrical charge
properties, but only the product of the reaction, and not the
substrate, binds to, or reacts with, the microbead, thereby
changing the optical and/or electrical charge properties of the
microbead.
[0045] The change in optical and/or electrical charge properties of
the microcapsules or microbeads can also be due to the different
optical and/or electrical charge properties of the target and the
product of the reaction being selected. Where both target and
product have similar optical and/or electrical charge properties,
only the product of the reaction being selected, and not the
target, binds to, or reacts with, the microbead, thereby changing
the optical and/or electrical charge properties of the
microcapsules or microbeads.
[0046] In a further configuration, further reagents specifically
bind to, or specifically react with, the product (and not the
substrate) attached to or contained in the microcapsule or
microbead, thereby altering the optical and/or electrical charge
properties of the microcapsule or microbead.
[0047] Advantageously, microbeads modified directly or indirectly
by the activity of the compound are further modified by Tyramide
Signal Amplification (TSA.TM.; NEN), resulting directly or
indirectly in a change in the optical properties of said
microcapsules or microbeads thereby enabling their separation.
[0048] It is to be understood that the detected change in the
compartment may be caused by the direct action of the compound, or
indirect action, in which a series of reactions, one or more of
which involve the compound having the desired activity leads to the
detected change.
[0049] Where the compounds are attached to beads, the density with
which compounds are coated onto the microbeads, combined with the
size of the microcapsule will determine the concentration of the
compound in the microcapsule. High compound coating densities and
small microcapsules will both give higher compound concentrations
which may be advantageous for the selection of molecules with a low
affinity for the target. Conversely, low compound coating densities
and large microcapsules will both give lower compound
concentrations which may be advantageous for the selection of
molecules with a high affinity for the target.
[0050] Preferably, microencapsulation is achieved by forming an
emulsion.
[0051] The microbead can be nonmagnetic, magnetic or
paramagnetic.
[0052] Repertoires of compounds can be encapsulated so as to have
multiple copies of a single compound in a microcapsule in different
ways. For example, thin tubes connected to the microfluidic device
can be dipped into reservoirs containing the desired compounds, and
capillary action can be used to draw the desired compound from the
reservoir into the microfluidic device. This method allows the
microfluidic device to be loaded with compounds prepared outside
the device.
[0053] Moreover, compound libraries can be be compartmentalised in
highly monodisperse microcapsules produced using microfluidic
techniques. For example, aliquots of each compound can be
compartmentalised into one or more aqueous microcapsules (with less
than 1.5% polydispersity) in water-in-oil emulsions created by
droplet break off in a co-flowing stream of oil (Umbanhowar et al.,
2000). Advantageously, the aqueous microcapsules are then
transported by laminar-flow in a stream of oil in microfluidic
channels (Thorsen et al., 2001). These microcapsules containing
single compounds can, optionally, be split into two or more smaller
microcapsules using microfluidics (Link et al., 2004; Song et al.,
2003). The microcapsules containing single compounds can,
optionally be fused with other microcapsules (Song et al., 2003)
containing a target. A single microcapsule containing a target can,
optionally, be split into two or more smaller microcapsules which
can subsequently be fused with microcapsules containing different
compounds, or compounds at different concentrations.
Advantageously, a compound and a target can be mixed by
microcapsule fusion prior to a second microcapsule fusion which
delivers the necessary to assay the activity of the target (e.g.
the substrate for the target if the target is an enzyme). This
allows time for the compound to bind to the target. The
microcapsules can be analysed and, optionally, sorted using
microfluidic devices (Fu et al., 2002).
[0054] Methods of controlling and manipulating of fluidic species
are also described, for example, in U.S. Provisional Patent
Application Ser. No. 60/498,091, filed Aug. 27, 2003, by Link, et.
al; U.S. Provisional Patent Application Ser. No. 60/392,195, filed
Jun. 28, 2002, by Stone, et. al; U.S. Provisional Patent
Application Ser. No. 60/424,042, filed Nov. 5, 2002, by Link, et
al; U.S. Pat. No. 5,512,131, issued Apr. 30, 1996 to Kumar, et al;
International Patent Publication WO 96/29629, published Jun. 26,
1996 by Whitesides, et al; U.S. Pat. No. 6,355,198, issued Mar. 12,
2002 to Kim, et al; International Patent Application Serial No.:
PCT/US01/16973, filed May 25, 2001 by Anderson, et al., published
as WO 01/89787 on Nov. 29, 2001; International Patent Application
Serial No. PCT/US03/20542, filed Jun. 30, 2003 by Stone, et al,
published as WO 2004/002627 on Jan. 8, 2004; International Patent
Application Serial No. PCT/US2004/010903, filed Apr. 9, 2004 by
Link, et al; and U.S. Provisional Patent Application Ser. No.
60/461,954, filed Apr. 10, 2003, by Link, et al; each of which is
incorporated herein by reference.
[0055] In various aspects of the invention, a fluidic system as
disclosed herein may include a droplet formation system, a droplet
fusing system, a droplet splitting system, a sensing system, a
controller, and/or a droplet sorting and/or separation system, or
any combination of these systems. Such systems and methods may be
positioned in any suitable order, depending on a particular
application, and in some cases, multiple systems of a given type
may be used, for example, two or more droplet formation systems,
two or more droplet separation systems, etc. As examples of
arrangements, systems of the invention can be arranged to form
droplets, to dilute fluids, to control the concentration of species
within droplets, to sort droplets to select those with a desired
concentration of species or entities (e.g., droplets each
containing one molecule of reactant), to fuse individual droplets
to cause reaction between species contained in the individual
droplets, to determine reaction(s) and/or rates of reaction(s) in
one or more droplets, etc. Many other arrangements can be practiced
in accordance with the invention.
[0056] One aspect of the invention relates to systems and methods
for producing droplets of a first liquid surrounded by a second
liquid2. The first and second liquids may be essentially immiscible
in many cases, i.e., immiscible on a time scale of interest (e.g.,
the time it takes a fluidic droplet to be transported through a
particular system or device). In certain cases, the droplets may
each be substantially the same shape or size, as further described
below. The first liquid may also contain other species, for
example, certain molecular species (e.g., as further discussed
below), cells, particles, etc.
[0057] In one set of embodiments, electric charge may be created on
a first liquid surrounded by a second liquid, which may cause the
first liquid to separate into individual droplets within the second
liquid, hi some embodiments, the first liquid and the second liquid
may be present in a channel, e.g., a microfluidic channel, or other
constricted space that facilitates application of an electric field
to the first liquid (which may be "AC" or alternating current, "DC"
or direct current etc.), for example, by limiting movement of the
first liquid with respect to the second liquid. Thus, the first
liquid can be present as a series of individual charged and/or
electrically inducible droplets within the second liquid, hi one
embodiment, the electric force exerted on the fluidic droplet may
be large enough to cause the droplet to move within the second
liquid. In some cases, the electric force exerted on the fluidic
droplet may be used to direct a desired motion of the droplet
within the second liquid, for example, to or within a channel or a
microfluidic channel.
[0058] Electric charge may be created in the first liquid within
the second liquid using any suitable technique, for example, by
placing the first liquid within an electric field (which may be AC,
DC, etc.), and/or causing a reaction to occur that causes the first
liquid to have an electric charge, for example, a chemical
reaction, an ionic reaction, a photocatalyzed reaction, etc. In one
embodiment, the first liquid is an electrical conductor. As used
herein, a "conductor" is a material having a conductivity of at
least about the conductivity of 18 megohm (MOhm or M.OMEGA.) water.
The second liquid surrounding the first liquid may have a
conductivity less than that of the first liquid. For instance, the
second liquid may be an insulator, relative to the first liquid, or
at least a "leaky insulator," i.e., the second liquid is able to at
least partially electrically insulate the first liquid for at least
a short period of time. Those of ordinary skill in the art will be
able to identify the conductivity of fluids, m one non-limiting
embodiment, the first liquid may be substantially hydrophilic, and
the second liquid surrounding the first liquid may be substantially
hydrophobic. In an alternative embodiment, the microcapsules or
microbeads are analysed by detection of a change in their
fluorescence. For example, microbeads can be analysed by flow
cytometry and, optionally sorted using a fluorescence activated
cell sorter (FACS). The different fluorescence properties of the
target and the product can be due to fluorescence resonance energy
transfer (FRET).
[0059] hi a further embodiment, the internal environment of the
microcapsules can be modified by the addition of one or more
reagents to the continuous phase of the emulsion. This allows
reagents to be diffused in to the microcapsules during the
reaction, if necessary.
[0060] The invention moreover relates to a method according to the
preceding aspects, further comprising the step of isolating the
secondary compound produced by reaction of the primary compounds
and optionally further comprising the step of manufacturing one or
more secondary compounds.
[0061] The invention also provides for a product when identified
according to the invention. As used in this context, a "product"
may refer to any compound, selectable according to the
invention.
[0062] Further embodiments of the invention are described in the
detailed description below and in the accompanying claims.
BRIEF DESCRIPTION OF THE FIGURES
[0063] FIGS. 1A and 1B illustrate the splitting of droplets in
accordance with one embodiment of the invention;
[0064] FIGS. 2A and 2B illustrate an apparatus in accordance with
an embodiment of the invention, before the application of an
electric field thereto;
[0065] FIGS. 3 A and 3B illustrate the apparatus of FIGS. 2A and 2B
after the application of an electric field thereto;
[0066] FIGS. 4A and 4B illustrate the apparatus of FIGS. 2A and 2B
after the application of a reversed electric field thereto;
[0067] FIG. 5 is a schematic diagram of droplet splitting, in
accordance with one embodiment of the invention;
[0068] FIGS. 6A and 6B are schematic diagrams of additional
embodiments of the invention;
[0069] FIGS. 7a and 7b are schematic diagrams of the formation of
micro fluidic droplets in accordance with the present
invention;
[0070] FIGS. 8a-f illustrate the splitting of droplets in
accordance with the invention;
[0071] FIGS. 9a-d illustrate the induction of dipoles in droplets
in accordance with the invention;
[0072] FIGS. 10a-d illustrate the sorting of microcasules by
altering the flow of carrier fluid in a microfluidic system;
[0073] FIGS. 11a-c illustrate the use of pressure changes in the
microfluidic system to control the direction of flow of
droplets;
[0074] FIGS. 12a-j illustrate flow patterns for droplets in
microfluidic systems in accordance with the invention;
[0075] FIGS. 13a-d illustrate the use of oppositely charged
droplets in the invention;
[0076] FIGS. 14a-c are illustrations of the formation and
maintenance of microfluidic droplets using three immiscible
liquids;
[0077] FIG. 15. Compound screening using microdroplets in a
microfluidic system. Panel A: schematic of the core system. Panel
B: process block diagram showing the modules in the core system.
Microdroplets containing a target enzyme are fused with
microdroplets each of which contain a different compound from a
compound library. After allowing time for the compounds to bind to
the target enzyme each microdroplet is fused with another
microdroplet containing a fluorogenic enzyme substrate. The rate of
the enzymatic reaction is determined by measuring the fluorescence
of each microdroplet, ideally at multiple points (corresponding to
different times).
[0078] Microdroplets containing compounds with desired activities
can, if required, be sorted and collected.
[0079] FIG. 16. Examples of microdroplet formation and manipulation
using microfluidics. Panel A: microdroplets can be created at up to
10.sup.4 sec.sup.-1 by hydrodynamic-focussing (top two panels) and
show <1.5% polydispersity (bottom panel). Panel B: microdroplets
can be split symmetrically or asymmetrically. Panel C:
microdroplets carrying positive (+q) and negative (-q) electrical
charges fuse spontaneously. Panel D: charged microdroplets can also
be steered using an applied electrical field (E).
[0080] FIG. 17. Examples of PTP1B inhibitors. Compounds with a
to-difluoromethylene phosphonate moiety (e.g. 2) have significantly
more potency than those with a single moiety (e.g. 1).
[0081] FIG. 18. Screening PTP1B inhibitors using
microencapsulation. Polystyrene beads with surface carboxylate
groups, died with orange or red fluorochromes(Fulton et al., 1997),
are derivatised with a phosphopeptide PTP1B substrate, and either
PTP1B inhibitors or non-inhibitory compounds, attached via a
cleavable linker (1). After mixing the beads, single beads and
target enzyme (PTP1B) are colocalised in a microcompartment by
forming a water-in-oil emulsion using a microfluidic device (2).
The compound is released (photochemically) (3). Inhibitors reduce
the amount of substrate converted to product (dephosphorylated
peptide) (4). The enzyme reaction is stopped and the emulsion is
broken (5). After labelling with green fluorescent anti-substrate
antibodies, beads are analysed by 3-colour flow cytometry to
simultaneously determine extent of inhibition and the compound on
the beads (6). Compound libraries can be coupled to optically
tagged beads (see below) and rapidly decoded by flow cytometry (at
up to 100,000 beads s.sup.-1). Hit compounds are re-synthesised for
further characterisation (7) or elaborated and rescreened in a
process of synthetic evolution (8).
[0082] FIG. 19. Synthesising PTP1B inhibitors in an emulsion. Two
types of beads are created, differentially labelled with orange and
red fluorochromes, and derivatised with two types of molecule, A or
B (neither, one, or both of which contain a difluoromethylene
phosphonate moiety), attached via a reversible connection (a Schiff
base). Beads are emulsified using a microfluidic device to give, on
average, two beads per compartment. The molecules, A & B, are
released from the beads in the compartment and react to form a new
molecule, A-B, (in solution). If A-B is a PTP1B inhibitor the PTP1B
substrate also on the beads is not dephosphorylated and these beads
identified by flow cytometry as FIG. 18.
[0083] FIG. 20. Small molecule evolution using four-component
reactions. Four sets of 25 beads are created, each derivatised with
one of 25 variants of molecules A, B, C or D, emulsified to give,
on average, 4 beads per compartment, the compounds released to
synthesise a large combinatorial repertoire (4.times.10.sup.5) in
situ and screened as FIG. 18. Low affinity inhibitors will be
`recombined` by re-screening mixtures of beads carrying moieties
identified in inhibitors. Beads carrying a moiety found in
inhibitors (e.g. A.sub.10) can also be mixed with complete sets of
beads coated with B, C and D and screened. If a moiety (say
B.sub.8) is then identified as a component of an inhibitor. beads
coated with A10 and B8 can be mixed with complete sets of beads C
and D and the process repeated. This process of `mutation` also
results in deconvolution. After fixing three of the four moieties
in active compounds, deconvolution can be completed using multiplex
bead analysis as above. Compounds can be re-diversified or
`mutated` using bead sets carrying variant, exploded sets of the
molecules used in the original libraries.
[0084] FIG. 21. Compartmentalisation of small molecules in
water-in-fluorocarbon emulsions. Water-in-perfluorooctyl bromide
emulsions were made containing texas red (1 mM) and calcein (1 mM)
in the aqueous phase by homogenisation as described in example 6
The two emulsions were mixed by vortexing and imaged by
epifluorescence microscopy after 24 hours. No exchange of texas-red
(red fluorescence) and calcein (green fluorescence) between
microdroplets could be observed.
[0085] FIG. 22. Primary compounds for the synthesis of PTP1B
inhibitors. An amine (A) and an aldehyde (B) with difluoromethylene
phosphonate moieties. Amine A reacts with aldehyde B in the aqueous
microcapsules of a water-in-oil emulsion to generate the imine C
which is a potent PTP1B inhibitor. C can be reduced in situ using
cyanoborohydride to generate the stable amine D.
[0086] FIG. 23 Charged droplet generation. (A), Oil and water
streams converge at a 30 micron orifice. A voltage V applied to
indium-tin-oxide (ITO) electrodes on the glass produces an electric
field E to capacitively charges the aqueous-oil interface. Drop
size is independent of charge at low field strengths but decreases
at higher fields, as shown in the photomicrographs, [(B) V=O, (C)
V=400, (D) V=600 and (E) V=800] at higher fields. (F) Droplet size
as a function of voltage showing the crossover between
flow-dominated and field-dominated snap-off for three different
flow rates of the continuous phase oil (Qc=80 nL/s, 110 nL/s, and
140 nL/s). The infusion rate of the water is constant Qd=20
nL/s.}
[0087] FIG. 24 Coalescing drops. (A) Drops having opposite sign of
electrostatic charge can be generated by applying a voltage across
the two aqueous streams. (B) In the absence of the field the
frequency and timing of drop formation at the two nozzles are
independent and each nozzle produces a different size drop at a
different frequency; infusion rates are the same at both nozzles.
After the confluence of the two streams, drops from the upper and
lower nozzles stay in their respective halves of the stream and due
to surfactant there are no coalescence events even in the case of
large slugs that fill the channel width. (C) With an applied
voltage of 200V across the 500 micron separation of the nozzles,
the drops simultaneously break-off from the two nozzles and are
identical; simultaneous drop formation can be achieved for unequal
infusion rates of the aqueous streams even up to a factor of two
difference in volumes. (D) The fraction of the drops that encounter
each other and coalesce increases linearly above a critical field
when a surfactant, sorbiton-monooleate 3% is present.
[0088] FIG. 25: (A) Droplets carrying a pH sensitive dye coalesce
with droplets of a different pH fluid. (B) Chaotic advection
rapidly mixes the two fluids through a combination of translation
and rotation as the droplets pass around corners.
[0089] FIG. 26: Diffusion limited and rapid mixing strategies. (A)
Drops meet and coalesce along the direction of E and then move off
in a perpendicular direction, as sketched the counter rotating
vortices after coalescence do not mix the two fluid parts as each
vortex contains a single material. (B) As the drops approach each
other the increasing field causes there interfaces to deform and
(C) a bridge to jump out connecting the drops, to create (D) in the
case of 20 nm silica particles and MgCl_2 a sharp interface where
the particles begin to gel. (E) A typical unmixed droplet with
particles in one hemisphere. (F) To achieve fast mixing, droplets
are brought together in the direction perpendicular to the electric
field and move off in the direction parallel to the direction they
merged along. Counter rotating vortexes are then created where each
vortex is composed of half of the contentes from each of the
premerger-droplets. (G) Shows a pH sensitive dye in the lower drop
and a different pH fluid in the upper droplet. (H) After merger the
droplets are split by a sharp line. (I) A uniform intensity
indicating that mixing has been occurred is achieved in the droplet
after it translates one diameter, typically this takes 1 to 2
MS.
[0090] FIG. 27 Time delay reaction module. (A) Droplets of
perfluorodecaline alternate with aqueous droplets in a hexadecane
carrier fluid. The `single-file` ordering of the droplets provides
for long delays with essentially no deviation in the precise
spacing of aqueous droplets or droplet order. (B) Increasing the
width and height of the channel to create a `large cross-sectional
area` channel provides for extremely long time delays from minutes
to hours. The exact ordering and spacing between the droplets is
not maintained in this type of delay line.
[0091] FIG. 28 Recharging neutral drops. (A) Schematic to recharge
neutral drops by breaking them in the presence of an electric
field. Uncharged drops (q=0) are polarized in an electric field
(Es.noteq.0), and provided Es is sufficiently large, as shown in
the photomicrograph of (B), they break into two oppositely charged
daughter drops in the extensional flow at a bifurcation. The
enlargement of the dashed rectangle, shown in (C), reveals that the
charged drops are stretched in the electric field E.sub.s but
return to spherical on contacting the electrodes indicated by
dashed vertical lines.
[0092] FIG. 29 Detection module. One or more lasers are coupled to
an optical fibre that is used to excite the fluorescence in each
droplet as it passes over the fibre. The fluorescence is collected
by the same fibre and dichroic beam splitters separate off specific
wavelengths of the fluorescent light and the intensity of the
fluorescence is measured with a photomultiplier tube (PMT) after
the light passes through a band-pass filter.
[0093] FIG. 30 Manipulating charged drops. In (A) charged drops
alternately enter the right and left channels when there is no
field applied (E.sub.s=0). The sketch in (B) shows the layout for
using an electric field E.sub.s to select the channel charged drops
will enter at a bifurcation. When an electric field is applied to
the right (C), the drops enter the right branch at the bifurcation;
they enter the left branch when the field is reversed (D). After
the bifurcation, the distance between drops is reduced to half what
it was before indicating the oil stream is evenly divided. The
inset of (D) shows the deformation in the shape of a highly charged
drop in an electric field.
DETAILED DESCRIPTION OF THE INVENTION
Definitions
[0094] The term "microcapsule" is used herein in accordance with
the meaning normally assigned thereto in the art and further
described hereinbelow. In essence, however, a microcapsule is an
artificial compartment whose delimiting borders restrict the
exchange of the components of the molecular mechanisms described
herein which allow the identification of the molecule with the
desired activity. The delimiting borders preferably completely
enclose the contents of the microcapsule. Preferably, the
microcapsules used in the method of the present invention will be
capable of being produced in very large numbers, and thereby to
compartmentalise a library of compounds. Optionally, the compounds
can be attached to microbeads. The microcapsules used herein allow
mixing and sorting to be performed thereon, in order to facilitate
the high throughput potential of the methods of the invention.
Microcapsules according to the present invention can be a droplet
of one fluid in a different fluid, where the confined components
are soluble in the droplet but not in the carrier fluid, and in
another embodiment there is another material defining a wall, such
as a membrane (e.g. in the context of lipid vesicles; liposomes) or
non-ionic surfactant vesicles, or those with rigid, nonpermeable
membranes, or semipermeable membranes. Arrays of liquid droplets on
solid surfaces, multiwell plates and "plugs" in microfluidic
systems, that is fluid droplets that are not completely surrounded
by a second fluid as defined herein, are not microcapsules as
defined herein.
[0095] A "proportion" of the microcapsules, which is defined as
comprising two or more compounds, or two or microbeads, is any
fraction of the microcapsules in question, including all of said
microcapsules. Advantageously, it is at least 25% thereof,
preferably 50%, and more preferably 60%, 70%, 80%, 90% or 95%.
[0096] The term "microbead" is used herein in accordance with the
meaning normally assigned thereto in the art and further described
hereinbelow. Microbeads, are also known by those skilled in the art
as microspheres, latex particles, beads, or minibeads, are
available in diameters from 20 run to 1 mm and can be made from a
variety of materials including silica and a variety of polymers,
copolymers and terpolymers. Highly uniform derivatised and
non-derivatised nonmagnetic and paramagnetic microparticles (beads)
are commercially available from many sources (e.g. Sigma, Bangs
Laboratories, Luminex and Molecular Probes) (Fornusek and Vetvicka,
1986).
[0097] Microbeads can be "compartmentalised" in accordance with the
present invention by distribution into microcapsules. For example,
in a preferred aspect the microbeads can be placed in a water/oil
mixture and emulsified to form a water-in-oil emulsion comprising
microcapsules according to the invention. The concentration of the
microbeads can be adjusted to control the number of microbeads,
which on average, appear in each microcapsule. Advantageously, the
concentration of the microbeads can be adjusted such that, on
average a single microbead appears in only 10-20% of the
microcapsules, thus assuring that there are very few microcapsules
with more than one microbead.
[0098] The term "compound" is used herein in accordance with the
meaning normally assigned thereto in the art. The term compound is
used in its broadest sense i.e. a substance comprising two or more
elements in fixed proportions, including molecules and
supramolecular complexes. This definition includes small molecules
(typically <500 Daltons) which make up the majority of
pharmaceuticals. However, the definition also includes larger
molecules, including polymers, for example polypeptides, nucleic
acids and carbohydrates, and supramolecular complexes thereof.
[0099] The term "primary compound" is used herein to indicate a
compound which is compartmentalised in a microcapsule or coupled to
a bead.
