Patent Application
20110096620
The present invention relates to devices, systems, and methods for preparing emulsions, including emulsions useful in biological reaction processes, such as, for example, amplification processes.
A number of biological sample analysis methods rely on sample preparation steps as a precursor to carrying out the analysis methods. For example, a precursor to performing many biological sequencing techniques (e.g., sequencing of nucleic acid) includes amplification of nucleic acid templates in order to obtain a large number of copies (e.g., millions of copies) of the same template.
One amplification method includes encapsulating a plurality of biological samples (e.g., nucleic acid samples) individually in a microcapsule of an emulsion and performing amplification on each of the plurality of encapsulated nucleic acid samples simultaneously. Such microcapsules are often referred to as “microreactors” since the amplification reaction occurs within the microcapsule.
In some cases, the microcapsule is a capture bead and the amplification process is referred to as bead emulsion amplification. In such a technique, beads containing DNA templates are suspended in an aqueous reaction mixture and then encapsulated in a water-in-oil emulsion. The template DNA may be either bound to the bead prior to emulsification or may be included in solution in the amplification reaction mixture. For further details regarding techniques for bead emulsion amplification, reference is made to PCT publication WO 2005/073410 A2, entitled “NUCLEIC ACID AMPLIFICATION WITH CONTINUOUS FLOW EMULSION,” which published internationally on Aug. 11, 2005, and is incorporated by reference in its entirety herein.
Performing bead emulsion amplification requires the formation of an emulsion containing the beads encapsulating the template DNA and a reagent mixture for supporting the amplification reaction. As noted above, the emulsion typically comprises a water-in-oil emulsion with the aqueous phase (e.g., dispersed phase) including the reagent mixture and the beads, and the continuous phase including oil.
Various emulsion preparation techniques have been used. For example, WO 2005/073410 A2, incorporated by reference herein, teaches a cross-flow emulsification system in which emulsion oil is pumped into one of a plurality of tees having a tapered area that is in flow communication with a syringe configured to inject a plurality of microreactors into the emulsion oil to form the emulsion. This system may generate droplets of 80 to 120 μm with the dispense channel diameter of 120 μm. Therefore, the droplet size is generally comparable to the dispense channel size. Using such a system one may encounter difficulties in employing the described cross-flow system to generate smaller droplets for example below 10 um (including in the range of 4 to 9 μ) in diameter. Considerations in this regard is that manufacture of tees with channels smaller than 10 μm may be expensive and the emulsification may take an long time due to a generally low flow rate that can be achieved through the such dispense channel in addition, the process may require application of high pressure to push the PCR mixture with the beads through the narrow opening, and may in turn limit the choice of materials capable to withstand the applied pressure. As a simplified example, to achieve the same flow rate though the opening of 6 μm as through 120 μm, having the channel length the same, one might be required to increase pressure substantially 400-fold or more. Such systems may also be prone to clogging and beads sedimentation.
An emulsification system based on agitation of the continuous phase may address some of the aforementioned issues and allow for various methods of the dispersed phase addition. One technique (Dressman et al, PNAS, Jul. 22, 2003, vol. 100, no. 15, 8817-8822) describes a technique for emulsion preparation using a magnetic stirrer and a magnet bar agitating the continuous oil phase while aqueous phase (PGR mixture with beads) is being added dropwise to it using a manual pipettor. A drawback of this system is a necessity to agitate an open tube with the emulsion, which makes it prone to splashing of oil and emulsion, leading to sample losses and possible contamination of the stirrer, pipettor and the bench with DNA. Furthermore, addition of the aqueous phase is done manually, which can be tedious and can result in poor uniformity and reproducibility of the emulsion due to inconsistency of the droplet size and position of the pipet tip during dispense. Finally, in this system, magnetic beads may become oriented in the strong magnetic field of the stirrer, thus resulting in a non-random beads distribution in the emulsion.
Another technique involves pipetting controlled amounts of the dispersed aqueous phase (including the microreactors which may be in the form of beads) into a test tube containing oil and then placing the test tube on a vortex mixer to form the emulsion. This technique, however, may be relatively time-consuming since the emulsion formation may require iterative steps of adding the dispersed phase followed by vortexing until the desired emulsion is obtained. Moreover, typically the test tube in which the emulsion is formed is moved between a location at which the dispersed aqueous phase is pipetted or otherwise added into the continuous phase in the test tube and a location at which the vortexing occurs. During the vortexing step, a user often places a bottom, closed end of the test tube onto a mounting piece of the vortex mixer, while holding an upper portion of the test tube as the vortex mixer imparts motion to the test tube.
