Patent Application
20250059587
The invention pertains to the field of materials for analytical methods and relates to a composition for a microfluidic device.
In the mid-1990s, advances in microfabrication techniques allowed the production of devices with feature sizes as small as few microns. Micromachining, photolithography, etching of silicon and glass substrates, all produced networks of flow channels that could sort reagents and molecules, partition chemical reactions, and act as droplet generators for mixture of aqueous and oil-based fluids. These microfluidic devices are well suited for performing biochemical assays, such as single-cell assays, studies of macromolecules e.g. proteins and nucleic acids, and polymerase chain reactions (PCR).
By the early 2000s, water-in-oil emulsions were being studied for potential applications designed to partition biological materials into nanoliter/picoliter-scale droplets. A significant advance was the use of surfactants in the oil-based continuous phase to maintain the integrity of droplets formed after the introduction of the discontinuous aqueous phase. Thanks to the use of surfactants in the oil-filled microfluidic devices, droplets can be pooled in widened channels or reservoirs, touching each other without breaking or fusing. Extensive fluidic networks of oil-and-surfactant filled channels can be designed to coordinate the intentional mixing of plugs or droplets to mediate biochemical reactions.
Fluorinated oils combined with fluorinated surfactants are particularly useful for handling biomolecules within aqueous droplets (Holtze et al., Biocompatible surfactants for water-in-fluorocarbon emulsions, 2008, 8(10), 1632-1639).
Emulsions containing fluorinated oil, however, can suffer from various disadvantages identified in the art. For example, aqueous droplets are typically buoyant in fluorinated oil (the density of fluorinated oil being higher than that of water), which may increase the complexity of droplet formation and manipulation: in some cases, the PCR mix deposition needs to be visually inspected; emulsions may require removal of excess oil below the droplets to position the droplets closer to a heat source, and/or the PCR mix position in the inlet well may be sensitive to inclination of the microfluidic chip.
Furthermore, the buoyant droplets may be more likely to be damaged by exposure to air above the emulsion, particularly when heated, the PCR mix is sensitive to evaporation leading to time constraints between sample deposition and sample analysis, and in some instances to the use of a sealing oil to prevent evaporation is necessary.
Hence, alternative systems have been proposed such as in WO2014/145582 which describes emulsions comprising aqueous droplets disposed in a continuous phase that includes a silicone oil and a silicone surfactant, wherein the silicone surfactant is described by the following general formula [SILICONE BACKBONE][ALKYL]x[POLYETHER]y[POLYSILOXANE]z, where x is 0-5, y is 1-35, and z is 2-50.
WO2017070363 also discloses filler fluids for microfluidic devices comprising a silicone oil and a siloxane block co-polymer solubilized in the silicone oil, wherein the siloxane block co-polymer is substantially immiscible with an aqueous liquid.
However, the identification of a suitable surfactant/oil system, compatible with molecular biology, is a major aim for improving digital PCR performances.
The compatibility with molecular biology means that the system should not impair with the main reaction protocols used in molecular biology, such as PCR.
Digital PCR performances encompass, notably, droplets stability (meaning that the droplets are substantially prevented from mixing and merging when in contact with each other), increase of the number of droplets for a given volume of PCR mix, with the consequential increase of the analyzed volume, and finally, avoidance of buoyant droplets.
It is also a significant goal to simplify, when loading microfluidic chips, PCR mix deposition and positioning, to prevent PCR mix evaporation to avoid sample wasting, and finally to minimize dead volume, i.e. the volume of sample that cannot be analyzed.
The applicant identified a new category of surfactants and an oil/surfactant system, which are compatible with molecular biology, which improve digital PCR performances and limit sample wasting and dead volume.
The applicant indeed demonstrated that surfactants according to the invention prevent droplets from mixing and merging when in contact with each other and increase the droplets number and the analyzed volume compared to other surfactants.
This increase of droplets number and analyzed volume ensures the precision of digital PCR quantification and the separability of fluorescence signals between different populations, which are key parameters to determine robustness and precision of digital PCR.
