U.S. patent application number 13/408071 was filed with the patent office on 2012-07-19 for emulsion compositions.
Invention is credited to Farid Ghadessy, Phillip Holliger.
Application Number | 20120184011 13/408071 |
Document ID | / |
Family ID | 9925928 |
Filed Date | 2012-07-19 |
United States Patent
Application |
20120184011 |
Kind Code |
A1 |
Holliger; Phillip ; et
al. |
July 19, 2012 |
Emulsion Compositions
Abstract
An emulsion is useful in allowing a wide variety of gene
products to be expressed via eukaryotic in vitro expression. The
emulsion comprises a silicone based surfactant, a hydrophobic phase
and a hydrophilic phase; wherein the hydrophilic phase comprises a
plurality of compartments containing a functional in vitro
eukaryotic expression system.
Inventors: |
Holliger; Phillip;
(Cambridge, GB) ; Ghadessy; Farid; (London,
GB) |
Family ID: |
9925928 |
Appl. No.: |
13/408071 |
Filed: |
February 29, 2012 |
Related U.S. Patent Documents
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Application
Number |
Filing Date |
Patent Number |
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12587432 |
Oct 6, 2009 |
8153402 |
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13408071 |
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10866392 |
Jun 11, 2004 |
7622280 |
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12587432 |
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10844720 |
May 13, 2004 |
7429467 |
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10866392 |
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PCT/GB02/05216 |
Nov 18, 2002 |
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10844720 |
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Current U.S.
Class: |
435/174 |
Current CPC
Class: |
A61K 47/24 20130101;
A61K 47/44 20130101; A61K 9/107 20130101; C12Q 1/6844 20130101;
A61K 47/26 20130101; C12Q 1/6844 20130101; A61K 9/1676 20130101;
C12N 15/1075 20130101; C12Q 2527/125 20130101 |
Class at
Publication: |
435/174 |
International
Class: |
C12N 11/00 20060101
C12N011/00 |
Foreign Application Data
Date |
Code |
Application Number |
Nov 16, 2001 |
GB |
0127564.3 |
Claims
1. An emulsion comprising a surfactant, a hydrophobic phase and a
hydrophilic phase comprising a plurality of microcapsules
containing a functional in vitro eukaryotic expression system,
wherein the surfactant is a chemically inert silicone-based
surfactant.
Description
CROSS-REFERENCE TO RELATED APPLICATIONS
[0001] This application is a continuation of U.S. patent
application Ser. No. 12/587,432, filed Oct. 6, 2009 (now allowed),
which is a continuation of U.S. patent application Ser. No.
10/866,392 (now U.S. Pat. No. 7,622,280), filed Jun. 11, 2004,
which is a continuation of U.S. patent application Ser. No.
10/844,720 (now U.S. Pat. No. 7,429,467), filed May 13, 2004, which
was a continuation of International Application PCT/GB02/05216,
filed Nov. 18, 2002, which claimed the priority of Great Britain
application GB 0127564.3, filed Nov. 16, 2001. The entire teachings
of these applications are incorporated herein by reference in their
entirety.
FIELD OF THE INVENTION
[0002] The present invention relates, inter alia, to emulsions
suitable for compartmentalisation of transcription/translation
reactions and methods using such emulsions. In particular, the
emulsions are useful for compartmentalisation of in vitro
eukaryotic transcription/translation reactions.
BACKGROUND TO THE INVENTION
[0003] Compartmentalisation methods based on water-in-oil emulsions
have recently been developed for use in repertoire selection
methods (Tawfik & Griffths 1998, Ghadessy et al 2001).
Compartmentalisation segregates individual genes and their encoded
products (delivered either via cells (Ghadessy et al, 2001) or
expressed in situ (Tawfik & Griffiths, 1998)) into discrete,
physically separate aqueous compartments, thus ensuring the linkage
of genotype and phenotype during the selection process.
[0004] WO99/02671 (which is incorporated herein by reference)
describes a method for isolating one or more genetic elements
encoding a gene product having a desired activity. Genetic elements
are first compartmentalised into microcapsules, which are
preferably formed by emulsification, and are then transcribed
and/or translated to produce their respective gene products (RNA or
protein) within the microcapsules. Alternatively, the genetic
elements may be contained within microcapsules of the emulsion and
transcription and/or translation (expression) of the gene product
can take place within using the cellular machinery. Genetic
elements that produce a gene product having a desired activity can
be subsequently sorted. For example, in some cases sorting may be
due to the desired activity inducing a change in the microcapsule.
In other cases sorting may be due to the desired activity inducing
a change in the genetic element.
[0005] The method disclosed in WO99/02671 works well with bacteria.
Although the cellular subcompartmentalisation approach could in
principle be extended to include eukaryotic cells, e.g. yeast,
insect or mammalian cells, for some applications it would be
desirable to provide in situ expression directly in microcapsules
using an in vitro eukaryotic transcription/translation system.
[0006] Previous successful expression of a prokaryotic enzyme, Hae
methylase, has been reported using bacterial S30 extracts in
emulsion (Tawfik D. & Griffiths A. D. 1998). However, such
methods are not suitable for some proteins of interest, for example
large multi-domain proteins and ribonucleoproteins which frequently
cannot be expressed in functional form using bacterial
extracts.
[0007] Thus it can be seen that a method which enables in situ
expression directly in microcapsules using an in vitro eukaryotic
transcription/translation system would provide a contribution to
the art.
SUMMARY OF THE INVENTION
[0008] Accordingly, in a first aspect of the present invention,
there is provided an emulsion comprising a surfactant, a
hydrophobic phase and a hydrophilic phase comprising a plurality of
microcapsules containing a functional in vitro eukaryotic
expression system, wherein the surfactant is a chemically inert
silicone-based surfactant.
[0009] In developing such a method, the present inventors have
encountered repeated problems in maintaining efficient
transcriptional/translational ability of an eukaryotic system, in
particular the rabbit reticulocyte lysate system, when in emulsion.
As described below, a number of modifications to emulsion
compositions used with prokaryotic expression systems were
unsuccessful in conferring such ability. However, it was
surprisingly found that, when chemically inert silicone-based
surfactants were employed in the emulsion composition, the
efficiency of transcription of the eukaryotic
transcription/translation system was markedly improved.
[0010] The emulsion allows the linkage of genotype and phenotype
due to compartmentalization of the eukaryotic expression system,
whilst avoiding many of the disadvantages of cell-based systems.
Thus, for example, it allows gene products to be obtained without
the need for extraction or secretion from cells.
[0011] Accordingly, in a second aspect of the invention, there is
provided a method of isolating one or more genetic elements
encoding a gene product having a desired activity, comprising the
steps of: [0012] (a) compartmentalising the genetic elements into
microcapsules formed from an emulsion of the invention [0013] (b)
expressing the genetic elements to produce their respective gene
products within the microcapsules; [0014] (c) sorting the genetic
elements which produce gene product(s) having the desired
activity.
[0015] In a third aspect, the invention provides a method for
preparing a gene product, comprising the steps of [0016] (a)
preparing a genetic element encoding the gene product; [0017] (b)
compartmentalising genetic elements into microcapsules formed from
an emulsion of the invention; [0018] (c) expressing the genetic
elements to produce their respective gene products within the
microcapsules; [0019] (d) sorting the genetic elements which
produce the gene product(s) having the desired activity; and [0020]
(e) expressing the gene product having the desired activity.
[0021] In accordance with this aspect of the invention, step (a)
preferably comprises preparing a repertoire of genetic elements,
wherein each genetic element encodes a potentially differing gene
product. Repertoires may be generated by conventional techniques,
such as those employed for the generation of libraries intended for
selection by methods such as phage display. Gene products having
the desired activity may be selected from the repertoire, according
to the present invention.
[0022] A fourth aspect of the invention provides a product selected
using the method of the second aspect of the invention or prepared
according to the third aspect of the invention. As used in this
context, a "product" may refer to a gene product selected or
prepared according to these aspects, or the genetic element (or
genetic information comprised therein).
