WO2016170345A1

WO2016170345A1 - Mifrofluidic apparatus and method for producing an emulsion, use of the apparatus, method for making a microfluidic apparatus and a surfactant

Info

Publication number: WO2016170345A1
Application number: PCT/GB2016/051112
Authority: WO
Inventors: Andrew Hudson
Original assignee: University Of Leicester
Priority date: 2015-04-22
Filing date: 2016-04-21
Publication date: 2016-10-27
Also published as: GB201506807D0

Abstract

A microfluidic apparatus for producing an emulsion, comprising at least one fluid inlet channel (4) configured to allow an aqueous solution to flow therealong and at least one fluid inlet channel (2) configured to allow an oil phase to flow therealong. Each inlet channel converges at a junction (8) at which an emulsion is formed upon contact between the oil phase and aqueous solution. The apparatus further comprises a fluid outlet channel (22) extending away from the junction, and configured to allow the emulsion to flow therealong. Each inlet channel comprises a restricted section (10, 16) disposed at least adjacent to the junction, and an expanded section (14, 20) disposed upstream of the restricted section, wherein the expanded section has an aspect ratio which is greater than 20:1.

Description

M IFROFLUIDIC APPARATUS AND METHOD FOR PRODUCING AN EMULSION, USE OF THE APPARATUS, METHOD FOR MAKING A M ICROFLUIDIC APPARATUS AND A SURFACTANT

The present invention is concerned with emulsions, and particularly, although not exclusively, microfluidic emulsions. The invention extends to apparatuses and methods for producing emulsions, and to the emulsions per se. The invention also extends to novel surfactants and their ability to stabilise microfluidic emulsions.

Single molecule experiments are used increasingly for the investigation of biological reactions. Among the most common single molecule measurements is fluorescence resonance energy transfer (FRET), which has contributed much to the understanding of macromolecular dynamics and reaction pathways. FRET measurements can be made using total internal reflection fluorescence (TIRF) microscopy. One component must, however, be attached (i.e. tethered) to the surface of a glass or silica cover slip, but this procedure suffers from the possibility that tethering affects the subsequent dynamics of biological transformations. In addition, if freely-diffusing components of the reaction are labelled they may adsorb to the surface and obscure events on the target site. An alternative strategy is to detect FRET or interactions in freely-diffusing molecules as they pass through a confocal laser (such as fluorescence correlation spectroscopy or alternating laser excitation spectroscopy methods), but this precludes following the sequence of events in a single molecule (or molecular complex) over a long period.

A promising method for following the reactions of single entities for a prolonged time without tethering them is to encapsulate them into emulsion droplets. The isolated molecules can then be imaged and analysed individually by confocal observation on a single droplet, or a larger number of droplets can be imaged concurrently in a wide field mode, using highly inclined thin illumination (ΗΓΓΙ) by a laser beam,¹ or TIRF microscopy. Indeed, it would be more desirable to image droplets in a wide field mode. For both HITI and TIRF, the emulsion droplets would need to be small (approx.≤ 1 μπι in length normal to the imaging surface) and positioned directly above the imaging surface; although the intensity of the evanescent field used in TIRF microscopy falls significantly beyond distances of 50-100 nm from the imaging surface, the excitation light can be coupled efficiently into aqueous droplets dispersed in a low index perfluorocarbon oil. Droplets² or vesicles³ used for single molecule studies have for the most part been either relatively large in size (>0.5 pi), or produced individually, or necessitated imaging by confocal methods. There has been relatively little success in forming droplets with volumes in the region of a few femtolitres (fl). Tawfik and Griffiths were the first to show the utility of water-in-oil emulsions for in vitro biology by compartmentalising the transcription and translation of single genes within aqueous droplets of variable size (mean spherical diameter, 2 - 3 μηι).ι In these early experiments, the emulsion droplets were formed by stirring the aqueous reaction mixture with mineral oil and surfactant, and the products of gene expression were measured after breaking the emulsion to extract the aqueous solution. Goldner and coworkers demonstrated the in situ measurement of single fluorescent molecules within similar-sized droplets (or hydrosomes) that were also formed by stirring aqueous and oil phases together.s In this example, the continuous phase of the emulsion was a perfluorocarbon oil with low refractive index, which meant that the aqueous droplets could be held by optical tweezers and a single encapsulated-molecule could be monitored for a long period of time by confocal fluorescence microscopy. The authors showed that two droplets could be fused together using a pair of independent optical traps and, in subsequent work, they demonstrated a droplet-on-demand method for producing and mixing aqueous droplets of monodisperse size in optical traps (both fl and sub-fl volume).⁶ Although the combination of optical trapping and droplet-on- demand is an elegant methodology, it is a relatively slow procedure for gathering datasets on a large number of single molecules. Large statistics are essential for understanding the static and dynamic heterogeneity in single molecule experiments. Therefore, the rapid production of emulsion droplets, with monodisperse femtolitre size suitable for encapsulating single molecules, by microfluidic flow focusing would be an enabling technology for single-molecule research, and it will address the main disadvantage of limited datasets obtained in experiments using either droplet-on- demand techniques or tethered lipid vesicles. Both flow focusing, and other microfluidic methods for droplet production using co-flowing streams of immiscible liquids, have found applications in in vitro biology,^10-^ but their utility for

encapsulation and detection of a single fluorophore, or a single fluorescently-labelled analyte, has not been reported before. Flow-focusing has previously been used for the controlled production of normal and reverse emulsions over a wide range of large droplet sizes from 500 nl down to 4 pi.⁸ The microfluidic method is passive and relies on an upstream flow field ahead of a 4-way junction in which one liquid phase is sandwiched between immiscible liquid phases in co-flowing streams, as illustrated in Figure 1. The pressure in the upstream fluidic channels is not in equilibrium and subject to periodic oscillations that lead to competition between the aqueous and oil flow. In the example shown in Figure 1, a transient increase in the pressure of the aqueous solution limits the flow of the oil phases and a pendant-like droplet forms at the 4-way junction. Whilst the droplet size increases, the pressure of the oil flow at the 4-way junction also increases until the aqueous droplet is pinched off. At this time, the flow of the oil phase dominates and temporarily blocks the aqueous solution. The pressure of the aqueous solution increases again and the process continues ad infinitum to generate a downstream flow of aqueous droplets dispersed in an immiscible oil. A theoretical description of the droplet-formation process is given in reference 9. The size of droplets formed by flow focusing will normally be dependent on the geometry of the 4-way junction, see Figure 1. Until now, the design of microfluidic devices with feature sizes of the order of a few micrometres has been a challenge. The formation of oil droplets of approx. 1 fL (1 μιη diameter) has been described in a microfluidic component where the exit-channel dimension of the junction was reduced (to approx. 1 μπι) following the swelling of the polydimethylsiloxane (PDMS) substrate after it had been left in contact with water.? However, the manufacture of microfluidic devices with a narrow junction by aging in a moist environment is unreliable. The production of droplets on the scale of 1 fL by microfluidic flow focusing is possible using junction dimensions of 10 μιη, or larger. A narrow thread must be formed in an aqueous solution sandwiched between fast flowing oil phases. Breakup of the thread can occur by a process called tipstreaming to generate small droplet sizes²⁶; however, the flow conditions for microdroplet formation by tip streaming cannot be maintained for longer than transient timescales and precise control of droplet size is highly challenging.

The present invention arises from the inventors' work in trying to overcome the problems associated with the prior art.

Thus, in accordance with a first aspect of the invention, there is provided a microfluidic apparatus for producing an emulsion, the apparatus comprising at least one fluid inlet channel configured to allow an aqueous solution to flow therealong and at least one fluid inlet channel configured to allow an oil phase to flow therealong, each inlet channel converging at a junction at which an emulsion is formed upon contact between the oil phase and aqueous solution, and a fluid outlet channel extending away from the junction, and configured to allow the emulsion to flow therealong, characterised in that each inlet channel comprises a restricted section disposed at least adjacent to the junction, and an expanded section disposed upstream of the restricted section, wherein the expanded section has an aspect ratio which is greater than 20: 1.

The inventors have demonstrated that a microfluidic device with channels that have a high aspect ratio in areas that are not immediately adjacent to the junction enables the apparatus of the first aspect to be used to rapidly produce, under very tight control, microfluidic emulsions containing uniform, monodisperse aqueous droplets with a size of approximately 1 fl volume. Hence, such droplets are suitable for confining single fluorophores using the technique of microfluidic flow-focusing. The apparatus can be used in an efficient and low cost manner for high throughput biology experiments, for example using fluorescent detection of a single molecule analyte (e.g. DNA or protein etc.) in an aqueous droplet. To date, it has not been possible to produce microfluidic devices with such a high aspect ratio, which is why current devices can only produce aqueous droplets with a size of approximately 1000 fl volume (or 10 - 20 μιη diameter) meaning that they are unsuitable for single molecule experiments, unlike the apparatus of the first aspect.

In a preferred embodiment, however, the microfluidic apparatus comprises at least three inlet channels, wherein at least two inlet channels are configured to allow an oil phase to flow therealong, and one inlet channel is configured to allow an aqueous solution to flow therealong. At least one of the inlet channels may be configured to allow both an oil phase and an aqueous solution to flow therealong.

Preferably, the junction comprises a 3- way or a 4-way junction. Preferably, the inlet channel which is configured to allow aqueous solution to flow therealong is disposed on substantially the opposite side of the junction to the outlet channel.

It will be understood that the aspect ratio can mean the ratio of the width of the expanded section to the depth of the expanded section of the inlet channel. Hence, it is preferred that the ratio of the width to the depth of the expanded section of each inlet channel is greater than 20: 1. Preferably, the aspect ratio of the expanded section of each inlet channel is greater than 25: 1, more preferably greater than 30:1, and most preferably greater than 35:1. Preferably, the aspect ratio of the expanded section of each inlet channel is between 20: 1 and 60: 1, more preferably between 25:1 and 55: 1, and even more preferably between 30:1 and 50:1. Most preferably, the aspect ratio of the expanded section of each inlet channel is between 35:1 and 45:1. In a most preferred embodiment, the aspect ratio of the expanded section of each inlet channel is about 40:1. Preferably, the restricted section of the inlet channel configured to allow aqueous solution to flow therealong is disposed adjacent to an intermediate section of the same inlet channel which is itself disposed adjacent to the expanded section of the inlet channel. Accordingly, it will be understood that the expanded section of that inlet channel is in fluid communication with the restricted section.

Preferably, the width of the restricted section of the inlet channel along which aqueous solution may flow is less than 5 μπι, more preferably less than 4.5 μπι, 4.0 μιη or 3.5 μπι. Preferably, the width of the restricted section of the inlet channel along which aqueous solution flows is between 1.0 μπι and 4.5 μπι, more preferably between 2.0 μιη and 4.0 μπι, and most preferably between 2.5 μπι and 3.5 μπι. In a preferred embodiment, the width of the restricted section of the inlet channel along which aqueous solution flows is about 3 μπι.

Preferably, the width of the expanded section of the inlet channel along which aqueous solution may flow is between 10 μπι and 150 μπι, more preferably between 20 μπι and 125 μπι, between 30 μπι and 100 μιη, or between 40 μιη and 80 μπι. Most preferably, the width of the expanded section is between 50 μπι and 70 μπι. In a preferred embodiment, the width of the expanded section of the inlet channel along which aqueous solution can flow is about 60 μπι.

In a preferred embodiment, the depth of the restricted section, expanded section and intermediate section, in embodiments where one is present, of the inlet channel configured to allow aqueous solution to flow therealong are approximately the same depth.

