Patent Application
20100294665
Aspects of the invention relate to methods and systems for transferring and/or concentrating a sample and more particularly to systems and methods which utilize an electric field to transfer and/or concentrate the sample.
When analyzing a biomaterial sample, such as a nucleic acid sample, there is often a need to transfer and/or concentrate the sample. Some prior approaches to transferring or concentrating a sample utilize a mechanical pump to hydrodynamically move and concentrate the sample. However, many types of nucleic acid samples are fragile and some mechanical approaches may damage the sample.
Other approaches utilize an electric field to concentrate a nucleic acid sample. However, an electric field may also damage a sample. For example, an electric field is created by the flow of current which may cause the temperature to increase in areas of greater electrical resistance. This is known as joule heating and it may damage the sample.
Aspects of the present invention are directed to improved methods and systems for transferring and/or concentrating a sample while minimizing sample damage.
In one illustrative embodiment, a system for concentrating a sample is provided. The system includes a first concentrator and a second concentrator positioned downstream of the first concentrator. The first concentrator includes a first chamber, a first semi-permeable membrane positioned within the first chamber having a first sample contacting surface, and an electrode assembly configured to selectively create an electric field across the first membrane to move a sample at least partially through the first chamber, from a starting position to the first sample contacting surface. The second concentrator includes a second chamber in selective fluid communication with the first chamber, and a second semi-permeable membrane positioned within the second chamber having a second sample contacting surface. The electrode assembly is also configured to selectively create an electric field across the second membrane to move a sample at least partially through the second chamber from an intermediate position to the second sample contacting surface, where the area of the first sample contacting surface of the first membrane is greater than the area of the second sample contacting surface of the second membrane.
In another illustrative embodiment, a system for concentrating a sample is provided. The system includes a chamber having an inlet port, a plurality of substantially parallel microchannels outwardly extending from the channel, and a semi-permeable membrane extending within the chamber. The membrane has a first sample contacting surface and the membrane extends along the plurality of microchannels. The system further includes an electrode assembly configured to selectively create an electric field through the plurality of microchannels and across the membrane to move a sample at least partially through the chamber, from a starting position to the first sample contacting surface of the membrane.
In yet another illustrative embodiment, a pipette is provided. The pipette includes a body having a passageway therethrough, where the body has a first end and a second end, and a semi-permeable membrane is positioned within the passageway, where the semi-permeable membrane is spaced apart from the first end of the body. A conductive buffer solution is within the passageway, and a positive electrode is at the second end of the body, where the positive electrode may selectively create an electric field through the passageway to the first end of the body when used in association with a negative electrode.
In a further illustrative embodiment, a method of transferring and concentrating a sample is provided. The method includes the acts of providing a pipette having a body with a passageway therethrough, a semi-permeable membrane positioned within the passageway, and a electrolytic buffer solution within the passageway, and placing a first end of the pipette in contact with a negatively charged sample contained within a reservoir. An electric field is created through the passageway of the pipette body such that a first portion of the negatively charged sample is drawn into a first end of the pipette body, whereby the concentration of the first portion of the sample is greater than the concentration of the sample in the reservoir.
In yet another illustrative embodiment, a system for transferring a sample is provided. The system includes a first chamber, a first semi-permeable membrane positioned within the first chamber, where the first membrane has a first sample contacting surface, and an assembly configured to move a sample at least partially through the first chamber, from a starting position to the first sample contacting surface. The system further includes a second chamber, where the second chamber is in selective fluid communication with the first chamber and a second semi-permeable membrane positioned within the second chamber, where the second membrane has a second sample contacting surface. The assembly is also configured to move a sample at least partially through the second chamber from an intermediate position to the second sample contacting surface, where the assembly includes an electrode assembly configured to selectively create an electric field across the second membrane to move a sample to the second sample contacting surface, and the area of the first sample contacting surface is greater than the area of the second sample contacting surface.