Furthermore, the density ratio of the oil/surfactant system according to the invention is reversed compared to a fluorinated system, thus facilitating chip loading, preventing sample wasting and minimizing dead volume. These are major improvements for assay accuracy and reproducibility.
Finally, due to the density ratio inversion of a silicone oil compared to a fluorinated oil, the PCR mix is also protected against evaporation, thus allowing an extended operating time between chip loading and processing.
In an embodiment, the present invention relates to a method for analyzing a biological material comprising:
In an embodiment, the present invention relates to the use of a silicone oil and a surfactant as an oily phase in digital PCR, wherein the surfactant is a block copolymer comprising blocks [A], [B] and [C], wherein:
In an embodiment, the present invention relates to continuous oily phase for a microfluidic device comprising a silicone oil and a surfactant, wherein the surfactant is a block copolymer comprising blocks [A], [B] and [C], wherein:
In an embodiment, the present invention relates to a microfluidic device comprising at least one chamber containing a silicone oil and a surfactant, wherein the surfactant is a block copolymer comprising blocks [A], [B] and [C], wherein:
According to the invention, the surfactant is a block copolymer comprising blocks [A], [B] and [C].
In an embodiment, block [A] of the surfactant corresponds to a block of formula (I)
In the above general formula, unless specified otherwise:
In an embodiment, m is comprised between 10 and 35, preferably between 10 and 17 or between 17 and 25.
In an embodiment, m is comprised between 25 and 75.
In an embodiment, R1 is a C12 alkyl.
In an embodiment, R1 is a C16 alkyl.
In an embodiment, R1 is a C12 alkyl and m is comprised between 10 and 35, preferably between 10 and 17 or between 17 and 25.
In an embodiment, R1 is a C16 alkyl and m is comprised between 25 and 75.
In an embodiment, block [B] of the surfactant corresponds to a block of formula (II)
In an embodiment, q is 3.
In an embodiment, n is comprised between 1 and 15, preferably 1 and 5.
In an embodiment, n is comprised between 5 and 15.
In an embodiment, r, s, t, u, v and w are comprised between 1 and 18, preferably between 1 and 12 and more preferably between 6 and 9.
In an embodiment, r, s, t, u, v and w are independently equal to 1 or 10.
In an embodiment, R3 is —OH.
In an embodiment, R2 is a compound of formula (III)
In an embodiment, R2 is a compound of formula (V)
In an embodiment, R2 is a compound of formula (III)
In an embodiment, R2 is a compound of formula (V)
In an embodiment, block [C] of the surfactant corresponds to a block of formula (VII)
In an embodiment, p is comprised between 5 and 200, preferably between 75 and 175 and more preferably between 95 and 140.
In an embodiment, p is comprised between 100 and 300.
In an embodiment, the block copolymer comprising blocks [A], [B] and [C] comprises terminal groups selected from the group consisting of —H, —CH3 and —Si(CH3)3.
In an embodiment, the terminal groups are —CH3 or —Si(CH3)3.
In an embodiment, the surfactant is a block polymer comprising blocks [A], [B] and [C], wherein
In an embodiment, the surfactant is a block polymer comprising blocks [A], [B] and [C], wherein
In an embodiment, the general formula of the surfactant is [A]-[B]—[C].
In an embodiment, the general formula of the surfactant is [B]—[C]-[A].
In an embodiment, the general formula of the surfactant is [C]-[A]-[B].
In an embodiment, the general formula of the surfactant is [B]-[A]-[C].
In an embodiment, the general formula of the surfactant is [A]-[C]—[B].
In an embodiment, the general formula of the surfactant is [C]—[B]-[A].
According to an embodiment, surfactants that can be used in the system according to the invention can be selected from the group consisting of the surfactant commercialized by Gelest® under the commercial name ABE 3642 (CAS No 212335-52-9), the surfactant commercialized by Siltech Corporation, under the commercial name Silube®J208-812 (CAS No 212335-52-9) and the surfactant also commercialized by Siltech Corporation, under the commercial name Silube® T310-A-16 (CAS No 145686-34-6).