[0100] The term "secondary compound" is used herein to indicate a
compound which is formed by the reaction between two or more
primary compounds in a microcapsule, optionally after the release
of at least one of the primary molecules from a microbead.
Advantageously, all primary molecules are released from the
microbeads. The secondary compound may be the result of a covalent
or non-covalent reaction between the primary compounds.
[0101] The term "scaffold" is used herein in accordance with the
meaning normally assigned thereto in the art. That is to say a core
portion of a molecule common to all members of a combinatorial
library (Maclean et al., 1999). Secondary compounds may optionally
comprise scaffolds.
[0102] A "repertoire" of compounds is a group of diverse compounds,
which may also be referred to as a library of compounds.
Repertoires of compounds may be generated by any means known in the
art, including combinatorial chemistry, compound evolution, or
purchased from commercial sources such as Sigma Aldrich, Discovery
Partners International, Maybridge and Tripos. A repertoire
advantageously comprises at least 10.sup.2, 10.sup.3, 10.sup.4,
10.sup.5, 10.sup.6, 10.sup.7, 10.sup.8, 10.sup.9, 10.sup.10,
10.sup.11 or more different compounds, which may be related or
unrelated in structure or function.
[0103] A "set" of compounds may be a repertoire of compounds or any
part of a repertoire, including a single compound species. The
invention envisages the use of two or more sets of compounds, which
are reacted together. The sets may be derived from a single
repertoire, or a plurality of different repertoires.
[0104] Compounds can be "released" from a microbead by cleavage of
a linker which effects the attachment of the compound to the
microbead. Release of the compounds from the microbead allows the
compounds to interact more freely with other contents of the
microcapsule, and to be involved in reactions therein and
optionally to become combined with other reagents to form new
compounds, complexes, molecules or supramolecular complexes.
Cleavage of linkers can be performed by any means, with means such
as photochemical cleavage which can be effected from without the
microcapsule being preferred. Photochemically cleavable linkers are
known in the art (see for example (Gordon and Balasubramanian,
1999)) and further described below.
[0105] As used herein, the "target" is any compound, molecule, or
supramolecular complex. Typical targets include targets of medical
significance, including drug targets such as receptors, for example
G protein coupled receptors and hormone receptors; transcription
factors, protein kinases and phosphatases involved in signalling
pathways; gene products specific to microorganisms, such as
components of cell walls, replicases and other enzymes;
industrially relevant targets, such as enzymes used in the food
industry, reagents intended for research or production purposes,
and the like.
[0106] An "activity", as referred to herein in connection with the
modulation of an activity of a target, can be any activity of the
target or an activity of a molecule which is influenced by the
target, which is modulatable directly or indirectly by a compound
or compounds as assayed herein. The activity of the target may be
any measurable biological or chemical activity, including binding
activity, an enzymatic activity, an activating or inhibitory
activity on a third enzyme or other molecule, the ability to cause
disease or influence metabolism or other functions, and the like.
Activation and inhibition, as referred to herein, denote the
increase or decrease of a desired activity 1.5 fold, 2 fold, 3
fold, 4 fold, 5 fold, 10 fold, 100 fold or more. Where the
modulation is inactivation, the inactivation can be substantially
complete inactivation. The desired activity may moreover be purely
a binding activity, which may or may not involve the modulation of
the activity of the target bound to.
[0107] A compound defined herein as "low molecular weight" or a
"small molecule" is a molecule commonly referred to in the
pharmaceutical arts as a "small molecule". Such compounds are
smaller than polypeptides and other, large molecular complexes and
can be easily administered to and assimilated by patients and other
subjects. Small molecule drugs can advantageously be formulated for
oral administration or intramuscular injection. For example, a
small molecule may have a molecular weight of up to 2000 Dalton;
preferably up to 1000 Dalton; advantageously between 250 and 750
Dalton; and more preferably less than 500 Dalton.
[0108] A "selectable change" is any change which can be measured
and acted upon to identify or isolate the compound which causes it.
The selection may take place at the level of the microcapsule, the
microbead, or the compound itself, optionally when complexed with
another reagent. A particularly advantageous embodiment is optical
detection, in which the selectable change is a change in optical
properties, which can be detected and acted upon for instance in a
FACS device to separate microcapsules or microbeads displaying the
desired change.
[0109] As used herein, a `change in optical properties` refers to
any change in absorption or emission of electromagnetic radiation,
including changes in absorbance, luminescence, phosphorescence or
fluorescence. All such properties are included in the term
"optical".
[0110] Microcapsules or microbeads can be identified and,
optionally, sorted, for example, by luminescence, fluorescence or
phosphorescence activated sorting. In a preferred embodiment, flow
cytometry is employed to identify and, optionally, sort
microcapsules or microbeads. A variety of optical properties can be
used for analysis and to trigger sorting, including light
scattering (Kerker, 1983) and fluorescence polarisation (Rolland et
al., 1985). In a highly preferred embodiment microcapsules or
microbeads are analysed and, optionally, sorted using a
fluorescence activated cell sorter (FACS) (Norman, 1980; Mackenzie
and Pinder, 1986).
[0111] The compounds in microcapsules or on beads can be identified
using a variety of techniques familiar to those skilled in the art,
including mass spectroscopy, chemical tagging or optical
tagging.
[0112] As used herein, "or" is understood to mean "inclusively or,"
i.e., the inclusion of at least one, but including more than one,
of a number or list of elements. In contrast, the term "exclusively
or" refers to the inclusion of exactly one element of a number or
list of elements.
[0113] The indefinite articles "a" and "an," as used herein in the
specification and in the claims, should be understood to mean "at
least one."
[0114] The term "about," as used herein in reference to a numerical
parameter (for example, a physical, chemical, electrical, or
biological property), will be understood by those of ordinary skill
in the art to be an approximation of a numerical value, the exact
value of which may be subject to errors such as those resulting
from measurement errors of the numerical parameter, uncertainties
resulting from the variability and/or reproducibility of the
numerical parameter (for example, in separate experiments), and the
like.
[0115] As used herein, a "cell" is given its ordinary meaning as
used in biology. The cell may be any cell or cell type. For
example, the cell may be a bacterium or other single-cell organism,
a plant cell, or an animal cell. If the cell is a single-cell
organism, then the cell may be, for example, a protozoan, a
trypanosome, an amoeba, a yeast cell, algae, etc. If the cell is an
animal cell, the cell may be, for example, an invertebrate cell
(e.g., a cell from a fruit fly), a fish cell (e.g., a zebrafish
cell), an amphibian cell (e.g., a frog cell), a reptile cell, a
bird cell, or a mammalian cell such as a primate cell, a bovine
cell, a horse cell, a porcine cell, a goat cell, a dog cell, a cat
cell, or a cell from a rodent such as a rat or a mouse. If the cell
is from a multicellular organism, the cell may be from any part of
the organism. For instance, if the cell is from an animal, the cell
may be a cardiac cell, a fibroblast, a keratinocyte, a heptaocyte,
a chondracyte, a neural cell, a osteocyte, a muscle cell, a blood
cell, an endothelial cell, an immune cell (e.g., a T-cell, a
B-cell, a macrophage, a neutrophil, a basophil, a mast cell, an
eosinophil), a stem cell, etc. hi some cases, the cell may be a
genetically engineered cell. In certain embodiments, the cell may
be a Chinese hamster ovarian ("CHO") cell or a 3T3 cell.
[0116] "Microfluidic," as used herein, refers to a device,
apparatus or system including at least one fluid channel having a
cross-sectional dimension of less than 1 mm, and a ratio of length
to largest cross-sectional dimension of at least 3:1. A
"microfluidic channel," as used herein, is a channel meeting these
criteria.
[0117] Accordingly the term `microfluidic control` (of a
system/method) as described herein refers to a method/system which
comprises the use of device or apparatus including at least one
fluid channel having a cross-sectional dimension of less than 1 mm,
and a ratio of length to largest cross-sectional dimension of at
least 3:1.
[0118] Electronic microfluidic control (of a method/system) as
referred to herein refers to a microfluidic method/system in which
one or more steps of the method/system involves the production of
an electronic charge on at least a proportion of the microcapsules
used in the microfulidic method/system.
[0119] The "cross-sectional dimension" of the channel is measured
perpendicular to the direction of fluid flow. Most fluid channels
in components of the invention have maximum cross-sectional
dimensions less than 2 mm, and in some cases, less than 1 mm. In
one set of embodiments, all fluid channels containing embodiments
of the invention are microfluidic or have a largest cross sectional
dimension of no more than 2 mm or 1 mm. In another embodiment, the
fluid channels may be formed in part by a single component (e.g. an
etched substrate or molded unit). Of course, larger channels,
tubes, chambers, reservoirs, etc. can be used to store fluids in
bulk and to deliver fluids to components of the invention. In one
set of embodiments, the maximum cross-sectional dimension of the
channel(s) containing embodiments of the invention are less than
500 microns, less than 200 microns, less than 100 microns, less
than 50 microns, or less than 25 microns.
[0120] A "channel," as used herein, means a feature on or in an
article (substrate) that at least partially directs the flow of a
fluid. The channel can have any cross-sectional shape (circular,
oval, triangular, irregular, square or rectangular, or the like)
and can be covered or uncovered. In embodiments where it is
completely covered, at least one portion of the channel can have a
cross-section that is completely enclosed, or the entire channel
may be completely enclosed along its entire length with the
exception of its inlet(s) and outlet(s). A channel may also have an
aspect ratio (length to average cross sectional dimension) of at
least 2:1, more typically at least 3:1, 5:1, or 10:1 or more. An
open channel generally will include characteristics that facilitate
control over fluid transport, e.g., structural characteristics (an
elongated indentation) and/or physical or chemical characteristics
(hydrophobicity vs. hydrophilicity) or other characteristics that
can exert a force (e.g., a containing force) on a fluid. The fluid
within the channel may partially or completely fill the channel. In
some cases where an open channel is used, the fluid may be held
within the channel, for example, using surface tension (i.e., a
concave or convex meniscus).
[0121] The channel may be of any size, for example, having a
largest dimension perpendicular to fluid flow of less than about 5
mm or 2 mm, or less than about 1 mm, or less than about 500
microns, less than about 200 microns, less than about 100 microns,
less than about 60 microns, less than about 50 microns, less than
about 40 microns, less than about 30 microns, less than about 25
microns, less than about 10 microns, less than about 3 microns,
less than about 1 micron, less than about 300 nm, less than about
100 nm, less than about 30 nm, or less than about 10 nm. In some
cases the dimensions of the channel may be chosen such that fluid
is able to freely flow through the article or substrate. The
dimensions of the channel may also be chosen, for example, to allow
a certain volumetric or linear flowrate of fluid in the channel. Of
course, the number of channels and the shape of the channels can be
varied by any method known to those of ordinary skill in the art.
In some cases, more than one channel or capillary may be used. For
example, two or more channels may be used, where they are
positioned inside each other, positioned adjacent to each other,
positioned to intersect with each other, etc.
[0122] As used herein, "integral" means that portions of components
are joined in such a way that they cannot be separated from each
other without cutting or breaking the components from each
other.
[0123] A "droplet," as used herein is an isolated portion of a
first fluid that is completely surrounded by a second fluid. It is
to be noted that a droplet is not necessarily spherical, but may
assume other shapes as well, for example, depending on the external
environment. In one embodiment, the droplet has a minimum
cross-sectional dimension that is substantially equal to the
largest dimension of the channel perpendicular to fluid flow in
which the droplet is located.
[0124] The "average diameter" of a population of droplets is the
arithmetic average of the diameters of the droplets. Those of
ordinary skill in the art will be able to determine the average
diameter of a population of droplets, for example, using laser
light scattering or other known techniques. The diameter of a
droplet, in a non-spherical droplet, is the mathematically-defined
average diameter of the droplet, integrated across the entire
surface. As non-limiting examples, the average diameter of a
droplet may be less than about 1 mm, less than about 500
micrometers, less than about 200 micrometers, less than about 100
micrometers, less than about 75 micrometers, less than about 50
micrometers, less than about 25 micrometers, less than about 10
micrometers, or less than about 5 micrometers. The average diameter
of the droplet may also be at least about 1 micrometer, at least
about 2 micrometers, at least about 3 micrometers, at least about 5
micrometers, at least about 10 micrometers, at least about 15
micrometers, or at least about 20 micrometers in certain cases.
[0125] As used herein, a "fluid" is given its ordinary meaning,
i.e., a liquid or a gas. Preferably a fluid is a liquid. The fluid
may have any suitable viscosity that permits flow. If two or more
fluids are present, each fluid may be independently selected among
essentially any fluids (liquids, gases, and the like) by those of
ordinary skill in the art, by considering the relationship between
the fluids. The fluids may each be miscible or immiscible. For
example, two fluids can be selected to be immiscible within the
time frame of formation of a stream of fluids, or within the time
frame of reaction or interaction. Where the portions remain liquid
for a significant period of time then the fluids should be
significantly immiscible. Where, after contact and/or formation,
the dispersed portions are quickly hardened by polymerization or
the like, the fluids need not be as immiscible. Those of ordinary
skill in the art can select suitable miscible or immiscible fluids,
using contact angle measurements or the like, to carry out the
techniques of the invention.
[0126] As used herein, a first entity is "surrounded" by a second
entity if a closed loop can be drawn around the first entity
through only the second entity. A first entity is "completely
surrounded" if closed loops going through only the second entity
can be drawn around the first entity regardless of direction. In
one aspect, the first entity is a particle. In yet another aspect
of the invention, the entities can both be fluids. For example, a
hydrophilic liquid may be suspended in a hydrophobic liquid, a
hydrophobic liquid may be suspended in a hydrophilic liquid, a gas
bubble may be suspended in a liquid, etc. Typically, a hydrophobic
liquid and a hydrophilic liquid are substantially immiscible with
respect to each other, where the hydrophilic liquid has a greater
affinity to water than does the hydrophobic liquid. Examples of
hydrophilic liquids include, but are not limited to, water and
other aqueous solutions comprising water, such as cell or
biological media, ethanol, salt solutions, etc. Examples of
hydrophobic liquids include, but are not limited to, oils such as
hydrocarbons, silicon oils, fluorocarbon oils, organic solvents
etc.
[0127] The term "determining," as used herein, generally refers to
the analysis or measurement of a species, for example,
quantitatively or qualitatively, or the detection of the presence
or absence of the species. "Determining" may also refer to the
analysis or measurement of an interaction between two or more
species, for example, quantitatively or qualitatively, or by
detecting the presence or absence of the interaction. Example
techniques include, but are not limited to, spectroscopy such as
infrared, absorption, fluorescence, UV/visible, FTIR ("Fourier
Transform Infrared Spectroscopy"), or Raman; gravimetric
techniques; ellipsometry; piezoelectric measurements; immunoassays;
electrochemical measurements; optical measurements such as optical
density measurements; circular dichroism; light scattering
measurements such as quasielectric light scattering; polarimetry;
refractometry; or turbidity measurements.
General Techniques
[0128] Unless defined otherwise, all technical and scientific terms
used herein have the same meaning as commonly understood by one of
ordinary skill in the art (e.g., in cell culture, molecular
genetics, nucleic acid chemistry, hybridisation techniques and
biochemistry).
[0129] Standard techniques are used for molecular, genetic and
biochemical methods (see generally, Sambrook et al., Molecular
Cloning: A Laboratory Manual, 2d ed. (1989) Cold Spring Harbor
Laboratory Press, Cold Spring Harbor, N.Y. and Ausubel et al.,
Short Protocols in Molecular Biology (1999) 4th Ed, John Wiley
& Sons, Inc. which are incorporated herein by reference) and
chemical methods. In addition Harlow & Lane, A Laboratory
Manual Cold Spring Harbor, N. Y, is referred to for standard
Immunological Techniques.
(A) General Description
[0130] The microcapsules of the present invention require
appropriate physical properties to allow the working of the
invention.
[0131] First, to ensure that the compounds and the target may not
diffuse between microcapsules, the contents of each microcapsule
must be isolated from the contents of the surrounding
microcapsules, so that there is no or little exchange of compounds
and target between the microcapsules over the timescale of the
experiment.
[0132] Second, the method of the present invention requires that
there are only a limited number of beads per microcapsule. This
ensures that the compounds and the target will be isolated from
other beads.
[0133] Third, the formation and the composition of the
microcapsules must not abolish the activity of the target.
[0134] Consequently, any microencapsulation system used must fulfil
these three requirements. The appropriate system(s) may vary
depending on the precise nature of the requirements in each
application of the invention, as will be apparent to the skilled
person.
[0135] A wide variety of microencapsulation procedures are
available (see Benita, 1996) and may be used to create the
microcapsules used in accordance with the present invention.
Indeed, more than 200 microencapsulation methods have been
identified in the literature (Finch, 1993).
[0136] These include membrane enveloped aqueous vesicles such as
lipid vesicles (liposomes) (New, 1990) and non-ionic surfactant
vesicles (van Hal et al., 1996). These are closed-membranous
capsules of single or multiple bilayers of non-covalently assembled
molecules, with each bilayer separated from its neighbour by an
aqueous compartment. In the case of liposomes the membrane is
composed of lipid molecules; these are usually phospholipids but
sterols such as cholesterol may also be incorporated into the
membranes (New, 1990). A variety of enzyme-catalysed biochemical
reactions, including RNA and DNA polymerisation, can be performed
within liposomes (Chakrabarti et al., 1994; Oberholzer et al.,
1995a; Oberholzer et al., 1995b; Walde et al., 1994; Wick &
Luisi, 1996).
[0137] With a membrane-enveloped vesicle system much of the aqueous
phase is outside the vesicles and is therefore
non-compartmentalised. This continuous, aqueous phase should be
removed or the biological systems in it inhibited or destroyed in
order that the reactions are limited to the microcapsules (Luisi et
al., 1987).
[0138] Enzyme-catalysed biochemical reactions have also been
demonstrated in microcapsules generated by a variety of other
methods. Many enzymes are active in reverse micellar solutions (Bru
& Walde, 1991; Bru & Walde, 1993; Creagh et al., 1993;
Haber et al., 1993; Kumar et al., 1989; Luisi & B., 1987; Mao
& Walde, 1991; Mao et al., 1992; Perez et al., 1992; Walde et
al., 1994; Walde et al., 1993; Walde et al., 1988) such as the
AOT-isooctane-water system (Menger & Yamada, 1979).
[0139] Microcapsules can also be generated by interfacial
polymerisation and interfacial complexation (Whateley, 1996).
Microcapsules of this sort can have rigid, nonpermeable membranes,
or semipermeable membranes. Semipermeable microcapsules bordered by
cellulose nitrate membranes, polyamide membranes and
lipid-polyamide membranes can all support biochemical reactions,
including multienzyme systems (Chang, 1987; Chang, 1992; Lim,
1984). Alginate/polylysine microcapsules (Lim & Sun, 1980),
which can be formed under very mild conditions, have also proven to
be very biocompatible, providing, for example, an effective method
of encapsulating living cells and tissues (Chang, 1992; Sun et al.,
1992).
[0140] Non-membranous microencapsulation systems based on phase
partitioning of an aqueous environment in a colloidal system, such
as an emulsion, may also be used.
[0141] Preferably, the microcapsules of the present invention are
formed from emulsions; heterogeneous systems of two immiscible
liquid phases with one of the phases dispersed in the other as
droplets of microscopic or colloidal size (Becher, 1957; Sherman,
1968; Lissant, 1974; Lissant, 1984).
[0142] Emulsions may be produced from any suitable combination of
immiscible liquids.
[0143] Preferably the emulsion of the present invention has water
(containing the biochemical components) as the phase present in the
form of finely divided droplets (the disperse, internal or
discontinuous phase) and a hydrophobic, immiscible liquid (an oil`)
as the matrix in which these droplets are suspended (the
nondisperse, continuous or external phase). Such emulsions are
termed water-in-oil` (W/O). This has the advantage that the entire
aqueous phase containing the biochemical components is
compartmentalised in discreet droplets (the internal phase). The
external phase, being a hydrophobic oil, generally contains none of
the biochemical components and hence is inert.
[0144] The emulsion may be stabilised by addition of one or more
surface-active agents (surfactants). These surfactants are termed
emulsifying agents and act at the water/oil interface to prevent
(or at least delay) separation of the phases. Many oils and many
emulsifiers can be used for the generation of water-in-oil
emulsions; a recent compilation listed over 16,000 surfactants,
many of which are used as emulsifying agents (Ash and Ash, 1993).
Suitable oils include light white mineral oil and decane. Suitable
surfactants include: non-ionic surfactants (Schick, 1966) such as
sorbitan monooleate (Span.TM.80; ICI), sorbitan monostearate
(Span.TM.60; ICI), polyoxyethylenesorbitan monooleate (Tween.TM.
80; ICI), and octylphenoxyethoxyethanol (Triton X-100); ionic
surfactants such as sodium cholate and sodium taurocholate and
sodium deoxycholate; chemically inert silicone-based surfactants
such as polysiloxane-polycetyl-polyethylene glycol copolymer (Cetyl
Dimethicone Copolyol) (e.g. AbilTMEM90; Goldschmidt); and
cholesterol.
[0145] Emulsions with a fluorocarbon (or perfluorocarbon)
continuous phase (Krafft et al., 2003; Riess, 2002) may be
particularly advantageous. For example, stable
water-in-perfluorooctyl bromide and water-in-perfluorooctylethane
emulsions can be formed using F-alkyl dimorpholinophosphates as
surfactants (Sadtler et al., 1996). Non-fluorinated compounds are
essentially insoluble in fluorocarbons and perfluorocarbons
(Curran, 1998; Hildebrand and Cochran, 1949; Hudlicky, 1992; Scott,
1948; Studer et al., 1997) and small drug-like molecules (typically
<500 Da and Log P<5) (Lipinski et al., 2001) are
compartmentalised very effectively in the aqueous microcapsules of
water-in-fluorocarbon and water-in-perfluorocarbon emulsions--with
little or no exchange between microcapsules.
[0146] Advantageously, compounds can be compartmentalised in
microcapsules comprising non-aqueous (organic) solvents.
Non-fluorinated organic solvents are essentially insoluble and
immiscible with fluorocarbons and perfiuorocarbons (Curran, 1998;
Hildebrand and Cochran, 1949; Hudlicky, 1992; Scott, 1948; Studer
et al., 1997) allowing the formation of emulsions with a
fluorocarbon (or perfluorocarbon) continuous phase and a
discontinous phase formed from a non-aqueous solvent such as
dichloromethane, chloroform, carbon tetrachloride, toluene,
tetrahydrofuran, diethyl ether, and ethanol. The ability to form
secondary compounds in microcapsules comprising non-aqueous
solvents greatly expands the repertoire of chemical reactions that
can be performed and secondary molecules that can be synthesised
therein. Most of synthetic organic chemistry is carried out in
organic solvents including dichloromethane, chloroform, carbon
tetrachloride, toluene, tetrahydrofuran, diethyl ether, and
ethanol. Organic molecules dissolve better in organic solvents.
Electrostatic interactions are enhanced in organic solvents (due to
the low dielectric constant), whereas they can be solvated and made
less reactive in aqueous solvents. For example, much of
contemporary organic chemistry involves reactions relating to
carbonyl chemistry, including the use of metal enolates. Likewise
for a growing number of other organometallic interactions. These
reactions are often carried out under an inert atmosphere in
anhydrous solvents (otherwise the reagents would be quenched by
water). There are also a large number of reactions which use
palladium catalysis including the Suzuki reaction and the Heck
reaction.
[0147] Creation of an emulsion generally requires the application
of mechanical energy to force the phases together. There are a
variety of ways of doing this which utilise a variety of mechanical
devices, including stirrers (such as magnetic stir-bars, propeller
and turbine stirrers, paddle devices and whisks), homogenisers
(including rotor-stator homogenisers, high-pressure valve
homogenisers and jet homogenisers), colloid mills, ultrasound and
`membrane emulsification` devices (Becher, 1957; Dickinson,
1994).