In a further illustrative embodiment, a method of transferring and concentrating a sample is provided. The method includes the acts of providing a chamber with a semi-permeable membrane positioned within the chamber, with the membrane having a sample contacting surface, and a channel opposing the sample contacting surface, and placing a negatively charged sample within the chamber. An electric field is created across the membrane such that the negatively charged sample is drawn through the chamber and to the sample contacting surface of the membrane, and an electric field is then created into the channel opposing the sample contacting surface to move the negatively charged sample away from the sample contacting surface and towards the channel. Then, an electric field is created between the chamber and the channel to compress the sample in the chamber.
Various embodiments of the present invention provide certain advantages. Not all embodiments of the invention share the same advantages and those that do may not share them under all circumstances.
Further features and advantages of the present invention, as well as the structure of various embodiments of the present invention are described in detail below with reference to the accompanying drawings.
The accompanying drawings are not intended to be drawn to scale. In the drawings, each identical or nearly identical component that is illustrated in various figures is represented by a like numeral. For purposes of clarity, not every component may be labeled in every drawing. Various embodiments of the invention will now be described, by way of example, with reference to the accompanying drawings, in which:
Aspects of the invention are directed to systems and methods for transferring and/or concentrating a sample. The systems and methods may be employed with various types of samples including charged particles and/or biomaterials, and may, for example, be incorporated into biodefense applications and other single molecule biology applications. In some embodiments, the systems and methods may be used to transfer and/or concentrate a nucleic acid sample. The systems and methods may be used to concentrate DNA samples and/or RNA samples. In other embodiments, the systems and methods may be used to transfer and/or concentrate other types of samples, such as proteins and/or any negatively-charged polymer. It should be appreciated that in some embodiments, the systems and methods may be used to transfer and/or concentrate one or more components in the sample. The systems may be configured in any of numerous ways, and the present invention is not limited to the particular systems described below. Furthermore, it should be appreciated that the below described methods for transferring and/or concentrating a sample are not limited to be performed only with the various systems described below. Furthermore, it is also contemplated that the below described methods and systems could be used to determine the presence and/or absence of a nucleic acid sample.
The systems and methods for transferring and/or concentrating a sample utilize an electric field. The sample may include negatively charged particles, such as, for example, nucleic acids, diluted within a buffer solution. When an electric field is created between a positive electrode and a negative electrode, the negatively charged particles in the sample are electrically attracted toward the positive electrode. In certain embodiments, the buffer solution is less attracted towards the electrodes.
The system for concentrating a sample may include a chamber with at least one membrane. To concentrate the sample, the sample is placed within the chamber and an electric field is created across the membrane such that the negatively charged sample moves toward the positive electrode. In one embodiment, the membrane may be positioned between the sample and the positive electrode such that the negatively charged sample will collect and concentrate on the membrane. In another embodiment, the membrane may be positioned between the sample and the negative electrode, for example, when the sample is eluted from the membrane after concentration.
Certain aspects of the invention are directed to systems and methods for concentrating a sample with an electric field having a substantially uniform current density across the membrane. In an electric field, negatively charged particles/molecules (such as nucleic acids) will follow the path of least resistance (i.e. current streamlines) towards the positive electrode. When a substantially uniform current density is created across the membrane, the sample may collect more evenly across the membrane. Without a substantially uniform current density across the membrane, the particles may tend to pile up more on portions of the membrane where there is a higher current. Then, the particles/molecules moving off the membrane may not travel at the same rate causing them to become more distributed in space, i.e. less concentrated.
As discussed in greater detail below, one approach to creating a substantially uniform current density across a membrane is to include a plurality of substantially parallel microchannels positioned between the membrane and the electrode such that the current travels through the microchannels. Such a configuration may alter the electrical resistance which may force current streamlines to spread uniformly across the width of the membrane. The electric field may be substantially evenly distributed through the microchannels to provide a substantially uniform current density across the membrane.
Another approach to creating a substantially uniform current density across a membrane, which is discussed in greater detail below, is to include a shallow depth region positioned between the membrane and the electrode. The shallow depth region may alter the electrical resistance which may force current streamlines to spread more uniformly across the width of the membrane.