Preferably, the depth of the inlet channel along which aqueous solution may flow is less than 15 μιη, more preferably less than 10 μπι, 7.5 μιη or 5 μπι. Most preferably, the depth of the inlet channel along which aqueous solution may flow is less than 4 μιη, 3 μπι or 2 μπι. Preferably, the depth of the inlet channel along which aqueous solution may flow is between 0.1 μιη and 10 μπι, more preferably between 0.25 μιη and 7.5 μιη, or between 0.5 μπι and 5 μπι. Even more preferably, the depth of the inlet channel along which aqueous solution may flow is between 0.7 μιη and 4 μπι, between 0.8 μπι and 3 μιη, or between 1 μπι and 2 μm. In a most preferred embodiment, the depth of the inlet channel along which aqueous solution may flow is about 1.3 μπι. Preferably, the restricted section of the or each inlet channel along which oil may flow is disposed adjacent to an intermediate section of the or each oil channel which is disposed adjacent to the expanded section of the or each oil channel. Accordingly, it will be understood that the expanded section of the or each oil channel is in fluid communication with the restricted section of the or each oil channel.

Preferably, the width of the restricted section of the or each inlet channel along which oil flows is less than 15 μπι, more preferably less than 14 μιη, 13 μπι, 12 μπι, ιι μπι or 10 μπι. Preferably, the width of the restricted section of the or each inlet channel along which oil phase flows is between 1 μιη and 14 μπι, more preferably between 3 μπι and 13 μπι, between 5 μιη and 12 μιη, or between 7 μιη and 11 μπι. Most preferably, the width of the restricted section of the or each oil channel is between 8 μπι and 10 μπι. In a preferred embodiment, the width of the restricted section of the or each oil channel is about 9 μΐΏ. Preferably, the width of the expanded section of the or each inlet channel along which oil phase flows is between 10 μπι and 150 μπι, more preferably between 20 μπι and 125 μπι, between 30 μιη and 100 μιη, or between 40 μιη and 80 μπι. Most preferably, the width of the expanded section of the or each oil channel is between 50 μπι and 70 μπι. In a preferred embodiment, the width of the expanded section of the or each oil channel is about 60 μπι.

In a preferred embodiment, the depth of the restricted section, expanded section and intermediate section, in embodiments where one is present, of the inlet channel configured to allow oil to flow therealong are approximately the same depth.

Preferably, the depth of the inlet channel along which oil may flow is less than 15 μιη, more preferably less than 10 μιη, 7.5 μπι or 5 μπι. Most preferably, the depth of the inlet channel along which oil may flow is less than 4 μπι, 3 μπι or 2 μπι. Preferably, the depth of the inlet channel along which oil may flow is between 0.1 μπι and 10 μιη, more preferably between 0.25 μπι and 7.5 μιη, or between 0.5 μιη and 5 μπι. Even more preferably, the depth of the inlet channel along which oil may flow is between 0.7 μπι and 4 μηι, between 0.8 μηι and 3 μηι, or between 1 μηι and 2 μηι. In a most preferred embodiment, the depth of the inlet channel along which oil may flow is about 1.3 μπι.

Preferably, the apparatus comprises an aqueous chamber disposed upstream of, and in fluid communication with, the inlet channel along which aqueous solution may flow. Preferably, the aqueous chamber has a cylindrical cross-section. Preferably, the aqueous chamber has a diameter of at least 1 mm. Preferably, the aqueous chamber has a diameter of about 2 mm. Preferably, the aqueous chamber itself comprises an aqueous inlet through which aqueous solution can be fed. Preferably, the aqueous chamber comprises a ceiling and a floor, and a plurality of spaced apart columns extending therebetween. Preferably, the columns are configured to prevent the ceiling of the aqueous chamber from sagging.

Preferably, the apparatus comprises a first fluid delivery line which extends from the aqueous inlet and is configured to allow aqueous solution to flow therealong.

Preferably, the first fluid delivery line comprises plastic tubing. Preferably, the first fluid delivery line has a diameter of at least 0.5 mm. Preferably, the first fluid delivery line has a diameter of about 1 mm. In one embodiment, the aqueous chamber comprises an internal aqueous filter configured to trap particles present in the aqueous solution which could otherwise block the inlet channel along which aqueous solution flows to the junction. The internal aqueous filter may comprise a plurality of spaced apart filter blocks between which aqueous solution can flow. Preferably, the plurality of spaced apart filter blocks are disposed circumferentially around the aqueous inlet. More preferably, the internal aqueous filter comprises two or more radially spaced apart concentric rows of filter blocks which are disposed around the aqueous inlet.

Preferably, the aqueous filter blocks forming an outer row are separated from each other by less than 8 μιη, more preferably by about 5 μπι. Preferably, the aqueous filter blocks forming an inner row are separated from each other by less than 11 μπι, more preferably by about 8 μπι.

It will be appreciated that the aqueous filter blocks may be a variety of shapes.

However, preferably the aqueous filter blocks have a trapezoid cross-section, and more preferably an isosceles trapezoid cross-section. However, in an alternative and preferred embodiment, the aqueous chamber does not comprise an internal aqueous filter. In this embodiment, the first fluid delivery line may comprise a junction, wherein upstream of the junction the first fluid delivery line is split into an oil phase delivery line configured to allow an oil phase to flow therealong, and an aqueous solution delivery line configured to allow an aqueous solution to flow therealong and be injected as an aqueous plug into the oil phase. A first external filter maybe disposed in the oil phase delivery line upstream of the junction. A second external filter may be disposed in the aqueous solution delivery line upstream of the junction.

Advantageously, this enables the apparatus to be used with a small aqueous sample which maybe delivered as an aqueous plug in a stream of oil. Preferably, the apparatus comprises an oil chamber disposed upstream of, and in fluid communication with, the at least one inlet channel along which oil may flow to the junction. Preferably, the oil chamber is disposed upstream of, and in fluid

communication with, two inlet channels along which oil flows to the junction.

Preferably, the oil chamber has a cylindrical cross-section. Preferably, the oil chamber has a diameter of at least ι mm. Preferably, the oil chamber has a diameter of about 2 mm.

Preferably, the oil chamber itself comprises an oil inlet through which oil can be fed into the oil chamber. Preferably, the oil chamber comprises an outlet which is in fluid communication with each oil inlet channel. Preferably, the oil chamber comprises a ceiling and a floor, and a plurality of spaced apart columns extending therebetween. Preferably, the columns are configured to prevent the ceiling of the oil chamber from sagging. Preferably, the apparatus comprises a second fluid delivery line which extends from the oil inlet and is configured to allow an oil phase to flow therealong. Preferably, the second fluid delivery line comprises plastic tubing. Preferably, the second fluid delivery line has a diameter of at least 0.5 mm. Preferably, the second fluid delivery line has a diameter of about 1 mm. Preferably, the oil chamber comprises an internal oil filter configured to trap particles present in the oil which could otherwise block the inlet channel along which oil flows to the junction. The internal oil filter may comprise a plurality of spaced apart oil filter blocks between which oil can flow. Preferably, the plurality of spaced apart filter blocks are disposed circumferentially around the oil inlet. More preferably, the internal oil filter comprises two or more radially spaced apart concentric rows of filter blocks which are disposed around the oil inlet.

Preferably, an outer row of oil filter blocks are separated from each other by less than 8 μπι, more preferably by about 5 μπι. Preferably, an inner row of oil filter blocks are separated from each other by less than 11 μιη, more preferably by about 8 μπι.

It will be appreciated that the oil filter blocks may be a variety of shapes. However, preferably the oil filter blocks have a trapezoid cross-section, and more preferably an isosceles trapezoid cross-section.

Preferably, the emulsion comprises aqueous droplets in oil.

Preferably, the inlet channels and outlet channel comprise hydrophilic inner surfaces. Advantageously, channels with hydrophilic surfaces will not resist the flow of an aqueous solution. Additionally, it has been found that the formation of water-in-oil emulsions is not hindered by channels with a hydrophilic surface.

Preferably, the outlet channel comprises a restricted section disposed at least adjacent to the junction, and an expanded section disposed downstream of the restricted section. Preferably, the restricted section of the outlet channel is disposed at least adjacent to an intermediate section of the outlet channel, which is disposed at least adjacent to the expanded section of the outlet channel. Accordingly, it will be understood that the restricted section of the outlet channel is in fluid communication with the expanded section of the outlet channel.

Preferably, the width of the restricted section of the outlet channel is less than 10 μπι. More preferably, the width of the restricted section of the outlet channel is less than 7.3 μπι, 5 μιη, 4.5 μιη, 4.0 μιη or 3-5 μηΐ· Preferably, the width of the restricted section of the outlet channel is between 1.0 μπι and 4.5 μιη, more preferably between 2.0 μπι and 4.0 μηι, and most preferably between 2.5 μιη and 3.5 μπι. In a preferred embodiment, the width of the restricted section of the outlet channel is about 3 μπι.

Preferably, the width of the expanded section of the outlet channel is between 5 μπι and 150 μπι, more preferably between 20 μπι and 125 μιη, between 30 μιη and 100 μιη, or between 40 μιη and 80 μπι. Most preferably, the width of the expanded section of the outlet channel is between 50 μπι and 70 μπι. In a preferred embodiment, the width of the expanded section of the outlet channel is about 60 μπι. Preferably, the aspect ratio of the expanded section of the outlet channel is greater than 20: 1. It will be understood that the aspect ratio of the outlet channel can mean the ratio of the width of the expanded section to the depth of the expanded section of the outlet channel. Hence, it is preferred that the aspect ratio of the width to the depth of the expanded section of the outlet channel is greater than 20:1. Preferably, the aspect ratio of the expanded section of the outlet channel is greater than 25:1, more preferably greater than 30:1, and most preferably greater than 35: 1.

Preferably, the aspect ratio of the expanded section of the outlet channel is between 20: 1 and 60: 1, more preferably between 25:1 and 55: 1, and even more preferably between 30:1 and 50:1. Most preferably, the aspect ratio of the expanded section of the outlet channel is between 35:1 and 45:1. In a most preferred embodiment, the aspect ratio of the expanded section of the outlet channel is about 40:1.

In a preferred embodiment, the depth of the restricted section, expanded section and intermediate section, in embodiments where one is present, of the outlet channel are approximately the same depth.

Preferably, the depth of the outlet channel is less than 15 μπι, more preferably less than 10 μπι, 7·5 μπι or 5 μιη. Most preferably, the depth of the outlet channel is less than 4 μπι, 3 μπι or 2 μπι. Preferably, the depth of the outlet channel is between 0.1 μιη and 10 μπι, more preferably between 0.25 μιη and 7.5 μπι, or between 0.5 μπι and 5 μπι. Even more preferably, the depth of the outlet channel is between 0.7 μπι and 4 μιη, between 0.8 μπι and 3 μιη, or between 1 μπι and 2 μπι. In a most preferred embodiment, the depth of the outlet channel is about 1.3 μπι. In a preferred embodiment, each inlet channel and the outlet channel are

approximately the same depth.

Preferably, the apparatus comprises a droplet collection chamber disposed downstream of, and in fluid communication with, the outlet channel. Preferably, the collection chamber is disposed adjacent to the outlet channel. The collection chamber is configured to collect aqueous droplets in oil which form the emulsion.

It will be appreciated that the size of the droplet collection chamber is not critical to the functioning of the apparatus of the invention. However, the inventors have had success using a droplet collection chamber which is approximately 3 mm in length and approximately 3 mm in width.

Preferably, the collection chamber comprises a ceiling and a floor, and a plurality of spaced apart columns extending therebetween. Preferably, and advantageously, the columns are configured to prevent the sagging of the ceiling, and also spread the flow of an emulsion entering the chamber from the outlet channel. It will be appreciated that a variety of columns could be provided. Accordingly, the columns could have a square cross-section, circular cross-section, rectangular cross-section, triangular cross-section, and/ or trapezoid cross-section etc. As shown in Figure 4, the inventors have used columns with a square cross-section.

Preferably, the columns have a width of between 1 μιη and 100 μπι, more preferably between 5 μπι and 50 μπι, and most preferably between 10 μιη and 30 μπι. In a preferred embodiment, the columns have a width of about 20 μπι.