[0148] Complicated biochemical processes, notably gene
transcription and translation are also active in aqueous
microcapsules formed in water-in-oil emulsions. This has enabled
compartmentalisation in water-in-oil emulsions to be used for the
selection of genes, which are transcribed and translated in
emulsion microcapsules and selected by the binding or catalytic
activities of the proteins they encode (Doi and Yanagawa, 1999;
Griffiths and Tawfik, 2003; Lee et al., 2002; Sepp et al., 2002;
Tawfik and Griffiths, 1998). This was possible because the aqueous
microcapsules formed in the emulsion were generally stable with
little if any exchange of nucleic acids, proteins, or the products
of enzyme catalysed reactions between microcapsules.
[0149] The technology exists to create emulsions with volumes all
the way up to industrial scales of thousands of litres (Becher,
1957; Sherman, 1968; Lissant, 1974; Lissant, 1984).
[0150] The preferred microcapsule size will vary depending upon the
precise requirements of any individual screening process that is to
be performed according to the present invention. In all cases,
there will be an optimal balance between the size of the compound
library and the sensitivities of the assays to determine the
identity of the compound and target activity.
[0151] The size of emulsion microcapsules may be varied simply by
tailoring the emulsion conditions used to form the emulsion
according to requirements of the screening system. The larger the
microcapsule size, the larger is the volume that will be required
to encapsulate a given compound library, since the ultimately
limiting factor will be the size of the microcapsule and thus the
number of microcapsules possible per unit volume.
[0152] Water-in-oil emulsions can be re-emulsified to create
water-in-oil-in water double emulsions with an external
(continuous) aqueous phase. These double emulsions can be analysed
and, optionally, sorted using a flow cytometer (Bernath et al.,
2004).
[0153] Highly monodisperse microcapsules can be produced using
microfiuidic techniques. For example, water-in-oil emulsions with
less than 1.5% polydispersity can be generated by droplet break off
in a co-flowing stream of oil (Umbanhowar et al., 2000).
Microfiuidic systems can also be used for laminar-flow of aqueous
microdroplets dispersed in a stream of oil in microfiuidic channels
(Thorsen et al., 2001). This allows the construction of
microfiuidic devices for flow analysis and, optionally, flow
sorting of microdroplets (Fu et al., 2002).
[0154] Advantageously, highly monodisperse microcapsules can be
formed using using systems and methods for the electronic control
of fluidic species. [One aspect of the invention relates to systems
and methods for producing droplets of fluid surrounded by a liquid.
The fluid and the liquid may be essentially immiscible in many
cases, i.e., immiscible on a time scale of interest (e.g., the time
it takes a fluidic droplet to be transported through a particular
system or device). In certain cases, the droplets may each be
substantially the same shape or size, as further described below.
The fluid may also contain other species, for example, certain
molecular species (e.g., as further discussed below), cells,
particles, etc.
[0155] In one set of embodiments, electric charge may be created on
a fluid surrounded by a liquid, which may cause the fluid to
separate into individual droplets within the liquid. In some
embodiments, the fluid and the liquid may be present in a channel,
e.g., a microfluidic channel, or other constricted space that
facilitates application of an electric field to the fluid (which
may be "AC" or alternating current, "DC" or direct current etc.),
for example, by limiting movement of the fluid with respect to the
liquid. Thus, the fluid can be present as a series of individual
charged and/or electrically inducible droplets within the liquid.
In one embodiment, the electric force exerted on the fluidic
droplet may be large enough to cause the droplet to move within the
liquid. In some cases, the electric force exerted on the fluidic
droplet may be used to direct a desired motion of the droplet
within the liquid, for example, to or within a channel or a
microfluidic channel (e.g., as further described herein), etc. As
one example, in apparatus 5 in FIG. 3A, droplets 15 created by
fluid source 10 can be electrically charged using an electric filed
created by electric field generator 20.
[0156] Electric charge may be created in the fluid within the
liquid using any suitable technique, for example, by placing the
fluid within an electric field (which may be AC, DC, etc.), and/or
causing a reaction to occur that causes the fluid to have an
electric charge, for example, a chemical reaction, an ionic
reaction, a photocatalyzed reaction, etc. In one embodiment, the
fluid is an electrical conductor. As used herein, a "conductor" is
a material having a conductivity of at least about the conductivity
of 18 megohm (MOhm or M.OMEGA.) water. The liquid surrounding the
fluid may have a conductivity less than that of the fluid. For
instance, the liquid may be an insulator, relative to the fluid, or
at least a
[0157] "leaky insulator," i.e., the liquid is able to at least
partially electrically insulate the fluid for at least a short
period of time. Those of ordinary skill in the art will be able to
identify the conductivity of fluids. In one non-limiting
embodiment, the fluid may be substantially hydrophilic, and the
liquid surrounding the fluid may be substantially hydrophobic.
[0158] In some embodiments, the charge created on the fluid (for
example, on a series of fluidic droplets) may be at least about
10.sup.-22 C/micrometer.sup.3. In certain cases, the charge may be
at least about 10.sup.-21 C/micrometer.sup.3, and in other cases,
the charge may be at least about 10.sup.-20 C/micrometer.sup.3, at
least about 10.sup.-19 C/micrometer.sup.3, at least about
10.sup.-18 C/micrometer.sup.3, at least about 10.sup.-17
C/micrometer.sup.3, at least about 10.sup.-16 C/micrometer.sup.3,
at least about 10-15 C/micrometer.sup.3, at least about 10.sup.-14
C/micrometer.sup.3, at least about 10.sup.-13 C/micrometer.sup.3,
at least about 10.sup.-12 C/micrometer.sup.3, at least about
10.sup.-11 C/micrometer.sup.3, at least about 10.sup.-10
C/micrometer.sup.3, or at least about 10.sup.-9 C/micrometer.sup.3
or more. In certain embodiments, the charge created on the fluid
may be at least about 10.sup.-21 C/micrometer2, and in some cases,
the charge may be at least about 10.sup.-20 C/micrometer2, at least
about 10.sup.-19 C/micrometer2, at least about 10.sup.-18
C/micrometer2, at least about 10.sup.-17 C/micrometer2, at least
about 10.sup.-16 C/micrometer2, at least about 10.sup.-15
C/micrometer2, at least about 10.sup.-14 C/micrometer2, or at least
about 10'' 13 C/micrometer2 or more, hi other embodiments, the
charge may be at least about 10.sup.-14 C/droplet, and, in some
cases, at least about 10.sup.-13 C/droplet, in other cases at least
about 10.sup.-12 C/droplet, in other cases at least about
10.sup.-11 C/droplet, in other cases at least about 10.sup.-10
C/droplet, or in still other cases at least about 10.sup.-9
C/droplet.
[0159] The electric field, in some embodiments, is generated from
an electric field generator, i.e., a device or system able to
create an electric field that can be applied to the fluid. The
electric field generator may produce an AC field (i.e., one that
varies periodically with respect to time, for example,
sinusoidally, sawtooth, square, etc.), a DC field (i.e., one that
is constant with respect to time), a pulsed field, etc. The
electric field generator may be constructed and arranged to create
an electric field within a fluid contained within a channel or a
microfluidic channel. The electric field generator may be integral
to or separate from the fluidic system containing the channel or
microfluidic channel, according to some embodiments. As used
herein, "integral" means that portions of the components integral
to each other are joined in such a way that the components cannot
be manually separated from each other without cutting or breaking
at least one of the components.
[0160] Techniques for producing a suitable electric field (which
may be AC, DC, etc.) are known to those of ordinary skill in the
art. For example, in one embodiment, an electric field is produced
by applying voltage across a pair of electrodes, which may be
positioned on or embedded within the fluidic system (for example,
within a substrate defining the channel or microfluidic channel),
and/or positioned proximate the fluid such that at least a portion
of the electric field interacts with the fluid. The electrodes can
be fashioned from any suitable electrode material or materials
known to those of ordinary skill in the art, including, but not
limited to, silver, gold, copper, carbon, platinum, copper,
tungsten, tin, cadmium, nickel, indium tin oxide ("ITO"), etc., as
well as combinations thereof. In some cases, transparent or
substantially transparent electrodes can be used. In certain
embodiments, the electric field generator can be constructed and
arranged (e.g., positioned) to create an electric field applicable
to the fluid of at least about 0.01 V/micrometer, and, in some
cases, at least about 0.03 V/micrometer, at least about 0.05
V/micrometer, at least about 0.08 V/micrometer, at least about 0.1
V/micrometer, at least about 0.3 V/micrometer, at least about 0.5
V/micrometer, at least about 0.7 V/micrometer, at least about 1
V/micrometer, at least about 1.2 V/micrometer, at least about 1.4
V/micrometer, at least about 1.6 V/micrometer, or at least about 2
V/micrometer. In some embodiments, even higher electric field
intensities may be used, for example, at least about 2
V/micrometer, at least about 3 V/micrometer, at least about 5
V/micrometer, at least about 7 V/micrometer, or at least about 10
V/micrometer or more.
[0161] In some embodiments, an electric field may be applied to
fluidic droplets to cause the droplets to experience an electric
force. The electric force exerted on the fluidic droplets may be,
in some cases, at least about 10.sup.-16 N/micrometer.sup.3. In
certain cases, the electric force exerted on the fluidic droplets
may be greater, e.g., at least about 10.sup.-15 N/micrometer.sup.3,
at least about 10.sup.-14 N/micrometer.sup.3, at least about
10.sup.-13 N/micrometer.sup.3, at least about 10.sup.-12
N/micrometer.sup.3, at least about 10.sup.-11 N/micrometer.sup.3,
at least about 10.sup.-10 N/micrometer.sup.3, at least about
10.sup.-9 N/micrometer.sup.3, at least about 10.sup.-8
N/micrometer.sup.3, or at least about 10.sup.-7 N/micrometer.sup.3
or more. In other embodiments, the electric force exerted on the
fluidic droplets, relative to the surface area of the fluid, may be
at least about 10.sup.-15 N/micrometer.sup.2, and in some cases, at
least about 10.sup.-14 N/micrometer.sup.2, at least about
10.sup.-13 N/micrometer.sup.2, at least about 10.sup.-12
N/micrometer.sup.2, at least about 10.sup.-11 N/micrometer.sup.2,
at least about 10.sup.-10 N/micrometer.sup.2, at least about
10.sup.-9 N/micrometer.sup.2, at least about 10.sup.-8
N/micrometer.sup.2, at least about 10.sup.-7 N/micrometer.sup.2, or
at least about 10.sup.-6 N/micrometer.sup.2 or more. In yet other
embodiments, the electric force exerted on the fiuidic droplets may
be at least about 10.sup.-9N, at least about 10.sup.-8N, at least
about 10.sup.-7 N, at least about 10.sup.-6 N, at least about
10.sup.-5 N, or at least about 10.sup.-4 N or more in some
cases.
[0162] In some embodiments of the invention, systems and methods
are provided for at least partially neutralizing an electric charge
present on a fiuidic droplet, for example, a fiuidic droplet having
an electric charge, as described above. For example, to at least
partially neutralize the electric charge, the fiuidic droplet may
be passed through an electric field and/or brought near an
electrode, e.g., using techniques such as those described
herein.
[0163] Upon exiting of the fiuidic droplet from the electric field
(i.e., such that the electric field no longer has a strength able
to substantially affect the fluidic droplet), and/or other
elimination of the electric field, the fluidic droplet may become
electrically neutralized, and/or have a reduced electric
charge.
[0164] In another set of embodiments, droplets of fluid can be
created from a fluid surrounded by a liquid within a channel by
altering the channel dimensions in a manner that is able to induce
the fluid to form individual droplets. The channel may, for
example, be a channel that expands relative to the direction of
flow, e.g., such that the fluid does not adhere to the channel
walls and forms individual droplets instead, or a channel that
narrows relative to the direction of flow, e.g., such that the
fluid is forced to coalesce into individual droplets. One example
is shown in FIG. 7A, where channel 510 includes a flowing fluid 500
(flowing downwards), surrounded by liquid 505. Channel 510 narrows
at location 501, causing fluid 500 to form a series of individual
fiuidic droplets 515. In other embodiments, internal obstructions
may also be used to cause droplet formation to occur. For instance,
baffles, ridges, posts, or the like may be used to disrupt liquid
flow in a manner that causes the fluid to coalesce into fiuidic
droplets.
[0165] In some cases, the channel dimensions may be altered with
respect to time (for example, mechanically or electromechanically,
pneumatically, etc.) in such a manner as to cause the formation of
individual fluidic droplets to occur. For example, the channel may
be mechanically contracted ("squeezed") to cause droplet formation,
or a fluid stream may be mechanically disrupted to cause droplet
formation, for example, through the use of moving baffles, rotating
blades, or the like. As a non-limiting example, in FIG. 7B, fluid
500 flows through channel 510 in a downward direction. Fluid 500 is
surrounded by liquid 505. Piezoelectric devices 520 positioned near
or integral to channel 510 may then mechanically constrict or
"squeeze" channel 510, causing fluid 500 to break up into
individual fluidic droplets 515.
[0166] In yet another set of embodiments, individual fluidic
droplets can be created and maintained in a system comprising three
essentially mutually immiscible fluids (i.e., immiscible on a time
scale of interest), where one fluid is a liquid carrier, and the
second fluid and the third fluid alternate as individual fluidic
droplets within the liquid carrier. In such a system, surfactants
are not necessarily required to ensure separation of the fluidic
droplets of the second and third fluids. As an example, with
reference to FIG. 14A, within channel 700, a first fluid 701 and a
second fluid 702 are each carried within liquid carrier 705. First
fluid 701 and second fluid 702 alternate as a series of
alternating, individual droplets, each carried by liquid carrier
705 within channel 700. As the first fluid, the second fluid, and
the liquid carrier are all essentially mutually immiscible, any two
of the fluids (or all three fluids) can come into contact without
causing droplet coalescence to occur. A photomicrograph of an
example of such a system is shown in FIG. 14B, illustrating first
fluid 701 and second fluid 702, present as individual, alternating
droplets, each contained within liquid carrier 705.
[0167] One example of a system involving three essentially mutually
immiscible fluids is a silicone oil, a mineral oil, and an aqueous
solution (i.e., water, or water containing one or more other
species that are dissolved and/or suspended therein, for example, a
salt solution, a saline solution, a suspension of water containing
particles or cells, or the like).
[0168] Another example of a system is a silicone oil, a
fluorocarbon oil, and an aqueous solution.
[0169] Yet another example of a system is a hydrocarbon oil (e.g.,
hexadecane), a fluorocarbon oil, and an aqueous solution. In these
examples, any of these fluids may be used as the liquid
carrier.
[0170] Non-limiting examples of suitable fluorocarbon oils include
octadecafluorodecahydronaphthalene:
##STR00001##
or 1-(1,2,2,3,3,4,4,5,5,6,6,-undecafluorocyclohexytyethanol:
##STR00002##
[0171] A non-limiting example of such a system is illustrated in
FIG. 14B. In this figure, fluidic network 710 includes a channel
containing liquid carrier 705, and first fluid 701 and second fluid
702. Liquid carrier 705 is introduced into fluidic network 710
through inlet 725, while first fluid 701 is introduced through
inlet 721, and second fluid 702 is introduced through inlet 722.
Channel 716 within fluidic network 710 contains liquid carrier 715
introduced from inlet 725. Initially, first fluid 701 is introduced
into liquid carrier 705, forming fluidic droplets therein. Next,
second fluid 702 is introduced into liquid 705, forming fluidic
droplets therein that are interspersed with the fluidic droplets
containing first fluid 701. Thus, upon reaching channel 717, liquid
carrier 705 contains a first set of fluidic droplets containing
first fluid 701, interspersed with a second set of fluidic droplets
containing second fluid 702. In the embodiment illustrated, channel
706 optionally comprises a series of bends, which may allow mixing
to occur within each of the fluidic droplets, as further discussed
below. However, it should be noted that in this embodiment, since
first fluid 701 and second fluid 702 are essentially immiscible,
significant fusion and/or mixing of the droplets containing first
fluid 701 with the droplets containing second fluid 702 is not
generally expected.
[0172] Other examples of the production of droplets of fluid
surrounded by a liquid are described in International Patent
Application Serial No. PCT/US2004/010903, filed Apr. 9, 2004 by
Link, et al. and International Patent Application Serial No.
PCTYUS03/20542, filed Jun. 30, 2003 by Stone, et al, published as
WO 2004/002627 on Jan. 8, 2004, each incorporated herein by
reference.
[0173] hi some embodiments, the fluidic droplets may each be
substantially the same shape and/or size. The shape and/or size can
be determined, for example, by measuring the average diameter or
other characteristic dimension of the droplets. The term
"determining," as used herein, generally refers to the analysis or
measurement of a species, for example, quantitatively or
qualitatively, and/or the detection of the presence or absence of
the species. "Determining" may also refer to the analysis or
measurement of an interaction between two or more species, for
example, quantitatively or qualitatively, or by detecting the
presence or absence of the interaction. Examples of suitable
techniques include, but are not limited to, spectroscopy such as
infrared, absorption, fluorescence, UV/visible, FTIR ("Fourier
Transform Infrared Spectroscopy"), or Raman; gravimetric
techniques; ellipsometry; piezoelectric measurements; immunoassays;
electrochemical measurements; optical measurements such as optical
density measurements; circular dichroism; light scattering
measurements such as quasielectric light scattering; polarimetry;
refractometry; or turbidity measurements.
[0174] The "average diameter" of a plurality or series of droplets
is the arithmetic average of the average diameters of each of the
droplets. Those of ordinary skill in the art will be able to
determine the average diameter (or other characteristic dimension)
of a plurality or series of droplets, for example, using laser
light scattering, microscopic examination, or other known
techniques. The diameter of a droplet, in a non-spherical droplet,
is the mathematically-defined average diameter of the droplet,
integrated across the entire surface. The average diameter of a
droplet (and/or of a plurality or series of droplets) may be, for
example, less than about 1 mm, less than about 500 micrometers,
less than about 200 micrometers, less than about 100 micrometers,
less than about 75 micrometers, less than about 50 micrometers,
less than about 25 micrometers, less than about 10 micrometers, or
less than about 5 micrometers in some cases.
[0175] The average diameter may also be at least about 1
micrometer, at least about 2 micrometers, at least about 3
micrometers, at least about 5 micrometers, at least about 10
micrometers, at least about 15 micrometers, or at least about 20
micrometers in certain cases.
[0176] Li certain instances, the invention provides for the
production of droplets consisting essentially of a substantially
uniform number of entities of a species therein (i.e., molecules,
compounds, cells, particles, etc.). For example, about 90%, about
93%, about 95%, about 97%, about 98%, or about 99%, or more of a
plurality or series of droplets may each contain the same number of
entities of a particular species. For instance, a substantial
number of fluidic droplets produced, e.g., as described above, may
each contain 1 entity, 2 entities, 3 entities, 4 entities, 5
entities, 7 entities, 10 entities, 15 entities, 20 entities, 25
entities, 30 entities, 40 entities, 50 entities, 60 entities, 70
entities, 80 entities, 90 entities, 100 entities, etc., where the
entities are molecules or macromolecules, cells, particles, etc. In
some cases, the droplets may each independently contain a range of
entities, for example, less than 20 entities, less than 15
entities, less than 10 entities, less than 7 entities, less than 5
entities, or less than 3 entities in some cases. In one set of
embodiments, in a liquid containing droplets of fluid, some of
which contain a species of interest and some of which do not
contain the species of interest, the droplets of fluid may be
screened or sorted for those droplets of fluid containing the
species as further described below (e.g., using fluorescence or
other techniques such as those described above), and in some cases,
the droplets may be screened or sorted for those droplets of fluid
containing a particular number or range of entities of the species
of interest, e.g., as previously described. Thus, in some cases, a
plurality or series of fluidic droplets, some of which contain the
species and some of which do not, may be enriched (or depleted) in
the ratio of droplets that do contain the species, for example, by
a factor of at least about 2, at least about 3, at least about 5,
at least about 10, at least about 15, at least about 20, at least
about 50, at least about 100, at least about 125, at least about
150, at least about 200, at least about 250, at least about 500, at
least about 750, at least about 1000, at least about 2000, or at
least about 5000 or more in some cases. In other cases, the
enrichment (or depletion) may be in a ratio of at least about
10.sup.4, at least about 10.sup.5, at least about 10.sup.6, at
least about 10.sup.7, at least about 10.sup.8, at least about
10.sup.9, at least about 10.sup.10, at least about 10.sup.11, at
least about 10.sup.12, at least about 10.sup.13, at least about
10.sup.14, at least about 10.sup.15, or more. For example, a
fluidic droplet containing a particular species may be selected
from a library of fluidic droplets containing various species,
where the library may have about 10.sup.5, about 10.sup.6, about
10.sup.7, about 10.sup.8, about 10.sup.9, about 10.sup.10, about
10.sup.11, about 10.sup.12, about 10.sup.13, about 10.sup.14, about
10.sup.15, or more items, for example, a DNA library, an RNA
library, a protein library, a combinatorial chemistry library, etc.
In certain embodiments, the droplets carrying the species may then
be fused, reacted, or otherwise used or processed, etc., as further
described below, for example, to initiate or determine a
reaction.
[0177] The use of micro fluidic handling to create microcapsoules
according to the invention has a number of advantages:
a) They allow the formation of highly monodisperse microcapsules
(<1.5% polydispersity), each of which functions as an almost
identical, very small microreactor, b) The microcapsules can have
volumes ranging from about 1 femtolitre to about 1 nanolitre. c)
Compartmentalisation in microcapsules prevents diffusion and
dispersion due to parabolic flow. d) By using a perfluorocarbon
carrier fluid it is possible to prevent exchange of molecules
between microcapsules. e) Compounds in microcapsules cannot react
or interact with the fabric of the microchannels as they are
separated by a layer of inert perfluorocarbon carrier fluid. f)
Microcapsules can be created at up to and including 10,000 s.sup.-1
and screened using optical methods at the same rate. This is a
throughput of .about.10.sup.9 per day.
[0178] Microcapsules can, advantageously, be fused or split. For
example, aqueous microdroplets can be merged and split using
microfluidics systems (Link et al., 2004; Song et al., 2003).
Microcapsule fusion allows the mixing of reagents. Fusion, for
example, of a microcapsule containing the target with a
microcapsule containing the compound could initiate the reaction
between target and compound. Microcapsule splitting allows single
microcapsules to be split into two or more smaller microcapsules.
For example a single microcapsule containing a compound can be
split into multiple microcapsules which can then each be fused with
a different microcapsule containing a different target. A single
microcapsule containing a target can also be split into multiple
microcapsules which can then each be fused with a different
microcapsule containing a different compound, or compounds at
different concentrations.
[0179] In one aspect, the invention relates to microfluidic systems
and methods for splitting a fluidic droplet into two or more
droplets. The fluidic droplet may be surrounded by a liquid, e.g.,
as previously described, and the fluid and the liquid are
essentially immiscible in some cases. The two or more droplets
created by splitting the original fluidic droplet may each be
substantially the same shape and/or size, or the two or more
droplets may have different shapes and/or sizes, depending on the
conditions used to split the original fluidic droplet. In many
cases, the conditions used to split the original fluidic droplet
can be controlled in some fashion, for example, manually or
automatically (e.g., with a processor, as discussed below). In some
cases, each droplet in a plurality or series of fluidic droplets
may be independently controlled. For example, some droplets may be
split into equal parts or unequal parts, while other droplets are
not split.