[0023] In a fifth aspect, the invention provides a method for
screening a compound or compounds capable of modulating the
activity of a gene product, comprising the steps of: [0024] (a)
preparing a repertoire of genetic elements encoding gene product;
[0025] (b) compartmentalising the genetic elements into
microcapsules formed from an emulsion of the invention; [0026] (c)
expressing the genetic elements to produce their respective gene
products within the microcapsules; [0027] (d) sorting the genetic
elements which produce the gene product(s) having the desired
activity; and [0028] (e) contacting a gene product having the
desired activity with the compound or compounds and monitoring the
modulation of an activity of the gene product by the compound or
compounds.
[0029] In the context of the present invention, a surfactant is
considered to be "chemically inert" if it is substantially free of
oxidating species, such as peroxides and aldehydes, and protein
denaturing species. Surfactants having 40%, preferably 50%, more
preferably 60%, 70%, 80%, 90%, 95%, or 98% less oxidating species
and protein denaturing species than either one of conventional
sorbitan monooleate (Span.TM.80; ICI) and polyoxyethylenesorbitan
monooleate (Tween.TM.80; ICI) emulsifiers are considered to be
"substantially free" of oxidating species and denaturing
species.
[0030] The terms "isolating", "sorting" and "selecting", as well as
variations thereof, are used herein. Isolation, according to the
present invention, refers to the process of separating an entity
from a heterogeneous population, for example a mixture, such that
it is free of at least one substance with which it was associated
before the isolation process. In a preferred embodiment, isolation
refers to purification of an entity essentially to homogeneity.
Sorting of an entity refers to the process of preferentially
isolating desired entities over undesired entities. In as far as
this relates to isolation of the desired entities, the terms
"isolating" and "sorting" are equivalent. The method of the present
invention permits the sorting of desired genetic elements from
pools (libraries or repertoires) of genetic elements which contain
the desired genetic element. Selecting is used to refer to the
process (including the sorting process) of isolating an entity
according to a particular property thereof.
[0031] In preferred embodiments of the methods of the invention,
the sorting of genetic elements may be performed in one of
essentially four techniques, details of which are given in
WO99/02671.
[0032] (I) In a first embodiment, the microcapsules are sorted
according to an activity of the gene product or a derivative
thereof which makes the microcapsule detectable as a whole.
Accordingly, the invention provides a method according to the
second aspect of the invention wherein a gene product 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 gene product and the
genetic element encoding it to be sorted. In this embodiment,
therefore, the microcapsules are physically sorted from each other
according to the activity of the gene product(s) expressed from the
genetic element(s) contained therein, which makes it possible
selectively to enrich for microcapsules containing gene products of
the desired activity.
[0033] (II) In a second embodiment, the genetic elements are sorted
following pooling of the microcapsules into one or more common
compartments. In this embodiment, a gene product having the desired
activity modifies the genetic element which encoded it (and which
resides in the same microcapsule) in such a way as to make it
selectable 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. Selection for the modified
genetic elements enables enrichment of the genetic elements
encoding the gene product(s) having the desired activity.
Accordingly, the invention provides a method according to the
second aspect of the invention, wherein in step (b) the gene
product having the desired activity modifies the genetic element
encoding it to enable the isolation of the genetic element. It is
to be understood, of course, that modification may be direct, in
that it is caused by the direct action of the gene product on the
genetic element, or indirect, in which a series of reactions, one
or more of which involve the gene product having the desired
activity, leads to modification of the genetic element.
[0034] (III) In a third embodiment, the genetic elements are sorted
following pooling of the microcapsules into one or more common
compartments. In this embodiment, a gene with a desired activity
induces a change in the microcapsule containing the gene product
and the genetic element encoding it. This change, when detected,
triggers the modification of the gene within the microcapsule. The
reactions are stopped and the microcapsules are then broken so that
all the contents of the individual microcapsules are pooled.
Selection for the modified genetic elements enables enrichment of
the genetic elements encoding the gene product(s) having the
desired activity. Accordingly the invention provides a method
according to the second aspect of the invention, where in step (b)
the gene product having the desired activity induces a change in
the microcapsule which is detected and triggers the modification of
the genetic element within the microcapsule so as to allow its
isolation. It is to be understood that the detected change in the
microcapsule may be caused by the direct action of the gene
product, or indirect action, in which a series of reactions, one or
more of which involve the gene product having the desired activity
leads to the detected change.
[0035] (IV) In a fourth embodiment, the genetic elements may be
sorted by a multi-step procedure, which involves at least two
steps, for example, in order to allow the exposure of the genetic
elements to conditions which permit at least two separate reactions
to occur. As will be apparent to a persons skilled in the art, the
first microencapsulation step of the invention must result in
conditions which permit the expression of the genetic elements--be
it transcription, transcription and/or translation, replication or
the like. Under these conditions, it may not be possible to select
for a particular gene product activity, for example because the
gene product may not be active under these conditions, or because
the expression system contains an interfering activity. The
invention therefore provides a method according to the second
aspect of the present invention, wherein step (b) comprises
expressing the genetic elements to produce their respective gene
products within the microcapsules, linking the gene products to the
genetic elements encoding them and isolating the complexes thereby
formed. This allows for the genetic elements and their associated
gene products to be isolated from the microcapsules before sorting
according to gene product activity takes place. In a preferred
embodiment, the complexes are subjected to a further
compartmentalisation step prior to isolating the genetic elements
encoding a gene product having the desired activity. This further
compartmentalisation step, which advantageously takes place in
microcapsules, permits the performance of further reactions, under
different conditions, in an environment where the genetic elements
and their respective gene products are physically linked. Eventual
sorting of genetic elements may be performed according to
embodiment (I), (II) or (III) above.
[0036] The "secondary encapsulation" may also be performed with
genetic elements linked to gene products by other means, such as by
phage display, polysome display, RNA-peptide fusion or lac
repressor peptide fusion.
[0037] The selected genetic element(s) may also be subjected to
subsequent, possibly more stringent rounds of sorting in
iteratively repeated steps, reapplying the method of the invention
either in its entirety or in selected steps only. By tailoring the
conditions appropriately, genetic elements encoding gene products
having a better optimised activity may be isolated after each round
of selection.
[0038] Additionally, the genetic elements isolated after a first
round of sorting may be subjected to mutagenesis before repeating
the sorting by iterative repetition of the steps of the method of
the invention as set out above. After each round of mutagenesis,
some genetic elements will have been modified in such a way that
the activity of the gene products is enhanced.
[0039] Moreover, the selected genetic elements can be cloned into
an expression vector to allow further characterisation of the
genetic elements and their products. A multitude of suitable
vectors are known to the person skilled in the art. The vectors may
be, for example, virus, plasmid or phage vectors provided with an
origin of replication, optionally a promoter for the expression of
the genetic element and optionally a regulator of the promoter. The
vectors may contain a selectable marker gene, for example the
neomycin resistance gene for a mammalian vector.
BRIEF DESCRIPTION OF THE FIGURES
[0040] FIG. 1 shows emulsions formed by mixing oil-phase with
rabbit reticulocyte lysate (RRL) for 1.5 min and photographed in
visual spectrum after 15 min incubation at 30.degree. C. From left
to right: 1) CSR mix, 2) CSR mix+DTT, 3) 1.5% Span80 in mineral
oil, 4) 1.5% Span80 in mineral oil+DTT, 5) 4% Abil EM90, 6) 4% Abil
EM90+DTT
[0041] FIG. 2 shows a 4% Abil EM90 in mineral oil emulsion imaged
in phase-contrast mode. The distance between the bars is 10
.mu.M
[0042] FIG. 3 shows the results of telomerase expression:
[0043] Panel A (Non-emulsified): Lane 1, hTERT (75 ng); Lane 2, hTR
(75 ng); Lane 3, hTERT+hTR; Lane 4, No construct; Lane 5, Tandem WT
expression construct (150 ng) Lane 6, Tandem deletion mutant
construct (150 ng)
[0044] Panel B: In emulsion, lane annotation same as in panel
A.
DETAILED DESCRIPTION
Emulsions
[0045] Emulsions are 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, 1984). Emulsions of the invention must enable the
formation of microcapsules.
[0046] Emulsions may be produced from any suitable combination of
immiscible liquids. The emulsion of the present invention has a
hydrophilic phase (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.
[0047] 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).