Preferably, the plurality of columns is configured to capture aqueous droplets present in an emulsion entering the chamber from the outlet channel. Preferably, the columns are arranged into groups of at least two, three or four columns, wherein each group is configured to capture aqueous droplets feeding in from the outlet channel. It is preferred that each group of columns is arranged in an open curvilinear configuration, wherein the open section faces the outlet channel. Hence, as droplets leave the outlet channel and pass through the collection chamber, they are captured in the curved arrangement of columns. In a preferred embodiment, the columns are disposed in groups of four columns. It may be appreciated that once captured, the droplets remain substantially static within the collection chamber, where they may be analysed. In another embodiment, however, the droplets may be analysed whilst moving in the outlet before the collection chamber.

Preferably, the droplet collection chamber comprises a mixed-phase outlet configured to allow excess fluid to be removed from the collection chamber.

In a preferred embodiment, the depth of the inlet channels, the outlet channel, the aqueous chamber, the oil chamber and the collection chamber are all approximately the same depth.

Accordingly, the depth of the channels and chambers is preferably less than 15 μιη, more preferably less than 10 μιη, 7.5 μπι or 5 μπι. Most preferably, the depth of the channels and chambers is less than 4 μπι, 3 μιη or 2 μπι. Preferably, the depth of the channels and chambers is between 0.1 μιη and 10 μιη, more preferably between 0.25 μιη and 7.5 μπι, or between 0.5 μπι and 5 μπι. Even more preferably, the depth of the channels and chambers is between 0.7 μιη and 4 μπι, between 0.8 μιη and 3 μπι, or between 1 μιη and 2 μπι. In a most preferred embodiment, the depth of the channels and chambers is about 1.3 μπι. Advantageously, this will mean the apparatus can be made from a template which is made using a soft lithographic process. Additionally, due to the shallow depth, the droplets formed are sandwiched between the floor and ceiling of the microfluidic device, and consequently, a user will never lose sight of the droplets on the microscope. The droplets can therefore be analysed more easily.

It will be appreciated that the apparatus is configured to create microfluidic emulsions containing aqueous droplets using a stable flow regime. Preferably, the droplets have a equivalent mean spherical diameter of less than 10 μιη, 5 μιη, 4 μπι, 3 μιη, 2 μπι or 1 μπι. Preferably, the droplets have an average volume of less than 50ofl, loofl, 5ofl, 25 fl, 10 fl, 5 fl or 2.5 fl.

The inventors believe that their method of making the apparatus of the first aspect is novel and inventive. Hence, in accordance with a second aspect, there is provided a method of making a microfluidic apparatus for producing an emulsion, the method comprising: using a suitable template with a patterned surface to produce an elastomer replica with a correspondingly patterned surface;

activating the patterned surface of the elastomer replica and a solid support; covering the patterned surface of the elastomer replica in a volatile solvent; and contacting the solid support with the patterned surface of the elastomer replica, to thereby produce a microfluidic apparatus.

Advantageously, by covering the patterned surface of the silicone replica in a volatile solvent prior to sealing the channels against the solid support the volatile solvent layer prevents the surfaces from bonding instantly. Instead, the volatile solvent can then evaporate allowing the elastomer replica to bond to the solid support in the absence of an external force. This prevents the collapse of channels in sections of the apparatus which have a high aspect ratio.

Preferably, the apparatus made according to the method of the second aspect is the apparatus as defined in the first aspect.

It will be understood that the template may comprise a negative three-dimensional image of the apparatus of the first aspect. The template may comprise a silicon surface patterned with an epoxy negative photoresist.

Preferably, the elastomer replica comprises a silicone replica. Preferably, the silicone replica comprises a polydimethylsiloxane (PDMS) replica.

Preferably, the step of producing the elastomer replica comprises:

mixing base and hardener components of an eleastomer, and using the mixture to coat the patterned surface of the template; and

degassing and curing the elastomer to produce an elastomer replica with a patterned surface.

Preferably, subsequent to the step of producing the elastomer replica the method comprises:

- boring holes into the elastomer replica to provide an aqueous inlet, an oil inlet and a mixed-phase outlet; and

inserting tubing into the bored holes. The holes may be bored using a punch, preferably a biopsy punch.

The solid support preferably comprises a transparent material. Accordingly, the solid support may comprise a cover slip or slide. The cover slip or slide may comprise glass or silica. The inventors have used a glass cover slip. It will be understood that the thickness of the solid support is not important. The inventors have used a no. 1 cover slip, i.e. the cover slip used by the inventors comprised a glass cover slip with a thickness of between 0.13 and 0.16 mm thick. However, other thicknesses or glass or silica cover slips could also be used, such as a no. 1.5 cover slip.

Advantageously, using a transparent solid support allows a user to see what is going on in the apparatus when it is used.

Preferably, the step of activating the patterned surface of the silicone replica and the cover slip comprises contacting the silicone replica and the cover slip with an oxygen plasma.

It will be understood that any volatile and inert solvent could be used. Accordingly, the volatile solvent may comprise an alcohol, a nitrile, an ester or a ketone. The alcohol may comprise methanol, ethanol or propanol. The nitrile may comprise acetonitrile. The ester may comprise methylacetate or ethyl acetate. The ketone may comprise acetone. Preferably, the volatile solvent comprises methanol.

Preferably, the step of contacting the solid support with the patterned surface of the elastomer replica comprises placing the solid support against the patterned surface of the elastomer replica, which is covered with the volatile solvent, and allowing the volatile solvent to evaporate. Preferably, once the solid support has been placed against the patterned surface of the elastomer replica, which is covered with the volatile solvent, the solid support and elastomer replica are heated to cause the volatile solvent to evaporate.

Preferably, the heating step comprises heating the solid support and elastomer replica to at least 30°C, 40°C, 50°C or 6o°C. Preferably, the heating step comprises heating the solid support and elastomer replica for at least 10 minutes, 20 minutes, 30 minutes, 40 minutes, 50 minutes or 1 hour. Preferably, the method does not comprise a final step of flushing the apparatus with a hydrophobic solution, such as a 1% solution of 3-aminopropyltriethoxysilane in FC-40, to create hydrophobic channels. The apparatus of the first aspect may be used to produce an emulsion.

Thus, in accordance with a third aspect, there is provided use of the apparatus of the first aspect to produce an emulsion. Preferably, the emulsion can be used in single molecule encapsulation methods.

Moreover, in accordance with a fourth aspect there is provided a method of producing an emulsion, the method comprising:

feeding an aqueous solution along an aqueous channel;

- feeding an oil phase along at least one oil channel;

contacting the aqueous solution with the oil phase at a junction to produce an emulsion,

characterised in that the aqueous channel and at least one oil channel comprises a restricted section disposed at least adjacent to the junction, and an expanded section disposed upstream of the restricted section, wherein the expanded section has an aspect ratio which is greater than 20:1.

The method is preferably used to create a microfluidic emulsion containing

monodisperse droplets. Preferably, the droplets have an equivalent mean spherical diameter of less than 10 μπι, 5 μπι, 4 μιη, 3 μπι, 2 μπι or 1 μπι. Preferably, the droplets have an average volume of less than 50ofl, loofl, 5ofl, 25 fl, 10 fl, 5 fl or 2.5 fl.

Preferably, the method comprises producing a stream of monodisperse droplets with a volume of less than 500 fl. More preferably, the method comprises producing a stream of monodisperse droplets with a volume of less than 300 fl, 200 fl, 100 fl, 50 fl or 25 fl. Most preferably, the method comprises producing a stream of monodisperse droplets with a volume of less than 20 fl, 15 fl or 10 fl. In a preferred embodiment, the method comprises producing a stream of monodisperse droplets with a volume of between 0.1 fl and 10 fl. Most preferably, the method comprises producing a stream of monodisperse droplets with a volume of between 0.5 fl and 7.5 fl. The term monodisperse maybe used to mean that all droplets produced in a stream have a volume that is within +/- 20% of the average volume. More preferably, the term monodisperse may be used to mean that all droplets produced in a stream have a volume that is within +/- 10% of the average volume.

The inventors can report a monodispersity of +/- 10% based on their observations from using the apparatus of the first aspect to carry out the method of the fourth aspect. It should be noted that while the inventors can only confirm that all droplets are within 10% of the average volume, this is due to difficulties in determining the size of the droplets accurately. It is possible that the droplets produced by the inventors were all within 5% of the average volume, but this cannot be verified due to the small size of the droplets.

The stream of monodisperse droplets may be produced for at least 1 minute. The stream of monodisperse droplets may be produced for at least 2 minutes, 3 minutes, 4 minutes, 5 minutes, 6 minutes, 7 minutes 8 minutes 9 minutes or 10 minutes.

It should be noted that the inventors have successfully been able to produce a stream of monodisperse droplets for longer than 10 minutes. However, using the apparatus of the first aspect, the collection chamber is sufficiently filled with the droplets after about 3 minutes and there is no need to continue.

Accordingly, in a preferred embodiment the stream of monodisperse droplets is produced for approximately 3 minutes.

Preferably, the method of the fourth aspect maybe conducted using the apparatus of the first aspect.

Preferably, the method comprises feeding a first stream of the oil phase along a first oil channel and a second stream of oil phase along a second oil channel to the junction.

Preferably, the step of contacting the aqueous solution with the oil phase comprises simultaneously contacting the aqueous solution with both the first and second streams of the oil phase. Preferably, the aqueous solution is fed at a rate of between 0.0001 μΐ/hr and 200 μΐ/hr. More preferably, the aqueous solution is fed at a rate of between 0.0005 μΐ/hr and 100 μΐ/hr, between 0.001 μΐ/hr and 50 μΐ/hr, between 0.005 μΐ/hr and 25 μΐ/hr, between 0.01 μΐ/hr and 10 μΐ/hr, or between 0.05 μΐ/hr and 5 μΐ/hr. Most preferably, the aqueous solution is fed at a rate of between 0.1 μΐ/hr and 4 μΐ/hr, between 0.1 μΐ/hr and 3 μΐ/hr, between 0.1 μΐ/hr and 2 μΐ/hr, or between 0.1 μΐ/hr and 1 μΐ/hr.

Preferably, the aqueous solution is fed at a rate of less than 200 μΐ/hr. More preferably, the aqueous solution is fed at a rate of less than 100 μΐ/hr, 50 μΐ/hr, 25 μΐ/hr, 10 μΐ/hr, or 5 μΐ/hr. Most preferably, the aqueous solution is fed at a rate of less than 4 μΐ/hr, 3 μΐ/hr, 2 μΐ/hr, or 1 μΐ/hr.

In a preferred embodiment, the aqueous solution is fed at a rate of about 0.5 μΐ/hr. Alternatively, the aqueous solution may be fed at a rate of less than 500 nl/hr. More preferably, the aqueous solution is fed at a rate of less than 400 nl/hr, 300 nl/hr, 200 nl/hr or 100 nl/hr. Most preferably, the aqueous solution is fed at a rate of less than 50 nl/hr, 40 nl/hr, 30 nl/hr, or 20 nl/hr. In a preferred embodiment, the aqueous solution is fed at a rate of about 10 nl/hr.

Preferably, the oil phase is fed at a rate of between 0.1 μΐ/hr and 200 μΐ/hr. More preferably, the oil phase is fed at a rate of between 1 μΐ/hr and 175 μΐ/hr, between 5 μΐ/hr and 150 μΐ/hr, or between 10 μΐ/hr and 125 μΐ/hr. Most preferably, the oil phase is fed at a rate of between 15 μΐ/hr and 100 μΐ/hr, between 25 μΐ/hr and 75 μΐ/hr, between 35 μΐ/hr and 65 μΐ/hr, between 40 μΐ/hr and 60 μΐ/hr, or between 45 μΐ/hr and 55 μΐ/hr. In a preferred embodiment, the oil phase is fed at a rate of about 50 μΐ/hr.

Alternatively, the oil phase may be fed at a rate of between 1 nl/hr and 750 nl/hr. More preferably, the oil phase is fed at a rate of between 10 nl/hr and 600 nl/hr, between 100 nl/hr and 500 nl/hr, or between 150 nl/hr and 450 nl/hr. Most preferably, the oil phase is fed at a rate of between 200 nl/hr and 400 nl/hr, or between 250 nl/hr and 350 nl/hr.

