Patent Application
20230102093
The present invention relates to fluids selected to mimic pipetting characteristics of target fluids so that the fluids can function as replacement fluids for the target fluids. In particular, the present invention relates to fluids having rheological and other characteristics that enable substantially mimicking of the pipettability of PCR Mastermix.
Pipettes are used to transfer fluids of interest from a source location to a target location. Pipettes may be operated manually or automatically, such as with an automated liquid handler. Pipettes may be used singly or grouped together. The fluids that are analyzed to gather information contained therein may be referred to herein as a “target fluid.” Fluids transferred with pipettes can be of all sorts, with varying transfer volume size and accuracy requirements dependent on the availability of the target fluid at the source, the type of target fluid, the target location conditions, and the target fluid analysis to be conducted, to name a few. The analysis of the target fluid may be greatly impacted by the accuracy of the volume of the target fluid transferred with the pipette. As a result, achieving optimal analysis performance from pipette usage is more difficult than users may expect—particularly when the target fluid volume transferred is small or when the physical and chemical properties of various target fluids used within an assay are significantly different from each other.
Pipetting characteristics of fluids are dependent upon physical characteristics of those fluids, including density, viscosity, surface tension and other properties. These characteristics are determined by the chemical components in those fluids. The accurate and repeatable delivery of specified volumes of fluid from pipetting devices depends in part on those characteristics. For example, pipetting settings selected to deliver a certain volume of serum manually or automatically are different than those needed to deliver the same volume of pure water. Conducting pipetting operations with unreliable target fluid characteristics can result in over-delivered, under-delivered, or inconsistently-delivered target fluid volumes in assays used for clinical diagnostics, pharmaceutical development, and other areas of life sciences and other analysis environments where quality assurance is of most importance. PCR Mastermix is required for any PCR-based assay. It is a critical component needed to achieve DNA amplification. PCR Mastermix contains various components necessary to carry out the DNA amplification process. It is a subject of extensive pipetting.
The task of pipetting an accurate volume of fluid reliably and repeatably is not simple, particularly when very small volumes of fluid are involved—on the order of 2 mL or less, and especially for volumes less than 200 μL, for example. When that target fluid is expensive and/or in short supply, any user training, automated dispensing equipment calibration, test protocol optimization, or analysis equipment calibration is also expensive. As a result, there may be a reluctance to conduct such training, optimization or calibration steps, which can lead to inaccuracies and lack of repeatability when necessary fluid dispensing is carried out. There exist some fluids that can be used to conduct training, optimization, and calibration but they do not match the pipetting characteristics of target fluids of interest including the ones that are expensive or are in short supply. These possible replacement fluids can be useful, but because they do not match the pipetting characteristics of target fluids of interest, they also can lead to inaccuracies and lack of repeatability.
There are several parameters that can effect pipetting, including the speed at which a fluid is aspirated into the pipette, the speed with which a fluid is dispensed from the tip, the amount of fluid left inside the tip (as a thin layer coating the inner wall), the insertion depth of the pipette tip into the solution to aspirate, the insertion depth into the solution to dispense, etc. All of these parameters collectively impact the final volume that is ultimately dispensed by the pipette and can be referred to as the pipettability or pipetting characteristics of the fluid. While some parameters are somewhat universal to any solution that is being pipetted, others are strongly effected by the identity of the solution that is being used. For any solution being pipetted, a sufficient replacement fluid must ultimately dispense the same way the target fluid does. Thus, the best measure of how good a replacement fluid is, is in how closely the replacement pipettes a specific volume when it is aspirated and dispense in the exact same manner as the target fluid of interest.
What is needed is a replacement fluid or replacement fluids that substantially match or mimic the pipetting characteristics of PCR Mastermix. Further, what is needed is such a replacement fluid or replacement fluids that impart pipetting characteristics that substantially mimic PCR Mastermix without being unreasonably expensive and are more likely to be available for use. Yet further, what is needed is a related method available to pipette users to produce such replacement fluid(s) through identification of those replacement fluid characteristics necessary to enable pipetting in a substantially similar manner as the PCR Mastermix that the replacement fluids intends to mimic.