In certain embodiments, the system for concentrating may be formed into a microfluidic chip. Microfluidic chips are structures designed for processing small fluid samples. Microfluidic chips may be stacked on top of each other and/or along side one another with fluid ports connecting adjacent chips. Each microfluidic chip may include one or more passageways so that a fluid sample may travel through the chip for various types of analyses.
In some embodiments where a chamber is formed in a microchip, the geometry of the chamber may be constrained by shallow etch depth microlithographic manufacturing techniques. A minimum surface area may be required for a particular embodiment, (for example, the need to avoid joule heating can cause the minimum membrane area within a chamber to be high). Achieving this minimum area given manufacturing constraints may require low aspect ratio features (for example, 500:1). This area may be coupled to another device or chamber via a higher aspect ratio channel (for example, 5:1). Certain aspects of the invention are directed to systems and methods for concentrating a sample having a substantially uniform current density across the membrane in such chamber geometries with low aspect ratios.
In other embodiments, the systems and methods for concentrating a sample may utilize a pipette. The pipette may also be used to transfer a sample from one location to another. A pipette may be used to transfer a sample between two locations that are not in fluid communication with each other (i.e. remote), for example, between two spaced apart reservoirs. As discussed in more detail below, the pipette includes a passageway with a semi-permeable membrane positioned within the passageway. According to one method, a first end of the pipette is placed in contact with a negatively charged sample contained within a reservoir. An electric field is created through the pipette passageway such that a first portion of the negatively charged sample is drawn into the first end of the pipette body to concentrate the first portion of the sample in the pipette.
Further aspects of the invention are directed to systems and methods for concentrating a sample which minimize damage to the sample. For example, in one embodiment, systems and methods for concentrating a nucleic acid sample are provided which are designed to minimize and/or eliminate damage to the nucleic acids which may occur due to shear forces acting on the nucleic acids. Such methods and systems are discussed in greater detail below and may be suitable for concentrating fragile nucleic acid samples, such as samples which include long DNA segments. Samples with long segments may be more apt to experience shear force damage while moving the sample. For example, in one embodiment, DNA segments having a length between approximately 100 kilobase to 1 megabase may be concentrated with the below described systems and methods without substantial shear damage. In some embodiments, the methods of the invention produce less than 1% shear damage. In other embodiments, the methods produce less than 20%, less than 10%, less than 5% or less than 2% shear damage. In other embodiments, systems and methods for concentrating a sample are provided which are designed to minimize and/or eliminate damage to the sample which may occur due to joule heating and temperature increases. Further embodiments are directed to systems and methods for concentrating a sample which are designed to minimize and/or eliminate damage to the sample which may occur due to harmful interactions between the sample and the membrane.
Turning to
The first and second concentrator systems 20, 30 according to one embodiment of the invention are shown in greater detail in
An electrode assembly (discussed in greater detail below) is configured to selectively create an electric field across the first and second membranes 24, 34 to move a sample through the concentrator systems 20, 30. The first and second concentrator systems may be filled with a fluid buffer such as Tris/Borate/EDTA(TBE) or Tris/Acetate/EDTA(TAE) to facilitate movement of the sample through the systems. In one embodiment, the first and second concentrator systems are filled with a buffering system stable under high electric fields for prolonged periods. The fluid must be an electrolytic (i.e. conductive) so that the electric field extends through the fluid to move a sample. In one embodiment, the fluid buffer has a sodium chloride concentration of approximately 20 millimolar.
An electric field may be created across the first membrane 24 to move a sample at least partially through the first chamber 22 from a starting position to the first sample contacting surface 26 on the first membrane 24. In one embodiment, the starting position is outside of the first chamber 22 and may, for example, be on a membrane 44 in a reaction chamber 40 which is positioned upstream of the first concentrator system 20. For example, in one illustrative embodiment, the sample may initially be positioned on a cellulose starting membrane 44 within the reaction chamber 40. Various types of sample preparation processes such as lysis, digestion, intercalation, nucleic acid extraction, uniform or sequence-specific labeling, and buffer exchanges may be performed within the upstream reaction chamber 40.