Preferably, the oil phase is fed at a rate of less than 750 nl/hr. More preferably, the oil phase is fed at a rate of less than 600 nl/hr, 500 nl/hr, or 450 nl/hr. Most preferably, the oil phase is fed at a rate of less than 400 nl/hr, or 350 nl/hr. In a preferred embodiment, the oil phase is fed at a rate of about 300 nl/hr.

Preferably, the aqueous solution comprises a detergent. Preferably, the detergent comprises between 0.01% m/v and 10% m/v of the aqueous solution, more preferably between 0.05% m/v and 5% m/v of the aqueous solution, and most preferably between 0.1% m/v and 1% m/v of the aqueous solution. In a preferred embodiment, the detergent comprises about 0.5% m/v of the aqueous solution. It will be appreciated that when the method is being used in a biological application then the detergent preferably comprises a non-ionic detergent, such as Tergitol-type NP-40 (nonyl phenoxypolyethocyethanol).

Alternatively, when the method is being used in a non-biological application then the detergent may comprise a non-ionic detergent, such as Tergitol-type NP-40 (nonyl phenoxypolyethocyethanol), or an ionic detergent.

Advantageously, the detergent reduces the surface tension of the aqueous solution and the resistance to flow thereby better enabling the water phase to flow along a microfluidic channel with a high aspect ratio.

It will be appreciated that the oil phase should have a low viscosity, thereby allowing the oil phase to pass along microfluidic channels with a high aspect ratio. The oil should also be compatible with any surfactant which is used, immiscible with water and the compound of interest must have a low affinity for the oil phase.

The inventors have found that perfluorinated amines, perfluorinated ethers and perfluorinated alkanes meet the above requirements. Accordingly, the oil phase may comprise a perfluorinated amine, such as Fluorinert® FC-40, a perfluorinated ether, such as Fluorinert®FC- 77 or methoxyperfluorobutane (HFE-7100), or a perfluorinated alkane, such as perfluoro(methylcyclohexane) (PPi) or perfluoro-i,3-dimethylcyclohexane (PP3).

Preferably, the oil phase comprises a surfactant. Preferably, the surfactant comprises between 0.1% m/v and 15% m/v of the oil phase, more preferably between 0.5% m/v and 10% m/v, or between 1% m/v and 8% m/v of the oil phase. Most preferably, the surfactant comprises between 3% m/v and 6% m/v of the oil phase.

Preferably, the surfactant in the oil phase comprises a perfluoropolyether - polyethylene glycol - perfluoropolyether (PFPE-PEG-PFPE) triblock copolymer.

Preferably, each perfluoropolyether (PFPE) block of the triblock copolymer comprises a PFPE unit with a molecular mass of 3750 Da or less, most preferably a molecular mass of 2500 Da or less.

Preferably, the polyethylene glycol (PEG) block of the triblock copolymer comprises a PEG unit with a molecular mass of 1000 Da or less, more preferably a molecular mass of 600 Da or less, more preferably a molecular mass of 400 Da or less, and more preferably a molecular mass of 300 Da or less.

Accordingly, it will be appreciated that the PFPE-PEG-PFPE triblock copolymer preferably has a molecular mass of 8500 Da or less, more preferably a molecular mass of 8100 Da or less, 7900 Da or less, 7800 Da or less, 6000 Da or less, 5600 Da or less, 5400 Da or less and most preferably a molecular mass of 5300 Da or less.

Preferably, the PFPE-PEG-PFPE triblock copolymer has hydrophilic-lipophilic balance (HLB) constant of between 1 and 5. More preferably, the PFPE-PEG-PFPE triblock copolymer has hydrophilic-lipophilic balance (HLB) constant of between 1 and 4. Most preferably, the PFPE-PEG-PFPE triblock copolymer has hydrophilic-lipophilic balance (HLB) constant of between 1.1 and 3.5.

Advantageously, 1 fl droplets made using this surfactant are stable for more than 24 hours and biocompatible as the surfactant developed by the inventors ensures that the oil-water interface is coated with polyethylene glycol and the single protein molecules do not bind to the surfactant, or the oil/water interface.

It will be appreciated that it may be desirable to trap an analyte in the aqueous droplets created in the above method. Preferably, the method comprises trapping a single analyte in an aqueous droplet. The analyte may comprise a biological molecule, an organic molecule, an inorganic molecule or a nanoparticle. In embodiments where the analyte comprises a biological molecule the biological molecule may comprise a protein or a nucleic acid, such as an RNA or DNA molecule. The biological molecule may comprise a genetic marker or a biomarker, for example a breast cancer marker, and so on. Accordingly, the aqueous solution may comprise an analyte.

In one of the examples below, green-fluorescent protein (GFP) was used as an analyte. However, GFP stuck to the polytetrafluoroethylene (PTFE) tubing which comprised the fluid delivery lines for delivering the aqueous solution to the aqueous chamber of the device, but the GFP did not stick to the surfaces of the inlets, outlets or chambers of the apparatus.

Accordingly, in a preferred embodiment the analyte would not bind to the fluid delivery lines. This could be due to use of a different analyte, or using fluid delivery lines comprising another material.

Accordingly, the aqueous solution preferably comprises the analyte, at a concentration of between o.oi nM and 50 nM, more preferably between 0.02 nM and 100 nM, or between 0.03 nM and 75 nM, or between 0.04 nM and 50 nM, or between 0.05 nM and 25 nM, and most preferably between 0.1 nM and 5 nM. In a most preferred

embodiment, the aqueous solution comprises the biological molecule at a concentration of about 0.3 nM.

The aqueous solution may comprise a salt. Any inert salt may be used. For instance, the inventors have obtained good results using magnesium chloride (MgCl₂). The aqueous solution may comprise the salt at a concentration of between 0.01 M and 1 M. Preferably, the aqueous solution comprises the salt at a concentration of between 0.05 M and 0.5 M. Most preferably, the aqueous solution comprises the salt at a

concentration of about 0.1 M.

Advantageously, the salt concentration inside the droplets will be higher than outside the droplets, and this will ensure that the droplets retain the water inside them.

In one preferred embodiment of the method, the step of feeding the aqueous solution along the aqueous channel comprises:

feeding a further oil phase along the aqueous channel; and injecting an aqueous plug into the further oil phase, wherein the aqueous plug comprises the aqueous solution.

Advantageously, this will allow aqueous samples of less than 100 μΐ to be used in the above method. This can be particularly useful when the method is being used to trap biological molecules in aqueous droplets as the availability of samples might be limited.

It will be appreciated that the further oil phase could be identical to the oil phase as defined above.

Preferably, the aqueous plug comprises less than 100 μΐ. More preferably, the aqueous plug comprises less than 90 μΐ, 8o μΐ, 70 μΐ, 6o μΐ or 50 μΐ. More preferably, the aqueous plug comprises less than 40 μΐ or 30 μΐ. In a preferred embodiment, the aqueous plug comprises between 1 and 20 μΐ.

It will be appreciated that it will not be possible to filter the plug after it has been injected into the further oil phase as this will cause the plug to break up. Accordingly, the aqueous solution may be injected into the further oil phase using a syringe with a filter.

Additionally, the further oil phase may be filtered upstream of where the point where the aqueous solution is injected.

The method preferably comprises analysing the or each droplet, for example detecting and/ or measuring fluorescence from the droplet or the analyte therein.

The method may comprise capturing the droplets, preferably in a collection chamber. The method may therefore comprise analysing a substantially static droplet, preferably within the collection chamber. The analysis may comprise measuring the fluorescence from the droplet or analyte therein.

Advantageously, analysing the static droplet allows the droplet to be analysed, and observations collected, over an extended period of time. This may be advantageous if the droplet is being used to monitor a dynamic process such as a reaction, or a time- dependent interaction. Alternatively, the method may comprise analysing the droplets immediately after they are produced, which maybe at or after the junction at which each inlet channel converges. Accordingly, the method may comprise analysing a droplet within a flowing stream. The analysis may comprise a digital detection method. The analysis may comprise measuring the fluorescence from the droplet or analyte therein. It will be appreciated that digital droplet detection could comprise an instantaneous

measurement of the fluorescence of a droplet, suitable for counting measurements.

The inventors believe that the surfactant they have developed is novel per se.

Accordingly, in accordance with a fifth aspect, there is provided a perfluoropolyether - polyethylene glycol - perfluoropolyether (PFPE-PEG-PFPE) triblock copolymer surfactant, wherein the PFPE block of the triblock copolymer comprises a PFPE unit with a molecular mass of 3750 Da or less and more preferably a molecular mass of 2500 Da or less, and each PEG block of the triblock copolymer comprises a PEG unit with a molecular mass of 1000 Da or less.

Preferably, each PEG block of the triblock copolymer comprises a PEG unit with a molecular mass of 600 Da or less, or 400 Da or less, or 300 Da or less.

In accordance with a sixth aspect there is provided use of the surfactant of the fifth aspect to produce an emulsion. The inventors believe that the emulsion produced is novel and inventive. Accordingly, in accordance with a seventh aspect there is provided an emulsion produced using the apparatus of the first aspect and/or the method of the fourth aspect.

All of the features described herein (including any accompanying claims, abstract and drawings), and/ or all of the steps of any method or process so disclosed, may be combined with any of the above aspects in any combination, except combinations where at least some of such features and/ or steps are mutually exclusive.

For a better understanding of the invention, and to show how embodiments of the same may be carried into effect, reference will now be made, by way of example, to the accompanying Figures, in which: -

Figure lA is a schematic diagram of a prior art flow focusing device; and Figure lB is a magnified image of the device of Figure lA taken using a high frame rate camera; Figure 2A is a series of sequential images showing droplet generation in the squeezing regime of flow focusing for the device of Figure 1. The sequential images were recorded using 50,000 frames per second (fps) and a 14 exposure time. From top to bottom, the frames shown were recorded at o, 5.54, 6.78, 7.10, 7.46, 7.76, 7.78 and 9.12 ms. The aqueous flow rate was 73 nL/ min and the oil flow was rate 479 nL/ min; Figure 2B is a series of sequential images showing droplet generation in an intermediate regime of flow focusing, between squeezing and dripping, for the device of Figure 1. The sequential images were recorded using 57,601 fps and a 14 exposure time. From top to bottom, the frames shown were recorded at o, 0.57, 0.62, 0.68, 0.71, 0.73, 0.76 and 0.92 ms. The aqueous flow rate was 59 nL/min and the oil flow rate was 899 nL/min; and Figure 2C is a series of sequential images showing droplet generation in the dripping regime of flow focusing for the device of Figure 1. The sequential images were recorded using 52,002 fps and a 12 exposure time. From top to bottom, the frames shown were recorded at o, 12.31, 14.92, 15.23, 15.27, 15.29, 15.33 and 15.55 ms. The aqueous flow rate was 5 nL/min and the oil flow rate was 965 nL/min;

Figure 3A shows the continuous and stable generation of monodisperse droplets (10 μπι diameter, 500 fl) with an aqueous flow rate of 59 nL/ min and an oil flow rate of 899 nL/min using the device of Figure 1. The images were taken from an image sequence recorded at 500 fps with an exposure time of 7 μβ; and Figures 3B and 3C show the unstable generation of polydisperse droplets (minimum 5 μιη diameter, 70 fl) with an aqueous flow rate of < 5 nL/min and an oil flow rate ~noo nL/min. The images were taken from an image sequence recorded at 500 fps with an exposure time of 7 μβ; Figures 4A to C is a schematic diagram of an embodiment of a flow focusing device in accordance with the present invention, and a template used to make the device, where Figure 4A shows the flow focusing device of the invention; Figure 4B shows images of the template used to make the flow focusing device in Figure 4A. The left hand side image is of the interior of one of the inlets and the right hand side image is of the interior of a droplet collection chamber and outlet; and Figure 4C is an enlarged view comparing a 4-way junction in (i) the flow focusing device of Figure 1, and (ii) the flow focusing device of Figures 4A and B;