It is an object of the present invention to enable the production of one or more replacement fluids having pipetting characteristics, which may also be referred to herein as “pipettability,” that mimic the pipetting characteristics of PCR Mastermix. This object is achieved by defining the replacement fluid rheology and other properties that when established produce in the replacement fluid pipetting characteristics that substantially mimic the pipetting characteristics of PCR Mastermix.
The present invention is a replacement fluid and related method for making the replacement fluid wherein the replacement fluid mimics the pipetting characteristics of PCR Mastermix. The replacement fluid is made of one or more components selected to substantially mimic pipettability while being either or both of less expensive and more available than the PCR Mastermix mimicked. Specifically, the replacement fluid mimics the rheology and other properties of the PCR Mastermix.
Rheology is the study of the deformation and flow of matter, including how materials respond to applied stress and strain. Rheological properties are important in pipetting based on the physical process in which a pipette aspirates and dispenses a fluid. Pipetting is achieved by applying a force to a fluid to cause it to either move into the pipette tip (i.e., aspirate), or to move out of the pipette tip (i.e., dispense). The rheological properties of a fluid dictate the rate at which that fluid will flow into or out of the pipette, as well as how much fluid coats the inside of the pipette tip, etc. Rheological properties include both chemical and physical characteristics and include viscosity, shear rate, surface tension and contact angle of the fluid with respect to a surface material. The viscosity of a material determines how gelatinous, syrupy or viscous that material is and is related to the chemical and physical attractions experienced by the molecules in a fluid. A common comparison to define viscosity is to compare water to honey, with the obvious observation that honey is much thicker or gelatinous than water and flows much slower when poured at room temperature. If honey is heated to near boiling and poured, it flows at nearly the same rate as water, because its viscosity has dropped to nearly the same as water. Thus, viscosity is impacted by the temperature of the material. Applying a force can also impact the viscosity of matter and is defined by a characteristic called shear rate; in some cases, applying force (e.g., shear stress) causes a material's viscosity to increase (i.e., shear thickening) and in other cases applied force causes the material's viscosity to decrease (i.e., shear thinning).
Yet another property is the surface tension of a fluid, which is a measure of the cohesive interactions between the molecules in a fluid specifically at the fluid's surface. The most common example of a fluid with very high surface tension is water wherein the strong cohesion of the water molecules with each other (as opposed to attraction between water molecules and air) results in a skin-like surface that can float more dense materials (e.g., a paper clip). Water's surface tension can be significantly reduced with a drop of dish soap, oil, or other hydrophobic materials. Contact angle is yet another property, which is defined as the angle that is formed between a fluid droplet and a surface it sits on. To envision this, think of a water droplet on a flat plastic sheet. Plastic is hydrophobic, so the water wants to exist in a tight ball and will have a strong radius of curvature as it attempts to minimize how much it has to touch the plastic. This results in a large contact angle (more than 90 degrees). Conversely, water on flat sheet of clean glass (glass is hydrophilic) will easily spread out, forming a sheet across the glass with a contact angle near zero.
Contact angle is a combination of the physical and chemical properties of the fluid and the physical and chemical properties of the material it is in contact with. Contact angle determines if the fluid wants to stick to the pipette tip and leave behind a thin layer or wants to get off the pipette tip and is thereby easily removed. There are also other properties that loosely relate to rheology but have a direct impact on the pipetting characteristics of a fluid which include the relative density, as well as the chemical interactions of the fluid components with their surroundings (e.g., surface adsorption of molecules onto a surface). For a replacement fluid to substantially mimic the pipetting characteristics of PCR Mastermix, it will need to substantially mimic most of the rheological and other properties of that target fluid.