[0048] Desirably, the emulsion is stable during incubation at
30.degree. C. for at least one hour. In some cases it is preferred
that it also be stable at higher temperatures, especially if
thermal cycling is used during PCR or other amplification
procedures.
Surfactants
[0049] Emulsions of the invention are 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).
[0050] However, as described in the examples, surfactants
conventionally used in emulsions applications such as non-ionic
surfactants (Schick, 1966), for example, sorbitan monooleate
(Span.TM.80; ICI) and polyoxyethylenesorbitan monooleate
(Tween.TM.80; ICI) are not suitable for efficient in vitro
eukaryotic expression with the rabbit reticulocyte lysate
[0051] However, as described herein, such expression may be
maintained when chemically inert silicone-based surfactants are
used.
[0052] Preferably, the chemically inert silicone-based surfactant
of the emulsion is a silicone copolymer.
[0053] More preferably the surfactant comprises a
polysiloxane-polycetyl-polyethylene glycol copolymer (Cetyl
Dimethicone Copolyol) e.g. Abil..RTM. EM90 (Goldschmidt).
[0054] The chemically inert silicone-based surfactant may be
provided as the sole surfactant in the emulsion composition or may
be provided as one of several surfactants. For example a mixture of
different surfactants may be used.
[0055] In preferred embodiments, the surfactant is provided at a
v/v concentration in the oil phase of the emulsion of 0.5 to 20%,
preferably 1 to 10%, more preferably 3-5%.
[0056] In a highly preferred embodiment, the surfactant is provided
at a v/v concentration in the oil phase of 4%.
[0057] In a highly preferred embodiment of the invention the
emulsion is made by adding an aqueous phase dropwise to an oil
phase in the presence of a surfactant comprising about 3-5% (v/v)
polysiloxane-polycetyl-polyethylene glycol copolymer in mineral
oil, preferably at a ratio of oil:water phase of 2.5:1.
[0058] The surfactant may be present initially with the hydrophobic
composition. A composition comprising the surfactant and the
hydrophobic composition therefore represents a further aspect of
the present invention.
[0059] Alternatively, the surfactant may be added at a later stage,
e.g. during or following the mixing of the hydrophobic and
hydrophilic phases.
[0060] In this embodiment the surfactant may be provided in a kit,
together with a hydrophobic composition. The kit may optionally
also include a eukaryotic expression system such as rabbit
reticulocyte lysate and/or a device for mixing the hydrophobic and
hydrophilic phases. It may further include instructions for use in
providing an emulsion of the present invention.
[0061] Alternatively, the surfactant may be present initially with
the hydrophilic composition.
Microcapsules
[0062] The term "microcapsule" is synonymous with "compartment" and
the terms are used interchangeably. In essence, a microcapsule is
an artificial compartment whose delimiting borders restrict the
exchange of the components of the molecular mechanisms described
herein which allow the sorting of genetic elements according to the
function of the gene products which they encode.
[0063] The microcapsules formed by the emulsion require appropriate
physical properties to allow the working of the invention. In
particular, the contents of each microcapsule must be isolated from
the contents of surrounding microcapsules.
[0064] Preferably, the microcapsules used in the methods of the
present invention will be capable of being produced in very large
numbers, and thereby to compartmentalise a library of genetic
elements which encodes a repertoire of gene products. The function
of the microcapsule is to enable co-localisation of the nucleic
acid and the corresponding polypeptide encoded by the nucleic acid.
This is preferably achieved by the ability of the microcapsule to
substantially restrict diffusion of template and product strands to
other microcapsules.
[0065] Second, the methods of the present invention require that
there are only a limited number of genetic elements per
microcapsule formed in the emulsion. This ensures that the gene
product of an individual genetic element will be isolated from
other genetic elements. Thus, coupling between genetic element and
gene product will be highly specific. The enrichment factor is
greatest with on average one or fewer genetic elements per
microcapsule, or two or more copies of a single genetic element per
microcapsule, the linkage between nucleic acid and the activity of
the encoded gene product being as tight as is possible, since the
gene product of an individual genetic element will be isolated from
the products of all other genetic elements. However, even if the
theoretically optimal situation of, on average, a single genetic
element or less per microcapsule is not used, a ratio of 5, 10, 50,
100 or 1000 or more genetic elements per microcapsule may prove
beneficial in sorting a large library. Subsequent rounds of
sorting, including renewed encapsulation with differing genetic
element distribution, will permit more stringent sorting of the
genetic elements. Preferably, there is a single genetic element, or
fewer, per microcapsule.
[0066] Thirdly, the formation and the composition of the
microcapsules must not abolish the function of the machinery for
the expression of the genetic elements and the activity of the gene
products using eukaryotic in vitro expression systems.
[0067] Consequently, the microcapsules formed by the emulsion must
fulfill these three requirements. The appropriate emulsion may vary
depending on the precise nature of the requirements in each
application of the invention, as will be apparent to the skilled
person.
[0068] The preferred microcapsule size will vary depending upon the
precise requirements of any individual selection process that is to
be performed according to the present invention. In all cases, the
principle consideration is the need for required concentration of
components in the individual compartments to achieve efficient
transcription/translation. This may be balanced with other
requirements which may relate to gene library size, enrichment, or
sorting procedures.
[0069] If small microcapsules are provided, a very large number of
discrete microcapsules can be provided within a small volume of
emulsion. Furthermore the provision of small microcapsules
increases selectivity by increasing the likelihood that only one
type of gene product will be produced within a given microcapsule.
It is therefore preferred that on average no more than one genetic
elements that is to be transcribed and/or translated is present per
compartment in order to keep the linkage between nucleic acid and
the activity of encoded gene product as tight as is possible.
However, even if the theoretically optimal situation of, on
average, a single genetic element or less per microcapsule is not
used, a ratio of 5, 10, 50, 100 or 1000 or more genetic elements
per microcapsule may prove beneficial in sorting a large library.
Subsequent rounds of sorting, including renewed encapsulation with
differing genetic element distribution, will permit more stringent
sorting of the genetic element. Preferably, there is on average no
more than a single genetic element per microcapsule.
[0070] Desirably, the mean volume of the microcapsules is less that
5.2.times.10.sup.-16 m.sup.3, (corresponding to a spherical
microcapsule of diameter less than 10 .mu.m), more desirably less
than 6.5.times.10.sup.-17 m.sup.3 (corresponding to a spherical
microcapsule of diameter less than 5 .mu.m), still more desirably
about 4.2.times.10.sup.-18 m.sup.3 (corresponding to a spherical
microcapsule of diameter of approximately 2 .mu.m).
[0071] The effective DNA or RNA concentration in microcapsules may
be artificially increased by various methods that will be
well-known to those versed in the art. These include, for example,
the addition of volume excluding chemicals such as polyethylene
glycols (PEG) and a variety of gene amplification techniques,
including transcription using RNA polymerases including those from
bacteria such as E. coli (Roberts, 1969; Blattner and Dahlberg,
1972; Roberts et al., 1975; Rosenberg et al., 1975, eukaryotes e.g.
(Weil et al., 1979; Manley et al., 1983) and bacteriophage such as
T7, T3 and SP6 (Melton et al., 1984); the polymerase chain reaction
(PCR) (Saiki et al., 1988); Q.beta. replicase amplification (Miele
et al., 1983; Cahill et al., 1991; Chetverin and Spirin, 1995;
Katanaev et al., 1995); the ligase chain reaction (LCR) (Landegren
et al., 1988; Barany, 1991); and self-sustained sequence
replication system (Fahy et al., 1991) and strand displacement
amplification (Walker et al., 1992). Gene amplification techniques
advantageously using thermal cycling (such as PCR and LCR) may be
used if the emulsions and the in vitro transcription or coupled
transcription-translation systems are thermostable.
[0072] Increasing the effective local nucleic acid concentration
enables microcapsules to be used more effectively. Thus
microcapsules having volumes of up to only about
5.2.times.10.sup.-16 m.sup.3 (corresponding to a sphere of diameter
10 .mu.m) can be used for many purposes, although of course
microcapsules with larger volumes can be used, if desired.
[0073] The microcapsule size must be sufficiently large to
accommodate all of the required components of the biochemical
reactions that are needed to occur within the microcapsule. For
example, in vitro, both transcription reactions and coupled
transcription-translation reactions often require a total
nucleoside triphosphate concentration of about 2 mM.