[0180] According to one set of embodiments, a fluidic droplet can
be split using an applied electric field. The electric field may be
an AC field, a DC field, etc. The fluidic droplet, in this
embodiment, may have a greater electrical conductivity than the
surrounding liquid, and, in some cases, the fluidic droplet may be
neutrally charged. In some embodiments, the droplets produced from
the original fluidic droplet are of approximately equal shape
and/or size. In certain embodiments, in an applied electric field,
electric charge may be urged to migrate from the interior of the
fluidic droplet to the surface to be distributed thereon, which may
thereby cancel the electric field experienced in the interior of
the droplet. In some embodiments, the electric charge on the
surface of the fluidic droplet may also experience a force due to
the applied electric field, which causes charges having opposite
polarities to migrate in opposite directions. The charge migration
may, in some cases, cause the drop to be pulled apart into two
separate fluidic droplets. The electric field applied to the
fluidic droplets may be created, for example, using the techniques
described above, such as with a reaction an electric field
generator, etc.
[0181] As a non-limiting example, in FIG. 1A, where no electric
field is applied, fluidic droplets 215 contained in channel 230 are
carried by a surrounding liquid, which flows towards intersection
240, leading to channels 250 and 255. hi this example, the
surrounding liquid flows through channels 250 and 255 at equal
flowrates. Thus, at intersection 240, fluidic droplets 215 do not
have a preferred orientation or direction, and move into exit
channels 250 and 255 with equal probability due to the surrounding
liquid flow. In contrast, in FIG. 1B, while the surrounding liquid
flows in the same fashion as FIG. 1A, under the influence of an
applied electric field of 1.4 V/micrometers, fluidic droplets 215
are split into two droplets at intersection 240, forming new
droplets 216 and 217. Droplet 216 moves to the left in channel 250,
while droplet 217 moves to the right in channel 255.
[0182] A schematic of this process can be seen in FIG. 5, where a
neutral fluidic droplet 530, surrounded by a liquid 535 in channel
540, is subjected to applied electric field 525, created by
electrodes 526 and 527. Electrode 526 is positioned near channel
542, while electrode 527 is positioned near channel 544. Under the
influence of electric field 525, charge separation is induced
within fluidic droplet 530, i.e., such that a positive charge is
induced at one end of the droplet, while a negative charge is
induced at the other end of the droplet. The droplet may then split
into a negatively charged droplet 545 and a positively charged
droplet 546, which then may travel in channels 542 and 544,
respectively. In some cases, one or both of the electric charges on
the resulting charged droplets may also be neutralized, as
previously described.
[0183] Other examples of splitting a fluidic droplet into two
droplets are described in International Patent Application Serial
No. PCT/US2004/010903, filed Apr. 9, 2004 by Link, et al.\ U.S.
Provisional Patent Application Ser. No. 60/498,091, filed Aug. 27,
2003, by Link, et. al\ and International Patent Application Serial
No. PCT/US03/20542, filed Jun. 30, 2003 by Stone, et al, published
as WO 2004/002627 on Jan. 8, 2004, each incorporated herein by
reference.
[0184] The invention, in yet another aspect, relates to systems and
methods for fusing or coalescing two or more fluidic droplets into
one droplet. For example, in one set of embodiments, systems and
methods are provided that are able to cause two or more droplets
(e.g., arising from discontinuous streams of fluid) to fuse or
coalesce into one droplet in cases where the two or more droplets
ordinarily are unable to fuse or coalesce, for example, due to
composition, surface tension, droplet size, the presence or absence
of surfactants, etc. In certain microfluidic systems, the surface
tension of the droplets, relative to the size of the droplets, may
also prevent fusion or coalescence of the droplets from occurring
in some cases.
[0185] In one embodiment, two fluidic droplets may be given
opposite electric charges (i.e., positive and negative charges, not
necessarily of the same magnitude), which may increase the
electrical interaction of the two droplets such that fusion or
coalescence of the droplets can occur due to their opposite
electric charges, e.g., using the techniques described herein. For
instance, an electric field may be applied to the droplets, the
droplets may be passed through a capacitor, a chemical reaction may
cause the droplets to become charged, etc. As an example, as is
shown schematically in FIG. 13 A, uncharged droplets 651 and 652,
carried by a liquid 654 contained within a microfluidic channel
653, are brought into contact with each other, but the droplets are
not able to fuse or coalesce, for instance, due to their size
and/or surface tension. The droplets, in some cases, may not be
able to fuse even if a surfactant is applied to lower the surface
tension of the droplets. However, if the fluidic droplets are
electrically charged with opposite charges (which can be, but are
not necessarily of, the same magnitude), the droplets may be able
to fuse or coalesce. For instance, in FIG. 13B, positively charged
droplets 655 and negatively charged droplets 656 are directed
generally towards each other such that the electrical interaction
of the oppositely charged droplets causes the droplets to fuse into
fused droplets 657.
[0186] In another embodiment, the fluidic droplets may not
necessarily be given opposite electric charges (and, in some cases,
may not be given any electric charge), and are fused through the
use of dipoles induced in the fluidic droplets that causes the
fluidic droplets to coalesce. In the example illustrated in FIG. 13
C, droplets 660 and 661 (which may each independently be
electrically charged or neutral), surrounded by liquid 665 in
channel 670, move through the channel such that they are the
affected by an applied electric field 675. Electric field 675 may
be an AC field, a DC field, etc., and may be created, for instance,
using electrodes 676 and 677, as shown here. The induced dipoles in
each of the fluidic droplets, as shown in FIG. 13 C, may cause the
fluidic droplets to become electrically attracted towards each
other due to their local opposite charges, thus causing droplets
660 and 661 to fuse to produce droplet 663. In FIG. 13D, droplets
651 and 652 flow together to fuse to form droplet 653, which flows
in a third channel.
[0187] It should be noted that, in various embodiments, the two or
more droplets allowed to coalesce are not necessarily required to
meet "head-on." Any angle of contact, so long as at least some
fusion of the droplets initially occurs, is sufficient. As an
example, in FIG. 12H, droplets 73 and 74 each are traveling in
substantially the same direction (e.g., at different velocities),
and are able to meet and fuse. As another example, in FIG. 121,
droplets 73 and 74 meet at an angle and fuse. In FIG. 12J, three
fluidic droplets 73, 74 and 68 meet and fuse to produce droplet
79.
[0188] Other examples of fusing or coalescing fluidic droplets are
described in International Patent Application Serial No.
PCT/US2004/010903, filed Apr. 9, 2004 by Link, et at, incorporated
herein by reference.
[0189] Fluidic handling of microcapsules therefore results in
further advantages:
a) Microcapsules can be split into two or more smaller
microdroplets allowing the reagents contained therein to be reacted
with a series of different molecules in parallel or assayed in
multiplicate. b) Microcapsules can be fused. This allows molecules
to be: (a) diluted, (b) mixed with other molecules, and (c)
reactions initiated, terminated or modulated at precisely defined
times. c) Reagents can be mixed very rapidly (in <2 ms) in
microcapsules using chaotic advection, allowing fast kinetic
measurements and very high throughput. d) Reagents can be mixed in
a combinatorial manner. For example, allowing the effect of all
possible pairwise combinations of compounds in a compound library
on a target to be tested
[0190] Creating and manipulated microcapsules in microfluidic
systems means that:
a) Stable streams of microcapsules can be formed in microchannels
and identified by their relative positions. b) If the reactions are
accompanied by an optical signal (e.g. a change in fluorescence) a
spatially-resolved optical image of the microfluidic network allows
time resolved measurements of the reactions in each microcapsules.
c) Microcapsules can be separated using a microfluidic flow sorter
to allow recovery and further analysis or manipulation of the
molecules they contain.
Screening/Sorting of Microcapsules
[0191] hi still another aspect, the invention provides systems and
methods for screening or sorting fluidic droplets in a liquid, and
in some cases, at relatively high rates. For example, a
characteristic of a droplet may be sensed and/or determined in some
fashion (e.g., as further described below), then the droplet may be
directed towards a particular region of the device, for example,
for sorting or screening purposes.
[0192] In some embodiments, a characteristic of a fluidic droplet
may be sensed and/or determined in some fashion, for example, as
described herein (e.g., fluorescence of the fluidic droplet may be
determined), and, in response, an electric field may be applied or
removed from the fluidic droplet to direct the fluidic droplet to a
particular region (e.g. a channel). In some cases, high sorting
speeds may be achievable using certain systems and methods of the
invention. For instance, at least about 10 droplets per second may
be determined and/or sorted in some cases, and in other cases, at
least about 20 droplets per second, at least about 30 droplets per
second, at least about 100 droplets per second, at least about 200
droplets per second, at least about 300 droplets per second, at
least about 500 droplets per second, at least about 750 droplets
per second, at least about 1000 droplets per second, at least about
1500 droplets per second, at least about 2000 droplets per second,
at least about 3000 droplets per second, at least about 5000
droplets per second, at least about 7500 droplets per second, at
least about 10,000 droplets per second, at least about 15,000
droplets per second, at least about 20,000 droplets per second, at
least about 30,000 droplets per second, at least about 50,000
droplets per second, at least about 75,000 droplets per second, at
least about 100,000 droplets per second, at least about 150,000
droplets per second, at least about 200,000 droplets per second, at
least about 300,000 droplets per second, at least about 500,000
droplets per second, at least about 750,000 droplets per second, at
least about 1,000,000 droplets per second, at least about 1,500,000
droplets per second, at least about 2,000,000 or more droplets per
second, or at least about 3,000,000 or more droplets per second
maybe determined and/or sorted in such a fashion.
[0193] hi one set of embodiments, a fluidic droplet may be directed
by creating an electric charge (e.g., as previously described) on
the droplet, and steering the droplet using an applied electric
field, which may be an AC field, a DC field, etc. As an example, in
reference to FIGS. 2-4, an electric field may be selectively
applied and removed (or a different electric field may be applied,
e.g., a reversed electric field as shown in FIG. 4A) as needed to
direct the fluidic droplet to a particular region. The electric
field may be selectively applied and removed as needed, in some
embodiments, without substantially altering the flow of the liquid
containing the fluidic droplet. For example, a liquid may flow on a
substantially steady-state basis (i.e., the average flowrate of the
liquid containing the fluidic droplet deviates by less than 20% or
less than 15% of the steady-state flow or the expected value of the
flow of liquid with respect to time, and in some cases, the average
flowrate may deviate less than 10% or less than 5%) or other
predetermined basis through a fluidic system of the invention
(e.g., through a channel or a microchannel), and fluidic droplets
contained within the liquid may be directed to various regions,
e.g., using an electric field, without substantially altering the
flow of the liquid through the fluidic system. As a particular
example, in FIGS. 2A, 3A and 4A, a liquid containing fluidic
droplets 15 flows from fluid source 10, through channel 30 to
intersection 40, and exits through channels 50 and 55. In FIG. 2 A,
fluidic droplets 15 are directed through both channels 50 and 55,
while in FIG. 3 A, fluidic droplets 15 are directed to only channel
55 and, in FIG. 4A, fluidic droplets 15 are directed to only
channel 50.
[0194] In another set of embodiments, a fluidic droplet may be
sorted or steered by inducing a dipole in the fluidic droplet
(which may be initially charged or uncharged), and sorting or
steering the droplet using an applied electric field. The electric
field may be an AC field, a DC field, etc. For example, with
reference to FIG. 9A, a channel 540, containing fluidic droplet 530
and liquid 535, divides into channel 542 and 544. Fluidic droplet
530 may have an electric charge, or it may be uncharged. Electrode
526 is positioned near channel 542, while electrode 527 is
positioned near channel 544. Electrode 528 is positioned near the
junction of channels 540, 542, and 544. In FIGS. 9C and 9D, a
dipole is induced in the fluidic droplet using electrodes 526, 527,
and/or 528. In FIG. 9C, a dipole is induced in droplet 530 by
applying an electric field 525 to the droplet using electrodes 527
and 528. Due to the strength of the electric field, the droplet is
strongly attracted to the right, into channel 544. Similarly, in
FIG. 9D, a dipole is induced in droplet 530 by applying an electric
field 525 to the droplet using electrodes 526 and 528, causing the
droplet to be attracted into channel 542. Thus, by applying the
proper electric field, droplet 530 can be directed to either
channel 542 or 544 as desired.
[0195] In other embodiments, however, the fluidic droplets may be
screened or sorted within a fluidic system of the invention by
altering the flow of the liquid containing the droplets. For
instance, in one set of embodiments, a fluidic droplet may be
steered or sorted by directing the liquid surrounding the fluidic
droplet into a first channel, a second channel, etc. As a
non-limiting example, with reference to FIG. 10A, fluidic droplet
570 is surrounded by a liquid 575 in channel 580. Channel 580
divides into three channels 581, 582, and 583. The flow of liquid
575 can be directed into any of channels 581, 582, and 583 as
desired, for example, using flow-controlling devices known to those
of ordinary skill in the art, for example, valves, pumps, pistons,
etc. Thus, in FIG. 10B, fluidic droplet 570 is directed into
channel 581 by directing liquid 575 to flow into channel 581
(indicated by arrows 574); in FIG. 10C, fluidic droplet 570 is
directed into channel 582 by directing liquid 575 to flow into
channel 582 (indicated by arrows 574); and in FIG. 10D, fluidic
droplet 570 is directed into channel 583 by directing liquid 575 to
flow into channel 583 (indicated by arrows 574).
[0196] However, it is preferred that control of the flow of liquids
in microfluidic systems is not used to direct the flow of fluidic
droplets therein, but that an alternative method is used.
Advantageously, therefore, the microcapsules are not sorted by
altering the direction of the flow of a carrier fluid in a
microfluidic system.
[0197] In another set of embodiments, pressure within a fluidic
system, for example, within different channels or within different
portions of a channel, can be controlled to direct the flow of
fluidic droplets. For example, a droplet can be directed toward a
channel junction including multiple options for further direction
of flow (e.g., directed toward a branch, or fork, in a channel
defining optional downstream flow channels). Pressure within one or
more of the optional downstream flow channels can be controlled to
direct the droplet selectively into one of the channels, and
changes in pressure can be effected on the order of the time
required for successive droplets to reach the junction, such that
the downstream flow path of each successive droplet can be
independently controlled. In one arrangement, the expansion and/or
contraction of liquid reservoirs may be used to steer or sort a
fluidic droplet into a channel, e.g., by causing directed movement
of the liquid containing the fluidic droplet. The liquid reservoirs
may be positioned such that, when activated, the movement of liquid
caused by the activated reservoirs causes the liquid to flow in a
preferred direction, carrying the fluidic droplet in that preferred
direction. For instance, the expansion of a liquid reservoir may
cause a flow of liquid towards the reservoir, while the contraction
of a liquid reservoir may cause a flow of liquid away from the
reservoir. In some cases, the expansion and/or contraction--of the
liquid reservoir may be combined with other flow-controlling
devices and methods, e.g., as described herein. Non-limiting
examples of devices able to cause the expansion and/or contraction
of a liquid reservoir include pistons and piezoelectric components.
In some cases, piezoelectric components may be particularly useful
due to their relatively rapid response times, e.g., in response to
an electrical signal.
[0198] As a non-limiting example, in FIG. 1 IA, fluidic droplet 600
is surrounded by a liquid 605 in channel 610. Channel 610 divides
into channels 611, 612. Positioned in fluidic communication with
channels 611 and 612 are liquid reservoirs 617 and 618, which may
be expanded and/or contracted, for instance, by piezoelectric
components 615 and 616, by a piston (not shown), etc. In Fig. HB,
liquid reservoir 617 has been expanded, while liquid reservoir 618
has been contracted. The effect of the expansion/contractions of
the reservoirs is to cause a net flow of liquid towards channel
611, as indicated by arrows 603. Thus, fluidic droplet 600, upon
reaching the junction between the channels, is directed to channel
611 by the movement of liquid 605. The reverse situation is shown
in Fig. HC, where liquid reservoir 617 has contracted while liquid
reservoir 618 has been expanded. A net flow of liquid occurs
towards channel 612 (indicated by arrows 603), causing fluidic
droplet 600 to move into channel 612. It should be noted, however,
that reservoirs 617 and 618 do not both need to be activated to
direct fluidic droplet 600 into channels 611 or 612. For example,
in one embodiment, fluidic droplet 600 may be directed to channel
611 by the expansion of liquid reservoir 617 (without any
alteration of reservoir 618), while in another embodiment, fluidic
droplet 600 may be directed to channel 611 by the contraction of
liquid reservoir 618 (without any alteration of reservoir 617). In
some cases, more than two liquid reservoirs may be used.
[0199] In some embodiments, the fluidic droplets may be sorted into
more than two channels. Non-limiting examples of embodiments of the
invention having multiple regions within a fluidic system for the
delivery of droplets are shown in FIGS. 6A and 6B. Other
arrangements are shown in FIGS. 10A-10D. In FIG. 6 A, charged
droplets 315 in channel 330 may be directed as desired to any one
of exit channels 350, 352, 354, or 356, by applying electric fields
to control the movement of the droplets at intersections 340, 341,
and 342, using electrodes 321/322, 323/324, and(325/326,
respectively. In FIG. 6A, droplets 315 are directed to channel 354
using applied electric fields 300 and 301, using principles similar
to those discussed above. Similarly, in FIG. 6B, charged droplets
415 in channel 430 can be directed to any one of exit channels 450,
452, 454, 456, or 458, by applying electric fields to control the
movement of the droplets at intersections 440, 441, 442, and 443,
using electrodes 421/422, 423/424, 425/426, and 427/428,
respectively. In this figure, droplets 415 are directed to channel
454; of course, the charged droplets may be directed to any other
exit channel as desired.
[0200] In another example, in apparatus 5, as schematically
illustrated in FIG. 2A, fluidic droplets 15 created by fluid source
10 are positively charged due to an applied electric field created
using electric field generator 20, which comprises two electrodes
22, 24. Fluidic droplets 15 are directed through channel 30 by a
liquid containing the droplets, and are directed towards
intersection 40. At intersection 40, the fluidic droplets do not
have a preferred orientation or direction, and move into exit
channels 50 and 55 with equal probability (in this embodiment,
liquid drains through both exit channels 50 and 55 at substantially
equal rates). Similarly, fluidic droplets 115 created by fluid
source 110 are negatively charged due to an applied electric field
created using electric field generator 120, which comprises
electrodes 122 and 124. After traveling through channel 130 towards
intersection 140, the fluidic droplets do not have a preferred
orientation or direction, and move into exit channels 150 and 155
with equal probability, as the liquid exits through exit channels
150 and 155 at substantially equal rates. A representative
photomicrograph of intersection 140 is shown in FIG. 2B.
[0201] In the schematic diagram of FIG. 3 A, an electric field 100
of 1.4 V/micrometer has been applied to apparatus 5 of FIG. 2 A, in
a direction towards the right of apparatus 5. Positively-charged
fluidic droplets 15 in channel 30, upon reaching intersection 40,
are directed to the right in channel 55 due to the applied electric
field 100, while the liquid containing the droplets continues to
exit through exit channels 50 and 55 at substantially equal rates.
Similarly, negatively-charged fluidic droplets 115 in channel 130,
upon reaching intersection 140, are directed to the left in channel
150 due to the applied electric field 100, while the liquid fluid
continues to exit the device through exit channels 150 and 155 at
substantially equal rates. Thus, electric field 100 can be used to
direct fluidic droplets into particular channels as desired. A
representative photomicrograph of intersection 140 is shown in FIG.
3B.
[0202] FIG. 4A is a schematic diagram of apparatus 5 of FIG. 2A,
also with an applied electric field 100 of 1.4 V/micrometer, but in
the opposite direction (i.e., -1.4 V/micrometer). hi this figure,
positively-charged fluidic droplets 15 in channel 30, upon reaching
intersection 40, are directed to the left into channel 50 due to
the applied electric field 100, while negatively-charged fluidic
droplets 115 in channel 130, upon reaching intersection 140, are
directed to the right into channel 155 due to applied electric
field 100. The liquid containing the droplets exits through exit
channels 50 and 55, and 150 and 155, at substantially equal rates.
A representative photomicrograph of intersection 140 is shown in
FIG. 4B.
[0203] In some embodiments of the invention, a fluidic droplet may
be sorted and/or split into two or more separate droplets, for
example, depending on the particular application. Any of the
above-described techniques may be used to spilt and/or sort
droplets. As a non-limiting example, by applying (or removing) a
first electric field to a device (or a portion thereof), a fluidic
droplet may be directed to a first region or channel; by applying
(or removing) a second electric field to the device (or a portion
thereof), the droplet may be directed to a second region or
channel; by applying a third electric field to the device (or a
portion thereof), the droplet may be directed to a third region or
channel; etc., where the electric fields may differ in some way,
for example, in intensity, direction, frequency, duration, etc. In
a series of droplets, each droplet may be independently sorted
and/or split; for example, some droplets may be directed to one
location or another, while other droplets may be split into
multiple droplets directed to two or more locations.
[0204] As one particular example, in FIG. 8A, fluidic droplet 550,
surrounding liquid 555 in channel 560 may be directed to channel
556, channel 557, or be split in some fashion between channels 562
and 564. In FIG. 8B, by directing surrounding liquid 555 towards
channel 562, fluidic droplet 550 may be directed towards the left
into channel 562; in FIG. 8C, by directing surrounding liquid 555
towards channel 564, fluidic droplet 550 may be directed towards
the right into channel 564, In FIG. 8D, an electric field may be
applied, in combination with control of the flow of liquid 555
surrounding fluidic droplet 550, that causes the droplet to impact
junction 561, which may cause the droplet to split into two
separate fluidic droplets 565, 566. Fluidic droplet 565 is directed
to channel 562, while fluidic droplet 566 is directed to channel
566. A high degree of control of the applied electric field may be
achieved to control droplet formation; thus, for example, after
fluidic droplet 565 has been split into droplets 565 and 566,
droplets 565 and 566 may be of substantially equal size, or either
of droplets 565 and 566 may be larger, e.g., as is shown in FIGS.
8E and 8F, respectively.
[0205] As another example, in FIG. 9 A, channel 540, carrying
fluidic droplet 530 and liquid 535, divides into channel 542 and
544. Fluidic droplet 530 may be electrically charged, or it may
uncharged. Electrode 526 is positioned near channel 542, while
electrode 527 is positioned near channel 544. Electrode 528 is
positioned near the junction of channels 540, 542, and 544. When
fluidic droplet 530 reaches the junction, it may be subjected to an
electric field, and/or directed to a channel or other region, for
example, by directing the surrounding liquid into the channel. As
shown in FIG. 9B, fluidic droplet 530 may be split into two
separate droplets 565 and 566 by applying an electric field 525 to
the droplet using electrodes 526 and 527. In FIG. 9C, a dipole can
be induced in droplet 530 by applying an electric field 525 to the
droplet using electrodes 527 and 528. Due to the strength of the
applied electric field, the droplet may be strongly attracted to
the right, into channel 544. Similarly, in FIG. 9D, a dipole may be
induced in droplet 530 by applying an electric field 525 to the
droplet using electrodes 526 and 528, causing the droplet to be
attracted into channel 542. By controlling which electrodes are
used to induce an electric field across droplet 530, and/or the
strength of the applied electric field, one or more fluidic
droplets within channel 540 may be sorted and/or split into two
droplets, and each droplet may independently be sorted and/or
split.
[0206] For example, highly monodisperse microcapsules containing a
target enzyme can be fused with highly monodisperse microcapsules
each of which contain a different compound from a compound library.