The second chamber 32 of the second concentrator system 30 is in selective fluid communication with the first chamber 22 of the first concentrator system 20. The electrode assembly is configured to selectively create an electric field to move the sample from the first chamber 22 at least partially through the second chamber 32. The electrode assembly may create an electric field across the second membrane 34 to move the sample from an intermediate position to the second sample contacting surface 36 on the second membrane 34.
In one embodiment, the first membrane 24 is smaller than the starting membrane 44, and the second membrane 34 is smaller than the first membrane 24, so that the concentration of the sample which collects on these membranes 44, 24, 34 increases through each stage of the system 10.
The electric field is created within a chamber when current flows through the chamber. At a substantially constant current, the strength of the electric field will vary with the cross-sectional area of the chamber. In general, the strength of an electric field within the chamber increases as the cross-sectional area of a chamber decreases. In one embodiment, where the second membrane 34 is smaller than the first membrane 24, the strength of the electric field may increase through the system 10 from the first membrane 24 in the first concentrator system 20 to the second smaller membrane 34 in the second concentrator system 30.
In some embodiments, it is desirable for the charged particles/molecules in the sample to move faster through the chamber. This allows for faster processing of a sample and/or larger volumes of samples to be concentrated. As the strength of the electric field increases, the speed of the negatively charged particles through the chamber towards a positive electrode may also increase. Conversely, when the electric field is weak, the particles may move more slowly through the chamber.
However, as the strength of the electric field increases, the sample may be damaged due to the increase in electric field. As the current travels through a concentrator system, portions of the concentrator system may heat up as a result of resistance in the flow of current. This is a concept known as joule heating and this heat may damage the sample. Joule heating may damage a sample, such as a DNA sample, by denaturing the DNA strands, by the release of bonds that retain the dye or tags, and/or by damaging the fluorescence mechanisms of the dye or tags. Independent of joule heating, an increase in electric field may also cause damage by creating an excessive force along the polymer chain on a tethered molecule in a uniform field and/or by creating an excessive force along the polymer chain in a free solution due to an electric field gradient.
Aspects of the present invention are directed to a multi-stage concentrator system which helps to balance the benefits of a stronger electric field, while reducing the amount of damage to the sample. In one embodiment, the electric field strength may be chosen such that the charged particles/molecules may move faster to the first membrane 24 than to the second downstream membrane 34. For example, in one embodiment of a multi-stage concentrator system, the area of the starting membrane contacting surface 46 in the reaction chamber 40 is greater than the area of the first sample contacting surface 26, and the area of the first sample contacting surface 26 is greater than the area of the second sample contacting surface 36. A first electric field may be used to move the sample from the starting membrane contacting surface 46 to the first sample contacting surface 26. A second weaker electric field may then be used to move the sample to the second smaller sample contacting surface 36. In one embodiment, the applied voltage is between approximately 500-1000 volts. In another embodiment, the applied voltage is between approximately 100-200 volts.
The first and second electric fields may be chosen in a manner which minimizes damage of the samples caused by the electric field. Without a multi-stage concentrator system, the maximum electric field strength may be based upon the smallest membrane configuration of the overall system 10, so as to prevent damage to the sample which may be caused by the electric field. With a multi-stage concentrator system, a maximum electric field strength may be different for each concentrator system 20, 30, allowing the sample to move and thus concentrate at different rates based upon the size and configuration of each stage. More specifically the electric field may be stronger in stages where the area of the membrane contacting surface is larger. Thus, the speed of the sample to the first membrane 24 may be greater than the speed of the same sample to the second membrane 34.