[0074] It can also be noted that, in order to transcribe a gene to
a single short RNA molecule of 500 bases in length, this would
require a minimum of 500 molecules of nucleoside triphosphate'per
microcapsule (8.33.times.10.sup.-22 moles). In order to constitute
a 2 mM solution, this number of molecules must be contained within
a microcapsule of volume 4.17.times.11.sup.-19 litres
(4.17.times.10.sup.-22 m.sup.3), which, if spherical, would have a
diameter of 93 nm.
[0075] Furthermore, particularly in the case of reactions involving
translation, it is to be noted that the eukaryotic ribosomes
necessary for the translation to occur are themselves approximately
30 nm in diameter. Hence, the preferred lower limit for
microcapsules is a diameter of approximately 0.1 .mu.m (100
nm).
[0076] Therefore, the microcapsule volume is preferably of the
order of between 5.2.times.10.sup.-22 m.sup.3 and
5.2.times.10.sup.-16 m.sup.3 corresponding to a sphere of diameter
between 0.1 .mu.m and 10 .mu.m, more preferably of between about
5.2.times.10.sup.-19 m.sup.3 and 6.5.times.10.sup.-17 m.sup.3 (1
.mu.m and 5 .mu.m).
[0077] Although small microcapsules are preferred for certain
applications, such as the methods disclosed in WO99/02671, it is
important to note that the present invention is in no way limited
to the provision of small microcapsules and that transcription and
translation systems also function in large microcapsules.
[0078] The size of emulsion microcapsules may be varied simply by
tailoring the emulsification conditions used to form the emulsion
according to requirements of the selection system.
[0079] Compartment size may be varied (within limits of emulsion
stability and inactivation of RRL) by 1) increased mixing time, 2)
different W/O ratios, 3) different concentrations of
surfactant.
[0080] The size distribution of microcapsules in emulsions can be
determined by any method known to skilled person. For example, the
size distribution may be assessed using laser diffraction (e.g.
using a Coulter LS230 Particle Size Analyser) or by microscopic
examination.
Expression
[0081] "Expression", as used herein, is used in its broadest
meaning, to signify that a nucleic acid contained in the genetic
element is converted into its gene product. Thus, where the nucleic
acid is DNA, expression refers to the transcription of the DNA into
RNA; where this RNA codes for protein, "expression" may also refer
to the translation of the RNA into protein. Where the nucleic acid
is RNA, "expression" may refer to the replication of this RNA into
further RNA copies, the reverse transcription of the RNA into DNA
and optionally the transcription of this DNA into further RNA
molecule(s), as well as optionally the translation of any of the
RNA species produced into protein. Preferably, therefore,
"expression" is performed by one or more processes selected from
the group consisting of transcription, reverse transcription,
replication and translation.
[0082] "Expression" of the genetic element may thus be directed
into either DNA, RNA or protein, or a nucleic acid or protein
containing unnatural bases or amino acids (the gene product) within
the microcapsule of the invention, so that the gene product is
confined within the same microcapsule as the genetic element.
Expression Systems
[0083] Any appropriate in vitro eukaryotic expression system can be
used in the emulsion of the invention provided that it includes
components needed for transcription and/or translation. If
glycosylation is desired then one or more glycosylases can also be
present, as appropriate, in order to achieve a desired
glycosylation pattern.
[0084] The expression system may, for example, comprise all or part
of a cell lysate or extract. For example wheat germ extract may be
used (Anderson et al., 1983) and is available commercially from
Promega. Desirably, however, the cell lysate is a mammalian cell
lysate. It may be a reticulocyte lysate. A preferred reticulocyte
lysate is a rabbit reticulocyte lysate (an "RRL"). The RRL system
is well characterised (see e.g. Pelham and Jackson, 1976) and is
available commercially from Promega.
[0085] However, any convenient eukaryotic expression system
prepared from other cell extracts may be used. The extracts should
contain all the components required for translation of RNA (e.g.
ribosomes, tRNAs, aminoacyl-tRNA synthetases, initiation,
elongation and termination factors etc with the extracts preferably
supplemented with amino acids, ATP, GTP, creatine phosphate and
creatine phosphokinase, other co-factors such as Mg.sup.2+.
[0086] By using emulsions of the present invention it is possible
to obtain appreciable expression of a genetic element and/or
activity of a gene product using an in vitro eukaryotic expression
system present within an emulsion. Expression and/or activity is
desirably at a level of at least 1% of that of the gene product
achievable with the expression system prior to formation of the
emulsion. More preferably it is at least 10%, 20% or 30% of said
level and/or activity.
Genetic Elements
[0087] A "genetic element" is a molecule or molecular construct
comprising a nucleic acid. The genetic elements of the present
invention may comprise any nucleic acid (for example, DNA, RNA or
any analogue, natural or artificial, thereof).
[0088] Nucleic acids encoding any appropriate gene product can be
used in the in vitro transcription and/or translation systems. In
addition to coding sequences, the nucleic acids may, for example,
comprise promoters, operators, enhancers, translational and
transcriptional initiation and termination sequences,
polyadenylation sequences, splice sites, upstream and downstream
regulatory regions, etc., as required for transcription and/or
translation. In some cases it may be preferred to use inducible
and/or temperature sensitive promoters in order to ensure
expression occurs only at a particular stage.
[0089] The nucleic acid component of the genetic element may
moreover be linked, covalently or non-covalently, to one or more
molecules or structures, including polypeptides, peptides, chemical
entities and groups, solid-phase supports such as magnetic beads,
and the like. In the methods of the invention, these structures or
molecules can be designed to assist in the sorting and/or isolation
of the genetic element encoding a gene product with the desired
activity.
[0090] As will be apparent from the following, in many cases the
polypeptide or other molecular group or construct is a ligand or a
substrate which directly or indirectly binds to or reacts with the
gene product in order to tag the genetic element. This allows the
sorting of the genetic element on the basis of the activity of the
gene product.
[0091] The ligand or substrate can be connected to the nucleic acid
by a variety of means that will be apparent to those skilled in the
art (see, for example, Hermanson, 1996). Any tag will suffice that
allows for the subsequent selection of the genetic element. Sorting
can be by any method which allows the preferential separation,
amplification or survival of the tagged genetic element. Examples
include selection by binding (including techniques based on
magnetic separation, for example using Dynabeads.TM.), and by
resistance to degradation (for example by nucleases, including
restriction endonucleases).
[0092] One way in which the nucleic acid molecule may be linked to
a ligand or substrate is through biotinylation. This can be done by
PCR amplification with a 5'-biotinylation primer such that the
biotin and nucleic acid are covalently linked. A biotinylated
nucleic acid may be coupled to a polystyrene microbead (0.035 to
0.2 .mu.m in diameter) that is coated with avidin or streptavidin,
that will therefore bind the nucleic acid with very high affinity.
This bead can be derivatised with substrate or ligand by any
suitable method such as by adding biotinylated substrate or by
covalent coupling.
[0093] Alternatively, a biotinylated nucleic acid may be coupled to
avidin or streptavidin complexed to a large protein molecule such
as thyroglobulin (669 Kd) or ferritin (440 Kd). This complex can be
derivatised with substrate or ligand, for example by covalent
coupling to the -amino group of lysines or through a non-covalent
interaction such as biotin-avidin. The substrate may be present in
a form unlinked to the genetic element but containing an inactive
"tag" that requires a further step to activate it such as
photoactivation (e.g. of a "caged" biotin analogue, (Sundberg et
al., 1995; Pirrung and Huang, 1996)). The catalyst to be selected
then converts the substrate to product. The "tag" could then be
activated and the "tagged" substrate and/or product bound by a
tag-binding molecule (e.g. avidin or streptavidin) complexed with
the nucleic acid. 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.
[0094] An alternative is to couple the nucleic acid to a
product-specific antibody (or other product-specific molecule). In
this scenario, the substrate (or one of the substrates) is present
in each microcapsule unlinked to the genetic element, but has a
molecular "tag" (for example biotin, DIG or DNP). When a catalyst
to be selected converts the substrate to product, the product
retains the "tag" and is then captured in the microcapsule by the
product-specific antibody. In this way the genetic element only
becomes associated with the "tag" when it encodes or produces an
enzyme capable of converting substrate to product.