In a preferred embodiment, the surfactant commercialized by Gelest® under the commercial name ABE 3642 (CAS No 212335-52-9) can be used as a surfactant according to the present invention.
In a preferred embodiment, the surfactant comprises 15 to 50% by weight of the surfactant of block [A], preferably 18 to 50%, more preferably 20 to 40%.
In a preferred embodiment, the surfactant comprises 3 to 10% by weight of the surfactant of block [B].
In a preferred embodiment, the surfactant comprises 20 to 40% by weight of the surfactant of block [A], 3 to 10% by weight of the surfactant of block [B], and the remaining weight of the surfactant of block [C].
In an embodiment, the surfactant comprises 30 to 35% by weight of the surfactant of block [A], 7 to 10% by weight of the surfactant of block [B], and the remaining weight of the surfactant of block [C].
Typically, the percentages by weight are estimated by RMN 1H analysis.
According to the invention, the continuous oily phase comprises a silicone oil.
A silicone oil as used herein encompasses molecules having a skeleton structure of alternating silicon and oxygen atoms bonded one to another with hydrocarbon attached to silicon atoms. The silicon atoms may be substituted by various moieties, such as hydrocarbon moieties.
The silicon oil may be chosen according to its viscosity and optionally according to the design of the microfluidic device in which the continuous oily phase may be used.
Viscosity can be measured by any method known by the one skilled in the art. Typically, the viscosity can be measured using usual viscometer such as a rotational viscometer. Typically, the viscosimeter can be a viscosimeter adapted to low viscosity material. For example, Brookfield viscosimeters (AMETEK Brookfield, 11 Commerce Blvd., Middleboro, MA 02346 USA) such as LVT, LVDV-E, DV1MLV, DV2TLV, DV3LTV can be used, together with Brookfield low viscosity accessories.
In an embodiment, the continuous oily phase comprises a silicone oil with a viscosity between 0.5 and 500 centistokes at 25° C.
In an embodiment, the continuous oily phase comprises a silicone oil with a viscosity between 0.5 and 100 centistokes at 25° C.
In an embodiment, the continuous oily phase comprises a silicone oil with a viscosity between 0.5 and 50 centistokes at 25° C.
In an embodiment, the continuous oily phase comprises a silicone oil with a viscosity between 0.5 and 10 centistokes at 25° C.
In an embodiment, the continuous oily phase comprises a silicone oil with a viscosity between 0.7 and 5 centistokes at 25° C.
In an embodiment, the viscosity of the continuous oily phase is comprised between 0.8 and 4.0 centistokes at 25° C., preferably between 0.9 and 3.0 centistokes at 25° C., and more preferably between 1.0 and 2.0 centistokes at 25° C.
Typically, the viscosity of the continuous oily phase is between 1.1 and 1.5 centistokes at 25° C.
Silicone oils with a viscosity between 0.7 and 5 centistokes at 25° C. are particularly advantageous when used in Opal™ microfluidic devices, described, for example, in patent applications WO2020/109379 and WO2020/109388.
In an embodiment, the silicone oil comprises decamethyltetrasiloxane.
In another embodiment, the silicone oil comprises at least 60% by weight relative to the total weight of the silicone oil of decamethyltetrasiloxane, preferably 70% by weight, relative to the total weight of the silicone oil of decamethyltetrasiloxane, more preferably 80% by weight relative to the total weight of the silicone oil of decamethyltetrasiloxane and even preferably 90% by weight relative to the total weight of the silicone oil of decamethyltetrasiloxane.
In another embodiment, the silicone oil further comprises octamethyltrisiloxane and/or dodecamethylpentasiloxane.
In an embodiment, the continuous oily phase comprises 1 to 10% by weight of octamethyltrisiloxane and/or 1 to 10% by weight of dodecamethylpentasiloxane.
In an embodiment, the product DMS-T01.5 (CAS No: 63148-62-9) commercialized by Gelest® can be used as the silicone oil.
In an embodiment, the continuous oily phase comprises the surfactant according to the invention.