In one embodiment, the ratio between the first sample contacting surface 26 and the second sample contacting surface is approximately 2. In another embodiment, the ratio between the first sample contacting surface 26 and the second sample contacting surface is approximately 10, and in yet another embodiment, the ratio between the first sample contacting surface 26 and the second sample contacting surface is approximately 20. For example, in one exemplary embodiment the area of the first sample contacting surface 26 of the first membrane 24 is approximately 0.4 mm2. From the first membrane 24, the sample is moved to the second membrane 34 where the area of the second sample contacting surface 36 of the second membrane 34 is approximately 0.02 mm2.
In one embodiment, the ratio between the area of the starting membrane 44 in the reaction chamber and the area of the first sample contacting surface 26 is approximately 100, and in another embodiment, the ratio between the area of the starting membrane 44 and the area of the first sample contacting surface 26 is approximately 250. For example, in an embodiment where the first sample contacting surface 26 is approximately 0.4 mm2, the area of the starting membrane 44 in the reaction chamber may be approximately 100 mm2.
It should be appreciated that aspects of the present invention are directed to multi-stage concentrators which may include three, four or more concentrator systems (not shown) which may be in fluid communication with and positioned downstream of the first and second concentrators systems 20, 30. Each concentrator system may include a membrane, where the area of the sample contacting surface of the membrane is smaller than the membrane in the upstream concentrator system. The number of concentrator systems in a multi-stage concentrator system may vary based upon the geometry of the overall system, the heat dissipation characteristics, and the desired concentration time.
To create an electric field across the membrane portion 24a, the electrode assembly may include a first electrode 52 positioned within the concentrator system 20. For example, in one embodiment, a positive electrode may be positioned within port A and/or port B, and a negative electrode (not shown) may be positioned at a location upstream from the sample. When an electric field is created between the positive and negative electrodes, the negatively charged sample will move into the chamber, towards the positive electrode, and will collect and concentrate on the membrane portion 24a. The membrane 24 is configured such that the sample cannot easily pass through the membrane so that the sample collects on the sample contacting surface 26.
In one embodiment, the concentrator system 20 includes a plurality of substantially parallel microchannels 60 extending outwardly from at least a portion of the channel 20. As shown, in this particular embodiment, a first set 62 of substantially parallel microchannels 60 extends outwardly from one portion of the channel 22 and a second set 64 of substantially parallel microchannels 60 extends outwardly from another spaced apart portion of the channel 22. In this embodiment, the first and second sets 62, 64 of microchannels extend along opposite sides of the chamber 22 and the two portions 24a, 24b of the first membrane 24 extend along the length of the first and second sets 62, 64 of microchannels, respectively.
As discussed above, aspects of the present invention are directed to systems and methods for concentrating a sample with an electric field which creates a substantially uniform current density across the membrane. The above-described substantially parallel microchannels 62 which are proximate to the membrane portion 24a may provide a substantially uniform current density across the membrane 24a, such that the sample may collect and concentrate more evenly across the membrane 24a. In particular, the current travels through the microchannels such that the current density across the membrane is substantially uniform.
To create an electric field across the membrane portion 24b, the electrode assembly may include a positive electrode 54, which may for example, be positioned within port E and/or port F. When an electric field is created between the positive electrode and an upstream negative electrode, the sample will move into the chamber 22 towards the positive electrode 54 collecting and concentrating on the membrane 24b. With the second set of substantially parallel microchannels 64 which are proximate to the membrane portion 24b, a substantially uniform current density across the membrane 24b may be provided, so that the sample may collect and concentrate substantially evenly across the membrane 24b.
It should be appreciated that in some embodiments, the sample may collect and concentrate on either one or both of the membrane portions 24a, 24b. In one embodiment, an electric field may be created across both membrane portions 24a, 24b, such that the sample may collect simultaneously on the membrane portions 24a, 24b. In another embodiment, the electric field across the membrane portions 24a, 24b may be created sequentially, such that a first portion of the sample is concentrated onto membrane portion 24a, and thereafter a second portion of the sample is concentrated onto membrane portion 24b.