[0095] When all reactions are stopped and the microcapsules are
combined, the genetic elements encoding active enzymes can be
enriched using an antibody or other molecule which binds, or reacts
specifically with the "tag". Although both substrates and product
have the molecular tag, only the genetic elements encoding active
gene product will co-purify.
[0096] In a highly preferred application, the methods of the
present invention are useful for sorting libraries of genetic
elements. The invention accordingly provides a method according to
preceding aspects of the invention, wherein the genetic elements
are isolated from a library of genetic elements encoding a
repertoire of gene product. Herein, the terms "library",
"repertoire" and "pool" are used according to their ordinary
signification in the art, such that a library of genetic elements
encodes a repertoire of gene products. In general, libraries are
constructed from pools of genetic elements and have properties
which facilitate sorting.
[0097] Initial selection of a genetic element from a genetic
element library using the present invention will in most cases
require the screening of a large number of variant genetic
elements. Libraries of genetic elements can be created in a variety
of different ways, including the following.
[0098] Pools of naturally occurring genetic elements can be cloned
from genomic DNA or cDNA (Sambrook et al., 1989); for example,
phage antibody libraries, made by PCR amplification repertoires of
antibody genes from immunised or unimmunised donors have proved
very effective sources of functional antibody fragments (Winter et
al., 1994; Hoogenboom, 1997). Libraries of genes can also be made
by encoding all (see for example Smith, 1985; Parmley and Smith,
1988) or part of genes (see for example Lowman et al., 1991) or
pools of genes (see for example Nissim et al., 1994) by a
randomised or doped synthetic oligonucleotide. Libraries can also
be made by introducing mutations into a genetic element or pool of
genetic elements `randomly` by a variety of techniques in vivo,
including; using `mutator strains`, of bacteria such as E. coli
mutD5 (Liao et al., 1986; Yamagishi et al., 1990; Low et al.,
1996); using the antibody hypermutation system of B-lymphocytes
(Yelamos et al., 1995). Random mutations can also be introduced
both in vivo and in vitro by chemical mutagens, and ionising or UV
irradiation (see Friedberg et al., 1995), or incorporation of
mutagenic base analogues (Freese, 1959; Zaccolo et al., 1996).
`Random` mutations can also be introduced into genes in vitro
during polymerisation for example by using error-prone polymerases
(Leung et al., 1989).
[0099] Further diversification can be introduced by using
homologous recombination either in vivo (see Kowalczykowski et al.,
1994) or in vitro (Stemmer, 1994a; Stemmer, 1994b).
Gene Product
[0100] The present invention can thus be used to produce specific,
desired gene products or to produce a range of diverse gene
products (which may be partially or wholly unknown) for screening
purposes.
[0101] The term "gene product" is used herein in its broadest sense
to include not only polypeptides but also RNA gene products. Thus
it includes the products of transcription alone, as well as the
products of both transcription and translation.
[0102] Preferred gene products are polypeptides that occur
naturally in eukaryotic cells (especially mammalian or human cells)
but not in prokaryotic cells, or mutant forms of such polypeptides
having one or more amino acid changes relative to the wild type
eukaryotic polypeptide. Mutant forms are useful in generating
diversity, e.g. for screening purposes. However, if amino acid
changes are made it is preferred that there is a limited number of
such changes, e.g. that less than 50, less than 25, less than 10 or
less than 5 amino acids are changed relative to a wild type
polypeptide. Mutant forms may, for example, act as antagonists or
agonists of one or more of the biological activities of a wild-type
polypeptide. They may therefore be useful in studying
structure-function relationships, in screening, in drug development
programs, etc. Mutations can be introduced into nucleic acids by
any appropriate method. For example, a nucleic acid sequence
incorporating a desired sequence change can be provided by
site-directed mutagenesis. This can then be used to allow the
expression of an RNA or a polypeptide having a corresponding change
in its sequence. Alternatively, a nucleic acid may be synthesised
to include a given mutation. Mutations can also be provided by
using mutagenic agents and/or irradiation.
[0103] For certain applications the expression system may be used
to express a gene product useful in the replication, repair,
maintenance or replication of a nucleic acid of a eukaryotic cell,
preferably of a mammalian or human cell. The gene product may
therefore have activity as a polymerase, a reverse transcriptase, a
ligase, or a telomerase, for example. It may have more than one
such activity. If it is involved in nucleic acid repair, it may
have proofreading activity. Gene products can be produced in the
compartments formed by the hydrophilic phase of the emulsion and
containing the expression system.
Selection Procedures
[0104] The methods can be configured to select for RNA, DNA or
protein gene product molecules with catalytic, regulatory or
binding activity.
(i) Affinity Selection
[0105] In the case of selection for a gene product with affinity
for a specific ligand the genetic element may be linked to the gene
product in the microcapsule via the ligand. Only gene products with
affinity for the ligand will therefore bind to the genetic element
itself and therefore only genetic elements that produce active
product will be retained in the selection step. In this embodiment,
the genetic element will thus comprise a nucleic acid encoding the
gene product linked to a ligand for the gene product.
[0106] In this embodiment, all the gene products to be selected
contain a putative binding domain, which is to be selected for, and
a common feature--a tag. The genetic element in each microcapsule
is physically linked to the ligand. If the gene product produced
from the genetic element has affinity for the ligand, it will bind
to it and become physically linked to the same genetic element that
encoded if resulting in the genetic element being `tagged`. At the
end of the reaction, all of the microcapsules are combined, and all
genetic elements and gene products pooled together in one
environment. Genetic elements encoding gene products exhibiting the
desired binding can be selected by affinity purification using a
molecule that specifically binds to, or reacts specifically with,
the "tag".
[0107] In an alternative embodiment, genetic elements may be sorted
on the basis that the gene product, which binds to the ligand,
merely hides the ligand from, for example, further binding
partners. In this eventuality, the genetic element, rather than
being retained during affinity purification step, may be
selectively eluted whilst other genetic elements are bound.
[0108] In an alternative embodiment, the invention provides a
method according to the second aspect of the invention, wherein in
step (b) the gene products bind to genetic elements encoding them.
The gene products together with the attached genetic elements are
then sorted as a result of binding of a ligand to gene products
having the desired activity. For example, all gene products can
contain an invariant region which binds covalently or
non-covalently to the genetic element, and a second region which is
diversified so as to generate the desired binding activity.
[0109] 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 (Stofko et al., 1992;
Montigiani et al., 1996)), 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.
[0110] However, the usefulness of certain affinity based selection
methods may be limited. Especially with low to medium affinity
interactions, the half-life of the interactions may often be too
short compared with the time required to detect the
interactions.
[0111] Thus in one embodiment of the present invention, selection
methods are based on increasing the affinity of intermolecular
interactions by allowing multivalent interactions to occur. The
resulting apparent increase in affinity gained by multivalent
interaction, also termed avidity, is due to the fact that when two
or more binding interactions take place within the same molecular
complex, there is only a very small additional entropic price to be
paid for the second or further interactions. This is because most
degrees of freedom have already been lost when binding through one
binding site immobilised the multivalent ligand. However, avidity
can have particularly drastic effects on the dissociation kinetics
(k.sub.off), as all interactions must be broken before dissociation
can take place.
[0112] Thus, in this embodiment, molecules that interact may be
selected by allowing multivalent interactions to occur between the
molecules, thus increasing the stability of any complex formed as
compared with a corresponding monovalent interaction.
[0113] Preferably, the first and/or second interacting molecules,
e.g. the gene product and the ligand molecule to which it binds,
have been modified to increase their valency. Preferably, one or
more reactive groups is present on the gene product or ligand
molecules, or both, such that the gene product (and/or ligand)
molecules associate with each other to form multivalent gene
product complexes and/or multivalent ligand molecule complexes. The
multivalent complexes may then be selected for binding according to
the invention. Preferably, the reactive groups form a covalent bond
on interaction.
[0114] The term "multivalent complex" as used herein means a
molecular complex comprising (i) at least two molecules of the gene
product or at least one molecule of a multivalent gene product and
(ii) a multivalent ligand molecule, wherein the at least two
molecules of the gene product are interacting with the ligand
molecule or the at least one molecule of a multivalent gene product
is interacting with the ligand molecule via at least two
valencies.