In an embodiment, the continuous oily phase comprises 0.5 to 5% by weight, relative to the total weight of the continuous oily phase, of the surfactant as previously defined, preferably, 0.5 to 2.5% by weight, relative to the total weight of the continuous oily phase, of the surfactant as previously defined, and more preferably, 0.5 to 1.5% by weight, relative to the total weight of the continuous oily phase, of the surfactant as previously defined.
In an embodiment, the continuous oily phase comprises about 1.0% by weight, relative to the total weight of the composition, of the surfactant as previously defined.
In a preferred embodiment, the continuous oily phase comprises a silicone oil comprising at least 60% of decamethyltetrasiloxane and a surfactant which is a block copolymer surfactant comprising blocks [A], [B] and [C], wherein
In another preferred embodiment, the continuous oily phase comprises silicone oil comprising at least 60% of decamethyltetrasiloxane and a surfactant which is a block copolymer surfactant comprising blocks [A], [B] and [C], wherein
In an embodiment, the dispersed phase comprises water and any water miscible co-solvent, such as for example ethers glycol and polyether glycols, dimethyl sulfoxide (DMSO), short organic alcohols, acetone, short fatty acids, glycerol short organic amines, hydrogen peroxide, or organic and inorganic acids.
In an embodiment, the dispersed phase comprises reagents for performing a biological reaction and biological material.
Biological material refers, without limitation, to organisms, organs, tissues, cells (including eukaryotic and prokaryotic cells), viruses or virus particles, nucleic acids (including double stranded and single stranded DNA or RNA), plasmids, proteins, peptides, antibodies, enzymes, hormones, growth factors, carbohydrates and lipids, and derivatives, combinations, or polymers thereof. A “biological material” according to the present invention may be a material of natural or of synthetic origin. A “biological material” may be extracted, recovered, or obtained directly from a biological sample, such as, without limitation, blood, urine, cerebrospinal fluid, seminal fluid, saliva, sputum, stool, tissues or cells.
In a preferred embodiment, biological material refers to nucleic acids.
“Emulsion” refers to a composition comprising at least two liquids, each of them being substantially immiscible in the other, wherein one of the liquids (which is referred to as the “dispersed phase”) is partitioned into the other liquid (which is referred to as the “continuous phase”). The dispersed phase of an emulsion is typically suspended in the form of colloids, micelles, capsules and/or droplets. The dispersed phase and the continuous phase are typically fully immiscible. Emulsions are typically stabilized by inclusion in the emulsion of one or more surfactants and/or emulsifying agents.
In an embodiment, the present invention also relates to a population of droplets comprising an aqueous phase, dispersed in a continuous oily phase comprising a silicone oil and a surfactant.
All features detailed in the previous paragraphs entitled “dispersed aqueous phase”, “continuous oily phase” and “surfactant” also apply to the emulsion and the population of droplets.
In an embodiment, the step of processing the biological material comprises amplifying the biological material, preferably by digital PCR, more preferably digital PCR in droplets.
Digital PCR may be seen to encompass three technologies, as follows:
With microfluidic-based digital PCR becoming well-known and more widely practiced, in 2006 Fluidigm Corporation commercialized the technology in an integrated microfluidic circuit. The BioMark system was based on the 1275 Digital Array, a chip of 12 panels, wherein each panel partitioned the reaction fluid into 765 6-nL chambers. After loading the PCR reaction mixture through 12 carrier inputs, the chip was thermocycled, fluorescence was detected, and the signal was processed and analysed by the Digital PCR Analysis software.
An alternative approach that further enhanced throughput and sensitivity while addressing the cost per reaction limitation was to generate picoliter-sized microdroplet reactors by flow-focusing offering many more partitions than the chamber-based systems. Droplets are generated in a microfluidic system, thermocycled to perform single-molecule digital PCR within the droplets, and end-point amplification is detected and quantified via real-time fluorescence curves. These droplet-based lab-on-chip systems were also adapted to perform reverse transcription PCR (RT-PCR) to detect single copies of RNA genomes and to perform multiplex reactions directed to multiple targets within a single droplet.