The fused microcapsules flow along a microfluidic channel, allowing
time for the compounds to bind to the target enzyme. Each
microcapsule is then fused with another microdroplet containing,
for example, a fluorogenic enzyme substrate. The rate of the
enzymatic reaction is determined by measuring the fluorescence of
each microdroplet, ideally at multiple points (corresponding to
different times).
[0207] Microcapsules can be optically tagged by, for example,
incorporating fluorochromes. In a preferred configuration, the
microcapsules are optically tagged by incorporating quantum dots:
quantum dots of 6 colours at 10 concentrations would allow the
encoding of 106 microcapsules (Han et al., 2001). Microcapsules
flowing in an ordered sequence in a microfluidic channel can be
encoded (wholly or partially) by their sequence in the stream of
microcapsules (positional encoding).
[0208] Microbeads, also known by those skilled in the art as
microspheres, latex particles, beads, or minibeads, are available
in diameters from 20 nm to 1 mm and can be made from a variety of
materials including silica and a variety of polymers, copolymers
and terpolymers including polystyrene (PS), polymethylmethacrylate
(PMMA), polyvinyltoluene (PVT), styrene/butadiene (S/B) copolymer,
and styrene/vinyltoluene (S/VT) copolymer. They are available with
a variety of surface chemistries from hydrophobic surfaces (e.g.
plain polystyrene), to very hydrophilic surfaces imparted by a wide
variety of functional surface groups: aldehyde, aliphatic amine,
amide, aromatic amine, carboxylic acid, chloromethyl, epoxy,
hydrazide, hydroxyl, sulfonate and tosyl. The functional groups
permit a wide range of covalent coupling reactions for stable or
reversible attachment of compounds to the microbead surface.
[0209] Microbeads can be optically tagged by, for example,
incorporating fluorochromes. For example, one hundred different
bead sets have been created, each with a unique spectral address
due to labelling with precise ratios of red (>650 nm) and orange
(585 nm) fluorochromes (Fulton et al., 1997) and sets of up to 106
beads can be encoded by incorporating quantum dots of 10
intensities and 6 colours (Han et al., 2001).
[0210] The compounds can be connected to the microbeads either
covalently or non-covalently by a variety of means that will be
familiar to those skilled in the art (see, for example,
[0211] (Hermanson, 1996)). Advantageously, the compounds are
attached via a cleavable linker.
[0212] A variety of such linkers are familiar to those skilled in
the art (see for example (Gordon and Balasubramanian, 1999)),
including for example, linkers which can be cleaved photochemically
and reversible covalent bonds which can be controlled by changing
the pH (e.g. imines and acylhydrazones), by adjusting the
oxido-reductive properties (e.g. disulphides), or using an external
catalyst (e.g. cross-metathesis and transamidation).
[0213] The method of the present invention permits the
identification of compounds which modulate the activity of the
target in a desired way in pools (libraries or repertoires) of
compounds.
[0214] In a highly preferred application, the method of the present
invention is useful for screening libraries of compounds. The
invention accordingly provides a method according to preceding
aspects of the invention, wherein the compounds are identified from
a library of compounds.
[0215] The compounds identified according to the invention are
advantageously of pharmacological or industrial interest, including
activators or inhibitors of biological systems, such as cellular
signal transduction mechanisms suitable for diagnostic and
therapeutic applications. In addition the compounds identified
according to the invention may be non-biological in nature. In a
preferred aspect, therefore, the invention permits the
identification of clinically or industrially useful products. In a
further aspect of the invention, there is provided a product when
isolated by the method of the invention.
[0216] The selection of suitable encapsulation conditions is
desirable. Depending on the complexity and size of the compound
library to be screened, it may be beneficial to set up the
encapsulation procedure such that one or less than one secondary
compound is formed per microcapsule. This will provide the greatest
power of resolution. Where the library is larger and/or more
complex, however, this may be impracticable; it may be preferable
to form several secondary compounds together and rely on repeated
application of the method of the invention to identify the desired
compound. A combination of encapsulation procedures may be used to
identify the desired compound.
[0217] Theoretical studies indicate that the larger the number of
compounds created the more likely it is that a compound will be
created with the properties desired (see (Perelson and Oster, 1979)
for a description of how this applies to repertoires of
antibodies). It has also been confirmed practically that larger
phage-antibody repertoires do indeed give rise to more antibodies
with better binding affinities than smaller repertoires (Griffiths
et al., 1994). To ensure that rare variants are generated and thus
are capable of being identified, a large library size is desirable.
Thus, the use of optimally small microcapsules is beneficial.
[0218] The largest repertoires of compounds that can be screened in
a single experiment to date, using two dimensional microarrays of 1
nl volume spots, is -10.sup.3 (Hergenrother et al., 2000). Using
the present invention, at a microcapsule diameter of 2.6 mm (Tawfik
and Griffiths, 1998), by forming a three-dimensional dispersion, a
repertoire size of at least 10n can be screened using 1 ml aqueous
phase in a 20 ml emulsion.
[0219] In addition to the compounds, or microbeads coated with
compounds, described above, the microcapsules according to the
invention will comprise further components required for the
screening process to take place. They will comprise the target and
a suitable buffer. A suitable buffer will be one in which all of
the desired components of the biological system are active and will
therefore depend upon the requirements of each specific reaction
system. Buffers suitable for biological and/or chemical reactions
are known in the art and recipes provided in various laboratory
texts, such as (Sambrook and Russell, 2001).
[0220] Other components of the system will comprise those necessary
for assaying the activity of the target. These may for example
comprise substrate(s) and cofactor(s) for a reaction catalysed by
the target, and ligand(s) bound by the target. They may also
comprise other catalysts (including enzymes), substrates and
cofactors for reactions coupled to the activity of the target which
allow for the activity of the target to be detected.
(B) Screening Procedures
[0221] To screen compounds which bind to or modulate the activity
of a target, the target is compartmentalised in microcapsules
together with one or more compounds or compound-coated microbeads.
Advantageously each microcapsule contains only a single sort of
secondary compound, but many copies thereof. Advantageously each
microbead is coated with only a single sort of compound, but many
copies thereof. Advantageously the compounds are connected to the
microbeads via a cleavable linker, allowing them to be released
from the microbeads in the compartments. Advantageously, each
microcapsule or microbead is optically tagged to allow
identification of the compounds contained within the microcapsule
of attached to the microbead.
(I) Screening for Binding
[0222] Compounds can be screened directly for binding to a target.
In this embodiment, if the compound is attached to a microbead and
has affinity for the target it will be bound by the target. At the
end of the reaction, all of the microcapsules are combined, and all
microbeads pooled together in one environment. Microbeads carrying
compounds exhibiting the desired binding can be selected by
affinity purification using a molecule that specifically binds to,
or reacts specifically with, the target.
[0223] In an alternative embodiment, the target can be attached to
microbeads by a variety of means familiar to those skilled in the
art (see for example (Hermanson, 1996)). The compounds to be
screened contain a common feature--a tag. The compounds are
released from the microbeads and if the compound has affinity for
the target, it will bind to it. At the end of the reaction, all of
the microcapsules are combined, and all microbeads pooled together
in one environment. Microbeads carrying compounds exhibiting the
desired binding can be selected by affinity purification using a
molecule that specifically binds to, or reacts specifically with,
the "tag".
[0224] In an alternative embodiment, microbeads may be screened on
the basis that the compound, which binds to the target, merely
hides the ligand from, for example, further binding partners, hi
this eventuality, the microbead, rather than being retained during
an affinity purification step, may be selectively eluted whilst
other microbeads are bound.
[0225] Sorting by affinity is dependent on the presence of two
members of a binding pair in such conditions that binding may
occur. Any binding pair may be used for this purpose. As used
herein, the term binding pair refers to any pair of molecules
capable of binding to one another. Examples of binding pairs that
may be used in the present invention include an antigen and an
antibody or fragment thereof capable of binding the antigen, the
biotin-avidin/streptavidin pair (Savage et al., 1994), a
calcium-dependent binding polypeptide and ligand thereof (e.g.
calmodulin and a calmodulin-binding peptide (Montigiani et al.,
1996; Stofko et al., 1992), pairs of polypeptides which assemble to
form a leucine zipper (Tripet et al., 1996), histidines (typically
hexahistidine peptides) and chelated Cu.sup.2+, Zn.sup.2+ and
Ni.sup.2+, (e.g. Ni-NTA; (Hochuli et al., 1987)), RNA-binding and
DNA-binding proteins (Klug, 1995) including those containing
zinc-finger motifs (Klug and Schwabe, 1995) and DNA
methyltransferases (Anderson, 1993), and their nucleic acid binding
sites.
[0226] hi an alternative embodiment, compounds can be screened for
binding to a target using a change in the optical properties of the
microcapsule or the microbead.
[0227] The change in optical properties of the microcapsule or the
microbead after binding of the compound to the target may be
induced in a variety of ways, including:
(1) the compound itself may have distinctive optical properties,
for example, it is fluorescent (2) the optical properties of the
compound may be modified on binding to the target, for example, the
fluorescence of the compound is quenched or enhanced on binding
(Voss, 1993; Masui and Kuramitsu, 1998). (3) the optical properties
of the target may be modified on binding of the compound, for
example, the fluorescence of the target is quenched or enhanced on
binding (Guixe et al., 1998; Qi and Grabowski, 1998) (4) the
optical properties of both target and compound are modified on
binding, for example, there can be a fluorescence resonance energy
transfer (FRET) from target to compound (or vice versa) resulting
in emission at the "acceptor" emission wavelength when excitation
is at the "donor" absorption wavelength (Heim & Tsien,
1996;
[0228] Mahajan et al, 1998; Miyawaki et al, 1997).
[0229] The invention provides a method wherein a compound with the
desired activity induces a change in the optical properties of the
microcapsule, which enables the microcapsule containing the
compound and the microbeads contained therein to be identified, and
optionally, sorted.
[0230] In an alternative embodiment, the invention provides a
method wherein microbeads are analysed following pooling of the
microcapsules into one or more common compartments. In this
embodiment, a compound having the desired activity modifies the
optical properties of the microbead which carried it (and which
resides in the same microcapsule) to allow it to be identified, and
optionally, sorted.
[0231] In this embodiment, it is not necessary for binding of the
compound to the target to directly induce a change in optical
properties.
[0232] In this embodiment, if the compound attached to the
microbead has affinity for the target it will be bound by the
target. At the end of the reaction, all of the microcapsules are
combined, and all microbeads pooled together in one environment.
Microbeads carrying compounds exhibiting the desired binding can be
identified by adding reagents that specifically bind to, or react
specifically with, the target and thereby induce a change in the
optical properties of the microbeads allowing their identification.
For example, a fluorescently-labelled anti-target antibody can be
used, or an anti-target antibody followed by a second fluorescently
labelled antibody which binds the first.
[0233] In an alternative embodiment, the target can be attached to
the microbeads by a variety of means familiar to those skilled in
the art (see for example (Hermanson, 1996)). The compounds to be
screened contain a common feature--a tag. The compounds are
released from the microbeads and if the compound has affinity for
the target, it will bind to it. At the end of the reaction, all of
the microcapsules are combined, and all microbeads pooled together
in one environment. Microbeads carrying compounds exhibiting the
desired binding can be identified by adding reagents that
specifically bind to, or react specifically with, the "tag" and
thereby induce a change in the optical properties of the microbeads
allowing their identification. For example, a
fluorescently-labelled anti-"tag" antibody can be used, or an
anti-"tag" antibody followed by a second fluorescently labelled
antibody which binds the first.
[0234] In an alternative embodiment, microbeads may be identified
on the basis that the gene product, which binds to the ligand,
merely hides the ligand from, for example, further binding partners
which would otherwise modify the optical properties of the
microbeads. hi this case microbeads with unmodified optical
properties would be selected.
[0235] Fluorescence may be enhanced by the use of Tyramide Signal
Amplification (TSA.TM.) amplification to make the microbeads
fluorescent (Sepp et al., 2002). This involves peroxidase (linked
to another compound) binding to the microbeads and catalysing the
conversion of fluorescein-tyramine in to a free radical form which
then reacts (locally) with the microbeads. Methods for performing
TSA are known in the art, and kits are available commercially from
NEN.
[0236] TSA may be configured such that it results in a direct
increase in the fluorescence of the microbeads, or such that a
ligand is attached to the microbeads which is bound by a second
fluorescent molecule, or a sequence of molecules, one or more of
which is fluorescent.
(ii) Screening for Regulation of Binding
[0237] In an alternative embodiment, the invention can be used to
screen compounds which act to regulate a biochemical process. If
the compound activates a binding activity of a target, a ligand for
the target which is activated can be attached to microbeads by a
variety of means familiar to those skilled in the art (see for
example (Hermanson, 1996)). At the end of the reaction, all of the
microcapsules are combined, and all microbeads pooled together in
one environment. Microbeads carrying compounds exhibiting the
desired binding can be selected by affinity purification using a
molecule that specifically binds to, or reacts specifically with,
the target.
[0238] In an alternative embodiment, microbeads may be screened on
the basis that the compound inhibits the binding activity of a
target. In this eventuality, the microbead, rather than being
retained during an affinity purification step, may be selectively
eluted whilst other microbeads are bound.
[0239] In an alternative embodiment, compounds can be screened for
the ability to modulates a binding activity of a target using a
change in the optical properties of the microcapsule or the
microbead.
[0240] The change in optical properties of the microcapsule or the
microbead after binding of the target to its ligand may be induced
in a variety of ways, including:
(1) the ligand itself may have distinctive optical properties, for
example, it is fluorescent (2) the optical properties of the ligand
may be modified on binding to the target, for example, the
fluorescence of the ligand is quenched or enhanced on binding
(Voss, 1993; Masui and Kuramitsu, 1998). (3) the optical properties
of the target may be modified on binding of the ligand, for
example, the fluorescence of the target is quenched or enhanced on
binding (Guixe et al., 1998; Qi and Grabowski, 1998) (4) the
optical properties of both target and ligand are modified on
binding, for example, there can be a fluorescence resonance energy
transfer (FRET) from target to ligand (or vice versa) resulting in
emission at the "acceptor" emission wavelength when excitation is
at the "donor" absorption wavelength (Heim & Tsien, 1996;
[0241] Mahajan et al, 1998; Miyawaki et al, 1997).
[0242] The invention provides a method wherein a compound with the
desired activity induces a change in the optical properties of the
microcapsule, which enables the microcapsule containing the
compound and the microbeads contained therein to be identified, and
optionally, sorted.
[0243] In an alternative embodiment, the invention provides a
method wherein microbeads are analysed following pooling of the
microcapsules into one or more common compartments. In this
embodiment, a compound having the desired activity modifies the
optical properties of the microbead which carried it (and which
resides in the same microcapsule) to allow it to be identified, and
optionally, sorted.
[0244] hi this embodiment, it is not necessary for binding of the
target to the ligand to directly induce a change in optical
properties.
[0245] hi this embodiment, if a ligand attached to the microbead
has affinity for the target it will be bound by the target. At the
end of the reaction, all of the microcapsules are combined, and all
microbeads pooled together in one environment. Microbeads carrying
compounds which modulate the binding activity can be identified by
adding reagents that specifically bind to, or react specifically
with, the target and thereby induce a change in the optical
properties of the microbeads allowing their identification. For
example, a fluorescently-labelled anti-target antibody can be used,
or an anti-target antibody followed by a second fluorescently
labelled antibody which binds the first.
[0246] Li an alternative embodiment, the target can be attached to
the microbeads by a variety of means familiar to those skilled in
the art (see for example (Hermanson, 1996)). The ligand to be
screened contains a feature--a tag. At the end of the reaction, all
of the microcapsules are combined, and all microbeads pooled
together in one environment. Microbeads carrying compounds which
modulate binding can be identified by adding reagents that
specifically bind to, or react specifically with, the "tag" and
thereby induce a change in the optical properties of the microbeads
allowing their identification. For example, a
fluorescently-labelled anti-"tag" antibody can be used, or an
anti-"tag" antibody followed by a second fluorescently labelled
antibody which binds the first.
[0247] Fluorescence may be enhanced by the use of Tyramide Signal
Amplification (TSA.TM. amplification to make the microbeads
fluorescent (Sepp et al., 2002), as above.
(iii) Screening for Regulation of Catalysis
[0248] In an alternative embodiment, the invention provides a
method wherein a compound with the desired activity induces a
change in the optical properties of the microcapsule, which enables
the microcapsule containing the compound and, optionally, the
microbeads contained therein to be identified, and optionally,
sorted. The optical properties of microcapsules can be modified by
either:
(a) the substrate and product of the regulated reaction having
different optical properties (many fluorogenic enzyme substrates
are available commercially, see for example (Haugland, 1996
including substrates for glycosidases, phosphatases, peptidases and
proteases, or (b) the presence of reagents which specifically bind
to, or react with, the product (or substrate) of the regulated
reaction in the microcapsule and which thereby induce a change in
the optical properties of the microcapsules allowing their
identification.
[0249] A wide range of assays for screening libraries of compounds
for those which modulate the activity of a target are based on
detecting changes in optical properties and can be used to screen
compounds according to this invention. Such assays are well known
to those skilled in the art (see for example Haugland, 1996).
[0250] Alternatively, selection may be performed indirectly by
coupling a first reaction to subsequent reactions that takes place
in the same microcapsule. There are two general ways in which this
may be performed. First, the product of the first reaction could be
reacted with, or bound by, a molecule which does not react with the
substrate(s) of the first reaction. A second, coupled reaction will
only proceed in the presence of the product of the first reaction.
A regulatory compound can then be identified by the properties of
the product or substrate of the second reaction.
[0251] Alternatively, the product of the reaction being selected
may be the substrate or cofactor for a second enzyme-catalysed
reaction. The enzyme to catalyse the second reaction can be
incorporated in the reaction mixture prior to microencapsulation.
Only when the first reaction proceeds will the coupled enzyme
generate an identifiable product.
[0252] This concept of coupling can be elaborated to incorporate
multiple enzymes, each using as a substrate the product of the
previous reaction. This allows for selection of regulators of
enzymes that will not react with an immobilised substrate. It can
also be designed to give increased sensitivity by signal
amplification if a product of one reaction is a catalyst or a
cofactor for a second reaction or series of reactions leading to a
selectable product (for example, see (Johannsson, 1991; Johannsson
and Bates, 1988). Furthermore an enzyme cascade system can be based
on the production of an activator for an enzyme or the destruction
of an enzyme inhibitor (see (Mize et al., 1989)). Coupling also has
the advantage that a common screening system can be used for a
whole group of enzymes which generate the same product and allows
for the selection of regulation of complicated multi-step chemical
transformations and pathways.
[0253] In an alternative embodiment, if the target is itself an
enzyme, or regulates a biochemical process which is enzymatic, the
microbead in each microcapsule may be coated with the substrate for
the enzymatic reaction. The regulatory compound will determine the
extent to which the substrate is converted into the product. At the
end of the reaction the microbead is physically linked to the
product of the catalysed reaction. When the microcapsules are
combined and the reactants pooled, microbeads which were coated
with activator compounds can be identified by any property specific
to the product. If an inhibitor is desired, selection can be for a
chemical property specific to the substrate of the regulated
reaction.
[0254] It may also be desirable, in some cases, for the substrate
not to be attached to the microbead. In this case the substrate
would contain an inactive "tag" that requires a further step to
activate it such as photo activation (e.g. of a "caged" biotin
analogue, (Pirrung and Huang, 1996; Sundberg et al., 1995)). After
convertion of the substrate to product the "tag" is activated and
the "tagged" substrate and/or product bound by a tag-binding
molecule (e.g. avidin or strep tavidin) attached to the microbead.
The ratio of substrate to product attached to the nucleic acid via
the "tag" will therefore reflect the ratio of the substrate and
product in solution. A substrate tagged with caged biotin has been
used to select for genes encoding enzymes with phosphotriesterase
activity using a procedure based on compartmentalisation in
microcapsules (Griffiths and Tawfik, 2003). The phosphotriesterase
substrate was hydrolysed in solution in microcapsules containing
active enzyme molecules, and after the reaction was completed, the
caging group was released by irradiation to allow the product to
bind, via the biotin moiety, to microbeads to which the gene
encoding the enzyme was attached.
[0255] After the microbeads and the contents of the microcapsules
are combined, those microbeads coated with regulators can be
selected by affinity purification using a molecule (e.g. an
antibody) that binds specifically to the product or substrate as
appropriate.
[0256] In an alternative embodiment, the invention provides a
method wherein the microbeads are analysed following pooling of the
microcapsules into one or more common compartments. Microbeads
coated with regulator compounds can be identified using changes in
optical properties of the microbeads. The optical properties of
microbeads with product (or substrate) attached can be modified by
either:
(1) the product-microbead complex having characteristic optical
properties not found in the substrate-microbead complex, due to,
for example; (a) the substrate and product having different optical
properties (many fluorogenic enzyme substrates are available
commercially (see for example Haugland, 1996) including substrates
for glycosidases, phosphatases, peptidases and proteases, or (b)
the substrate and product having similar optical properties, but
only the product, and not the substrate binds to, or reacts with,
the microbead; (2) adding reagents which specifically bind to, or
react with, the product (or substrate) and which thereby induce a
change in the optical properties of the microbeads allowing their
identification (these reagents can be added before or after
breaking the microcapsules and pooling the microbeads). The
reagents; (a) bind specifically to, or react specifically with, the
product, and not the substrate, (or vice versa) if both substrate
and product are attached to the microbeads, or (b) optionally bind
both substrate and product if only the product, and not the
substrate binds to, or reacts with, the microbeads (or vice
versa).
[0257] In this scenario, the substrate (or one of the substrates)
can be present in each microcapsule unlinked to the microbead, but
has a molecular "tag" (for example biotin, DIG or DNP or a
fluorescent group). When the regulated enzyme converts the
substrate to product, the product retains the "tag" and is then
captured in the microcapsule by the product-specific antibody. When
all reactions are stopped and the microcapsules are combined, these
microbeads will be "tagged" and may already have changed optical
properties, for example, if the "tag" was a fluorescent group.
Alternatively, a change in optical properties of "tagged"
microbeads can be induced by adding a fluorescently labelled ligand
which binds the "tag" (for example fluorescently-labelled
avidin/streptavidin, an anti-"tag" antibody which is fluorescent,
or a non-fluorescent anti-"tag" antibody which can be detected by a
second fluorescently-labelled antibody).
(iv) Screening for Compound Specificity/Selectivity
[0258] Compounds with specificity or selectivity for certain
targets and not others can be specifically identified by carrying
out a positive screen for regulation of a reaction using one
substrate and a negative screen for regulation of a reaction with
another substrate. For example, two substrates, specific for two
different target enzymes, are each labelled with different
fluorogenic moieties. Each target enzymes catalyse the generation
of a product with with a different fluorescence spectrum resulting
in different optical properties of the microcapsules depending on
the specificity of the compound for two targets.
(v) Screening Using Cells
[0259] In the current drug discovery paradigm, validated
recombinant targets form the basis of in vitro high-throughput
screening (HTS) assays. Isolated proteins cannot, however, be
regarded as representative of complex biological systems; hence,
cell-based systems can provide greater confidence in compound
activity in an intact biological system. A wide range of cell-based
assays for drug leads are known to those skilled in the art. Cells
can be compartmentalised in microcapsules, such as the aqeous
microdroplets of a water-in-oil emulsion (Ghadessy, 2001). The
effect of a compound(s) on a target can be determined by
compartmentalising a cell (or cells) in a microcapsule together
with a compound(s) and using an appropriate cell-based assay to
identify those compartments containing compounds with the desired
effect on the cell(s). The use of water-in-fluorocarbon emulsions
may be particularly advantageous: the high gas dissolving
[0260] 61 capacity of fluorocarbons can support the exchange of
respiratory gases and has been reported to be beneficial to cell
culture systems (Lowe, 2002).