The rheological characteristics that should be substantially matched (or are at least sufficiently comparable) to produce a substantially similar pipettability include relative density, viscosity, shear rate, and surface tension. In addition to those characteristics of the replacement fluid itself, the pipettability that the replacement fluid needs to match may also be dependent on the contact angle of the replacement fluid in relation to the material of the tip of the pipette. This contact angle is dependent upon both the physical and chemical properties of the fluid and the physical and chemical properties of the pipette tip material. Thus, the contact angle of the replacement fluid with respect to the pipette tip material should be substantially similar to the contact angle of the PCR Mastermix with respect to the pipette tip material.
The present invention is a replacement fluid having a combination of the identified rheological properties and other characteristics of the replacement fluid that results in pipetting characteristics that are substantially similar to the pipetting characteristics of PCR Mastermix. The resulting replacement fluid should be capable of delivering a pipetted volume substantially similar to, and ideally within about +/−20%, of the same delivered volume of the PCR Mastermix.
Each replacement fluid of the present invention that is a pipetting equivalent of the PCR Mastermix target fluid of interest includes a primary equivalent fluid and may include one or more other pipettability modifying additives that impart chemical or physical properties to the primary equivalent fluid that render its pipettability substantially the same as that of the PCR Mastermix. The primary equivalent fluid is chosen for an approximation of the general chemical and physical properties of the target fluid (e.g., water for aqueous solutions, organic solvent for organic solutions). The at least one or more optional modifying additives are chosen to modify the relative density, the viscosity, the surface tension, the shear rate, and/or the contact angle of the replacement fluid such that the pipetting characteristics are substantially similar to the target fluid. A pipetted volume of the replacement fluid should be within about +/−20% of a corresponding volume of the PCR Mastermix. The one or more optional modifying additives are chosen to modify at least the viscosity and the surface tension characteristics of the primary equivalent fluid but not limited thereto.
The one or more optional modifying additives may also modify the relative density, shear rate, surface tension, and/or contact angle of the primary equivalent fluid. The primary equivalent fluid and the optional modifying additives are also chosen for relative availability and lower cost in comparison to the PCR Mastermix. Further consideration of the properties of the primary equivalent fluid and the one or more modifying additives is their temperature dependence. That is, the effect of temperature on the rheological characteristics of a combination of the primary equivalent fluid and the optional one or more pipetting modifying additives should be substantially equivalent to the temperature dependency of the PCR Mastermix.
Yet further consideration of the properties of the primary equivalent fluid and the one or more modifying additives is their dependence on applied force or stress. That is, the effect of applied force of shear stress on the rheological characteristics of the combination of the primary equivalent fluid and the one or more modifying additives should be substantially equivalent to the applied force or shear stress dependency of the target fluid of interest.
Examples of the optional one or more pipettability modifying additives that may be added to the primary equivalent fluid to adjust the rheological and other chemical and physical properties of the primary equivalent fluid include one or more of water, buffering salt, glycerol, sucrose, protein, lipid, surfactant, and water-soluble polymer. These modifying additives may be added to increase or decrease the relative density of the composition, the surface tension, the viscosity and shear rate, and the contact angle. For example, buffering salt may be added to change the relative density and surface tension of the composition, whereas glycerol, sucrose or protein may be added to change the viscosity of the composition, and whereas lipid or surfactant may be added to change the surface tension and contact angle of the composition with respect to the pipette tip material. Protein and soluble polymer may be added to increase viscosity or to produce an adsorbed layer on the inner pipette wall
The composition of the invention may further include optional additives which do not affect pipettability (called non-modifying additives herein). The optional non-modifying additives are selected to produce certain characteristics of specific interest without adversely impacting the equivalent rheological mimicking characteristics of the replacement fluid. These non pipetting modifying additives may have different purposes. For example, one or more dyes may be added to the replacement fluid to facilitate pipetting training and/or equipment calibration. The one or more dyes may be absorbance or fluorescence dyes useful for performing spectroscopic measurements to determine the volume of a reagent dispensed. Other additives may also include stabilizing buffers or chelators, and well as preservative agents to extend the shelf-life of the replacement fluid.