This technology was for example commercialized by QuantaLife, Inc. as the QX100 ddPCR™ System in 2011. The microfluidic consumables used on the ddPCR™ platform could accommodate up to eight samples per chip, generating 14,000-16,000 droplets per sample.
An advanced digital PCR equipment, the Naica© System was launched in 2016 by Stilla Technologies. This system performs digital PCR by partitioning the sample, using a confinement gradient, into a large 2D array of droplets, also called a droplet crystal. A PCR reaction occurs in each of the partitioned 25-30,000 droplets that make up the droplet crystal, and a fluorescence read-out is performed at end point by taking high resolution image of the crystal.
Hence, and as used herein, the term “digital PCR” encompasses but is not limited to Digital PCR in Microarrays, Digital PCR in Micro-droplets and Crystal Digital PCR™, and the term “digital PCR in droplets” encompasses Digital PCR in Micro-droplets and Crystal Digital PCR™.
In an embodiment, the step of processing the biological material comprises amplifying the biological material, preferably by digital PCR and more preferably by digital PCR in droplets.
The silicone oil/surfactant system according to the invention is advantageous in microfluidic devices comprising a droplet chamber.
As the density ratio of the oil/surfactant system according to the invention is reversed compared to that of a fluorinated system, chip loading is facilitated as the PCR mix sinks close to the droplet chamber, preventing sample wasting and minimizing dead volume.
The system according to the invention is particularly advantageous in Opal microfluidic devices, described, for example, in patent applications WO2020/109379 and WO2020/109388.
Opal microfluidic devices comprise at least one inlet microchannel, one droplet chamber, one output channel and a loading well configured to receive a drop of sample.
In the case of fluorinated system, the PCR mix floats in the loading well of the microfluidic chips. It may thus be necessary to inspect the mix deposition to ensure that the PCR mix is properly injected into the microfluidic chip. Furthermore, the mix position in the well is sensitive to inclination of the chip due to the floating nature of the droplets in the loading well.
On the contrary, in the case of the system according to the present invention, the PCR mix sinks into the loading well in proximity with the injector of the microfluidic chip. Hence, mix position is less sensitive to inclination and there is no need for inspection after mix pipetting. Chip loading is hence facilitated.
Furthermore, due to the density ratio inversion, the PCR mix is also protected against evaporation, allowing an extended operating time between chip loading and processing, and avoiding a supplementary step of dispensing sealing oil. This is also a major improvement for preventing sample wasting and minimizing dead volume.
The invention will be further illustrated by the following examples. However, these examples should not be interpreted in any way as limiting the scope of the present invention.
Use the following set up for 48 reactions of the 3-color run, using three Opal chips. Set up the PCR mix for all 48 samples in a batch mix to ensure equal conditions in each reaction.
Use the following set up for 48 reactions of the 3-color run, using three Opal chips. Set up the PCR mix for all 48 samples in a batch mix to ensure equal conditions in each reaction.
Use the following set up for 48 reactions of the 6-color run, using three Opal chips. Set up the PCR mix for all 48 samples in a batch mix to ensure equal conditions in each reaction.
In a first set of PCR experiments, 8 different surfactants were used at a concentration of 5% w/w in decamethyltetrasiloxane.
Results obtained for 4 chambers (four replicates) per surfactant are described in the table below:
ABE 3642 advantageously increases the droplets number and the analyzed volume, compared to the other surfactants tested. In a second set of experiments, three new surfactants were screened, together with ABE 3642 as reference, at 1% w/w (as detailed below) in decamethyltetrasiloxane, following the same procedure previously used.
Results obtained for 16 chambers (sixteen replicates) per surfactant are described in the following table:
The best results were obtained with ABE 3642 which enables to obtain the highest number of droplets and thus the highest analyzed volume. It is noteworthy that Silube J208-812 and Silube T310-A16 are also suitable to generate stable water-in-oil droplets while no stable droplets were observed with CMS-222 at 1% w/w or at 0.1% w/w.
CMS-222 is a siloxane block co-polymer represented by the following formula. This surfactant does not allow to obtain stable droplets.