[0115] In such avidity selection procedures, the ligand molecule is
preferably multivalent. For example, where the ligand molecule is a
polypeptide, the ligand molecule may be multivalent by virtue of
being expressed as a fusion protein to a third polypeptide which
multimerises.
[0116] The gene product and/or ligand molecules may comprise a tag,
for example a biotin or a myc epitope tag or moiety, to assist in
purifying complexes formed between them, and/or to assist in
recovering gene product and/or ligand molecules for analysis and
identification.
[0117] The ligand molecule is typically a multimer, such as a
dimer, or capable of forming a homomultimer under the reaction
conditions used in the methods of the invention. Alternatively, the
ligand molecule may be a heteromultimer. It is preferred to use
ligand molecules which are polypeptides that have been engineered
to be multimeric but whose constituent subunits do not normally
form multimers. This may be achieved by chemical linkage of two or
more molecules to form a covalently linked multimer. Alternatively,
in the case of ligand molecules which are polypeptides and which
bind to gene products which are polypeptides, the molecules may be
expressed as a fusion to a third polypeptide, the third polypeptide
forming homomultimers which effectively results in multimerisation
of the fused ligand polypeptide sequence. An example of a suitable
third polypeptide (referred to herein as a "hook" polypeptide) is
glutathione-S-transferase (GST), which forms dimers. Preferred hook
polypeptides provide for good levels of expression of soluble
products. In one embodiment, hook polypeptides that are suitable
for secretion into the bacterial periplasm (e.g. GST after the
removal of 3 surface Cys residues (Tudyka and Skerra, 1997) are
preferred. The ligand molecule may be provided as a plurality of
ligand molecules.
[0118] In a particularly preferred embodiments of the invention,
the gene products are polypeptides encoded by first polynucleotides
and the polynucleotides are associated with the corresponding
polypeptides such that when a first polypeptide is selected during
the screening methods of the present invention, the polynucleotide
sequence that encodes the selected polypeptide is physically
linked, or in close proximity, and can easily be recovered and, for
example, sequenced to determine the identity of the selected
polypeptide. In order to achieve this, the plurality of first
polynucleotides in a compartment may be such that there is on
average only one polynucleotide per using the emulsion of the
present invention.
[0119] Further details of avidity based selection methods, which
may be used in methods of the present invention, are described in
co-pending GB patent application 0114856.8, the contents of which
are herein incorporated by reference.
(ii) Catalysis
[0120] When selection is for catalysis, the genetic element in each
microcapsule may comprise the substrate of the reaction. If the
genetic element encodes a gene product capable of acting as a
catalyst, the gene product will catalyse the conversion of the
substrate into the product. Therefore, at the end of the reaction
the genetic element is physically linked to the product of the
catalysed reaction. When the microcapsules are combined and the
reactants pooled, genetic elements encoding catalytic molecules can
be enriched by selecting for any property specific to the
product.
[0121] For example, enrichment can be by affinity purification
using a molecule (e.g. an antibody) that binds specifically to the
product. Equally, the gene product may have the effect of modifying
a nucleic acid component of the genetic element, for example by
methylation (or demethylation) or mutation of the nucleic acid,
rendering it resistant to or susceptible to attack by nucleases,
such as restriction endonucleases.
[0122] 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 of the first reaction. A second, coupled reaction will
only proceed in the presence of the product of the first reaction.
An active genetic element can then be purified by selection for the
properties of the product of the second reaction.
[0123] 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 either be
translated in situ in the microcapsules or incorporated in the
reaction mixture prior to microencapsulation. Only when the first
reaction proceeds will the coupled enzyme generate a selectable
product.
[0124] 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 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 and Bates, 1988; Johannsson, 1991). 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 selection system can be used for a whole group of enzymes
which generate the same product and allows for the selection of
complicated chemical transformations that cannot be performed in a
single step.
[0125] Such a method of coupling thus enables the evolution of
novel "metabolic pathways" in vitro in a stepwise fashion,
selecting and improving first one step and then the next. The
selection strategy is based on the final product of the pathway, so
that all earlier steps can be evolved independently or sequentially
without setting up a new selection system for each step of the
reaction.
[0126] Expressed in an alternative manner, there is provided a
method of isolating one or more genetic elements encoding a gene
product having a desired catalytic activity, comprising the steps
of: [0127] (1) expressing genetic elements to give their respective
gene products; [0128] (2) allowing the gene products to catalyse
conversion of a substrate to a product, which may or may not be
directly selectable, in accordance with the desired activity;
[0129] (3) optionally coupling the first reaction to one or more
subsequent reactions, each reaction being modulated by the product
of the previous reactions, and leading to the creation of a final,
selectable product; [0130] (4) linking the selectable product of
catalysis to the genetic elements by either: [0131] a) coupling a
substrate to the genetic elements in such a way that the product
remains associated with the genetic elements, or [0132] b) reacting
or binding the selectable product to the genetic elements by way of
a suitable molecular "tag" attached to the substrate which remains
on the product, or [0133] c) coupling the selectable product (but
not the substrate) to the genetic elements by means of a
product-specific reaction or interaction with the product; and
[0134] (5) selecting the product of catalysis, together with the
genetic element to which it is bound, either by means of a specific
reaction or interaction with the product, or by affinity
purification using a suitable molecular "tag" attached to the
product of catalysis, wherein steps (1) to (4) each genetic element
and respective gene product is contained within a microcapsule
formed from an emulsion of the invention. (iii) Regulation
[0135] A similar system can be used to select for regulatory
properties of enzymes.
[0136] In the case of selection for a regulator molecule which acts
as an activator or inhibitor of a biochemical process, the
components of the biochemical process can either be translated in
situ in each microcapsule or can be incorporated in the reaction
mixture prior to microencapsulation. If the genetic element being
selected is to encode an activator, selection can be performed for
the product of the regulated reaction, as described above in
connection with catalysis. If an inhibitor is desired, selection
can be for a chemical property specific to the substrate of the
regulated reaction.
[0137] There is therefore provided a method of sorting one or more
genetic elements coding for a gene product exhibiting a desired
regulatory activity, comprising the steps of: [0138] (1) expressing
genetic elements to give their respective gene products; [0139] (2)
allowing the gene products to activate or inhibit a biochemical
reaction, or sequence of coupled reactions, in accordance with the
desired activity, in such a way as to allow the generation or
survival of a selectable molecule; [0140] (3) linking the
selectable molecule to the genetic elements either by [0141] a)
having the selectable molecule, or the substrate from which it
derives, attached to the genetic elements, or [0142] b) reacting or
binding the selectable product to the genetic elements, by way of a
suitable molecular "tag" attached to the substrate which remains on
the product, or [0143] c) coupling the product of catalysis (but
not the substrate) to the genetic elements, by means of a
product-specific reaction or interaction with the product; [0144]
(4) selecting the selectable product, together with the genetic
element to which it is bound, either by means of a specific
reaction or interaction with the selectable product, or by affinity
purification using a suitable molecular "tag" attached to the
product of catalysis, wherein steps (1) to (4) each genetic element
and respective gene product is contained within a microcapsule
formed by an emulsion of the invention.
(iv) Microcapsule Sorting
[0145] The invention provides for the sorting of intact
microcapsules where this is enabled by the sorting techniques being
employed. Microcapsules may be sorted as such when the change
induced by the desired gene product 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 gene product, or indirect, in which a series of
reactions, one or more of which involve the gene product having the
desired activity leads to the change. For example, the microcapsule
may be so configured that the gene product is displayed at its
surface and thus accessible to reagents. Where the microcapsule is
a membranous microcapsule, the gene product may be targeted or may
cause the targeting of a molecule to the membrane of the
microcapsule. This can be achieved, for example, by employing a
membrane localisation sequence, such as those derived from membrane
proteins, which will favour the incorporation of a fused or linked
molecule into the microcapsule membrane. Alternatively, where the
microcapsule is formed by phase partitioning such as with
water-in-oil emulsions, a molecule having parts which are more
soluble in the extra-capsular phase will arrange themselves such
that they are present at the boundary of the microcapsule.