In addition to creating a more uniform current density across the membrane 24, the plurality of microchannels 60 may also enable the fabrication of larger membrane surfaces by providing a greater surface to which the membrane 24 may attach. The greater surface area which may be provided by the microchannels 60 may make the membrane 24 more secure within the chamber 22 when the membrane 24 is subjected to pressure gradients and/or electrical gradients.
Turning now to
Similar to the membrane 24, a plurality of microchannels 80 are shown proximate the second membrane 34. This configuration may provide an electric field which creates a substantially uniform current density across the membrane 34 such that the sample may collect and concentrate more evenly across the sample contacting surface 36.
Although the schematic representation of concentrators illustrated in
Once the sample collects and concentrates on the second membrane 34, the electric field may be reversed so that the sample moves in the opposite direction. In one embodiment, the positive electrode 56 positioned at port H may be replaced with a negative electrode to repel the negatively charged sample back through the five channels 72. At this stage, the sample may either be moved into another concentrator (not shown) for further concentration or the sample may undergo further processing which may depend upon the type of sample. In one embodiment, where the sample is a nucleic acid sample including DNA, the sample may move into a reaction chamber 82 (see
As shown in
The concentrator systems 20, 30, 30b may be formed in a variety of ways, as the invention is not limited in this respect. The concentrator systems 20, 30, 30b may be formed of materials such as, but not limited to, plastic, glass (fused silica, borosolicate, etc.), insulated semiconductors (silicon dioxide on silicon, etc), or ceramics. In one embodiment, the concentrator systems 20, 30 are formed onto a microfluidic chip, where the channels 22, 32 and/or the microchannels 60, 80 may be pre-etched into the chip. As shown in
The membranes 24, 34 are conductive, such that an electric field may travel through the membranes. The membranes are semi-permeable and may be porous, but the membranes are configured such that the sample cannot easily pass completely through the membranes 24, 34. As discussed further below, the membranes 24, 34 may be configured such that a sample may pass partially into but not completely through the membranes, such that the sample becomes embedded within the membrane. However, in other embodiments, the membranes 24, 34 may be configured such that the sample cannot penetrate the sample contacting surface 26, 36. In one embodiment, the membranes 24, 34 may be formed from a semi-solid material, and may for example, be made from a dense polymer matrix.
The membranes 24, 34 may also be formed in a variety of ways. In one embodiment, a membrane is a semi-permeable polymer membrane formed from a material such as an acrylimide, polyacrylimide, agarose, polyethylene glycol (PEG), and/or other biocompatible gel, and may for example be formed from a mixture of both acrylimide and PEG. In another embodiment, one or both of the membranes may be formed from a cellulose membrane, such as a cellulose filter paper.
Hybrid designs, including at least two different types of semi-permeable membranes, are also contemplated as the present invention is not limited in this respect.
For example, in one embodiment, the first membrane 24 may be made of a regenerated cellulose membrane, and another membrane, such as the second membrane 34, may be made of a gel.
It is also contemplated that in certain embodiments, the membrane material may be formed to have a particular configuration and/or pore size to substantially limit the collection and/or concentration of nucleic acids having a certain particle size. In this respect, the membrane material may be configured to have a particular cut-off nucleic acid size. This fractionation functionality may be beneficial when the concentration of only longer and/or larger nucleic acids is desirable, as the shorter and/or smaller nucleic acids may either pass through the membrane or become embedded within the membrane.
In one embodiment, the membrane 24 may be fabricated with a gel, such as an acrylimide gel or agarose gel. To form the membrane 24, the chamber and microchannels of the microfluidic chip may first be filled with the gel. The gel may include a photo initiator such that when UV light is selectively exposed to portions of the gel, the gel crosslinks and solidifies within the chamber 22, 32 to form the membrane 24, 34. In one embodiment, azo-based photo initiator such as VA-086 and/or VA-50 obtained from Wako Chemicals (Richmond, Va.) may be used. In another embodiment, a photo initiator called Darocur® obtained from Ciba Specialty Chemicals is used. In certain embodiments having the Darocur® photo initiator, the polymerization and solidification of the gel may occur more rapidly. Due to the small dimensions associated with a microfluidic chip, the chip may be placed under a microscope to selectively expose portions of the gel to the UV light. Once the desired portions of the gel are exposed to the UV light, the remaining unsolidified gel may be flushed out to the microfluidic chip using a fluid wash.