Without wishing to be bound by theory, it is hypothesized that polyethylene glycol chain of the [B] block within the surfactants according to the invention is a key parameter for preventing droplets from mixing and merging when in contact with each other and therefore a key parameter for increasing the droplets number and the analyzed volume compared to other surfactants. The alkyl chain of the [A] block within the surfactants according to the invention is potentially also a key parameter for preventing droplets from mixing and merging when in contact with each other and therefore a key parameter for increasing the droplets number and the analyzed volume compared to other surfactants.
Best results were obtained when the percentage by weight of surfactant of block [A] is in the range going from 20% to 40% by weight of surfactant and the percentage by weight of surfactant of block [B] is in the range going from 3% to 10% by weight of surfactant.
The ABE 3642 surfactant was studied at a range of concentrations from 0.05% to 10% in decamethyltetrasiloxane in Opal chips.
Stability of the 2D monolayer can be observed for surfactant concentrations of 0.5% w/w and above (as described in the table above), while concentrations above 5% w/w may be detrimental to biocompatibility (PCR could be inhibited by the too high concentration of surfactant).
In addition to the number of droplets, the precision of dPCR quantification, and the separability of fluorescence signals between different populations, were then assessed. All these experiments were performed with ABE 3642 at 1% (w/w) in decamethyltetrasiloxane.
The quantification accuracy was directly evaluated by comparison with results obtained with Opal chips filled with fluorinated chemistry.
For each channel, a satisfactory separability between negative and positive droplets was observed (separability index calculated by the Crystal Miner software of the Naica® Digital PCR suite>4). No deviation of the quantification was observed compared to the reference concentration obtained with the chips filled with the fluorinated chemicals.
In addition to the 3-plex assay described above, a 6-plex assay was also performed to confirm suitability of the oil/surfactant mixture with other biological objects. This 6-plex assay uses Phage Lambda (blue channel), PhiX174 (teal channel), pUC18 MCS L1 (green channel), pBR 322 (yellow channel), Entero Cloaca (custom plasmid based on pUC57, red channel) and ALB (infra-red channel). The quantification accuracy was evaluated by comparison with target concentrations.
For all six channels, a satisfactory separability between negative and positive droplets was observed (separability>4). No deviation of the quantification was observed compared to the target concentrations.
A comparative study was performed between the fluorinated system (Opal chips) and the silicon system (ABE 3642 1% in DMS-T01.5) to evaluate the effect of incubation time between chip loading and processing. For this, the chambers of each chip were loaded with the PCR mixture at 2-minute intervals and the chips were then processed in PCR such that the first chamber loaded had 26 minutes of incubation between chip loading and PCR while the last chamber loaded was processed immediately. Two chips per chemical system were processed with the 3-plex assay validation and the related protocol described for Example 3.
A clear increase in calculated concentration with the incubation time was observed in the fluorinated system, most likely due to evaporation of the PCR before injection, while calculated concentrations remained stable with the silicon system (i.e. an increase of 25% was observed in the green channel after 26 minutes for the fluorinated system while no deviation was observed with the silicon system).
In addition to the comparative studies with the fluorinated system, extended incubation times between chip loading and PCR have been evaluated with the silicon system (ABE 3642 1% in DMS-T01.5). The chips were loaded at the same time and then processed in dPCR after 6 hours or 10 hours of incubation at room temperature. The changes in calculated concentrations were evaluated by comparison to the results obtained when the chips are processed immediately after loading. The 3-plex validation assay and the related protocol described for Example 3 were also used for these tests.
Results obtained for 24 chambers. Chambers with less than 10K droplets were excluded before the analysis.
A small deviation in quantification of less than 10% for the three channels was observed after 6 h and 10 h of incubation at room temperature between chip loading and dPCR processing.
These results demonstrate that the silicon chemistry system according to the invention allows for an extended operating time between chip loading and processing, contrary to the fluorinated system of the state of the art.
| Number | Date | Country | Kind |
|---|---|---|---|
| 21306849.7 | Dec 2021 | EP | regional |
| Filing Document | Filing Date | Country | Kind |
|---|---|---|---|
| PCT/EP2022/086592 | 12/19/2022 | WO |