Figure 5 shows the 4-way junction of the flow focusing device of Figure 4; where

Figure 5A is an image of the photoresist layer on the silicon wafer making up a portion of the template; Figure 5B is a surface profile of the photoresist layer on the silicon wafer of the template; and Figure 5C shows that the smallest width dimension of 3 μπι rendered on the UV-photomask is accurately transferred onto the photoresist layer, this reading was taken from the exit channel immediately following the convergence of the water and oil phases, the thickness of the photoresist layer transfers to the depth of the microfluidic channel is 1.3 μπι;

Figure 6 is an image of a polydimethylsiloxane (PDMS) flow focusing device produced from the template of Figure 4 by the standard method of soft lithography, where the step involving the addition of methanol solvent prior to sealing the microfluidic channels is not performed. The darker regions indicate where the ceiling of the microfluidic channels have collapsed due to the large aspect ratio of the channel dimensions;

Figure 7 shows droplet generation in the dripping regime of flow focusing within the device of Figure 4. Image sequence recorded at 52,002 fps and 5 exposure time; frames shown at o, 14.36, 16.71, 17.00, 17.08, 17.10, 17.15, 17.25 and 17.29 ms;

Figure 8 shows droplet generation at three different points within the flow focusing device of Figure 4, the frames shown in images A-C were taken from an image sequence recorded at 100 fps and 47 exposure time;

Figure 9 shows aqueous droplets with a diameter of approx. 1 μπι located next to two squares in the droplet collection chamber of the flow focusing device of Figure 4;

Figure 10 shows the photobleaching of droplet-confined quantum dots, where Figure 10A shows images of 9 by 9 μιτι, recorded at 100 fps. Clockwise from top left of image sequence, the first image is an average over 150 frames recorded prior to illuminating the droplet with a laser; the second, third and fourth images were taken after 7, 27 and 50 s, respectively, and the integrated intensity-time trace is shown on the right; Figure 10B shows images of 6.75 by 6.75 μιη, recorded at 25 fps. Clockwise from top left of image sequence, the first image is an average over 35 frames recorded prior to illuminating the droplet with the laser; the second, third and fourth images were taken after 0.08, 10.20 and 20.00 s, and the integrated intensity-time trace is shown on the right; and Figure 10C shows images of 6.75 by 6.75 μπι, recorded at 25 fps. From left to right of the image sequence, the first image is an average over 30 frames recorded prior to illuminating the droplet with the laser; the second, third, fourth and fifth images were recorded in intervals of 3 s;

Figure 11 shows photobleaching of droplet-confined green-fluorescent protein, where Figure 11A shows images of 8.4 by 8.4 μπι, recorded at 10 fps. From left to right of image sequence, the first image is an average over 35 frames recorded prior to illuminating the droplet with the laser; the second, third, fourth and fifth images were taken after 6.3, 8.4, 11.0 and 14.2 s, respectively; Figure 11B shows images of 8.4 by 8.4 μπι, recorded at 10 fps. Clockwise from the top of the image sequence, the first image is an average over 35 frames recorded prior to illuminating the droplet with the laser; the second and third images were taken after o and 2.7 s, respectively, and the integrated intensity-time trace is shown on the right; and Figure 11C shows images of 8.4 by 8.4 μιη, recorded at 10 fps. From left to right, the first image is an average over 41 frames recorded prior to illuminating the droplet with the laser; the second image was taken after 7.1 s, and the integrated intensity-time trace is shown on the right; Figure 12 is the synthesis of a non-ionic surfactant;

Figure 13A is a bright-field image of aqueous droplets in the collection chamber of the microfluidic device. The droplets are confined in a planar layer within the 1.3 μπι channel height; Figure 13B is a graph showing the pixel-intensity profile of an individual droplet, where the coordinates on the circumference of the droplet are determined that correspond to the longest-vertical distance between intensity minima on the 2D image. The ellipsoidal diameter, and equivalent spherical diameter, of the droplet is estimated using this data; Figure 13C is a histogram illustrating the frequency of equivalent spherical diameter for 86 droplets in the region highlighted at the top right of figure 13A. The coordinate positions could not be identified for an additional 16 droplets in the same region. The mean ellipsoidal diameter is 3.4 μπι

(standard deviation 0.4 μπι), with the axial dimension of the droplets restricted by the 1.3 μιτι channel height. The resulting equivalent mean spherical diameter of the droplets is 2.5 μπι (8 fl volume); and

Figure 14 shows water on glass and PDMS which is untreated, plasma-treated and plasma and aminosilane-treated. Examples

The inventors have designed a novel apparatus for producing emulsions. The device can be used to produce a water-in-oil emulsion where the water droplets are monodisperse and each droplet has a volume of down to about one femtolitre (fl). The emulsion can be used in a variety of applications such as conducting single molecule, or single particle, experiments on analytes.

Experimental Methods

A template to produce replicas of a prior art flow focusing device 1 was provided by A. D. Griffiths.²⁷ A schematic diagram of the flow focusing device 1 (also referred to as a "replica") made using the template is shown in Figure 1. The device 1 comprises an aqueous inlet channel 4 along which an aqueous solution is fed, two oil inlet channels 2 along which oil is fed, and an emulsion exit channel 6 along which a resultant emulsion exits. The oil channels 2, aqueous channel 4 and exit channel 6 are mutually disposed to define a 4-way junction 8, in which all four channels are mutually arranged at about 90⁰ with respect to each other on the same plane. The exit channel 6 extends away from the 4-way junction 8 along the same direction as the aqueous inlet channel.

The aqueous inlet channel 4 includes a narrowed or restricted section 10 which is immediately adjacent to the junction 8. Upstream of this restricted section 10 there is disposed an intermediate section 12, and upstream of this intermediate section 12 there is disposed an expanded section 14. Similarly, each oil inlet channel 2 also comprises a restricted section 16 which is disposed immediately adjacent to the junction 8.

Upstream of the restricted section 16 there is disposed an intermediate section 18, and upstream of the intermediate section 18 is disposed an expanded section 20. The emulsion exit channel 6 comprises a restricted section 22 which is disposed adjacent to the junction 8. Downstream of the restricted section 22 there is disposed an intermediate section 24, and downstream of the intermediate section 24 there is an expanded section 26.

In use, an aqueous solution 28 is fed along the aqueous inlet channel 4, and an oil phase 30 is fed along the oil inlet channels 2. The two phases 28, 30 meet at the 4-way junction 8 and create a water-in-oil emulsion 32, or reverse emulsion, which then flows along the emulsion exit channel 6. Using these replicas 1, monodisperse droplets 56 with sizes down to around 500 fl (10 μπι spherical diameter) could be generated continuously. The contraction of the aqueous inlet phase 28 at the 4-way junction 8 in a flow focusing device 1 leads to an elongated flow, and the mode of break-up of the aqueous solution 28 depends on the capillary number for the oil flow 30 upstream of the junction 8. It will be appreciated that the capillary number is a parameter known in the field of fluid dynamics and is calculated as: the dynamic viscosity * the fluid viscosity / the interfacial tension. However, the inventors have not calculated numerical values for this as they do not have an accurate number for the interfacial tension.

For small capillary numbers, the regime for droplet formation is called squeezing. ^¾ Under these conditions, the aqueous solution temporarily blocks the junction 8 and the flow of oil, see Figure 2A, which causes the pressure of the continuous phase to increase until an aqueous droplet 56 is pinched off from the elongated aqueous flow. The squeezing regime of flow focusing shown in Figure 2A was produced when the aqueous flow rate was 73 nl/min and the oil flow rate was 479 nl/min. Increasing the pressure applied to the oil phase and/ or reducing the pressure applied to the aqueous solution reduces the formation time of the droplet 56 resulting in a decrease in size. The intermediate regime of flow focusing shown in Figures 2B was produced using an aqueous flow rate of 59 nl/min and an oil flow rate of 899 nl/min. Similarly, the dripping regime of flow focusing shown in Figures 2C was produced using an aqueous flow rate of 5 nl/min and an oil flow rate of 965 nl/min.

The capillary number increases at higher flow rates of oil and the droplet-formation regime transitions from squeezing into dripping, see Figure 2C. In this case, the 4-way junction 8 is never blocked completely and, instead, the faster flow of oil causes the aqueous solution to deform into a focused flow. The droplets 56 are pinched off from the end of the focused flow with diameters that can be equal to, or smaller, than the width of the junction 8.

Increasing the pressure applied to the oil phase and/or reducing the pressure applied to the aqueous solution also increases the separation of droplets 56. This can be seen by comparing Figure 3A, where the evenly spaced and monodisperse droplets 56 were obtained using an aqueous flow rate of 59 nl/min and an oil flow rate of 899 nl/min, to Figures 3B and 3C, where the droplets 56 were obtained using an aqueous flow rate of < 5 nl/min and an oil flow rate of about 1100 nl/min. Using the prior art template, the smallest droplet sizes of 500 fL were produced continuously by the dripping mechanism, shown in Figure 2A and 3A. It was possible to generate droplet 56 sizes down to approx. 70 fL (approx. 5 μπι diameter) but a stable and continuous production of monodisperse droplet 56 sizes could not be maintained and variability in the droplet diameter is observed in the video images, see Figure 3B and C.

Another mechanism has been described in the literature as the flow rate of oil is increased further, where a thin thread of the aqueous solution extends a long distance into the channel downstream of the 4-way junction 8. The capillary breakup of the aqueous thread in the downstream channel can lead to various-sized droplets 56 depending on the ratio of the flow rates of the oil and aqueous solutions. At high ratios, the process is known as tip streaming, and very small droplets (≤ 1 μπι in diameter) have been observed.²⁵ _' ²⁶ _' ²⁸ This is the most widely reported method for generating droplets in the fl-volume range. However, the conditions for tip streaming are challenging to maintain for longer than transient timescales. Small fluctuations in the downstream flow conditions change the breakup distance, which leads to a dramatic change in the droplet 56 size. Using the prior art template 1, the flow conditions that lead transiently to the formation and breakup of a thread of dispersed phase could not be found. A final regime for droplet 56 formation at high capillary numbers is called jetting; this flow condition was also not observed in replicas from the prior art master. Hence, the smallest volume of aqueous droplets 56 that could be produced consistently was 500 fl (corresponding to 10 μπι diameter).

Referring now to Figure 4, the original prior art template 1 shown in Figure 1 was modified in a number of important respects to produce an embodiment of the device 34 of the invention, with which it is possible to produce smaller droplets 56. The flow focusing device 34 is made of polydimethylsiloxane (PDMS).

Initially, the inventors designed a device where the restricted section 10, 16 of the inlets 2, 4 had a width of 3 μπι and a depth of 1.3 micrometres. Due to the nature of the lithography process used to create the template, the depth of the channels has to be maintained throughout the device. Accordingly, the depth of the expanded sections 14, 20 also had to be 1.3 μπι.

The maximum reported aspect ratio for which the collapse of PDMS channels can be avoided is ~20.²⁹ Accordingly, initially the inventors tried to keep within an upper limit of 20 for the aspect ratio. In this case, the expanded sections 14, 20 of the inlet channels 2, 4 needed to be 30 μιη, and the overall surface area to volume ratio of the fluid inside the microfluidic device was very small. The inventors found that this made it impossible to push the fluid through the channels due to resistance at the liquid-solid interfaces.

Accordingly, the inventors realised that it was essential that the width of the channels 2,4 in the expanded sections 14, 20 needed to be much larger than 30 μπι, and the design therefore needed to exceed the maximum value of 20 for the aspect ratio reported previously.

Accordingly, as shown in Figure 4A, the device 34 of the invention comprises two oil inlet channels 2, an aqueous inlet channel 4 and an emulsion exit channel 6 which together define a 4-way junction 8. Upstream of the aqueous inlet channel 4 is a chamber 36 provided with an aqueous inlet 38 (shown with dotted lines in Figure 4A). Upstream of the junction 8, the two oil inlet channels 2 converge at a meeting point 40. Upstream of the meeting point 40 is an oil chamber 42 provided with an oil outlet 44 (shown with dotted lines in Figure 4A). Columns 50, shown as circles in Figure 4A, are located around the inlets to prevent sagging of the PDMS ceiling in the shallow microfluidic chambers.