The replacement fluid of the present invention is selected to mimic the pipettability of PCR Mastermix. Some of the components of PCR Mastermix include the four nitrogenous DNA base molecules (e.g., adenine, guanine, cytosine, thymine), stabilizing components (e.g., magnesium chloride), buffering and other salts (e.g., potassium chloride, etc.), DNA polymerase protein, DNA primer strands, preservatives (e.g., EDTA), and thickening and stabilizing reagents (e.g., glycerol). These components collectively determine the density, viscosity, surface tension, shear rate, and contact angle of the PCR Mastermix, which is substantially different than water. The different characteristics require different liquid handling steps as compared to the liquid handling steps needed for water. If a user does not account for the need for different liquid handling steps, he may be grossly over dispensing or under dispensing the PCR Mastermix without knowing it, or he may be delivering a variable volume without knowing it. An over-dispense results in wasting expensive reagent. An under-dispense my result in inadequate DNA amplification, which may result in erroneous data and conclusions. A variability in dispense results in variability and increased uncertainty in the assay results, which may result in erroneous data and conclusions.
PCR Mastermix is very expensive and so it is desirable to have available a pipetting equivalent. An example embodiment of the composition of the invention includes water as the primary equivalent fluid and added pipettability modifying additives of glycerol, and a nonionic surfactant such as octylphenol ethoxylate. The weight ratio of glycerol to water is in the range of about 20%-to-70%. As compared to pure water, the glycerol increases the viscosity from 1 centipoise (cP) to above 3 cP at 5° C. with no shear stress applied, and can be used to tailor the viscosity to have substantially the same shear rate as a PCR Mastermix of interest. The glycerol also increases the relative density and viscosity of water in creating the replacement fluid. The nonionic surfactant significantly decreases the surface tension to between 32-38 mN/m, which is well below the surface tension of water (75 mN/m), and also has an impact on the contact angle. These two components make a PCR Mastermix pipetting equivalent that is much more readily available and substantially less expensive than PCR Mastermix.
The present invention is a replacement fluid suitable to replace PCR Mastermix, wherein the replacement fluid is different from the PCR Mastermix. The replacement fluid includes a fluid having pipetting characteristics substantially equivalent to PCR Mastermix, wherein for a desired pipetted volume of the PCR Mastermix delivered by a pipette, a pipetted volume of the replacement fluid delivered by the pipette is substantially similar to the desired pipetted volume of the PCR Mastermix. The pipetted volume of the replacement fluid may be within about +/−20% of the desired pipetted volume of the PCT Mastermix. The replacement fluid has rheological and other properties substantially equivalent to rheological properties of PCR Mastermix. The rheological properties and other properties include viscosity, shear rate, surface tension, and contact angle. The replacement fluid may include one or more additives. The one or more additives include one or more pipetting-modifying additives selected to modify one or more of the rheological and other properties of the primary equivalent fluid. The one or more pipetting-modifying additives may be selected from the group consisting of water, a water-soluble polymer, buffering salt, glycerol, sucrose, protein, lipid, and surfactant. The one or more additives may include one or more non-pipetting-modifying additives selected not to modify one or more of the rheological and other properties of the primary equivalent fluid. The one or more non-pipetting-modifying additives are selected from the group consisting of stabilizing buffer, chelator, and preservative agent. The primary equivalent fluid may be a mix of water and 20% glycerol and the pipetting-modifying additive is a surfactant. The surfactant may be a nonionic surfactant, which may be octylphenol ethoxylate. The replacement fluid may also include one or more analysis-aiding components, wherein the one or more analysis-aiding components are selected to enable analysis of the replacement fluid as though it were the PCR Mastermix. The one or more analysis-aiding components may be one or more absorbance or fluorescence dyes selected to enable spectroscopic analysis of the replacement fluid.