In another method of emulsification, a more complex approach was taken (Diehl et al., PNAS, Nov. 8, 2005, vol. 102, no. 45, 16368-16373 ). Initially, both aqueous and oil phases were mixed together (no dispensing) and briefly vortexed followed by quick emulsification using an overhead homogenizer. This process involves multiple steps and at least two transfers of emulsion from one vessel into another, which can lead to sample losses. Furthermore, there is also a concern that existing disposable emulsion generators may not be effective in making uniform emulsions with the optimum droplet size on the scale larger than 1 ml.
Thus, conventional emulsion preparation techniques relying on vortexing may be relatively time-consuming. In addition, such conventional techniques are relatively user-intensive, requiring the user to perform iterative pipetting, or other dispersion phase adding steps and vortexing steps and/or to hold the test tube in position as it is being vortexed. Further, the iterative process of the dispersion phase adding steps and the vortexing steps may be labor intensive under conventional methods since the user typically removes the test tube from the vortex mixer during the dispersion phase adding step. Using magnetic forces to agitate the emulsion may be detrimental to the emulsion quality. Overhead homogenizers with disposable generators require multiple transfers of the emulsion and may not be suitable for making emulsions on the scale larger than 1 ml.
It may be desirable to provide a more automated emulsion preparation technique, for example, one that reduces the activity required by a user during formation of the emulsion. It also may be desirable to provide an emulsion preparation technique that facilitates increasing the throughput of biological sample analysis processes by Increasing the efficiency of sample preparation.
Moreover, it may be desirable to provide an emulsion preparation technique that yields substantially consistent bead emulsions, for example, emulsions containing no more than 1 bead per aqueous droplet. It may also be desirable to provide a vortexing technique that yields substantially consistent vortexing rates. In other words, it may be desirable to provide a technique that achieves constant velocity vortexing irrespective of factors such as the amount of solution in a tube that is being vortexed and/or the amount of force on the tube during vortexing, such as, for example, a force on the tube due to supporting the tube during vortexing.
The present invention may satisfy one or more of the above-mentioned desirable features. Other features may become apparent from the description which follows.
In accordance with the invention and in one embodiment the apparatus may comprise a vortex mixer further comprising: at least one base plate defining at least one first opening configured to receive a first closed end portion of at least one mixing tube and to permit the at least one mixing tube to pivot about the first closed end thereof; at least one motor configured to impart a substantially orbital movement to the base plate; and at least one support member disposed at a distance from the at least one base plate, the at least one support member being configured to receive a second end portion of the at least one mixing tube and to permit the at least one mixing tube to substantially freely pivot about the first closed end portion during orbital movement of the at least one base plate.
In another embodiment, a system is described for forming an emulsion, the system comprising: a mixing tube defining a reservoir configured to contain a continuous emulsion phase, the mixing tube defining an open end portion; a cap configured to engage with the open end portion of the mixing tube; and a dispensing tube having a first end positioned within the reservoir and a second end configured to be placed in flow communication with a supply of an aqueous phase, the dispensing tube being configured to flow the aqueous phase from the supply to the reservoir.
In still another embodiment, a method is described for forming a bead emulsion for amplifying nucleic acid, the method comprising: supplying a mixing tube with a continuous emulsion phase; imparting motion to the mixing tube via a vortex mixer so as to form vortexes in the continuous emulsion phase; and dispensing an aqueous phase comprising beads containing nucleic acid into the mixing tube while imparting the motion to the mixing tube.
These and other features of the present teachings are set forth herein. In the following description, certain aspects and embodiments will become evident. It should be understood that the invention, in its broadest sense, could be practiced without having one or more features of these aspects and embodiments. It should be understood that these aspects and embodiments are merely exemplary and explanatory and are not restrictive of the invention.
The accompanying drawings, which are incorporated in and constitute a part of this specification, illustrate exemplary embodiments and together with the description, serve to explain various principles. The skilled artisan will understand that the drawings, described below, are for illustration purposes only. The drawings are not intended to limit the scope of the present teachings in any way. In the drawings,
Reference will now be made in detail to various exemplary embodiments, examples of which are illustrated in the accompanying drawings. Wherever possible, the same reference numbers will be used throughout the drawings to refer to the same or like parts.