Two spaced apart concentric rows of isosceles trapezia 52 (see the left-hand image shown in Figure 4B) extending around the perimeter of the inlets 38, 44 act as internal filter blocks in the replicas to trap particles that might otherwise block the narrow junction 8 at the intersection of the aqueous and oil phases. The design of the filter blocks was taken from a design the inventors were given which was used in Andrew Griffiths' lab in Paris. The inventors modified the design by altering the separation between the filter blocks. The separation between the filter blocks 52 (i.e. the trapezia in Figure 4B) was reduced from 11 to 8 μπι in the inner circle of trapezia 52, and 8 to 5 μπι in the outer circle of trapezia 52. The depth of the microfluidic channels were reduced from 15 μπι, in the prior art template, to 1.3 μπι, in the new embodiment of the device 34. The initial width of both the aqueous and oil channels was reduced from 170 to 60 μπι. The width of the aqueous channel 4 along the restricted sections 10 and 22 that extends through the junction 8 was reduced from 5 to 3 μπι. The restricted section 16 of the oil channels 2 leading to the junction was also reduced from 15 to 9 μπι.

The channel downstream of the junction 8 contained the mixed flow of the immiscible phases. In the prior art template, it expanded to a width of 165 μπι beyond the region shown in Figure 4C(i), and was directed straight towards the outlet. In the new template, it expands to a 60 μπι-width via an intermediate section 24, beyond the region shown in Figure 4C(ii), and leads into a droplet collection chamber 46, see Figures 4A. The repeated pattern of squares 54, with sides of 20 μπι, see the right hand image of Figure 4B, located inside the collection chamber 46 had a dual function.

Firstly, they acted as columns to prevent sagging of the PDMS ceiling. Secondly, the square-based columns were arranged appropriately, in groups of four, to spread the flow of the water-in-oil emulsion, and capture the aqueous droplets ahead of the outlet in the microfluidic component. This enables the spectroscopic analysis of the aqueous droplets on-board the microfluidic component.

Fabricating a new master template for microfluidic components

A negative image of a large number of copies of the microfluidic design shown in Figure 4A was drawn in Adobe Illustrator software (Adobe Systems) and converted to a Gerber file format; a positive image of one copy of the microfluidic design is shown in Figure 4A. The image was reproduced at 128,000 dpi on a chrome layer supported on 0.060"- thick soda lime (JD Photo-Tools). Boron-doped silicon (100) wafers, with a diameter of 2." and a thickness of 280 μιη (ι-ιο Ω-cm), were used as substrates to manufacture the master template (MicroChemical GmbH). A permanent epoxy negative photoresist (SU-8 2002, MicroChem Corp.) was spin coated (500 rpm, 30 s, followed by 1500 rpm, 30s) onto the polished silicon surface to produce a uniform layer of 1.3 μπι thickness, which was cured by a soft bake at 95 °C for 1 min. Coated silicon wafers were clamped on a vacuum chuck in a home-built photolithography apparatus. A vertical linear stage brought the photoresist-coated surface of the wafer into contact with the photomask and uniform UV illumination of 550-650 mJ crrr² (incident on the photomask), across the 2." diameter area, was provided by a commercial 365 nm LED curing lamp (DELOLUX 80/365, Delo Industrial Adhesives). Following a post bake at 95 °C for 6 min, the photoresist was developed in Microposit EC solvent (MicroChem Corp.) and cleaned with acetone. The template (part of which is shown in Figure 5A) was fabricated in filtered air within a horizontal laminar flow hood.

An optical profilometer (Zeta-20, Zeta Instruments) was used to check the three dimensional surface pattern on the silicon wafers. The smallest feature size of the microfluidic design is the width of the aqueous channel immediately preceding the 4-way junction and the width of the exit channel immediately following the 4-way junction. The 3D profile of the exit channel immediately following the 4-way junction in the photoresist layer on a silicon wafer is shown in Figure 5B as a 3 dimenstional projection and 5C as a 2 dimensional profile of the cross section of the channel. The junction is reproduced precisely with a depth of 1.3 μπι and a width of 3.1 μπι. Producing replicas of the microfluidic components in PDMS

Replicas of the new template in Figure 4A were produced in polydimethylsiloxane (PDMS). The base and hardener components of the silicone adhesive were mixed in a ratio of approximately 10:1, and cast over the patterned surface on the silicon wafer in a disposable plastic petri dish. The thickness of the adhesive layer was approximately 5 mm. The PDMS was degassed in a vacuum desiccator prior to curing at 65 °C for 2 hr, with post-curing overnight at room temperature. The outline of a rectangle

(approximately 25 by 35 mm) surrounding 12 copies of the microfluidic design was cut into the cured PDMS, and the enclosed segment was separated from the silicon wafer. A 0.7 mm biopsy punch was used to bore holes at the positions indicated by the dotted circles in Figure 4A on the patterns transferred to the PDMS. After the microfluidic component was assembled, the connections to the inlet and outlet channels were made by inserting o.042"-O.D. tubing (Microbore PTFE tubing, Cole-Parmer) into the bored holes. The PDMS surface and a #1 cover slip (Menzel-Glaser, 24 mm by 50 mm) were activated with an oxygen plasma for 1 min at 0.1 mbar and 28 W (MiniFlecto-PC-MFC, Gala Instrumente). The cover slip was then pressed firmly against the patterned surface of the PDMS to seal the channels for the microfluidic components, and placed in an oven at 65 °C for 1 hr.

An additional step was required for producing replicas of the new template with a channel depth of 1.3 μπι. The reduced thickness of the photoresist layer means that the aspect ratio was high for the aqueous and oil channels both upstream and downstream of the 4-way junction (the ratio of width to height is approximately 40). In these regions, the sagging of the PDMS ceiling would normally block the channels and restrict fluid flow; this is illustrated in Figure 6. The maximum reported aspect ratio for which the collapse of PDMS channels can be avoided is ~20.²⁹ It was not practical to reduce the width of the channels throughout the microfluidic design in order to maintain an aspect ratio < 20 because the high pressure required for pushing the aqueous and oil phases through the channels would cause the PDMS to delaminate from the cover slip. The inventors found that it was possible to avoid the collapse of microfluidic channels in regions of high aspect ratio by covering the patterned PDMS surface in methanol (HPLC grade), prior to sealing the channels against the cover glass. The methanol layer prevented the surfaces from bonding instantaneously when brought into contact; it evaporated in the oven at 65 °C allowing the PDMS to bond to the cover slip in the absence of an applied force.³⁰ The microfluidic replicas produced from the original template, containing wider and deeper channels, were flushed with a 1% solution of 3-aminopropyltriethoxysilane in FC-40 (Fluorinert, 3M), and left overnight. Both the PDMS and glass surfaces are hydrophilic following plasma treatment, and water will tend to become the continuous phase in flow focussing under these conditions. As shown in Figure 14. the contact angle of pure water on untreated and plasma-treated glass is approximately 67⁰ and <5°, respectively, and, on untreated and plasma-treated PDMS is approximately 91⁰ and 12°, respectively. The effect of the silanizing agent was to reduce the hydrophilicity of the plasma-treated channels whilst still maintaining a sufficiently-low interfacial tension between the aqueous phase and the surfaces to facilitate the pressure-driven flow. Accordingly, as shown in Figure 14, the contact angle of water on glass and PDMS following additional treatment with the silanizing agent is 20⁰ and 19⁰, respectively. This pre-treatment was not performed for the microfluidic replicas produced from the new template containing a junction of 3 μπι-width and 1.3 μπι-depth. In this case, the narrow hydrophobic-modified channels resisted the flow of the aqueous solution, and it was critical that the original hydrophilic surfaces were retained. It was found that the formation of water-in-oil emulsion droplets was not hindered by the hydrophilic surface of the channels for the smaller dimensions in the new template, but it was necessary to reduce the interfacial surface tension by addition of the detergent, 0.5% m/v Tergitol-type NP-40 (nonyl phenoxypolyethoxylethanol). Pressure-driven flow of aqueous and oil phases and formation of aqueous

microdroplets

Custom triblock copolymers were synthesised from perfluoropolyether carboxylic acids (PFPE, 2500 to 7500 g-mol^"1) and polyethylene glycol (PEG, 300 to 1000 g-mol^-1), as shown in Figure 12. The product, PFPE-PEG-PFPE, is a non-ionic surfactant with ester linkages between the PFPE and PEG components. Similar surfactants have been described by others.^31-33

Krytox 157FSL, 157FSM and 157FSH were obtained from Dupont and were used as supplied. Perfluorohexane was purchased from Fluorochem Ltd. and dried by refluxing over calcium hydride. The polyethylene glycols (300, 400, 600 and 1000 Da) were purchased from Sigma-Aldrich. Each of the polyethylene glycols were dissolved in toluene, distilled to remove any trace water and then dried in vacuo at 110 °C for 4 hours. The triblock copolymers PFPE-PEG-PFPE were synthesised using a method modified from the literature.³⁴ The perfluoropolyether carboxylic acids were refluxed with 10 equivalents of oxalyl chloride in dry perfluorohexane for 24 hours under an atmosphere of nitrogen. After cooling the reaction mixture to room temperature, the perfluorohexane and the excess oxalyl chloride was removed on a Schlenk line to give the perfluoropolyether acid chloride as a clear oil which was stored under nitrogen. Two equivalents of the perfluoropolyether acid chloride were then reacted with one equivalent of the dry polyethylene glycol in the presence of dry pyridine in a solvent mixture of dry benzotrifluoride and dry perfluorohexane. The reaction mixture was refluxed under a nitrogen atmosphere for 24-72 h. After cooling the reaction mixture to room temperature, it was filtered and the excess solvent was removed using a rotary evaporator. The crude product was dissolved in perfluorohexane and was washed with water. The organic layer was dried over MgS0₄ and CaCl₂, filtered and the solvent was removed to give the fluorosurfactant as a clear oil.

The PEG component in the triblock copolymer provides an inert biocompatible surface in the interior of the aqueous droplet. The surfactant (3 to 6 % m/v) was added to the oil phase, FC-40. Both the aqueous and oil phases were delivered to a microfluidic component by a pressure-driven flow controller (MFCS, Fluigent). The pressure applied to the aqueous and oil phases can be manipulated separately to enable the droplet size to be adjusted. Flow conditions respond immediately following adjustment of pressures. Typical aqueous flow rates are about 0.01 μί/1ΐΓ. A much higher oil flow rate is used. In the example shown in Figure 8, this will be about 0.30 μΕ/hr. The formation of droplets at the junction between the aqueous and oil flows was visualised using a 5x objective lens (MPlan Apo, Mitoyo) with a zoom lens (Zoom 6000, Navitar Inc.) and a high frame rate camera (MotionXtra NX-4S3, IDT Ltd.). The internal volume of the PTFE tubing between the sample vial on the flow controller and the microfluidic component was approximately 50 μL. Accordingly, the minimum volume of aqueous sample required in an experiment to generate a stream of microdroplets was 100 μL·. If necessary, a smaller volume of sample could be used by injecting the aqueous solution (1 to 20 μΐ,) into a flow of the FC-40 oil using a high performance liquid chromatography sample-inlet valve (Rheodyne Model 7125 syringe loading injector). In this case, the aqueous solution travelled as a plug in the oil flow along the PTFE tubing and into the aqueous inlet of the microfluidic component. The aqueous plug flowed along the central channel leading to the 4-way junction where it was dispersed into a short stream of droplets. In this mode of operation, the internal filter for the aqueous channel must be eliminated as otherwise it would lead to the upstream breakup of the aqueous plug. However, the aqueous solution and oil phase are both filtered upstream from where the aqueous plug is injected into the oil phase.