[0146] In a preferred aspect of the invention, however,
microcapsule sorting is applied to sorting systems which rely 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 sorted by luminescence, fluorescence or
phosphorescence activated sorting. In a highly preferred
embodiment, fluorescence activated sorting is employed to sort
microcapsules in which the production of a gene product having a
desired activity is accompanied by the production of a fluorescent
molecule in the capsule. For example, the gene product itself may
be fluorescent, for example a fluorescent protein such as GFP.
Alternatively, the gene product may induce or modify the
fluorescence of another molecule, such as by binding to it or
reacting with it.
(v) Microcapsule Identification
[0147] Microcapsules may be identified by virtue of a change
induced by the desired gene product which either occurs or
manifests itself at the surface of the microcapsule or is
detectable from the outside as described in section (iv)
(Microcapsule Sorting). This change, when identified, is used to
trigger the modification of the gene 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 gene
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 genetic
element. A similar procedure has been described previously for the
rapid sorting of cells (Keij et al., 1994). Modification of the
genetic element may result, for example, from coupling a molecular
"tag", caged by a photolabile protecting group to the genetic
elements: bombardment with photons of an appropriate wavelength
leads to the removal of the cage. Afterwards, all microcapsules are
combined and the genetic elements pooled together in one
environment. Genetic elements encoding gene products exhibiting the
desired activity can be selected by affinity purification using a
molecule that specifically binds to, or reacts specifically with,
the "tag".
(vi) Multi-Step Procedure
[0148] It will be also be appreciated that according to the present
invention, it is not necessary for all the processes of
transcription/replication and/or translation, and selection to
proceed in one single step, with all reactions taking place in one
microcapsule. The selection procedure may comprise two or more
steps. First, transcription/replication and/or translation of each
genetic element of a genetic element library may take place in a
first microcapsule. Each gene product is then linked to the genetic
element which encoded it (which resides in the same microcapsule).
The microcapsules are then broken, and the genetic elements
attached to their respective gene products optionally purified.
Alternatively, genetic elements can be attached to their respective
gene products using methods which do not rely on encapsulation. For
example phage display (Smith, G. P., 1985), polysome display
(Mattheakkis et al., 1994), RNA-peptide fusion (Roberts and
Szostak, 1997) or lac repressor peptide fusion (Cull, et al.,
1992).
[0149] In the second step of the procedure, each purified genetic
element attached to its gene product is put into a second
microcapsule containing components of the reaction to be selected.
This reaction is then initiated. After completion of the reactions,
the microcapsules are again broken and the modified genetic
elements are selected. In the case of complicated multistep
reactions in which many individual components and reaction steps
are involved, one or more intervening steps may be performed
between the initial step of creation and linking of gene product to
genetic element, and the final step of generating the selectable
change in the genetic element.
(vii) Selection by Activation of Reporter Gene Expression In
Situ
[0150] The system can be configured such that the desired binding,
catalytic or regulatory activity encoded by a genetic element
leads, directly or indirectly to the activation of expression of a
"reporter gene" that is present in all microcapsules. Only gene
products with the desired activity activate expression of the
reporter gene. The activity resulting from reporter gene expression
allows the selection of the genetic element (or of the compartment
containing it) by any of the methods described herein.
[0151] For example, activation of the reporter gene may be the
result of a binding activity of the gene product in a manner
analogous to the "two hybrid system" (Fields and Song, 1989).
Activation might also result from the product of a reaction
catalysed by a desirable gene product. For example, the reaction
product could be a transcriptional inducer of the reporter gene.
For example arabinose could be used to induce transcription from
the araBAD promoter. The activity of the desirable gene product
could also result in the modification of a transcription factor,
resulting in expression of the reporter gene. For example, if the
desired gene product is a kinase or phosphatase the phosphorylation
or dephosphorylation of a transcription factor may lead to
activation of reporter gene expression.
(viii) Amplification
[0152] According to further aspects of methods of the present
invention the methods may comprise the further step of amplifying
the genetic elements. Selective amplification may be used as a
means to enrich for genetic elements encoding the desired gene
product.
[0153] In all the above configurations, genetic material comprised
in the genetic elements may be amplified and the process repeated
in iterative steps. Amplification may be by the polymerase chain
reaction (Saiki et al., 1988) or by using one of a variety of other
gene amplification techniques including; Q.beta. replicase
amplification (Cahill, Foster and Mahan, 1991; Chetverin and
Spirin, 1995; Katanaev, Kurnasov and Spirin, 1995); the ligase
chain reaction (LCR) (Landegren et al., 1988; Barany, 1991); the
self-sustained sequence replication system (Fahy, Kwoh and Gingers,
1991) and strand displacement amplification (Walker et al.,
1992).
EXAMPLES
Example 1
Conventional Emulsions do not Support Efficient Eukaryotic In Vitro
Translation
[0154] An oil phase formulation comprising 4.5% v/v sorbitan
monooleate (Span 80, Fluka; 85548) and 0.4% v/v
polyoxyethylenesorbitan monooleate (Tween 80, Sigma Ultra; P-8074,
and 0.05% v/v t-octylphenoxypolyethoxyethanol (Triton-X 100,
Sigma), in mineral oil (Sigma; M-3516) ("original CSR mix") was
used to emulsify a RRI expression reaction. All RRL reactions were
performed using the TNT T7 quick coupled transcription/translation
system (Promega) expressing firefly luciferase from a plasmid
template. A 50 .mu.l expression reaction was set up on ice
comprising 80% RRL (v/v), methionine 0.02 mM, and luciferase
plasmid template (1 .mu.g). A 40 .mu.l aliquot of this was
emulsified by dropwise addition (5 drop per 5 secs) to 100 pl of
ice-chilled oil phase under constant stirring (1000 rpm). After
addition of the last drop (approximately 20 secs) stirring was
continued for an additional 3-4 minutes.
[0155] Emulsified reactions were incubated at 30.degree. C. for 1
hour and extracted using ether as described above. Luciferase
activity was measured in a 96-well plate reader using luciferase
assay reagent (Promega). The non-emulsified reaction was also
extracted with ether to enable just comparison of activities. This
showed expression levels within emulsion to be typically a very low
0.1% that of the non-emulsified reaction.
[0156] Using a "reduced" oil phase formulation, comprising 1.5%
(v/v) Span 80 (SIGMA) in mineral oil (SIGMA), slightly improved
yields of up to 0.7% were noted, especially with addition of DTT to
20 .mu.M. Inclusion of DTT using the original CSR oil mix was
extremely detrimental to emulsion formation. Several ratios of
aqueous phase to oil phase were tested, and mixing times varied.
The conditions described above gave highest activity with retention
of emulsion integrity over the incubation period.
[0157] Thus emulsification of a RRL reaction using the "classic"
emulsion formulations based on Span80 either alone or in
combination with Tween80 and TritonX-100 resulted in a complete
loss of in vitro translation activity (<1% as expression outside
emulsion (Table 2)) as judged by expression of the enzyme firefly
luciferase.
[0158] Furthermore, we noted a colour change of the hemin component
of the RRL from a dark pink to a rusty brown colour within a matter
of minutes after emulsification (see FIG. 1), indicating oxidation
of the hemin, presumably attributable to a component of the oil
phase.
Example 2
Anti-Oxidants do not Restore Efficient Eukaryotic In Vitro
Translation
[0159] Mammalian translation is regulated, inter alia, by the
family of eIF-2.alpha. kinases in response to cellular stress
(reviewed by Dever (1999), TIBS, 24, 398-403). eIF-2.alpha. kinases
contain a sensor domain and a conserved eIF2 kinase domain. Their
function is to phosphorylate eIF-2.alpha. (which shuts down
translation) in response to stimuli received through the sensor
domain. This serves to protect the cell in circumstances of
cellular stress from wasting resources (protein translation
consumes large amounts of cellular energy) or as an antiviral
defence by preventing expression of the viral genome. Four
different kinases are known to respond to different types of stress
signals (Table 1).