An exemplary embodiment of a vortex mixer 100 in accordance with aspects of the present teachings is illustrated in
In various exemplary embodiments, the speed of the motors may be Individually controlled by respective control panels 190, which may include both speed increasing/decreasing controls and on/off switches. Further, the motors may be connected to a data bus line or the like (not shown) such that a user may program a speed of operation of the motors, including a speed versus time protocol. A user may input a speed protocol directly into a data input system integrated with the vortex mixer, for example, as part of a control panel 195 or 190 on the vortex mixer 100, or via a remotely located data input system (e.g., computer) configured to be placed in data communication with the vortex mixer 100.
As shown in the close-up, lop view in
The base plates 120 may define at least one opening 122 in a face of the base plate 120 that faces away from the base portion 112 of the vortex mixer 100. in the exemplary embodiment, three openings 122 are depicted. However, any number of openings may be provided depending on the number of mixing tubes it may be desired to vortex on each base plate 120. The number of openings may be selected based, for example, on the size of each mixing tube to be vortexed using a base plate 120, the power of the motor, and other factors. The openings 122 may extend at least partially or entirely through a thickness of the base plate 120 and have a substantially tapered configuration. More specifically, the openings 122 may taper inwardly in a direction from the face of the base plate 122 that faces upward and away from the base portion 112 toward a face of the base plate 122 that faces downward and toward the base portion 112. The openings 122 also may be provided with a radius 123 at an edge surrounding the opening 122 at the surface of the base plate 120 that faces away from the base portion 112, as illustrated in
In various exemplary embodiments, the size of the openings 122 may be configured to be compatible with various tube sizes and configurations. For example, the openings 122 may be configured to accommodate containers/tubes such as microtubes of approximately 1-5 mL, as well as larger containers/tubes of approximately 5-50 mL and even larger container/tubes as appropriate to the desired application. Such flexibility desirably allows smaller or larger volume emulsions to be prepared.
According to various exemplary embodiments, and as illustrated in
With reference again to
In various exemplary embodiments, the support member 130 may define the same number of openings 132 that are defined by the corresponding base plate 120. Each opening 132 may be substantially in alignment with an opening 122, and the openings 132 may be configured to support a top end portion of a mixing tube 50 of which the closed end portion is received in a corresponding opening 122 of a base plate 120, as depicted in
As shown in
With reference to
The clamping plate 138 may be coupled to the support bracket 135 in a manner that sandwiches the support member 135 between the clamping plate 138 and the support bracket 135. In various exemplary embodiments, the clamping plate 138 may be coupled to the support bracket 135 via bolts. However, any suitable coupling mechanisms may be used and are considered within the scope of the invention.
As noted above, the support bracket 135, and thus the clamping plate 138 and support member 130, are configured to move so that a distance between the support bracket 135 and the base plate 120 may be adjusted. In the exemplary embodiment of
Although the exemplary embodiments of
The vortex mixer 100 of
The syringe pump 150 also includes a movable bracket 158 that is configured to move along rails 160. The movable bracket 168 is configured to engage with the free end of the plunger 85 that remains external from the syringe hollow body 88. The movable bracket 158 is configured to exert a force on the plunger 86 to move the plunger 85 relative to the hollow body 88 in response to and in the same direction as the movable bracket 158 moving along the rails 160, e.g., up and down in
The syringe pump 150 may be programmable to modulate a rate at which the movable bracket 158 pushes down on the plunger 85. In addition to controlling the rate of motion of the movable bracket 158, the syringe pump 100 may be programmed to move in response to a time-rate protocol. By way of example, a keypad or other data input mechanism 195 may be provided on the vortex mixer 100 to select and/or program a rate and/or rate/time protocol at which the movable bracket 158 moves downward to actuate syringes 80 held in the syringe pump 150. The keypad or other data input mechanism in various alternate exemplary embodiments may be provided via a computer or other data input portal situated remotely from the vortex mixer 100 and connected thereto via a wireless or wired data interface mechanism.
Placing the syringe pump 150 in the orientation depicted in the exemplary embodiment of
With reference to
The mixing tube 50 may define an opening at one end portion thereof (e.g., the top end portion in the orientation shown in
The system of
The cap 60 may be configured to permit the passage of a dispensing tube 65 that is held in place via a fitting 68 disposed externally to the cap 60. The dispensing tube 65 may be open at both ends and hollow so as to be placed in flow communication with a supply of a substance and to deliver that substance into the reservoir 55 of the mixing tube 50. In various exemplary embodiments, the dispensing tube 65 may be made of stainless steel, PEEK or other known plastics compatible with DNA, PCR reagents, DNA beads and oil phase.