Single molecule fluorescence microscopy of droplets

Fluorescence measurements on the microdroplets trapped in the upstream collection chamber were made on a home-built inverted microscope with a 100 ^χ/ 1.25NA oil immersion objective lens. The back aperture of the objective lens was overfilled with the collimated beam of a 488 nm laser. The narrow beam waist of the laser was positioned on an aqueous microdroplet. The fluorescence light was collected by the objective lens and imaged onto an electron-multiplied charge-coupled device (iXon, Andor). The acquired data was saved in Tagged Image File Format and single images and intensity time traces were obtained manually using the open source image processing software, Fiji. Background corrected intensity time traces were obtained by determining the mean pixel intensity from an area twice as large as that occupied by a single aqueous droplet. Reversible and irreversible changes of the fluorescence intensity due to either variations in quantum yield or the bleaching of fluorophores were analysed. In the latter case, the assignment and counting of bleaching steps enabled the number of fluorescent proteins present in an aqueous droplet to be determined. Results and Discussion

Generation of fl-droplets by microfluidic flow focusing

Since the inventors could not identify conditions in which the replicas from the prior art template, with a 5 μπι- wide junction and a 15 μπι channel depth, would produce fl- droplets reliably, see Figures 2 and 3, the effects of reducing the dimensions of the microfluidic component, as shown in Figure 4C, were tested. The surface tension of the aqueous solution had to be lowered by the addition of NP-40. Without this detergent, the maximum possible applied flow pressure was not sufficient to cause the water phase to reach the narrow 3 μιη junction for producing droplets with sizes equal to, or less than, the junction diameter by the dripping mechanism.

Different variants of the PFPE-PEG-PFPE triblock copolymer were tested in the oil phase, at a concentration of 3 % m/v, to optimise the formation and stability of the aqueous droplets. The surfactant reduces the surface tension at the oil-water interface, which enables the aqueous droplets to be pinched off from the elongated flow and dispersed into the oil. The formation of large droplets by the squeezing mechanism was possible with a wide range of molecular masses for the PFPE (2500 to 7500 Da) and PEG (300 to 1000 Da) units. However, the generation of droplets with diameters < 10 μπι without coalescence in the collection chamber was only possible using the smallest molecular weight PFPE unit of 2500 Da in combination with PEG units of 300, 400 600 or 1000 Da and using the medium molecular weight PFPE unit of 3750 Da in combination with PEG units of either 600 or 1000 Da. The hydrophilic-lipophilic balance (HLB) values for these fluorosurfactants ranged from 1.13 to 3.33. Similar fluorosurfactants have been reported in the literature for stabilising larger droplets O500 fl) by microfluidic flow focusing but they are normally prepared from

Krytoxi57FSH (7500 Da). The advantage of using the much smaller molecular weight PFPE of 2500 Da is that the fluorosurfactants are much easier to synthesise, characterise and handle. Consequently, the results described below were obtained by adding the triblock copolymer, with 2500 Da for the PFPE unit and 300 Da for the PEG unit, to the oil phase.

The reduced dimensions for the 4-way junction together with the optimised surfactant enabled the controlled production of droplets with volumes of 1-5 fl under flow conditions that could be sustained for long periods (in excess of 10 min) to produce a continuous stream of monodisperse droplets. It was difficult to acquire video images showing the formation of droplets with a volume of a few femtolitres due to the much higher velocity of the fluids in channels of lower cross sectional area. The formation of a single droplet occurred on a timescale of < 1 ms. The video images shown in Figure 7 were obtained with an exposure time of 5 μβ, and a frame rate of 52002 fps. To enable the camera to capture the images shown in Figure 7 an exceptionally low flow rate was used. Accordingly, the aqueous flow rate was between about 0.2 and 2 nl/hr (i.e.

between 0.0002 μΐ/hr and 0.002 μΐ/hr). The oil flow rate was between about 100 nl/hr and 800 nl/hr (i.e. between 0.1 μΐ/hr and 0.8 μΐ/hr). The critical observation in this sequence of images is that the elongated flow of the aqueous solution protrudes into the 4-way junction, where the droplet is pinched off from the pendant-shaped tip of the elongated flow. This is followed by the aqueous solution retreating back into the upstream microchannel, which is consistent with the dripping mechanism of droplet formation. The elongated flow of the aqueous solution does not extend into the single downstream channel, and the process of droplet formation does not rely on thread formation (i.e. tipstreaming) which is a flow condition that is difficult to sustain. The video images in Figure 7 indicate that the increase in pressure of the aqueous solution leads to only a subtle change in the position of the tip of the elongated flow.

In the example shown in Figure 7, the droplet will have travelled a substantial distance along the downstream channel before the formation of a subsequent droplet at the tip of the elongated flow can be observed. This contrasts with the relatively short spacing between the 500 fl droplets obtained using replicas made from the prior art template design. By increasing the flow rate for the aqueous solution, a higher density of droplets can be generated (see Figure 8). As explained above, the aqueous flow rate used was about 0.01 μΐ ΐΐΓ, and the oil flow rate is used was about 300 μΙ-Jhr. At these higher rates, the process of individual droplet formation could not be visualised in the video images. The images shown in Figure 8 of a stream of droplets, with sizes of approx. 1 fl, were obtained at low magnification in order to use shorter exposure times for sharper image contrast. In this example, the faster flow rate for the aqueous solution does not appear to cause the regime for flow focusing to alter from dripping (see Figure 8A), and the elongated flow of the aqueous solution does not appear to enter the downstream channel during the formation of droplets. The size of the droplets remains

approximately the same following the increase in the aqueous flow rate, and the rate of droplet production is more rapid. The speed of the fl-sized droplets is reduced in the wider section of the downstream channel, and the separation between adjacent droplets is also reduced (Figure 8B and C). The flow conditions (i.e. the relative pressures applied for delivery of oil and water) could be adjusted within a few seconds for the generation of approximately 1 fl droplets and a stable flow could be sustained in excess of 10 minutes.

A pressure driven-flow controller (Fluigent) was found to enable the formation of femtolitre droplet sizes; in contrast, suitable flow conditions could not be identified and maintained with syringe pumps. Droplets with spherical or ellipsoidal diameters between ι to 3 μιη could be generated by applying between 200 mbar and 400 mbar pressure to the oil channel, with the aqueous channel pressure maintained at two thirds of the pressure in the oil channel. Increasing the aqueous pressure to three quarters of the pressure in the oil channel resulted in ellipsoidal droplets of approximate diameter 3 to 4 μπι. Similarly, increasing the aqueous pressure to four fifths of the pressure in the oil channel resulted in droplets of 4 to 5 μιη in diameter, and an aqueous pressure of nine tenths of the pressure in the oil channel resulted in droplets of >5 μπι in diameter. External measurement of flow rate could not be made accurately at the low values required to generate femtolitre droplets; however, an aqueous flow rate of approximately 10 nl/hr, and an oil flow rate of 300 nl/hr, was estimated from the frequency of droplet production in an image sequence recorded at 20,000 fps (47 exposure time) for the droplet train shown in Fig. 8. The fl droplets are collected in a downstream chamber after production at the 4-way junction by flow focussing. An outlet is located at the far end of the chamber. The microfluidic flow had to last for 1 minute in order to yield a sufficient number of trapped droplets in the collection chamber. A bright-field image of droplets, with a mean ellipsoidal diameter of 3.4 μπι (standard deviation of 0.4 μπι), is shown in Figure 13A. Diameter is estimated for individual droplets from the pixel-intensity profile, where the coordinates on the circumference of the droplet are determined from the intensity minima on the longest vertical secant of the 2D image (see Figure 13B). The histogram shown in Figure 13C illustrates the sizes determined for 86 droplets in the region highlighted at the top right of Figure 13A; there were an additional 16 droplets in the same region for which the diameters could not be identified from the pixel-intensity profile. Droplets with a diameter that is larger than the height of the collection chamber (i.e. 1.3 μπι) will be ellipsoidal, rather than spherical, in shape. The mean ellipsoidal diameter of the measured droplets is 3.4 μπι, and the resulting equivalent mean spherical diameter of the droplets is 2.5 μπι, equating to a volume of 8 fl. The pressure-driven flow controller enabled the desired target diameters to be obtained within a few seconds, meaning that relatively small numbers of different-sized droplets were formed whilst the pressure values were adjusted. There is a small back flow of both aqueous and oil phases into the upstream channels when the flows are halted after 1 minute. Conveniently, this prevents the inhomogeneously-sized droplets produced at this stage from replacing the previously generated droplets. The number of droplets trapped in the collection chamber of the microfluidic device is typically of the order of 104. The total viewing area of the collection chamber is approximately 6 mm², and the analysed section shown in Figure 13A containing 102 droplets represents 7400 μπι². Continued operation of the aqueous and oil flow leads to equal rates of population and loss of droplets from the collection chamber. Collected droplets do not show any signs of degradation over the course of 24 hours storage at -5 °C.

Single molecule fluorescence imaging in droplets of a few femtolitres

The fl droplets were collected in a downstream chamber after production at the 4-way junction by flow focusing. An outlet is located at the far end of the chamber. The microfluidic flow had to last for 1 minute in order to yield a sufficient number of trapped droplets in the collection chamber. A bright-field image of droplets, with a diameter of approximately 1 μπι, is shown in Figure 9. The pressure-driven flow controller enabled the desired target diameter of approx. 1 μιη to be obtained within a few seconds, meaning that relatively few larger droplets formed while the pressure was increasing. There is a small back flow of both aqueous and oil phases into the upstream channels when the flows are halted after 1 minute. Conveniently, this prevents the different-sized droplets produced at this stage from replacing the previously generated femtolitre droplets. The number of droplets trapped in the collection chamber is typically in the range of 2000 to 10000. Collected droplets did not show any signs of degradation over the course of 3 hours stored at 5 °C.

Additionally, it should be noted, the inventors were able to obtain data from droplets produced the day before and stored in a refrigerator over night. The inventors also observed that the droplets were stable for at least 3 hours at room temperature.

At this stage, the microfluidic device containing the generated droplets was transferred to a fluorescence microscope. Single droplets were moved into the focus of the 488 nm laser beam by the translation of the microscope stage, and the fluorescence of individual droplets recorded until the contents were photobleached by the excitation laser. The autofluorescence of the PDMS substrate was low and the emission from the encapsulated contents of a droplet can be easily discriminated from background light. The design of the microfluidic device means that wide-field imaging of a large number of droplets would also be possible using either highly-inclined thin illumination by a laser beam or total-internal-reflection fluorescence microscopy.

Quantum dots (QDot ITK 605 carboxyl, Invitrogen, Ltd.) were added initially to the aqueous solution and were encapsulated inside droplets on the microfluidic device. In these examples, the encapsulated volumes were larger than 1 fl in order that the diffusional motion of the quantum dot in the droplet volume could be observed.

Droplets with a diameter that is larger than the height of the collection chamber (i.e. 1.3 μπι) will be ellipsoidal, rather than spherical, in shape. In Figure 10A, the ellipsoidal droplets had a cross-sectional diameter of 4.5 μπι (± 0.5 μπι) and the encapsulated volume would have been approx. 14.8 fl. The concentration of quantum dots was 8 nM in the aqueous solution (containing 0.5% m/v NP-40 and 0.1 M MgCl₂) giving an average of 66 quantum dots in each aqueous droplet. Based on the absence of any light emission from the surrounding oil phase, the quantum dots must have been confined to the dispersed phase and did not leak into the continuous phase. Intense emission was observed from the illuminated droplets, see Figure 10A. Initially, a subset of dark quantum dots in the droplet appear to undergo photoactivation by the laser radiation and the cumulative emission intensity increases slowly. This process is counterbalanced by the photobleaching of bright quantum dots, which dominates after a short time resulting in the exponential-like decay of emission intensity. A lower concentration of quantum dots of 800 pM was used to obtain the data in Figure 10B. In this example, the ellipsoidal droplets were produced with a diameter of 2.5 μπι (±0.5 μπι ) and the encapsulated volume would have been approx. 4 fl. At this concentration level, there must be on average 2 quantum dots per droplet. Spatial fluctuations in the emission images, recorded by the EMCCD, are characteristic of the presence of discrete numbers of quantum dots in an isolated aqueous droplet. The intensity time plots show a series of bleaching steps, and the number of quantum dots contained in a droplet could be estimated. Further reducing the concentration of quantum dots to 80 pM in the aqueous solution led to an average of 0.2 quantum dots encapsulated in a single droplet with a diameter of 2.5 μπι (±0.5 μηι). In Figure 10C, an example of one of these droplets containing a single quantum dot is shown. The confined movement of a single quantum dot could be observed over time and there was no apparent interaction between the quantum dot and the droplet interface.