It can be seen that any replacement fluid can be made with selective rheological and other characteristics mimicking those of PCR Mastermix. The components of that replacement fluid may be chosen based on those equivalent characteristics as well as availability and cost. The invention is one or more replacement fluids with target fluid pipette mimicking characteristics. Those pipette mimicking characteristics are produced by selecting the primary equivalent fluid and, one or more optional pipettability modifying additives to generate substantially equivalent pipetting characteristics.
A replacement fluid of the present invention for mimicking the pipetting characteristics of PCR Mastermix is a primary equivalent fluid having substantially similar pipettability without being the PCR Mastermix. The primary equivalent fluid may be combined with one or more pipetting modifying additives that impart chemical and physical properties of pipettability interest. There may be additional optional non pipetting modifying additives forming part of the replacement fluid. The modifying additives and the ratio of such additives in the replacement fluid are selected to generate in the replacement fluid a pipettability that is substantially the same as the pipettability of the PCR Mastermix.
A first example of a fluid replacement for PCR Mastermix includes water as the primary fluid, and about 210 g/L of glycerol, about 4 g/L of KHP and about 5.3 g/L of octylphenol ethoxylate as pipettability modifying additives. Further non-pipettability modifying additives include about 4 g/L of the chelating agent ethylenediaminetetraacetic acid (EDTA) and about 0.6 g/L of the preservative Mergal (Troy Chemical, part number 100421). Yet further non-pipettability modifying additives include about 1.1 g/L of copper chloride dihydrate as one spectroscopic dye, and about 0.33 g/L of Ponceau S as a second spectroscopic dye (the amount of Ponceau S depends on the spectroscopic properties needed). Further additions of hydrochloric acid and/or sodium hydroxide are made to bring the fluid to a pH of 6.
A second example of a fluid replacement for PCR Mastermix includes water as the primary fluid, and about 210 g/L of glycerol, about 4 g/L of KHP and about 5.3 g/L of octylphenol ethoxylate as pipettability modifying additives. Further non-pipettability modifying additives include about 4 g/L of the chelating agent ethylenediaminetetraacetic acid (EDTA) and about 0.6 g/L of the preservative Mergal (Troy Chemical, part number 100421). Yet further non-pipettability modifying additives include about 1.1 g/L of copper chloride dihydrate as one spectroscopic dye, and about 1.6 g/L of Ponceau S as a second spectroscopic dye (the amount of Ponceau S depends on the spectroscopic properties needed). Further additions of hydrochloric acid and/or sodium hydroxide are made to bring the fluid to a pH of 6.
Test results for the first and second examples of a fluid replacement for PCR Mastermix include testing of rheological properties as shown in
The test data in
The present invention further includes a related method for replacing a target fluid for pipetting activities with a replacement fluid that functions substantially the same as the target fluid in terms of pipetting characteristics. A first step of the method is to determine pipetting characteristics for the PCR Mastermix. A second step is to identify one or more primary equivalent fluids that may substantially match the pipettability of the PCR Mastermix based on the identified pipetting characteristics of the target fluid. A third step is to analyze one or more rheological and/or other properties of the one or more identified primary equivalent fluids and compare them to the corresponding properties of the PCR Mastermix. The identified primary equivalent fluid(s) should be less expensive and/or more readily available as compared to the PCR Mastermix. A fourth step is optionally to introduce one or more additives to the primary equivalent fluid or fluids and evaluate adjustments made to the pipettability of the primary equivalent fluid(s) to determine mimicking of PCR Mastermix pipettability. The one or more additives may include pipettability-modifying and non-modifying additives. A fifth step of the method is to replace the PCR Mastermix with one or more selected ones of the identified primary equivalent fluids. An optional step is to carry out analysis of the primary equivalent fluid, which may include one or more spectroscopic analyses, wherein the primary equivalent fluid may include a non-modifying additive for that purpose.
While the invention has been described with respect to specific example embodiments, it is not intended to be limited to those specific embodiments. Instead, the invention covers those embodiments and all reasonable equivalents.
| Number | Date | Country | |
|---|---|---|---|
| 63250979 | Sep 2021 | US |