The dispensing tube 65 may be fixedly mounted to the cap 60, and the end of the dispensing tube 65 that supplies a substance to the reservoir 55 may be disposed at a distance ranging from about 1 mm to 15 mm, preferably 2 mm to 10 mm, from the bottom of the mixing tube 50. In an alternative embodiment, the dispensing tube 65 may be movable relative to the mixing tube 50 so that the distance of the end of the dispensing tube 65 that supplies substance to the mixing tube 50 to the bottom of the mixing tube 50 may be adjusted. In various embodiments the end of the tube 65 is immersed into the oil phase while dispensing the aqueous phase. Depending on the emulsification scale, one skilled in art may adjust the position of the tube 65 so that its end will be within the 1 to 15 mm from the bottom of the tube 50.
According to various exemplary embodiments, the dispending tube 65 may have a substantially circular cross-sectional configuration with a diameter ranging from about 0.3 to 1.0 mm, preferably 0.4 to 0.6 mm, most preferably 0.4 mm. The diameter of the dispensing tube 65 may be selected to permit dispensing of an aqueous emulsion phase (e.g., dispersion phase) comprising beads containing template, as has been described above. Dispensing tube 65 diameter may be selected based on anticipated dispense rate, desirable droplet size and related pressure buildup during dispensing. The higher dispense rate, the larger tube 65 diameter needs to be to allow aqueous phase to flow. On the other hand, if the diameter of the dispensing tube 65 is too large, it may result in formation larger than anticipated droplets. In various preferred exemplary embodiments, the dispensing tube diameter was 0.4 mm. As will be appreciated by one of skill in the art, based on the relationship between tube circumference, rpm and solution volume, one may empirically evaluate and/or calculate the effect that the diameter of the dispensing tube has on the forming of the emulsion and the appropriate diameter to optimize emulsion formation for a particular application.
In various exemplary embodiments, the dispensing tube 65 may be configured to be placed in flow communication with a supply of a substance, such as, for example, an aqueous phase (e.g., dispersion phase) of an emulsion, to be dispensed into the reservoir 55 of the mixing tube 50. As illustrated in the exemplary embodiments of
Thus, the exemplary system of
The dispensing tube 65 may be used to deliver an aqueous phase from a syringe 80 with which it is placed in flow communication and into the mixing tube reservoir 55, which may. In various exemplary embodiments, be filled with an oil, in various exemplary embodiments, the dispensing tube 65 may be placed in flow communication with a supply of an aqueous phase comprising microreactor beads carrying nucleic acid template. The supply of the aqueous phase also may contain a reagent and/or other constituents configured to support a biological reaction, such as, for example, PCR, for introducing with the beads into reservoir 55.
In various exemplary embodiments, one or more separate supplies of an aqueous phase may be placed in flow communication with the dispensing tube 65. For example, as schematically represented in the exemplary embodiment of
According to various exemplary embodiments, the components of the system shown in
Those having ordinary skill in the art would recognize a variety of ways to place the dispensing tube 65 in flow communication with one or more supplies of one or more aqueous phases (e.g., dispersion phases) to dispense such phases into the mixing tube reservoir 55. Although many exemplary embodiments described herein utilize a syringe as the supply of substance in flow communication with the dispensing tube, it should be understood that various other supply mechanisms may be used, such as, for example, a reservoir with a positive displacement pump to supply fluid into the dispensing tube.
In accordance with various exemplary embodiments, a method for forming an emulsion, such as, for example, a bead emulsion as described above, may include placing one or more mixing tubes 50 filled with oil to less than ½ of its capacity, preferably to less than ⅓ of its capacity and most preferably to between ¼ to ⅙ of its capacity. For a non-limiting example, in a preferred embodiment, a 9-ml aliquot of the continuous oil phase is placed into a 50-ml mixing tube 50. Oil phase may be introduced Into the mixing tube by dispensing using a serological pipette, a syringe or any other known measuring device. Oil phase can also be poured from a pre-measured container or may be pumped in using a peristaltic pump or any other means, it will be appreciated that the actual oil amount may depend on the selected tube/application. The emulsion may be formed, such as, for example, a bead emulsion as described above, by placing one or more mixing tubes 50 filled with oil in position in the vortex mixer 100, as shown in
The vortex mixer 100 may be turned on to provide an orbital movement to the base plate 120 via the motors, which in turn can impart a substantially orbital movement to the closed end portion of the mixing tube 50. The speed of the base plate movement may be adjusted, either programmably or manually, until vortexes are formed in the oil contained in the mixing tube reservoir 55. After vortexes are formed in the oil, the syringe pump 150 may be activated, for example, via a programmed protocol or manually, to depress the syringe plunger 85 at a controlled rate. An aqueous dispersion phase may thus be displaced from the syringe reservoir 86 at a predetermined and controlled rate based on the rate of the syringe pump 150. In accordance with various exemplary embodiments, the rate at which the syringe pump 150 bears down on the syringe piston 85 may range from about 0.1 to about 1.5 ml/min. Addition of aqueous phase to the oil phase can continue until the desired bead emulsion is formed.