In a second set of experiments, green-fluorescent protein (GFP) was added to the aqueous solution at a concentration of 50 nM, with 0.5% NP-40 and 0.1 M MgCl₂. Droplets were produced with a diameter of 3.0 μπι (±0.5 μπι) which would have been expected to encapsulate, on average, 180 molecules of GFP. A much smaller number was detected in these experiments; however, the origin of depletion of GFP levels was due to the protein adsorption on the surface of plastic tubing delivering the aqueous solution to the microfluidic device, rather than the transmission of GFP from aqueous droplets into the continuous oil phase. The fluorescence intensity of GFP is an order of magnitude less than the emission from a quantum dot and the fluorescent protein bleaches at a faster rate. The detected fluorescence signal from a single, droplet- encapsulated, GFP molecule is just above the background signal observed from the fluorocarbon oil. Droplets containing multiple GFP molecules are uniformly bright with a clearly-defined interface, which indicates that the GFP molecules are entirely confined to the aqueous droplets (see Figure 11A). A lower concentration of GFP of 5 nM was used to obtain the data in Fig. 11B and 11C. Spatial fluctuations in the fluorescent images are observed for droplets containing smaller numbers of confined molecules illustrating the free-diffusional motion of GFP.

The intensity-time plots shown in Figure 11 were background-signal corrected. The fluorescence-intensity levels were approximately the same for various droplets measured at time intervals up to 3 hr, indicating that GFP molecules remain encapsulated inside the aqueous droplets. Bleaching steps in the fluorescence intensity are observed in the background-corrected time plots, see Figure 11B and C, and it was possible to detect a single fluorescent protein encapsulated within an aqueous droplet (Figure 11C), where the intensity-time plot shows a single photobleaching step. Summary and Conclusion

The inventors have demonstrated the rapid and controlled formation of an emulsion containing monodisperse aqueous droplets with a size of approx. 1 fl volume (or 1 - 2 μπι equivalent spherical diameter) suitable for confining single fluorophores using the technique of microfluidic flow-focusing?. Droplets made according to the present invention are:

• Uniform - each droplet has essentially same volume; • Stable for more than 24 hours; and

• Biocompatible - the surfactant developed by the inventors ensures that the oil- water interface is coated with polyethylene glycol and the single protein molecules did not bind to interfacial surfaces.

Additionally, the process for producing the droplets of the present invention is:

• Efficient - the technique only requires a sample injection of about 10 μΐ of an aqueous sample; and

• Low cost - the process uses an inexpensive bench top instrument for pressure- driven fluid flow, and the instrument uses cheap consumable microfluidic components.

The present invention takes advantage of the control and precision offered by flow focusing for the production of monodisperse emulsion droplets, which can then be used in low throughput experiments for single molecule studies. Accordingly, the present invention offers a revolutionary new method for detecting and analysing single molecules encapsulated in water droplets surrounded by an immiscible oil. The present invention avoids the problems caused by tethering molecules to surfaces using immunosorbent techniques. Instead the isolated molecules can be imaged and analysed individually using ordinary fluorescence microscopes.

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Claims

1. A microfluidic apparatus for producing an emulsion, the apparatus comprising at least one fluid inlet channel configured to allow an aqueous solution to flow

5 therealong and at least one fluid inlet channel configured to allow an oil phase to flow therealong, each inlet channel converging at a junction at which an emulsion is formed upon contact between the oil phase and aqueous solution, and a fluid outlet channel extending away from the junction, and configured to allow the emulsion to flow therealong, characterised in that each inlet channel comprises a restricted sectiono disposed at least adjacent to the junction, and an expanded section disposed upstream of the restricted section, wherein the expanded section has an aspect ratio which is greater than 20:1.

2. A microfluidic apparatus according to claim 1, wherein the microfluidic

5 apparatus comprises at least three inlet channels, wherein at least two inlet channels are configured to allow an oil phase to flow therealong, and one inlet channel is configured to allow an aqueous solution to flow therealong, and the junction comprises a 4-way junction in which the inlet channel which is configured to allow aqueous solution to flow therealong is disposed on substantially the opposite side of the junction0 to the outlet channel.

3. A microfluidic apparatus according to any preceding claim, wherein the aspect ratio is the ratio of the width of the expanded section to the depth of the expanded section of the inlet channel.

5

4. A microfluidic apparatus according to any preceding claim, wherein the width of the restricted section of the inlet channel along which aqueous solution may flow is less than 5 μπι, 4.5 μπι, 4.0 μπι or 3.

5 μπι. θ 5. A microfluidic apparatus according to any preceding claim, wherein the width of the restricted section of the or each inlet channel along which oil flows is less than 15 μπι, 14 μιη, 13 μπι, 12 μιη, ιι μπι or 10 μπι.

6. A microfluidic apparatus according to any preceding claim, wherein the

5 apparatus comprises an aqueous chamber, an oil chamber and a droplet collection

chamber, wherein the aqueous chamber is disposed upstream of, and in fluid communication with, the inlet channel along which aqueous solution may flow, the oil chamber is disposed upstream of, and in fluid communication with, the at least one inlet channel along which oil may flow to the junction, and the droplet collection chamber is disposed downstream of, and in fluid communication with, the outlet channel.

7. A microfluidic apparatus according to claim 6, wherein the aqueous chamber does not comprise an internal aqueous filter.

8. A microfluidic apparatus according to either claim 6 or claim 7, wherein the collection chamber comprises a ceiling and a floor, and a plurality of spaced apart columns extending therebetween, and the columns are configured to capture aqueous droplets present in an emulsion entering the chamber from the outlet channel.

9. A microfluidic apparatus according to any preceding claim, wherein the emulsion comprises aqueous droplets in oil and the inlet channels and outlet channel comprise hydrophilic inner surfaces.

10. A microfluidic apparatus according to any preceding claim, wherein the outlet channel comprises a restricted section disposed at least adjacent to the junction, and an expanded section disposed downstream of the restricted section, wherein the aspect ratio of the expanded section of each inlet channel and the outlet channel is greater than 20: 1, 25:1, 30:1 or 35:1.

11. A microfluidic apparatus according to claim 9, wherein the width of the restricted section of the outlet channel is less than 10 μιη, 7.3 μπι, 5 μπι, 4.5 μιη, 4-0 μιτι or 3.5 μηι.

12. A microfluidic apparatus according to any preceding claim, wherein the depth of the inlet channels and the outlet channel is less than 15 μιη, ιο μπι, 7.5 μπι, 5 μπι, 4 μιη, 3 μιη or 2 μπι.

13· A method of making a microfluidic apparatus for producing an emulsion, the method comprising:

- using a suitable template with a patterned surface to produce an elastomer replica with a correspondingly patterned surface; activating the patterned surface of the elastomer replica and a solid support; covering the patterned surface of the elastomer replica in a volatile solvent; and contacting the solid support with the patterned surface of the elastomer replica, to thereby produce a microfluidic apparatus.

14. A method according to claim 13, wherein the template comprises a negative three-dimensional image of the apparatus of any one of claims 1 to 12.

15. A method according to either claim 13 or claim 14, wherein:

- the elastomer replica comprises a silicone replica;

the solid support comprises a cover slip or slide, wherein the cover slip or slide comprises glass or silica; and/or

- the volatile solvent comprises an alcohol, a nitrile, an ester or a ketone.

16. A method according to any of claims 13 to 15, wherein the step of activating the patterned surface of the silicone replica and the cover slip comprises contacting the silicone replica and the cover slip with an oxygen plasma.

17. A method according to any of claims 13 to 16, wherein the step of contacting the solid support with the patterned surface of the elastomer replica comprises placing the solid support against the patterned surface of the elastomer replica, which is covered with the volatile solvent, and allowing the volatile solvent to evaporate.

18. A method according to any of claims 13 to 17, wherein the method does not comprise a final step of flushing the apparatus with a hydrophobic solution to create hydrophobic channels.

Use of the apparatus of any one of claims 1 to 12 to produce an emulsion.

20. A method of producing an emulsion, the method comprising:

feeding an aqueous solution along an aqueous channel;

feeding an oil phase along at least one oil channel;

21. A method according to claim 20, wherein the method comprises producing a stream of monodisperse droplets with a volume of less than 500 fl, 300 fl, 200 fl, 100 fl, 50 fl or 25 fl.

22. A method according to claim 21, wherein the stream of monodisperse droplets is produced for at least 1 minute.

23. A method according to any of claims 20 to 22, wherein the method comprises feeding a first stream of the oil phase along a first oil channel and a second stream of oil phase along a second oil channel to the junction, and the step of contacting the aqueous solution with the oil phase comprises simultaneously contacting the aqueous solution with both the first and second streams of the oil phase.

24. A method according to any of claims 20 to 23, wherein the aqueous solution is fed at a rate of less than 200 μΐ/hr, 100 μΐ/hr, 50 μΐ/hr, 25 μΐ/hr, 10 μΐ/hr, 5 μΐ/hr, 4 μΐ/hr, 3 μΐ/hr, 2 μΐ/hr, or 1 μΐ/hr.

25. A method according to any of claims 20 to 24, wherein the oil phase is fed at a rate of between 1 nl/hr and 750 nl/hr, between 10 nl/hr and 600 nl/hr, between 100 nl/hr and 500 nl/hr, between 150 nl/hr and 450 nl/hr, between 200 nl/hr and 400 nl/hr, or between 250 nl/hr and 350 nl/hr.

26. A method according to any of claims 20 to 25, wherein the aqueous solution comprises a detergent and a salt, wherein the detergent comprises between 0.01% m/v and 10% m/v of the aqueous solution and the aqueous solution comprises the salt at a concentration of between 0.01 M and 1 M.

27. A method according to any of claims 20 to 26, wherein the oil phase comprises a perfluorinated amine, a perfluorinated ether or a perfluorinated alkane,

28. A method according to any of claims 20 to 27, wherein the oil phase comprises a surfactant which comprises between 0.1% m/v and 15% m/v of the oil phase, and the surfactant comprises a perfluoropolyether - polyethylene glycol - perfluoropolyether (PFPE-PEG-PFPE) triblock copolymer, and each perfluoropolyether (PFPE) block of the triblock copolymer comprises a PFPE unit with a molecular mass of 3750 Da or less, and the polyethylene glycol (PEG) block of the triblock copolymer comprises a PEG unit with a molecular mass of 1000 Da or less, and the PFPE-PEG-PFPE triblock copolymer has hydrophilic-lipophilic balance (HLB) constant of between 1 and 5.

29. A method according to any of claims 20 to 28, wherein the method comprises trapping a single analyte in an aqueous droplet, and the analyte comprises a biological molecule, an organic molecule, an inorganic molecule or a nanoparticle.

30. A method according to claims 29, wherein the method comprises analysing the or each droplet, for example detecting and/or measuring fluorescence from the droplet or the analyte therein.

31. A method according to any of claims 20 to 30, wherein the step of feeding the aqueous solution along the aqueous channel comprises:

feeding a further oil phase along the aqueous channel; and

injecting an aqueous plug into the further oil phase, wherein the aqueous plug comprises the aqueous solution, and comprises less than 100 μΐ.

32. A perfluoropolyether - polyethylene glycol - perfluoropolyether (PFPE-PEG- PFPE) triblock copolymer surfactant, wherein the PFPE block of the triblock copolymer comprises a PFPE unit with a molecular mass of 3750 Da or less, and each PEG block of the triblock copolymer comprises a PEG unit with a molecular mass of 1000 Da or less.

33. A triblock copolymer surfactant, according to claim 32, wherein the PFPE-PEG- PFPE triblock copolymer has hydrophilic-lipophilic balance (HLB) constant of between 1 and 5.

34. Use of the surfactant according to either claim 32 or claim 33 to produce an emulsion.

35. An emulsion produced using the apparatus of any of claims 1 to 12 and/ or the method of any of claims 20 to 31.