TABLE-US-00001 TABLE 1 Stress-responsive eIF2 kinases Name
Activating signal HRI oxidative stress (low heme) PKR viral
infection (dsRNA) GCN2 starvation (low amino acids, uncharged tRNA)
PERK heat stress, viral infection (unfolded protein)
[0160] We reasoned that one of the reasons for the complete shut
down in translation (given the discoloring of the hemin in the RRL)
was oxidative stress caused by the diffusion of oxidative species
from the oil into the water-phase.
[0161] The component responsible for discoloration and the
inhibition of translation was identified to be contained in both
the Span80 and Tween80 surfactant but not in the mineral oil.
[0162] We tried to buffer the redox change by providing
anti-oxidant or reducing compounds within the oil-phase (PDH, BDA)
and/or the water-phase (DTT, ascorbic acid). Furthermore, we tried
to remove oxidative species from the oil-phase by reaction of the
oil-phase (the mineral oil surfactant mixture) or Span80 alone with
(Polystyrylmethyl)trimethylammonium borohydride-beads (Novabiochem)
or DTT prior to emulsification. Although slowing discoloration
(FIG. 1), this yielded only slight improvements in translation
efficiencies (Table 2). Furthermore, treatment of the oil-phase
with borohydride-beads appeared to reduce the emulsion-forming
properties of the surfactant/oil-phase leading to much destabilized
emulsions.
[0163] Only DTT (at 20 .mu.M final conc.) produced a slight but
consistent improvement in expression levels within emulsion
compared to that of non-emulsified reaction (Table 2). Higher
levels of DTT proved detrimental to the RRL expression system (not
shown). In general DTT also proved destabilizing to the
emulsions.
Example 3
Neither cAMP Nor 2-Ap Enable Efficient Eukaryotic In Vitro
Translation
[0164] We also attempted a direct inhibition of the eIF2 kinase
pathway using cAMP or 2-aminopurine (2-AP). Although cAMP produced
a small improvement when used on its own, it proved not-additive
with the beneficial effects of DTT (not shown). Both cAMP and 2-AP
are rather unspecific inhibitors of eIF2 kinases (there are at
present no available specific inhibitors) and presumably interfere
with other processes within the RRL translation system.
Example 4
Neither HSP70 nor HSP90 Enable Efficient Eukaryotic In Vitro
Translation
[0165] The fact that even high concentrations of DTT did not rescue
more than residual translation activity suggested to us that other
factors than oxidation must be contributing to translation
inhibition. One suspect was protein denaturation as affected by the
emulsification process, i.e. the vigorous mixing of a hydrophilic
water phase and hydrophobic oil-phase. Indeed, it has been known
for some time that addition of BSA (presumably containing some
denatured protein produced by freeze-thawing) produces a
translation shutdown (Matts et al (1993), Biochemistry, 32,
7323-7328), even without emulsification. We confirmed the results
of Matts 93 with and without emulsification. We also tried to
buffer the effect by supplementing the RRL lysates with chaperones,
in particular HSP70 and HSP90 (SIGMA). Once again this produced
only small (non additive) improvements (not shown), which could be
equalled or surpassed by the addition of small amounts (5%) of
glycerol (not shown), which is known to protect proteins from
denaturation.
Example 5
Development of a Novel Oil-Phase and Water-in-Oil Emulsion
[0166] Given this low level of activity, efforts were made to
identify a novel oil phase formulation with diminished potential to
cause oxidative stress or protein denaturation during the
emulsification process.
[0167] After attempts to improve activity with Span80 based
emulsions had failed we tested novel surfactants.
[0168] Emulsification reactions were performed as described in
Example 1, but substituting the surfactants used in that reaction
(Span 80, Tween 80, and Triton) with silicone-based surfactants. Of
these, chemically inert silicone-based surfactants were found to be
successful.
[0169] Polysiloxane-polycetyl-polyethylene glycol copolymer (ABIL
EM90) (Goldschmidt) used at 4% (v/v) in mineral oil afforded
significant improvements. Emulsifying as described in Example 1,
with the exception of a reduced (1.5 minute) stirring time,
expression levels dramatically increased up to 39% (Table 2) of
that of the non-emulsified reaction. This emulsion was stable
throughout the incubation period, and microscopic visualisation
revealed the majority of compartments to have diameters in the
range of 2-5 microns (FIG. 2).
TABLE-US-00002 TABLE 2 Luciferase activity (in light units (LU)) of
luciferase expressed in rabbit 15 reticulocyte extract
non-emulsified and emulsified at two different mixing times (3 min
and 4 min) CSR 1.5% Non Emulsified: emulsion Span80 in emulsified
mixing time mix mineral oil 4% Abil -DTT 326879 3 min 945 832
127828 +DTT 231318 N.A*. 1632 78970 % activ- 0.2% 0.2%/0.6 39%/34%
ity Back- ground: 249 -DTT 154442 4 min 327 338 40155 +DTT 101702
N.A*. 843 29493 % activ- 0.13% 0.15%/0.7 26%/29% ity Back- ground:
114 *non-stable emulsion
Example 6
Expression of Human Telomerase in Emulsion Using Novel
Oil-Phase
[0170] Telomeres are specific DNA structures found at the ends of
chromosomes in eukaryotes. They are appended to the 3' end (left
after removal of the RNA primer used for DNA replication) by a
specialised enzyme telomerase, comprising a RNA component and a
protein component. In humans the enzyme comprises human telomeric
RNA (hTR) and the human telomerase polypeptide (hTERT) and appends
repeated copies of a hexamer repeat (TTAGGG) (SEQ ID NO: 1) to the
chromosome ends. Telomerase activity has been implicated in both
tumor development and progression as well as in senescence and
programmed cell death.
[0171] Telomerase has so far not been expressed successfully in
functional form in prokaryotes, presumably because it requires
specialised chaperones (e.g. HSP 90) and accessory factors both for
assembly and function. But it can be expressed in eukaryotic cells
and also in the rabbit reticulocyte lysate in vitro translation
system (Weinrich et al (1997), Nat. Genet., 17498-502/Beattie et al
(1998, 8, 177-180).
[0172] The oil phase from Example 5 was tested for expression of
functional human telomerase in RRL. Linear T7-driven templates
encoding either wt hTERT and hTR in tandem cloned downstream of the
IRES of pCITE4a (Novagen) or hTERT cloned into pCITE4a with hTR
cloned separately into a variant of pCITE 4a (in which the IRES was
deleted (pCITE-E)) or an inactive deletion mutant of telomerase
were prepared by PCR amplification using the respective parental
plasmids and primers CITET7ba (5'-GTTTTCCCAGTCACGACGTTGTAA-3') (SEQ
ID NO: 2) and CITEterfo (5 `-CCGGATATAGTTCCTCCTTTCAGC-3`) (SEQ ID
NO: 3).
[0173] Expression reactions (50 .mu.l) comprised RRL (80% v/v),
telomerase construct (see FIG. 3 legend), methionine (1 mM),
telomerase substrate (TS (telomerase substrate) primer
(5'-AATCCGTCGAGCAGAGTT-3') (SEQ ID NO: 4) (Intergen) 1 .mu.M), PCR
enhancer (Promega) (3 .mu.l), dNTPs (25 .mu.M), DTT (20 .mu.M).
Emulsions were formed under chilled conditions (on ice) exactly as
described above and incubated at 30.degree. C. for 1.5 hours.
Emulsions were then extracted with 200 .mu.l
chloroform-isoamylalcohol, followed by extraction of aqueous phase
with 1 volume phenol-chloroform.
[0174] Telomerase reaction products were ethanol precipitated and
resuspended in 20 ul sterile water. A PCR-based TRAP (Kim 94) assay
(Intergen) was then used to detect telomerase extension products
formed in the emulsion. Telomerase activity produces a
characteristic ladder (with 6 bp spacing for each repeat) (see FIG.
3).
[0175] The results indicated expression of functionally active
telomerase from the WT template in emulsion. Control experiments
either omitting addition of telomerase gene, or using an inactive
deletion mutant gave negative results (FIG. 3).
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Sequence CWU 1
1
3124DNAArtificial sequenceChemically synthesized primer 1gttttcccag
tcacgacgtt gtaa 24224DNAArtificial sequenceChemically synthesized
primer 2ccggatatag ttcctccttt cagc 24318DNAArtificial
sequenceChemically synthesized primer 3aatccgtcga gcagagtt 18
* * * * *