In some embodiments, before the microfluidic chip is filled with the gel, the microfluidic chip may first be flushed with a series of reagents, and/or a polymer coating, such as an acrylimide coating, may be used to coat the inner chamber and microchannel walls. This coating may form chemical bonds to act like an anchor for the gel so that the gel may bond more easily to the inner walls of the chamber and microchannels. Thereafter, the microfluidic chip may be flushed with water before introducing the gel into the chip to form the membrane.
In certain embodiments, one or more chambers may be configured to act as a mechanical anchor to the gel membrane. In particular, the chamber may be provided with positive or negative relief areas. The membrane may be positioned adjacent these positive or negative relief areas to prevent the membranes from moving. One example of a negative relief in the chamber according to one embodiment is illustrated in
In other embodiments, a positive relief may be provided in a chamber 22 to mechanically anchor a membrane. In a positive relief, a protrusion is formed in the inner chamber walls to help secure the membrane. In one embodiment, a post may be formed in the channel and may extend from the floor to the ceiling.
In certain embodiments, a negative relief anchoring system may be preferred over a positive relied anchoring system because the protrusions/posts associated with a positive relief anchoring system may disrupt the electric field lines flowing through the chamber. In some embodiments, the currently density may be more uniform with a negative relief furrow 410 anchoring system in comparison to a positive relief protrusion anchoring system.
In certain embodiments, it may be desirable to limit the amount of the nucleic acid sample that may become embedded within the membrane. In such embodiments, a passivation process may be used to fill voids within the membrane so that the sample does not later become embedded within those voids. For example, in one embodiment with a gel membrane, a “sacrificial material” may be flushed through the system to fill up voids and/or pores within the membrane. The sacrificial material is typically a negatively charged material that is capable of filling voids/pores in the membrane. In one embodiment, where the nucleic acid sample is a DNA sample, the sacrificial material may include another type of DNA. The sacrificial material that does not become to embedded within the membrane is then flushed out. It is also contemplated that the sacrificial material may be a positively charged material if the material is capable of remaining in the membrane during a concentration step, which may utilize an electric field. A repassivation step may also be performed to reintroduce the sacrificial material into the membrane after prolonged use.
As discussed below, in certain embodiments as shown in
It should be recognized that the above description regarding the formation of the membrane 24, 34 within the concentrator systems 20, 30, 30b is not intended to be limiting, as the membrane may be formed with other materials and/or with other methods. Furthermore, it should be recognized that one membrane 24 within the first concentrator system 20 may be formed with different materials and/or according to different methods than another membrane 34 in the second concentrator system 30, 30b.
Similar to the above-described first and second membranes 24, 34, in the embodiment illustrated in
Unlike the embodiments illustrated in
There may be several benefits associated with embodiments where the membrane 94 is spaced apart from the plurality of microchannels 100. First, the separation distance between the membrane and the microchannels permits the flow of the cooling liquid to circulate behind the membrane 94 through the backside flow branch 102 which may reduce the affects of the joule heating. As the current travels through the membrane, the membrane 94 and the surrounding areas may heat up as a result of the increased resistance in the flow of current through the membrane. The flow of the cooling liquid behind the membrane 94 helps to reduce the affects of the joule heating. Second, when the membrane 94 is spaced apart from the microchannels, the membrane 94 does not extend into the microchannels which may also minimize joule heating. As mentioned above, as the current travels through a concentrator system, portions of the system may heat up as a result of resistance in the flow of current. As the current travels through the buffer fluid, the resistance may be minimal, but the resistance may increase as the current travels through the membranes 94. For example, the resistance through the membrane material may be between approximately 3 and 10 times greater in comparison to the resistance through the buffer fluid. This can lead to undesirable localized hot-spots in to the microchannels 100. When the microchannels 100 are spaced apart from the membrane 94, the microchannels 100 may be filled with a buffer fluid which has a lower resistance in comparison to the resistance of the membrane 94 which may minimize hot-spots. Third, the flow of cooling fluid along the membrane 94 may also prevent ion concentration polarization. In certain embodiments, the pore size of the membrane 94 may be small enough that it is difficult for ions to move through the membrane 94. Ion concentration polarization may occur if ions build up on one side of the membrane. Over time, ion concentration polarization can result in an undesirable current drop. The flow of liquid adjacent the membrane through the backside flow branch 102 may reduce and/or prevent this ion build up and thus helps to stabilize the current.