(vi) Flow Cytometry
(vi) Flow Analysis and Sorting
[0261] In a preferred embodiment of the invention the microcapsules
or microbeads will be analysed and, optionally, sorted by flow
cytometry. Many formats of microcapsule can be analysed and,
optionally, sorted directly using flow cytometry.
[0262] In a highly preferred embodiment, microfluidic devices for
flow analysis and, optionally, flow sorting (Fu, 2002) of
microdroplets and microbeads will be used.
[0263] A variety of optical properties can be used for analysis and
to trigger sorting, including light scattering (Kerker, 1983) and
fluorescence polarisation (Rolland et al., 1985). In a highly,
preferred embodiment the difference in optical properties of the
microcapsules or microbeads will be a difference in fluorescence
and, if required, the microcapsules or microbeads will be sorted
using a microfluidic or conventional fluorescence activated cell
sorter (Norman, 1980; Mackenzie and Pinder, 1986), or similar
device. Flow cytometry has a series of advantages:
(1) fluorescence activated cell sorting equipment from established
manufacturers (e.g. Becton-Dickinson, Coulter, Cytomation) allows
the analysis and sorting at up to 100,000 microcapsules or
microbeads s''1. (2) the fluorescence signal from each microcapsule
or microbead corresponds tightly to the number of fluorescent
molecules present. As little as few hundred fluorescent molecules
per microcapsules or microbeads can be quantitatively detected; (3)
the wide dynamic range of the fluorescence detectors (typically 4
log units) allows easy setting of the stringency of the sorting
procedure, thus allowing the recovery of the optimal number
microcapsules or microbeads from the starting pool (the gates can
be set to separate microcapsules or microbeads with small
differences in fluorescence or to only separate out microcapsules
or microbeads with large differences in fluorescence, dependant on
the selection being performed); (4) fluorescence-activated cell
sorting equipment can perform simultaneous excitation and detection
at multiple wavelengths (Shapiro, 1995). allowing positive and
negative selections to be performed simultaneously by monitoring
the labelling of the microcapsules or microbeads with two to
thirteen (or more) fluorescent markers, for example, if substrates
for two alternative targets are labelled with different fluorescent
tags the microcapsules or microbeads can labelled with different
fluorophores dependent on the target regulated.
[0264] If the microcapsules or microbeads are optically tagged,
flow cytometry can also be used to identify the compound or
compounds in the microcapsule or coated on the microbeads (see
below). Optical tagging can also be used to identify the
concentration of the compound in the microcapsule (if more than one
concentration is used in a single experiment) or the number of
compound molecules coated on a microbead (if more than one coating
density is used in a single experiment). Furthermore, optical
tagging can be used to identify the target in a microcapsule (if
more than one target is used in a single experiment). This analysis
can be performed simultaneously with measuring activity, after
sorting of microcapsules containing microbeads, or after sorting of
the microbeads.
(vii) Microcapsule Identification and Sorting
[0265] The invention provides for the identification and,
optionally, the sorting of intact microcapsules where this is
enabled by the sorting techniques being employed. Microcapsules may
be identified and, optionally, sorted as such when the change
induced by the desired compound either occurs or manifests itself
at the surface of the microcapsule or is detectable from outside
the microcapsule. The change may be caused by the direct action of
the compound, or indirect, in which a series of reactions, one or
more of which involve the compound having the desired activity
leads to the change. For example, where the microcapsule is a
membranous microcapsule, the microcapsule may be so configured that
a component or components of the biochemical system comprising the
target are displayed at its surface and thus accessible to reagents
which can detect changes in the biochemical system regulated by the
compound on the microbead within the microcapsule.
[0266] In a preferred aspect of the invention, however,
microcapsule identification and, optionally, sorting relies on a
change in the optical properties of the microcapsule, for example
absorption or emission characteristics thereof, for example
alteration in the optical properties of the microcapsule resulting
from a reaction leading to changes in absorbance, luminescence,
phosphorescence or fluorescence associated with the microcapsule.
All such properties are included in the term "optical". In such a
case, microcapsules can be identified and, optionally, sorted by
luminescence, fluorescence or phosphorescence activated sorting. In
a highly preferred embodiment, flow cytometry is employed to
analyse and, optionally, sort microcapsules containing compounds
having a desired activity which result in the production of a
fluorescent molecule in the microcapsule.
[0267] The methods of the current invention allow reagents to be
mixed rapidly (in <2 ms), hence a spatially-resolved optical
image of microcapsules in micro fluidic network allows time
resolved measurements of the reactions in each microcapsule.
Microcapsules can, optionally, be separated using a microfluidic
flow sorter to allow recovery and further analysis or manipulation
of the molecules they contain. Advantageously, the flow sorter
would be an electronic flow sorting device. Such a sorting device
can be integrated directly on the microfluidic device, and can use
electronic means to sort the microcapsules. Optical detection, also
integrated directly on the microfluidic device, can be used to
screen the microcapsules to trigger the sorting. Other means of
control of the microcapsules, in addition to charge, can also be
incorporated onto the microfluidic device.
[0268] In an alternative embodiment, a change in microcapsule
fluorescence, when identified, is used to trigger the modification
of the microbead within the compartment. In a preferred aspect of
the invention, microcapsule identification relies on a change in
the optical properties of the microcapsule resulting from a
reaction leading to luminescence, phosphorescence or fluorescence
within the microcapsule. Modification of the microbead within the
microcapsules would be triggered by identification of luminescence,
phosphorescence or fluorescence. For example, identification of
luminescence, phosphorescence or fluorescence can trigger
bombardment of the compartment with photons (or other particles or
waves) which leads to modification of the microbead or molecules
attached to it. A similar procedure has been described previously
for the rapid sorting of cells (Keij et al., 1994). Modification of
the microbead may result, for example, from coupling a molecular
"tag", caged by a photolabile protecting group to the microbeads:
bombardment with photons of an appropriate wavelength leads to the
removal of the cage. Afterwards, all microcapsules are combined and
the microbeads pooled together in one environment. Microbeads
coated with compounds exhibiting the desired activity can be
selected by affinity purification using a molecule that
specifically binds to, or reacts specifically with, the "tag".
(C) Compound Libraries
(i) Primary Compound Libraries
[0269] Libraries of primary compounds can be obtained from a
variety of commercial sources. The compounds in the library can be
made by a variety of means well known to those skilled in the art.
Optionally, compound libraries can be made by combinatorial
synthesis using spatially resolved parallel synthesis or using
split synthesis, optionally to generate one-bead-one-compound
libraries. The compounds can, optionally, be synthesised on beads.
These beads can be compartmentalised in microcapsules directly or
the compounds released before compartmentalisation.
[0270] Advantageously, only a single type of compound, but multiple
copies thereof is present in each microcapsule.
[0271] The compounds can, optionally, be connected to microbeads
either covalently or non-covalently by a variety of means that will
be familiar to those skilled in the art (see, for example,
(Hennanson, 1996)).
[0272] Microbeads are available with a variety of surface
chemistries from hydrophobic surfaces (e.g. plain polystyrene), to
very hydrophilic surfaces imparted by a wide variety of functional
surface groups: aldehyde, aliphatic amine, amide, aromatic amine,
carboxylic acid, chloromethyl, epoxy, hydrazide, hydroxyl,
sulfonate and tosyl. The functional groups permit a wide range of
covalent coupling reactions, well known to those skilled in the
art, for stable or reversible attachment of compounds to the
microbead surface.
[0273] Advantageously, the compounds are attached to the microbeads
via a cleavable linker. A variety of such linkers are familiar to
those skilled in the art (see for example (Gordon and
Balasubramanian, 1999)), including for example, linkers which can
be cleaved photochemically and reversible covalent bonds which can
be controlled by changing the pH (e.g. imines and acylhydrazones),
by adjusting the oxido-reductive properties (e.g. disulphides), or
using an external catalyst (e.g. cross-metathesis and
transamidation).
[0274] Advantageously, only a single type of compound, but multiple
copies thereof is attached to each bead.
(II) Secondary Compound Libraries
[0275] Secondary compound libraries are created by reactions
between primary compounds in microcapsules. Secondary compounds can
be created by a variety of two component, and multi-component
reactions well known to those skilled in the art (Armstrong et al.,
1996; Domling, 2002; Domling and Ugi, 2000; Ramstrom and Lehn,
2002).
[0276] To form secondary compound libraries by a two-component
reaction, two sets of compounds are compartmentalised in
microcapsules such that many compartments contain two or more
compounds. Advantageously, the modal number of compounds per
microcapsule is two. Advantageously, the microcapsules contain at
least one type of compound from each set of compounds.
Advantageously, the microcapsules contain one type of compound from
each set of compounds. The secondary compounds are formed by
chemical reactions between primary compounds from different sets.
The secondary compound may be the result of a covalent or
non-covalent reaction between the primary compounds.
[0277] A variety of chemistries, familiar to those skilled in the
art, are suitable to form secondary compounds in two-component
reactions. For example, reversible covalent bonds which "can be
controlled by changing the pH (e.g. imines and acylhydrazones), by
adjusting the oxido-reductive properties (e.g. disulphides), or
using an external catalyst (e.g. cross-metathesis and
transamidation), can be used (Ramstrom and Lehn, 2002).
[0278] hi a further embodiment, the method can also be used to
create secondary compound libraries using three-component,
four-component and higher order multi-component reactions. Three,
four or more sets of compounds (as appropriate) are
compartmentalised in microcapsules. The compounds are
compartmentalised in microcapsules such that many compartments
contain multiple compounds. Advantageously, the modal number of
compounds per microcapsule is equal to the number of components in
the reaction. Advantageously, the microcapsules contain at least
one type of compound from each set of compounds. Advantageously,
the microcapsules contain one type of compound from each set of
compounds. The secondary compounds are formed by chemical reactions
between primary compounds from different sets. The secondary
compound may be the result of covalent or non-covalent reactions
between the primary compounds.
[0279] Examples of suitable multi-component reactions are the
Strecker, Hantzsch, Biginelli, Mannich, Passerini, Bucherer-Bergs
and Pauson-Khand three-component reactions and the Ugi
four-component reaction (Armstrong et al., 1996; Domling, 2002;
Domling and Ugi, 2000).
[0280] Secondary compound libraries may also be built using a
scaffold molecule which is common to all the secondary compounds
(Ramstrom and Lehn, 2002). This scaffold molecule may be
compartmentalised into microcapsules together with the other
primary compounds.
[0281] Li a further embodiment, to form secondary compound
libraries by a two-component reaction, two sets of compounds are
attached to microbeads, advantageously to give only a single type
of molecule per microbead. The microbeads are compartmentalised in
microcapsules such that many compartments contain two or more
microbeads. Advantageously, the modal number of beads per
microcapsule is two. The compounds comprising at least one of the
two sets are released from the microbeads. The secondary compounds
are formed by chemical reactions between primary compounds from
different sets. The secondary compound may be the result of a
covalent or non-covalent reaction between the primary
compounds.
[0282] In a further embodiment, the method can also be used to
create secondary compound libraries using three-component,
four-component and higher order multi-component reactions. Three,
four or more sets of compounds (as appropriate) are attached to
microbeads, advantageously to give only a single type of molecule
per microbead. The microbeads are compartmentalised in
microcapsules such that many compartments contain multiple
microbeads. Advantageously, the modal number of beads per
microcapsule is equal to the number of components in the reaction.
The compounds comprising either all, or all bar one, of the sets
are released from the microbeads. The secondary compounds are
formed by chemical reactions between primary compounds from
different sets. The secondary compound may be the result of
covalent or non-covalent reactions between the primary
compounds.
[0283] Advantageously, the same reversible covalent bond can used
to couple the primary compound to the microbead as is used to form
the secondary compound.
[0284] Secondary compound libraries may also be built using a
scaffold molecule which is common to all the secondary compounds
(Ramstrom and Lehn, 2002). This scaffold molecule may be
compartmentalised into microcapsules together with the
microbeads.
(D) Identification of Compounds
[0285] The compounds in microcapsules or on microbeads can be
identified in a variety of ways. If the identified microcapsules
are sorted (e.g. by using a fluorescence activated cell
sorter--FACS) the compounds can be identified by by direct
analysis, for example by mass-spectroscopy. If the compounds remain
attached to beads isolated as a result of selection (for example by
affinity purification) or sorting (for example using a FACS) they
can also be identified by direct analysis, for example by
mass-spectroscopy. The microcapsules or beads can also be tagged by
a variety of means well known to those skilled in the art and the
tag used to identify the compound attached to the beads (Czarnik,
1997). Chemical, spectrometric, electronic, and physical methods to
encode the compounds may all be used. In a preferred embodiment
microcapsules or beads have different optical properties and are
thereby optically encoded. In a preferred embodiment encoding is
based on microcapsules or beads having different fluorescence
properties, hi a highly preferred embodiment the microcapsules or
beads are encoded using fluorescent quantum dots present at
different concentrations in the microcapsule or bead (Han, 2001).
Microcapsules flowing in an ordered sequence in a microfluidic
channel can also be encoded (wholly or partially) by their sequence
in the stream of microcapsules (positional encoding).
[0286] Advantageously, each compounds is present in different
microcapsules at different concentrations (typically at
concentrations varying from mM to nM) allowing the generation of a
dose-response curve. Fusing microcapsules to give all possible
permutations of several different substrate concentrations and
compound concentrations would allow the determination of the mode
of inhibition (e.g. competitive, noncompetitive, uncompetitive or
mixed inhibition) and inhibition constant (K.sub.1) of an
inhibitory compound. The concentration of the compounds in the
microcapsules can be determined by, for example, optical encoding
or positional encoding of the microcapsules or microbeads as
above.
(E) Identification of Targets
[0287] Advantageously, multiple different targets can be
compartmentalised in microcapsules such that each microcapsule
contains multiple copies of the same target. For example, multiple
protein kinases, or multiple polymorphic variants of a single
target, can be compartmentalised to allow the specificity of
compounds to be determined. The identity of the target in a
microcapsule can be determined by, for example, optical encoding or
positional encoding of the microcapsules or microbeads as
above.
[0288] Expressed in an alternative manner, there is provided a
method for the synthesis and identification of compounds which bind
to a target component of a biochemical system or modulate the
activity of the target, comprising the steps of:
(a) compartmentalising two or more sets of primary compounds into
microcapsules together with the target such that many compartments
contain two or more primary compounds; (b) forming secondary
compounds in the microcapsules by chemical reactions between
primary compounds from different sets; and (c) identifying subsets
of primary compounds which react to form secondary compounds which
bind to or modulate the activity of the target.
[0289] There is also provided a method for the synthesis and
identification of compounds which bind to a target component of a
biochemical system or modulate the activity of the target,
comprising the steps of:
(1) attaching two or more sets of primary compounds onto
microbeads; (2) compartmentalising the microbeads into
microcapsules together with the target such that many compartments
contain two or more microbeads; (3) releasing the primary compounds
from the microbeads; (4) forming secondary compounds in the
microcapsules by chemical reactions between primary compounds from
different sets; and (5) identifying subsets of primary compounds
which react to form secondary compounds which bind to or modulate
the activity of the target.
[0290] If the primary compounds react, not only with other primary
compounds in the same compartment, but also with other microbeads
in the compartment, the primary compounds which react together to
form a secondary compound can be identified by direct analysis of
the compounds present on a microbeads isolated as a result of
selection or sorting. For example, if the primary compounds are
linked to the beads via a disulphide bond when they are released in
the compartment the primary compounds will react both with each
other to form a secondary compound and with the sulphydryl groups
on the beads. Hence, if two beads are co-compartmentalised, each
bead will end up carrying both primary compounds. After isolation
of these beads both primary compounds which reacted to form the
secondary compound can be identified.
(F) Rapid Mixing of Reagents in Microcapsules
[0291] Advantageously, after fusion of microcpasules, the reagents
contained in the fused microcapsule can be mixed rapidly using
chaotic advection. By passing the droplets through channels that
disrupt the laminar flow lines of the fluid within the droplets,
their contents can be rapidly mixed, fully initiating any chemical
reactions.
(G) Sensing Microcapsule Characteristics
[0292] In certain aspects of the invention, sensors are provided
that can sense and/or determine one or more characteristics of the
fluidic droplets, and/or a characteristic of a portion of the
fluidic system containing the fluidic droplet (e.g., the liquid
surrounding the fluidic droplet) in such a manner as to allow the
determination of one or more characteristics of the fluidic
droplets. Characteristics determinable with respect to the droplet
and usable in the invention can be identified by those of ordinary
skill in the art. Non-limiting examples of such characteristics
include fluorescence, spectroscopy (e.g., optical, infrared,
ultraviolet, etc.), radioactivity, mass, volume, density,
temperature, viscosity, pH, concentration of a substance, such as a
biological substance (e.g., a protein, a nucleic acid, etc.), or
the like.
[0293] In some cases, the sensor may be connected to a processor,
which in turn, cause an operation to be performed on the fluidic
droplet, for example, by sorting the droplet, adding or removing
electric charge from the droplet, fusing the droplet with another
droplet, splitting the droplet, causing mixing to occur within the
droplet, etc., for example, as previously described. For instance,
in response to a sensor measurement of a fluidic droplet, a
processor may cause the fluidic droplet to be split, merged with a
second fluidic droplet, sorted etc.
[0294] One or more sensors and/or processors may be positioned to
be in sensing communication with the fluidic droplet. "Sensing
communication," as used herein, means that the sensor may be
positioned anywhere such that the fluidic droplet within the
fluidic system (e.g., within a channel), and/or a portion of the
fluidic system containing the fluidic droplet may be sensed and/or
determined in some fashion. For example, the sensor may be in
sensing communication with the fluidic droplet and/or the portion
of the fluidic system containing the fluidic droplet fluidly,
optically or visually, thermally, pneumatically, electronically, or
the like. The sensor can be positioned proximate the fluidic
system, for example, embedded within or integrally connected to a
wall of a channel, or positioned separately from the fluidic system
but with physical, electrical, and/or optical communication with
the fluidic system so as to be able to sense and/or determine the
fluidic droplet and/or a portion of the fluidic system containing
the fluidic droplet (e.g., a channel or a microchannel, a liquid
containing the fluidic droplet, etc.). For example, a sensor may be
free of any physical connection with a channel containing a
droplet, but may be positioned so as to detect electromagnetic
radiation arising from the droplet or the fluidic system, such as
infrared, ultraviolet, or visible light. The electromagnetic
radiation may be produced by the droplet, and/or may arise from
other portions of the fluidic system (or externally of the fluidic
system) and interact with the fluidic droplet and/or the portion of
the fluidic system containing the fluidic droplet in such as a
manner as to indicate one or more characteristics of the fluidic
droplet, for example, through absorption, reflection, diffraction,
refraction, fluorescence, phosphorescence, changes in polarity,
phase changes, changes with respect to time, etc. As an example, a
laser may be directed towards the fluidic droplet and/or the liquid
surrounding the fluidic droplet, and the fluorescence of the
fluidic droplet and/or the surrounding liquid may be determined.
"Sensing communication," as used herein may also be direct or
indirect. As an example, light from the fluidic droplet may be
directed to a sensor, or directed first through a fiber optic
system, a waveguide, etc., before being directed to a sensor.
[0295] Non-limiting examples of sensors useful in the invention
include optical or electromagnetically-based systems. For example,
the sensor may be a fluorescence sensor (e.g., stimulated by a
laser), a microscopy system (which may include a camera or other
recording device), or the like. As another example, the sensor may
be an electronic sensor, e.g., a sensor able to determine an
electric field or other electrical characteristic. For example, the
sensor may detect capacitance, inductance, etc., of a fluidic
droplet and/or the portion of the fluidic system containing the
fluidic droplet.
[0296] As used herein, a "processor" or a "microprocessor" is any
component or device able to receive a signal from one or more
sensors, store the signal, and/or direct one or more responses
(e.g., as described above), for example, by using a mathematical
formula or an electronic or computational circuit. The signal may
be any suitable signal indicative of the environmental factor
determined by the sensor, for example a pneumatic signal, an
electronic signal, an optical signal, a mechanical signal, etc.
(H) Materials
[0297] A variety of materials and methods, according to certain
aspects of the invention, can be used to form any of the
above-described components of the microfluidic systems and devices
of the invention. In some cases, the various materials selected
lend themselves to various methods. For example, various components
of the invention can be formed from solid materials, in which the
channels can be formed via micromachining, film deposition
processes such as spin coating and chemical vapor deposition, laser
fabrication, photolithographic techniques, etching methods
including wet chemical or plasma processes, and the like. See, for
example, Scientific American, 248:44-55, 1983 (Angell, et at). In
one embodiment, at least a portion of the fluidic system is formed
of silicon by etching features in a silicon chip. Technologies for
precise and efficient fabrication of various fluidic systems and
devices of the invention from silicon are known. In another
embodiment, various components of the systems and devices of the
invention can be formed of a polymer, for example, an elastomeric
polymer such as polydimethylsiloxane ("PDMS"),
polytetrafluoroethylene ("PTFE" or TEFLON.RTM.), or the like.
[0298] Different components can be fabricated of different
materials. For example, a base portion including a bottom wall and
side walls can be fabricated from an opaque material such as
silicon or PDMS, and a top portion can be fabricated from a
transparent or at least partially transparent material, such as
glass or a transparent polymer, for observation and/or control of
the fluidic process. Components can be coated so as to expose a
desired chemical functionality to fluids that contact interior
channel walls, where the base supporting material does not have a
precise, desired functionality. For example, components can be
fabricated as illustrated, with interior channel walls coated with
another material. Material used to fabricate various components of
the systems and devices of the invention, e.g., materials used to
coat interior walls of fluid channels, may desirably be selected
from among those materials that will not adversely affect or be
affected by fluid flowing through the fluidic system, e.g.,
material(s) that is chemically inert in the presence of fluids to
be used within the device.
[0299] In one embodiment, various components of the invention are
fabricated from polymeric and/or flexible and/or elastomeric
materials, and can be conveniently formed of a hardenable fluid,
facilitating fabrication via molding (e.g. replica molding,
injection molding, cast molding, etc.). The hardenable fluid can be
essentially any fluid that can be induced to solidify, or that
spontaneously solidifies, into a solid capable of containing and/or
transporting fluids contemplated for use in and with the fluidic
network. In one embodiment, the hardenable fluid comprises a
polymeric liquid or a liquid polymeric precursor (i.e. a
"prepolymer"). Suitable polymeric liquids can include, for example,
thermoplastic polymers, thermoset polymers, or mixture of such
polymers heated above their melting point. As another example, a
suitable polymeric liquid may include a solution of one or more
polymers in a suitable solvent, which solution forms a solid
polymeric material upon removal of the solvent, for example, by
evaporation. Such polymeric materials, which can be solidified
from, for example, a melt state or by solvent evaporation, are well
known to those of ordinary skill in the art. A variety of polymeric
materials, many of which are elastomeric, are suitable, and are
also suitable for forming molds or mold masters, for embodiments
where one or both of the mold masters is composed of an elastomeric
material. A non-limiting list of examples of such polymers includes
polymers of the general classes of silicone polymers, epoxy
polymers, and acrylate polymers. Epoxy polymers are characterized
by the presence of a three-membered cyclic ether group commonly
referred to as an epoxy group, 1,2-epoxide, or oxirane. For
example, diglycidyl ethers of bisphenol A can be used, in addition
to compounds based on aromatic amine, triazine, and cycloaliphatic
backbones. Another example includes the well-known Novolac
polymers. Non-limiting examples of silicone elastomers suitable for
use according to the invention include those formed from precursors
including the chlorosilanes such as methylchlorosilanes,
ethylchlorosilanes, phenylchlorosilanes, etc.