In accordance with exemplary embodiments of the present teachings, the vortex mixer 100 may be configured such that the vortexing rate is substantially constant, irrespective of such factors as the amount of substance contained in the mixing tubes 50, the addition of the aqueous phase to the continuous oil phase, and/or the clamping force exerted on the tubes by the clamping plates 138, for example. The ability to maintain a predictable and substantially constant vortexing rate provides a technique that facilitates consistent emulsion formation.
In one exemplary embodiment, oil phase is prepared by dissolution of approximately 7.5% volume/volume SPAN80 and 0.4% volume/volume Tween80 in light mineral oil. Then a dispensing tube 50 is filled with approximately 9 ml oil phase, a cap 60 with mounted dispense tube 65 is screwed-in, and the tube 50 is placed in the vortex mixer 100. PCR reagent mixture is mixed with the approximately 1-μm beads, then aspirated into a syringe installed in the syringe pump 150. The syringe is connected to the dispensing tube 65 via adapter 72. Vortex mixer 100 is turned on and set at approximately 2000 rpm for approximately 9 min 53 sec. Total volume of the PCR mix (2.8 ml) is dispensed into oil after the vortex mixer 100 is stabilized at the set speed. Dispense rate is approximately 0.8 ml/min. Total dispense time is about 4.5 min. After dispensing is finished, the emulsion is vortexed for about 5 more minutes at the set speed until the preset time elapsed. In the described embodiment, about 1.7 Billion beads are emulsified in a single mixing tube 50. Droplet size is in the range of approximately 4 to 7 μm (33-180 fl volume). These reactors (droplets) provide sufficient amount of PCR reagents to amplify a single template molecule if it is present in the droplet.
Although
For the purposes of this specification and appended claims, unless otherwise indicated, all numbers expressing quantities, percentages or proportions, and other numerical values used in the specification and claims, are to be understood as being modified in all instances by the term “about.” Accordingly, unless indicated to the contrary, the numerical parameters set forth in the following specification and attached claims are approximations that may vary depending upon the desired properties sought to be obtained by the present invention. At the very least, and not as an attempt to limit the application of the doctrine of equivalents to the scope of the claims, each numerical parameter should at least be construed in light of the number of reported significant digits and by applying ordinary rounding techniques.
Notwithstanding that the numerical ranges and parameters setting forth the broad scope of the invention are approximations, the numerical values set forth in the specific examples are reported as precisely as possible. Any numerical value, however, inherently contains certain errors necessarily resulting from the standard deviation found in their respective testing measurements. Moreover, all ranges disclosed herein are to be understood to encompass any and all subranges subsumed therein. For example, a range of “less than 10” includes any and all subranges between (and including) the minimum value of zero and the maximum value of 10, that is, any and all subranges having a minimum value of equal to or greater than zero and a maximum value of equal to or less than 10, e.g., 1 to 5.
It is noted that, as used in this specification and the appended claims, the singular forms “a,” “an,” and “the,” include plural referents unless expressly and unequivocally limited to one referent. As used herein, the term “include” and its grammatical variants are intended to be non-limiting, such that recitation of items in a list is not to the exclusion of other like items that can be substituted or added to the listed items.
It will be apparent to those skilled in the art that various modifications and variations can be made to the devices, systems, and methods of the present disclosure without departing from the scope its teachings. Other embodiments of the disclosure will be apparent to those skilled in the art from consideration of the specification and practice of the teachings disclosed herein. It is intended that the specification and examples be considered exemplary only.
This application claims a priority benefit under 35 U.S.C. §118(e) to U.S. Provisional Application No. 60/890,817, filed Jun. 1, 2007, the contents of which are incorporated herein by reference.
| Number | Date | Country | |
|---|---|---|---|
| 60941505 | Jun 2007 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 12130502 | May 2008 | US |
| Child | 12981086 | US |