[0300] Silicone polymers are preferred in one set of embodiments,
for example, the silicone elastomer polydimethylsiloxane.
Non-limiting examples of PDMS polymers include those sold under the
trademark Sylgard by Dow Chemical Co., Midland, Mich., and
particularly Sylgard 182, Sylgard 184, and Sylgard 186. Silicone
polymers including PDMS have several beneficial properties
simplifying fabrication of the microfiuidic structures of the
invention. For instance, such materials are inexpensive, readily
available, and can be solidified from a prepolymeric liquid via
curing with heat. For example, PDMSs are typically curable by
exposure of the prepolymeric liquid to temperatures of about, for
example, about 65.degree. C. to about 75.degree. C. for exposure
times of, for example, about an hour. Also, silicone polymers, such
as PDMS, can be elastomeric and thus may be useful for forming very
small features with relatively high aspect ratios, necessary in
certain embodiments of the invention. Flexible (e.g., elastomeric)
molds or masters can be advantageous in this regard.
[0301] One advantage of forming structures such as microfiuidic
structures of the invention from silicone polymers, such as PDMS,
is the ability of such polymers to be oxidized, for example by
exposure to an oxygen-containing plasma such as an air plasma, so
that the oxidized structures contain, at their surface, chemical
groups capable of cross-linking to other oxidized silicone polymer
surfaces or to the oxidized surfaces of a variety of other
polymeric and non-polymeric materials. Thus, components can be
fabricated and then oxidized and essentially irreversibly sealed to
other silicone polymer surfaces, or to the surfaces of other
substrates reactive with the oxidized silicone polymer surfaces,
without the need for separate adhesives or other sealing means. In
most cases, sealing can be completed simply by contacting an
oxidized silicone surface to another surface without the need to
apply auxiliary pressure to form the seal. That is, the
pre-oxidized silicone surface acts as a contact adhesive against
suitable mating surfaces. Specifically, in addition to being
irreversibly sealable to itself, oxidized silicone such as oxidized
PDMS can also be sealed irreversibly to a range of oxidized
materials other than itself including, for example, glass, silicon,
silicon oxide, quartz, silicon nitride, polyethylene, polystyrene,
glassy carbon, and epoxy polymers, which have been oxidized in a
similar fashion to the PDMS surface (for example, via exposure to
an oxygen-containing plasma). Oxidation and sealing methods useful
in the context of the present invention, as well as overall molding
techniques, are described in the art, for example, in an article
entitled "Rapid Prototyping of Microfluidic Systems and
Polydimethylsiloxane," Anal. Chem., 70:474-480, 1998 (Duffy et al),
incorporated herein by reference.
[0302] Another advantage to forming microfluidic structures of the
invention (or interior, fluid-contacting surfaces) from oxidized
silicone polymers is that these surfaces can be much more
hydrophilic than the surfaces of typical elastomeric polymers
(where a hydrophilic interior surface is desired). Such hydrophilic
channel surfaces can thus be more easily filled and wetted with
aqueous solutions than can structures comprised of typical,
unoxidized elastomeric polymers or other hydrophobic materials.
[0303] hi one embodiment, a bottom wall is formed of a material
different from one or more side walls or a top wall, or other
components. For example, the interior surface of a bottom wall can
comprise the surface of a silicon wafer or microchip, or other
substrate. Other components can, as described above, be sealed to
such alternative substrates. Where it is desired to seal a
component comprising a silicone polymer (e.g. PDMS) to a substrate
(bottom wall) of different material, the substrate may be selected
from the group of materials to which oxidized silicone polymer is
able to irreversibly seal (e.g., glass, silicon, silicon oxide,
quartz, silicon nitride, polyethylene, polystyrene, epoxy polymers,
and glassy carbon surfaces which have been oxidized).
Alternatively, other sealing techniques can be used, as would be
apparent to those of ordinary skill in the art, including, but not
limited to, the use of separate adhesives, thermal bonding, solvent
bonding, ultrasonic welding, etc.
[0304] Various aspects and embodiments of the present invention are
illustrated in the following examples. It will be appreciated that
modification of detail may be made without departing from the scope
of the invention.
Examples
Example 1. Microfluidic Device for Combinatorial Chemistry and
Screening Using In Vitro Compartmentalisation
[0305] A schematic representation of the microfluidic device is
shown in FIG. 15. Microchannels are fabricated with rectangular
cross-sections using rapid prototyping in poly(dimethylsiloxane)
(PDMS) (McDonald and Whitesides, 2002) and rendered hydrophobic as
(Song and Ismagilov, 2003). Syringe pumps were used to drive
flows
[0306] (Harvard Apparatus PHD 2000 Infusion pumps). For aqueous
solutions, 250 .mu.l Hamilton Gastight syringes (1700 series, TLL)
with removeable needles of 27-gauge are used with 30-gauge
TEFLON.RTM. tubing (Weico Wire and Cable). For the carrier fluid, 1
ml Hamilton Gastight syringes (1700 series, TLL) are used with
30-gauge TEFLON.RTM. needles with one hub from Hamilton (Song and
Ismagilov, 2003). The carrier fluid is 9% (v/v)
C.sub.6F.sub.11C.sub.2H.sub.4OH in perfluorodecaline (PFD) (Song et
al., 2003). The microfluidic device consists of a series of
interconnected modules. Each module has a specific function. These
include modules that will produce droplets, fuse droplets, mix
droplets, react droplets, detect droplets, and sort droplets (see
FIG. 16). In one example, droplets are made, consisting of
different molecules or different concentrations of molecules.
Droplets are made at rates of up to 10.sup.4 sec.sup.-1, and are
made with a polydispersity of less than 1.5% and with sizes ranging
from 1 .mu.ra. to 100 .mu.m. Each droplet is fused with a second
droplet containing a second set of reactants, and is rapidly mixed
to initiate the chemical reaction. This chemical reaction is
allowed to proceed in each droplet by passing it through a delay
channel. Each droplet is then fused with another droplet containing
a second set of reactants, and is subsequently rapidly mixed to
initiate the second set of chemical reactions. After the second
reaction has proceeded in a delay module, the results of the
reaction is determined using an optical sensor or other form of
detection module. Finally, the desired droplets are sorted into two
populations based on signal form the optical detection module, one
population is kept for further processing and the other discarded.
These and other modules can be used in this combination, or in
other combinations.
[0307] Droplet generation module: We use a flow-focusing geometry
to form the drops. A water stream is infused from one channel
through a narrow constriction; counter propagating oil streams
hydrodynamically focus the water stream reducing its size as it
passes through the constriction as shown in FIG. 23A. This droplet
generator can be operated in a flow regime that produces a steady
stream of uniform droplets of water in oil. The size of the water
droplets is controlled by the relative flow rates of the oil and
the water; the viscous forces overcome surface tension to create
uniform droplets. If the flow rate of the water is too high a
longer jet of fluid passes through the orifice and breaks up into
droplets further down stream; these droplets are less uniform in
size. If the flow rate of the water is too low, the droplet breakup
in the orifice becomes irregular again, producing a wider range of
droplet sizes. While this emulsification technology is robust, it
is limited to producing droplets of one size at any given flow
rate; this droplet size is largely determined by the channel
dimensions. Moreover, the timing of the droplet production cannot
be controlled.
[0308] We overcome these limitations by incorporating electric
fields to create an electrically addressable emulsification system.
To achieve this, we apply high voltage to the aqueous stream and
charge the oil water interface, as shown schematically in FIG. 23
A. The water stream behaves as a conductor while the oil is an
insulator; electrochemical reactions charge the fluid interface
like a capacitor. At snap-off, charge on the interface remains on
the droplet. In addition, the droplet volume, Vd, and frequency, f,
can be tailored over nearly three orders of magnitude without
changing the infusion rate of the oil or water. Droplet size and
frequency are not independent; instead their product is determined
by the infusion rate of the dispersed phase Qd=f Vd. The droplet
size decreases with increasing field strength, as shown in FIGS.
23, B to E.
[0309] The dependence of the droplet size on applied voltage for
three different flow rates is summarized in FIG. 23F. At low
applied voltages the electric field has a negligible effect, and
droplet formation is driven exclusively by the competition between
surface tension and viscous flow. By contrast, at high electric
field strengths, there is a significant additional force on the
growing drop, F=qE, where q is the charge on the droplet. Since the
droplet interface behaves as a capacitor, q is proportional to the
applied voltage, V. This leads to a V.sup.2 dependence of the
force, which accounts for the decrease in droplet size with
increasing applied field shown in FIG. 23F. If the electric field
becomes too large, the charged interface of the water stream is
repelled by the highly charged drops; this destabilizes the
production and increases the variation in droplet size.
[0310] The electronic control afforded by the field-induced droplet
formation provides an additional valuable benefit: it allows the
phase of the droplet break-off to be adjusted within the production
cycle. This is accomplished by increasing the field above the
critical break-off field only at the instant the droplet is
required. This provides a convenient means to precisely synchronize
the production and arrival of individual droplets at specific
locations.
[0311] Droplet coalescer module: An essential component in any
droplet-based reaction-confinement system is a droplet coalescing
module which combines two or more reagents to initiate a chemical
reaction. This is particularly difficult to achieve in a
microfluidic device because surface tension, surfactant
stabilization, and drainage forces all hinder droplet coalescence;
moreover, the droplets must cross the stream lines that define
their respective flows and must be perfectly synchronized to arrive
at a precise location for coalescence.
[0312] Use of electrostatic charge overcomes these difficulties;
placing charges of opposite sign on each droplet and applying an
electric field forces them to coalesce. As an example we show a
device consisting of two separate nozzles that generate droplets
with different compositions and opposite charges, sketched in FIG.
24A. The droplets are brought together at the confluence of the two
streams. The electrodes used to charge the droplets upon formation
also provide the electric field to force the droplets across the
stream lines, leading to coalesce. Slight variations in the
structure of the two nozzles result in slight differences in the
frequency and phase of their droplet generation in the absence of a
field. Thus the droplets differ in size even though the infusion
rates are identical. Moreover, the droplets do not arrive at the
point of confluence at exactly the same time. As a result the
droplets do not coalesce as shown in FIG. 24B. By contrast, upon
application of an electric field, droplet formation becomes exactly
synchronized, ensuring that pairs of identically sized droplets
each reach the point of confluence simultaneously. Moreover, the
droplets are oppositely charged, forcing them to traverse the
stream lines and contact each other, thereby causing them to
coalesce, as shown in FIG. 24C. The remarkable synchronization of
the droplet formation results from coupling of the break-off of
each of the pair of droplets as mediated by the electric field; the
magnitude of the electric field varies as the separation between
the leading edges of the two droplets changes and the frequency of
droplet break-off is mode-locked to the electric field. A minimum
charge is required to cause droplets to coalesce, presumably
because of the stabilizing effects of the surfactant coating; this
is clear from FIG. 24D which shows the voltage dependence of the
percentage of drops that contact each other that actually
coalesce.
[0313] Droplet mixer module: Rapid mixing is achieved through
either successive iterations of translation and rotation, FIG. 25,
or by coalescing drops along the direction parallel to the flow
direction, FIG. 26.
[0314] Droplet reactor/time delay module: A delay line is used to
provide a fixed time for a reaction. Two non-limiting examples of
how this can be achieved are `single file` and `large
cross-section` channels. The `single file` delay line uses length
to achieve a fixed reaction time. As this often results in
exceptionally long channels, it is desirable to place spacer
droplets of a third fluid, immicible with both the carrier oil and
the aqueous droplets inbetween aqueous droplet pairs. There is then
an alternation between aqueous and non-aqueous droplets in a
carrier oil. This is shown in FIG. 27A. A second possibility for
achieving a long time delay is to use wide and deap channel having
a `large cross-sectiononal area` to slow the average velocity of
the droplets. An example of this is shown in FIG. 27B.
[0315] Recharging module: The use of oppositely charged droplets
and an electric field to combine and mix reagents is extremely
robust, and 100% of the droplets coalesce with their partner from
the opposite stream. However, after they coalesce the resultant
drops carry no electrostatic charge. While it is convenient to
charge droplets during formation, other methods must be employed in
any robust droplet-based microfluidic system to recharge the mixed
droplets if necessary for further processing. This is readily
accomplished through the use of extensional flow to split neutral
droplets in the presence of an electric field which polarizes them,
resulting in two oppositely charged daughter droplets; this is
sketched in FIG. 28A. The photomicrograph in FIG. 28B shows neutral
droplets entering a bifurcation and splitting into charged daughter
droplets. The dashed region in FIG. 28B is enlarged in FIG. 28C to
illustrate the asymmetric stretching of the charged droplets in the
electric field. The vertical dashed lines indicate the edges of the
electrodes where the droplets return to their symmetric spherical
shape. The electric field also allows precision control of the
droplet splitting providing the basis for a robust droplet division
module which allows the splitting of the contents into two or more
aliquots of identical reagent, facilitating multiple assays on the
contents of the same microreactor.
[0316] Detection module: The detection module consists of an
optical fiber, one or more laser, one or more dichroic beam
splitter, bandpass filters, and one or more photo multiplying tube
(PMT) as sketched in FIG. 29.
[0317] Sorting module: The contents of individual droplets must be
probed, and selected droplets sorted into discreet streams. The use
of electrostatic charging of droplets provides a means for sorting
that can be precisely controlled, can be switched at high
frequencies, and requires no moving parts. Electrostatic charge on
the droplets enables drop-by-drop sorting based on the linear
coupling of charge to an external electric field. As an example, a
T-junction bifurcation that splits the flow of carrier fluid
equally will also randomly split the droplet population equally
into the two streams, as shown in FIG. 30A. However, a small
electric field applied at the bifurcation precisely dictates which
channel the drops enter; a schematic of the electrode configuration
is shown in FIG. 30B. Varying the direction of the field varies the
direction of the sorted droplets as shown in FIGS. 30C and 30D. The
large forces that can be imparted on the droplets and the high
switching frequency make this a fast and robust sorting engine with
no moving parts; thus the processing rate is limited only by the
rate of droplet generation.
Example 2
Screening for Protein Tyrosine Phosphatase IB (PTP1B) Inhibitors
Using Microcapsules in Microfluidic Systems
[0318] PTP1B is a negative regulator of insulin and leptin signal
transduction. Resistance to insulin and leptin are hallmarks of
type 2 diabetes mellitus and obesity and hence PTP1B is an
attractive drug target for diabetes and obesity therapy (Johnson et
al., 2002). Using a microfluidic device as described in Example 1,
we describe how PTP1B inhibitors can be screened using
microcapsules in a microfluidic system.
[0319] All water-soluble reagents are dissolved in (25 mM HEPES, pH
7.4, 125 mM NaCl, 1 mM EDTA), a buffer compatible with PTP1B
activity. A solution of the target enzyme (human recombinant PTP1B,
residues 1-322; Biomol Research Laboratories, Inc.) at 50 mU/ml and
a solution of either a) 100 .mu.M compound 2 (FIG. 17), which has a
bis-difluoromethylene phosphonate and is a known PTP1B inhibitor
(Johnson et al., 2002), or b) 100 .mu.M hydrocinnamic acid
(Aldrich), a compound that is not a PTP1B inhibitor are
compartmentalised into microcapsules using the device. Each
microcapsule containing target enzyme is fused with a microcapsule
containing compound 2 or a microcapsule containing hydrocinnamic
acid. Microcapsules containing either compound 2 or hydrocinnamic
acid can be formed by switching between injection with syringes
containing compound 2 and hydrocinnamic acid.
[0320] After microcapsule fusion the contents are rapidly mixed.
After this point the microcapsules are run for up to 1 min through
a 60 cm long microchannel (to allow inhibitor binding). This
microchannel is then merged with a second microchannel containing
aqueous microcapsules containing the fluorogenic PTP1B substrate
6,8-difluoro-4-methylumbelliferyl phosphate (DiFMUP) (Molecular
Probes) in 25 mM HEPES, pH 7.4, 125 mM NaCl, 1 mM EDTA and the
microcapsules fused pairwise. The fused microcapsules are then run
for up to 2 min through a 60 cm long microchannel. Fluorescence of
the microcapsules due to production of DiFMU (excitation/emmission
maxima 358/452 nm; blue fluorescence) is measured. Predominantly,
microcapsules exhibiting blue fluorescence are those containing
hydrocinnamic acid whereas microcapsules containing compound 2
exhibit low fluorescence due to inhibition of PTP1B.
Example 3. Screening of PTP1B Inhibitors from a Compound
Library
[0321] 96 aqueous mixtures are made on ice (to prevent reaction).
The first mixture contains 100 .mu.M compound 2 (FIG. 17), which
has a ozs-difluoromethylene phosphonate and is a known PTP1B
inhibitor (Johnson et al., 2002), and a pre-defined ratio of
Qdot.TM. Streptavidin Conjugates with emmission maxima at 585 nm,
655 nm and 705 nm (Quantum Dot Corporation, Hayward Calif.) in a
buffer compatible with PTP1B activity (25 mM HEPES, pH 7.4, 125 mM
NaCl, 10% glycerol, 1 mM EDTA) (Doman et al., 2002). The 95 other
aqueous mixtures are identical to the above but each contain one of
95 carboxylic acids from the Carboxylic Acid Organic Building Block
Library (Aldrich) in place of compound 2, and different ratios of
Qdot.TM. Streptavidin Conjugates with emission maxima at 585 run,
655 nm and 705 nm. In all mixtures the concentration of the 705 nm
Qdot.TM. Streptavidin Conjugates is 100 nM, and the concentrations
of the 585 nm and 655 nm Qdot.TM. Streptavidin Conjugates is either
0, 11, 22, 33, 44, 55, 66, 77, 88 or 100 nM. Hence, there are 100
(10.times.10) permutations of Qdot.TM. Streptavidin Conjugate
concentrations which allows the microcapsules containing each
compound to have a unique fluorescence signature which is read by
determining the fluorescence ratio of fluorescence at at 705 nm,
585 nm and 655 nm.
[0322] The 96 mixtures are distributed into 96 wells of a
microtitre plate. Aliquots from each well of the plate are loaded
sequentially into the microfluidic device described in Example 1
using thin tubes connected to the microfluidic device which are
dipped into reservoirs containing the desired compounds, and
capillary action is used to draw the desired compound from the
reservoir into the microfluidic device. The mixtures are
compartmentalised into microcapsules in the device. Each
microcapsule is fused with another microcapsule containing the
target enzyme (human recombinant PTP1B, residues 1-322; Biomol
Research Laboratories, Inc.) at 5 mU/ml and rapidly mixed. After
incubating for 10 min, at 37.degree. C. in a delay line the
microcapsule is fused with a further microcapsule containing the
fluorogenic PTP1B substrate 6,8-difluoro-4-methylumbelliferyl
phosphate (DiFMUP) (Molecular Probes), and incubated at 370 C for
30 min. in a delay line. Inhibitors reduce the amount of
non-fluorescent substrate (DiFMUP) converted to the
dephosphorylated product (DiFMU; excitation/emmission maxima
358/452 nm; blue fluorescence). Microcapsule fluorescence is then
analysed. Predominantly, all microcapsules exhibited blue
fluorescence due to dephosphorylation of DiFMUP by PTP1B except
those with the Qdot fluorescence signature of the microcapsules
containing compound 2.
Example 4. Attachment of a Compound Library to Microbeads
[0323] 5.5 .mu.m diameter polystyrene microbeads that bear
carboxylate functional groups on the surface are commercially
available (Luminex Corporation) in an optically tagged form, as a
result of incorporation of precise ratios of orange (585 nm), and
red (>650 nm) fluorochromes (Fulton et al., 1997). A set of 100
such beads, each with a unique optical signature are modified with
an excess of ethylenediamine and EDC
(1-ethyl-3-(3-dimethylaminopropyl)carbodiimide hydrochloride
(Pierce) as (Hermanson, 1996) to create primary amino groups on the
surface. The photocleavable linker
4-(4-hydroxymethyl-2-methoxy-5-nitrophenoxy)butanoic acid
(NovaBiochem) (Holmes and Jones, 1995) is then attached to the
beads by forming an amide bond using EDC as above. 100 different
carboxylic acids from the Carboxylic Acid Organic Building Block
Library (Aldrich) are then coupled to the beads, by reacting with
the linker alcohol to form a carboxylate ester, each of the 100
different optically tagged beads being coupled to a different
carboxylic acid, and each bead being derivatised with .about.106
molecules of carboxylic acid. Irradiation for 4 min on ice using a
B100 AP 354 nm UV lamp (UVP) from a distance of .about.5 cm results
in release of the compounds from the beads as carboxylic acids.
Example 5. Screening for Inhibitors of the Enzyme Protein Tyrosine
Phosphatase IB (PTP1B) Using Compounds Attached to Microbeads
[0324] 5.5 .mu.m diameter polystyrene microbeads that bear
carboxylate functional groups on the surface are commercially
available (Luminex Corporation) in an optically tagged form, as a
result of incorporation of precise ratios of orange (585 nm), and
red (>650 nm) fluorochromes (Fulton et al., 1997). First, the
carboxylate functional groups on the microbeads are converted to
primary amines using ethylenediamine and EDC as in example 6. A
phosphopeptide substrate for PTP1B, the undecapeptide EGFR988-Qg8
(D ADEp YLIPQQG) (Zhang et al., 1993), is then coupled to both sets
of microbeads via the surface amino groups using EDC. This peptide
is made by solid phase synthesis on Sieber Amide resin
(9-Fmoc-amino-xanthen-3-yloxy-Merrifield resin) (Novabiochem) with
orthogonal protection on the side chain carboxylate groups using
carboxylate-O-allyl esters. A linker comprised of tetradecanedioic
acid is coupled to the N-terminus and the peptide cleaved from the
beads using 1% TFA to yield a peptide with a C-terminal amide The
peptide is coupled to the beads (using EDC) via the linker to give
.about.105 peptides per bead. The remaining surface amino groups
are then modified by attaching the photochemically cleavable linker
4-(4-hydroxymethyl-2-methoxy-5-nitrophenoxy)butanoic acid as in
example 6. The protecting groups on the side chain carboxylates of
the peptide are then removed using Pd(Ph3)4/CHCl3/HOAc/N-methyl
morpholine. A first set of microbeads is derivatised with
3-(4-difluorophosphonomethylphenyl)propanoic acid (compound 1, FIG.
17), a compound that is a known PTP1B inhibitor (Johnson et al.,
2002). A second set of beads, with a distinct optical tag from the
first set of beads, is derivatised with hydrocinnamic acid
(Aldrich), a compound that is not a PTP1B inhibitor. In each case
the compound is coupled by reacting with the linker alcohol to form
a carboxylate ester as in example 6. Each microbead is derivatised
with .about.10.sup.6 molecules (Fulton et al., 1997).
[0325] The microbeads are then screened using the microfluidic
system outlined in FIG. 15. The two sets of microbeads are mixed in
ratios varying from 1:1000 to 1:1 (compound 1 beads: hydrocinnamic
acid beads) and 10.sup.8 total microbeads are mixed with the target
enzyme (human recombinant PTP1B, residues 1-322; Biomol Research
Laboratories, Inc.) at a concentration of 10 nM, on ice (to prevent
reaction) in a buffer compatible with PTP1B activity (25 mM HEPES,
pH 7.4, 125 mM NaCl, 10% glycerol, 1 mM EDTA) (Doman et al., 2002).
Single beads and target enzyme (PTP1B) are then colocalised in
microcapsules by forming microcapsules using the microfluidic
system described in Example 1. The concentration of beads is such
that most microcapsules contain one or no beads. Each microcapsule
is fused with another microcapsule containing the target enzyme
(human recombinant PTP1B, residues 1-322; Biomol Research
Laboratories, Inc.) at 5 mU/ml and rapidly mixed. The compound is
released photochemically (as in example 4). After incubating for 10
min, at 37.degree. C. in a delay line the microcapsule is fused
with a further microcapsule containing the fluorogenic PTP1B
substrate 6,8-difluoro-4-methylumbelliferyl phosphate (DiFMUP)
(Molecular Probes), and incubated at 37.degree. C. for 30 min. in a
delay line. Inhibitors reduce the amount of substrate converted to
product (dephosphorylated peptide). The microcapsules are
collected, cooled to 4.degree. C. and broken as (Griffiths and
Tawfik, 2003) into 100 .mu.M vanadate to stop the reaction (Harder
et al., 1994). After labelling with an anti-substrate
(anti-phosphotyrosine) antibody labelled with the green (530 nm)
fluorochrome fluorescein isothiocyanate (mouse monoclonal IgG2b
PY20 (Santa Cruz) according to the manufacturer's instructions,
beads are analysed by 3-colour flow cytometry using a FACScan
(Becton-Dickinson), FACScalibur (Becton-Dickinson) or MoFIo
(Cytomation) flow cytometers to simultaneously determine the extent
of inhibition and the compound on the beads. Predominantly,
dephosphorylation of the peptide is only observed on those
microbeads which were coated with PTPIB inhibitors, and not on
other microbeads.
Example 6. Screening of PTP1B Inhibitors from a Compound Library
Attached to Microbeads
[0326] A set of 100 5.5 .mu.m diameter polystyrene microbeads,
bearing carboxylate functional groups on the surface and each with
a unique optical signature (Luminex Corporation) as a result of
incorporation of precise ratios of orange (585 nm), and red
(>650 run) fluorochromes (Fulton et al., 1997) are derivatised
with a phosphopeptide substrate for PTP1B, the undecapeptide
EGFR.sub.988-998 (DADEpYLIPQQG; SEQ ID NO: 1) (Zhang et al., 1993),
and 100 different carboxylic acids, each attached via a
photochemically cleavable linker, as in example 4. One of these
carboxylic acids is 3-(4-difluorophosphonomethylphenyl) propanoic
acid (compound 1, FIG. 17), a compound that is a known PTP1B
inhibitor (Johnson et al., 2002). The other 99 carboxylic acids are
from the Carboxylic Acid Organic Building Block Library (Aldrich)
as example 4. Equal numbers of each of the 100 bead sets are then
mixed and screened as for example 5. Predominantly,
dephosphorylation of the peptide is only observed on those
microbeads which were coated with the PTPIB inhibitor
3-(4-difluorophosphonomethylphenyl) propanoic acid (compound 1,
FIG. 17), and not on microbeads coated with other compounds.
Example 7. Compartmentalisation of Small Molecules in a
Water-in-Fluorocarbon Emulsions
[0327] Water-in-fluorocarbon emulsions containing 95% (v/v)
perfluorooctyl bromide, 5% (v/v) phosphate buffered saline
containing the molecule of interest in solution, and 2% (w/v)
C8F17C11H22OP(O)[N(CH2CH2)2O]2 (F8H1 IDMP) as surfactant were
formed essentially as (Sadtler et al., 1996) by extrusion (15
times) through 14 .mu.m filters (Osmonics) or by homogenising for 5
min at 25,000 r.p.m. using an Ultra-Turrax T8 Homogenizer (DCA)
with a 5 mm dispersing tool. Emulsions were made containing a
series of small fluorescent molecules dissolved in the aqueous
phase at concentrations from 100 .mu.m to 2 mM. These molecules,
including calcein, texas red, fluorescein, coumarin 102,
7-hydroxycoumarm-3-carboxylic acid and 7-diethylamino-4-methyl
coumarin (coumarin 1), had molecular weights from 203 to 625 Da and
Log P values--calculated using SRC's Log Kow/KowWin Program (Meylan
and Howard, 1995)--ranging from -0.49 to 4.09. Emulsions containing
different coloured fluorochromes were mixed by vortexing.
Compartmentalisation was observed by epifluorescence microscopy of
the mixed emulsions. No exchange between compartments was observed
24 hours after mixing (see FIG. 19).
Example 8. Compartmentalisation of Small Molecules in a
Water-in-Fluorocarbon Emulsions
[0328] made using microfluidic systems. Water-in-fluorocarbon
emulsions containing 95% (v/v) perfluorooctyl bromide, 5% (v/v)
phosphate buffered saline containing the molecule of interest in
solution, and 2% (w/v) C8F17CnH22OP(O)[N(CH2CH2)2O]2 (F8H1 IDMP) as
surfactant were formed essentially using multiple droplet
generation modules as described in Example 1. The aqueous phase at
each of the nozzles contained a different small fluorescent
molecules dissolved at concentrations from 100 .mu.M to 2 mM. These
molecules, including calcein, texas red, fluorescein, coumarin 102,
7-hydroxycoumarin-3-carboxylic acid and 7-diethylamino-4-methyl
coumarin (coumarin 1), had molecular weights from 203 to 625 Da and
Log P values--calculated using SRC's Log Kow/KowWin Program (Meylan
and Howard, 1995)--ranging from -0.49 to 4.09. Emulsions containing
different coloured fluorochromes were mixed by combining the
streams carrying the droplet having different fluorofers into a
single stream containing all types of droplets. The stream carrying
the collection of droplets then empties into a deep well on the
device where the droplets can be stored in close proximity and
monitored over time up to 24 hours. No cross contamination between
the droplets is observed.
Example 9. Determining Mode of Inhibition and Kx of PETG on
.beta.-Galactosidase
[0329] Using a microfluidic device as described in Example 1, we
demonstrate that the mode of inhibition of the enzyme E. coli
.beta.-galactosidase (LacZ), by phenylethyl
.beta.-D-thiogalactopyranoside (PETG), is competitive, and we show
how we can obtain the inhibition constant (K1) of PETG. In the
enzyme inhibition assay, the rate of catalysis is determined by
using a non-fluorescent substrate for LacZ, fluorescein
mono-.beta.-D-galactoside (FMG), and measuring the appearance of
the fluorescent product, fluorescein (excitation 488 ran, emission
514 nm). All components of the LacZ inhibition assay are dissolved
in assay buffer (10 mM MgCl2, 50 mM NaCl, 1 mM DTT, 100 .mu.g/ml
BSA, 10
[0330] Leading into each droplet forming module (FIG. 15) are two
TEFLON.RTM. tubes leading from syringe pumps. The channels leading
from each tube merge to create a single flow before entering the
droplet forming module. The two syringes feeding into the first
droplet forming module contain, (a) 50 .mu.M PETG in assay buffer,
and (b), assay buffer. The two syringes feeding into the second
droplet forming module contain, (c) 100 nM LacZ in assay buffer,
and (d), assay buffer. The two syringes feeding into the third
droplet forming module contain, (e) 5 mM FMG in assay buffer, and
(f), assay buffer. The final concentration of each component in
each droplet is independently controllable by adjusting relative
flow rates of each component and buffer solution while maintaining
a constant combined flow rate from both syringes.
[0331] The first droplet fusion mixes the inhibitor (PETG) with the
enzyme (LacZ). After the combined droplet has spent two minutes in
a delay line it is fused with a third droplet containing the
fluorogenic enzyme substrate (FMG). Finally, after all the
components are mixed the reaction is observed by measuring
fluorescence of individual droplets or by integrating fluorescent
light from droplets with the same concentration of each component
during 10-second exposure time at multiple points in the second 10
min long delay line. Each fluorescence intensity value at different
positions is proportional to the amount of product at different
reaction times. Rate of product formation is linear during initial
reaction time and initial rate (v) can be determined from linear
fitting. Data from the repeated measurement at different
concentration of FMG and PETG are expressed in a Lineweaver-Burk
plot (1/v vs. 1/[S]; where [S]=substrate concentration). The same
y-intercept values at different concentration of PETG show that the
mode of PETG inhibition is competitive. In competitive inhibition,
each slope divided by the y-intercept represents an apparent
Michaelis-Menten constant that is a linear function of the
concentration of inhibitor. The y-intercept in a graph of apparent
Michaelis-Menten constant versus competitive inhibitor
concentration gives the Michaelis-Menten constant, and the inverse
of its slope multiplied by the y-intercept is K.sub.1. Using the
following conditions (in the final fused microcapsule), 30 nM LacZ,
0 to 13 .mu.M PETG and 10 to 700 .mu.M FMG the XM of FMG for LacZ
can be determined to within 20% of the previously published value
(118 .mu.M; Huang, 1991), and the Ki of PETG for LacZ can be
determined to be within the range of the previously published value
(0.98 .mu.M; Huang, 1991).
Example 10
Synthesis of Secondary Compounds in Emulsion Microcapsules and
Screening for PTP1B Inhibition in Microfluidic Systems
[0332] Using a microfluidic device as described in Example 1, we
describe how PTP1B inhibitors can be synthesised and screened using
microcapsules in a microfluidic system.
[0333] All water-soluble reagents are dissolved in (25 mM HEPES, pH
7.4, 125 mM NaCl, 1 mM EDTA), a buffer compatible with PTP1B
activity. A compound which is a primary amine is compartmentalised
into microcapsules using the device. A second solution, of a
compound which is an aldehyde is also compartmentalised into
microcapsules using the device. The amines and aldehydes can either
a) contain a difluoromethylene phosphonate moiety (FIG. 22,
compounds A and B), or b) contain no difluoromethylene phosphonate
moiety. Each microcapsule containing a primary amine is fused with
a microcapsule containing an aldehyde. Microcapsules containing
compounds with and without difluoromethylene phosphonate moieties
can be formed by switching between injection with syringes
containing amines or aldehydes with or without a difluoromethylene
phosphonate moiety.
[0334] After microcapsule fusion the contents are rapidly mixed and
the microcapsules pass down a delay line. This allows the amine and
the aldehyde to react together by formation of a Schiff base to
create a secondary compound and allows inhibitors to bind to PTP1B.
Each microcapsules are then fused with a further microcapsule
containing a solution of the target enzyme (human recombinant
PTP1B, residues 1-322; Biomol Research Laboratories, Inc.) at 50
mU/ml, and the fluorogenic PTP1B substrate
6,8-difluoro-4-methylumbelliferyl phosphate (DiFMUP) (Molecular
Probes). The fused microcapsules then run along a further delay
line. Fluorescence of the microcapsules due to production of DiFMU
(excitation/emmission maxima 358/452 nm; blue fluorescence) is
measured.
[0335] Predominantly, when the amine and aldehyde concentrations
are low (<100 .mu.M) inhibition of PTP1B activity is only
observed in microcapsules containing both an amine with a
difluoromethylene phosphonate moiety (compound A,) and an aldehyde
with a difluoromethylene phosphonate moiety (compound B5). This is
because the Schiff base formed in these microcapsules (compound C,)
contains oz's-difluoromethylene phosphonate and is a much more
potent PTP1B inhibitor than a molecule with a single
difluoromethylene phosphonate moiety.
[0336] Predominantly, when the amine and aldehyde concentrations
are high (>100 .mu.M) inhibition of PTP1B activity is observed
in microcapsules containing either an amine with a
difluoromethylene phosphonate moiety (compound A, or an aldehyde
with a difluoromethylene phosphonate moiety (compound B,), or both,
but not in other microcapsules. This is because at higher
concentrations molecules with either a single difluoromethylene
phosphonate moiety or a ozs-difluorornethylene phosphonate
(compound C, FIG. 22) can inhibit PTP1B.
Example 11. Synthesis of a Library of 2304 Secondary Compounds in
Emulsion Microcapsules and Screening of PTP1B Inhibition in
Microfluidic Systems
[0337] 96 aqueous mixtures are made in a buffer compatible with
PTP1B activity (25 mM HEPES, pH 7.4, 125 mM NaCl, 10% glycerol, 1
mM EDTA) (Doman et al., 2002) and containing the target enzyme
(human recombinant PTP1B, residues 1-322; Biomol Research
Laboratories, Inc.) at a concentration of 5 mU/ml. The first 48
mixtures each contain a unique compound containing a primary amine.
One of these compounds (compound A, FIG. 22) contains a
difluoromethylene phosphonate moiety. The second 48 mixtures of
microbeads each contain a unique compound containing an aldehyde.
One of these compounds (compound B, FIG. 22) contains a
difluoromethylene phosphonate moiety.
[0338] The 96 mixtures are distributed into 96 wells of a
microtitre plate. Aliquots from each well of the plate are loaded
sequentially into the microfluidic device described in Example 1
using thin tubes connected to the microfluidic device which are
dipped into reservoirs containing the desired compounds, and
capillary action is used to draw the desired compound from the
reservoir into the microfluidic device. The mixtures are
compartmentalised into microcapsules in the device.
[0339] Each microcapsule containing an amine is fused with a
microdroplet containing an aldehyde and incubated for 10 min, at
370C in a delay line. The amine and the aldehyde react together by
forming a Schiff base, resulting in the creation of a new molecule
(an imine) in solution. The microcapsule is then fused with a
further microcapsule containing the fluorogenic PTP1B substrate
6,8-difluoro-4-methylumbelliferyl phosphate (DiFMUP) (Molecular
Probes), and incubated at 370C for 30 min. in a delay line.
Inhibitors reduce the amount of non-fluorescent substrate (DiFMUP)
converted to the dephosphorylated product (DiFMU;
excitation/emmission maxima 358/452 nm; blue fluorescence).
Microcapsule fluorescence is then analysed.
[0340] Microcapsules containing a primary compound which is itself
a PTP1B inhibitor, or which reacts with another primary compound to
form a second inhibitor are identified as little substrate has been
converted to product. When the compounds ar present in the
mcirocapsules at high concentration, the identified microcapsules
where little substrate has been converted to product include those
carrying compounds containing a difluoromethylene phosphonate
moiety. When the compounds are present in the microcapsules at low
concentration, the concentration of the compounds containing a
difluoromethylene phosphonate moieties in the microcapsules is
insufficient to efficiently inhibit PTP1B (see example 10).
However, in microcapsules where two primary compounds have reacted
to form an imine containing a to-difluoromethylene phosphonate
moiety, which is a highly potent PTP1B inhibitor (compound C, FIG.
22), this inhibits conversion of the PTP1B substrate to product and
little fluorescence is observed.
Example 12
Synthesis of Secondary Compounds in Emulsion Microcapsules and
Screening for PTP1B Inhibition Using Compounds Attached to
Microbeads in Microfiuidic Systems
[0341] 5.5 .mu.m diameter polystyrene microbeads that bear
carboxylate functional groups on the surface are commercially
available (Luminex Corporation) in an optically tagged form, as a
result of incorporation of precise ratios of orange (585 nm), and
red (>650 nm) fluorochromes (Fulton et al., 1997). First, the
carboxylate functional groups on the microbeads are converted to
primary amines using ethylenediamine and EDC as in example 4. A
phosphopeptide substrate for PTP1B, the undecapeptide
EGFR.sub.988-998 (D ADEp YLIPQQG) (Zhang et al., 1993), is then
coupled to both sets of microbeads via the surface amino groups
using EDC and the protecting groups on the side chain carboxylates
of the peptide removed as in example 5. A first set of microbeads
(set 1) is reacted with succinimidyl p-formylbenzoate to convert
the surface amino groups to aldehydes. A second set of microbeads
(set 2), with a distinct optical tag from the first set of
microbeads, is left unreacted (i.e. with primary amines on the
surface).
[0342] The first set of microbeads (set 1), are then reacted with a
compound containing a difluoromethylene phosphonate moiety and a
primary amine (compound A, FIG. 22) via reaction with the surface
aldehyde groups to form a Schiff base. The second set of microbeads
(set 2), with a distinct optical tag from the first set of beads,
are reacted with a compound containing a difluoromethylene
phosphonate moiety and an aldehyde
[0343] (compound B, FIG. 22) via reaction of the aldehyde with the
surface amine groups to form a Schiff base. The formation of Schiff
bases is enhanced by reaction at alkaline pH (i.e. pH9-10).
Microbeads coated with compounds at various densities are
created.
[0344] The two sets of microbeads are separately suspended in a
buffer compatible with PTP1B activity (25 rnM HEPES, pH 7.4, 125 mM
NaCl, 10% glycerol, 1 mM EDTA) (Doman et al., 2002). Each set of
microbeads is compartmentalised into microcapsules in the device
described in Example 1. The number of microbeads is varied such
that, at one extreme, most microcapsules contain one or no beads,
and at the other, the majority of microcapsules contain two or more
microbeads. Each microcapsule containing a set 1 microbead is fused
with a microcapsule containing a set 2 microbead and incubated for
10 min, at 37.degree. C. in a delay line. The Schiff base is a
relatively labile, reversible interaction, readily hydrolysed at
neutral pH, resulting in release of compounds from the beads. In
microcapsules containing a microbead from both set 1 and set 2, the
compounds released from the microbeads can react with each other,
forming a Schiff base and creating a new molecule in solution. This
new molecule (FIG. 22, compound C) contains a bis-difluoromethylene
phosphonate moiety and has significantly more potency as a PTP1B
inhibitor than compounds with a single difluoromethylene
phosphonate moiety (see FIG. 22). The microcapsule is then fused
with a further microcapsule containing the target enzyme (human
recombinant PTP1B, residues 1-322; Biomol Research Laboratories,
Inc.) at a concentration of 5 mU/ml in 25 mM FIEPES, pH 7.4, 125 mM
NaCl, 10% glycerol, 1 mM EDTA, and incubated at 37.degree. C. for
30 min. in a delay line. Inhibitors reduce the amount of substrate
converted to product (dephosphorylated peptide). The microcapsules
are collected, cooled to 4.degree. C., and broken into 100 .mu.M
vanadate to stop the reaction (Harder et al., 1994). After
labelling with an anti-substrate (anti-phosphotyrosine) antibody
labelled with the green (530 nm) fluorochrome fluorescein
isothiocyanate (mouse monoclonal IgG2b PY20 (Santa Cruz) according
to the manufacturer's instructions, beads are analysed by 3-colour
flow cytometry using a FACScan (Becton-Dickinson), FACScalibur
(Becton-Dickinson) or MoFIo (Cytomation) flow cytometers to
simultaneously determine the extent of inhibition and the compound
on the beads. With low microbead numbers, most microcapsules
contain only a single or no microbeads and PTP1B inhibition is only
detected on beads coated with a high density of inhibitor, when the
concentration of inhibitor released into solution in each
microcapsule is sufficiently high for effective inhibition. In
contrast, when the bead numbers are higher, many microbeads are
detected where little substrate has been converted to product, even
when the microbeads are coated with inhibitor at low density. This
is due to the formation of a highly potent PTP1B inhibitor (FIG.
22, compound C) containing a to-difluoromethylene phosphonate
moiety in microcapsules containing a microbead each from set 1 and
set 2.
Example 13
Synthesis of a Library of 2500 Secondary Compounds in Emulsion
Microcapsules and Screening for PTP1B Inhibition Using Compounds
Attached to Microbeads in Microfluidic Systems
[0345] A set of 100 5.5 .mu.m diameter polystyrene microbeads,
bearing carboxylate functional groups on the surface and each with
a unique optical signature (Luminex Corporation) as a result of
incorporation of precise ratios of orange (585 nm), and red
(>650 nm) fluorochromes (Fulton et al., 1997) are modified to
convert the carboxylate functional groups to primary amines as in
example 4, then derivatised with a phosphopeptide substrate for
PTP1B, the undecapeptide EGFR.sub.988-998 (DADEp YLIPQQG SEQ ID NO:
1) (Zhang et al., 1993), as in example 5. The first 50 sets of
microbeads are reacted to convert a proportion of the surface
carboxyl groups to aldehydes as in example 10. The second 50 sets
of microbeads are left unreacted (i.e. with primary amines on the
surface).
[0346] The first 50 sets of microbeads are each reacted with a
unique compound containing a primary amine via reaction with the
surface aldehyde groups to form a Schiff base which links the
compounds to the beads. One of these compounds (compound A, FIG.
22) contains a difluoromethylene phosphonate moiety. The second 50
sets of microbeads are each reacted with a unique compound
containing an aldehyde via reaction with the surface amine groups
to form a Schiff base which links the compounds to the beads. One
of these compounds (compound B, FIG. 22) contains a
difiuoromethylene phosphonate moiety. The formation of Schiff bases
is enhanced by reaction at alkaline pH (i.e. pH9-10).
[0347] The 50 sets of microbeads which were reacted with primary
amines (amine microbeads) are pooled and suspended in a buffer
compatible with PTP1B activity (25 mM HEPES, pH 7.4, 125 mM NaCl,
10% glycerol, 1 mM EDTA) (Doman et al., 2002). The 50 sets of
microbeads which were reacted with aldehydes (aldehyde microbeads)
are pooled and suspended in the same buffer. The amine microbeads
and the aldehyde microbeads are compartmentalised into
microcapsules in the device described in Example 1. The number of
microbeads is set such that the majority of microdroplets contain a
single microbead. Each microcapsule containing an amine microbead
is fused with a microcapsule containing an aldehyde microbead and
incubated for 10 min, St 37.degree. C. in a delay line. The
microcapsule is then fused with a further microcapsule containing
the target enzyme (human recombinant PTP1B, residues 1-322; Biomol
Research Laboratories, Inc.) at a concentration of 5 mU/ml in 25 mM
HEPES, pH 7.4, 125 mM NaCl, 10% glycerol, 1 mM EDTA, and incubated
at 370C for 30 min. in a delay line. The Schiff base is a
relatively labile, reversible interaction, readily hydrolysed at
neutral pH, resulting in release of compounds from the beads. In
microcapsules containing a microbead from one of the first 50 sets
and a microbead from one of the second 50 sets, the compounds
released from the microbeads can react with each other, forming a
Schiff base and creating a new molecule in solution. Inhibitors
reduce the amount of substrate converted to product
(dephosphorylated peptide). The microcapsules are collected, cooled
to 4.degree. C., and broken into 100 .mu.M vanadate to stop the
reaction (Harder et al., 1994). After labelling with an
anti-substrate (anti-phosphotyrosine) antibody labelled with the
green (530 nm) fluorochrome fluorescein isothiocyanate (mouse
monoclonal IgG2b PY20 (Santa Cruz) according to the manufacturer's
instructions, beads are analysed by 3-colour flow cytometry using a
FACScan (Becton-Dickinson), FACScalibur (Becton-Dickinson) or MoFIo
(Cytomation) flow cytometers to simultaneously determine the extent
of inhibition and the compound on the beads.
[0348] Beads which were coated with a primary compound which is
itself a PTP1B inhibitor, or which reacts with another primary
compound released from another co-compartmentalised bead to form a
second inhibitor are identified as little substrate has been
converted to product. The identified beads where as little
substrate has been converted to product include those carrying
compounds containing a difluoromethylene phosphonate moiety. When
the microbeads are coated with compounds at low density the
concentration of the released compounds containing a
difluoromethylene phosphonate moieties in the microcapsules is
insufficient to efficiently inhibit PTP1B (see example 12). However
in microcapsules containing two microbeads, one from the first set
of 50 beads and one from the second set of 50 beads, and where each
microbead carries a molecule with a difluoromethylene phosphonate
moiety, the released molecules can form a highly potent PTP1B
inhibitor (compound C, FIG. 22) containing a bis-difluoromethylene
phosphonate moiety in the microcapsules which inhibits conversion
of the PTP1B substrate to product.
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Sequence CWU 1
1
1111PRTHomo sapiens 1Asp Ala Asp Glu Tyr Leu Ile Pro Gln Gln Gly1 5
10
* * * * *