As discussed above, to form the membrane 94, the gel may fill the microfluidic chip and thereafter only selected portions of the gel may be exposed to a UV light to crosslink and thereby solidify those gel portions. The non-crosslinked gel portions are then flushed out of the chip and filled with the buffer fluid. When the microchannels are filled with the gel rather than the buffer fluid, the resistance for the current to travel through the gel may be greater. Thus, in certain embodiments, the gel which may be used to form the membrane may be flushed out of the plurality of microchannels to reduce the affects of the joule heating within the concentrator system.
Turning now to
A sample may initially be positioned on a starting membrane 142 within the reaction chamber 140. To initiate movement of the sample, an electric field may be created through electrodes SL and TG such that the electric field extends through the reaction chamber 140, but not through the first or second concentrator system 120, 130. For example, when electrode TG is a negative electrode and electrode SL is a positive electrode, the sample will travel away from the reaction chamber 140 and towards the selector valve 150.
In some embodiments, the membrane 122, 132 within the first and second concentrator systems 120, 130 may be more susceptible to joule heating damage. When an electric field is created between electrodes SL and TG, a greater current may be used to move the sample because this electric field is not created across either downstream membrane 122, 132. A greater current between electrodes SL and TG may thus be used to create a stronger electric field to free the sample from membrane entanglement with the starting membrane 142. As set forth above, a greater current may also make the sample move at a higher velocity.
Once the sample is removed from the starting membrane 142, the electric field may change. For example, the electric field may be created between electrodes C3a, C3b which may be positive electrodes, and electrode TG may be maintained as the negative electrode. In this respect, the sample travels into the first concentrator system 120 and collects and concentrates on the membrane 122. As discussed above with respect to
To move the sample from membrane 122a, 122b into the second concentrator system 130 an electric field may be created between electrodes C3a, C3b and downstream electrode G2. To move the sample towards electrode G2, electrode G2 may be a positive electrode and electrodes C3a, C3b may now be negative electrodes. In one embodiment, the sample on membrane portion 122a may be moved independent of a sample on membrane portion 122b. For example, an electric field may be created between electrode C3a and G2 to move the sample on membrane 122a, whereas an electric field may be created between electrodes C3b and G2 to move a sample on membrane 122b. The independent operation of membranes 122a,122b may allow one to create an electric field on only one membrane portion 122a or 122b which is strong enough to move a sample given the restraints of the current density on the second smaller downstream membrane 132 due to joule heating. Once the sample collects on membrane 132, an electric field may be created between electrodes G1, G2 and downstream electrode G4 to move the concentrated sample for further processing and/or analysis.
Turning to
In this particular embodiment shown in
In one embodiment, the depth of the shallow depth region 160 (i.e. distance into the page) is approximately 50% of the depth of the surrounding chamber 192. In another embodiment, the depth of the shallow depth region 160 is approximately 25% of the depth of the surrounding chamber 192, and in another embodiment, the depth of the shallow depth region 160 is approximately 10% of the depth of the surrounding chamber 192, is approximately 5% of the depth of the surrounding chamber 192, or approximately 1% of the depth of the surrounding chamber 192. In one particular embodiment where the depth of the shallow depth region 160 is approximately 5% of the depth of the surrounding chamber 192, the depth of the chamber is approximately 20 micrometers and the depth of the shallow depth region is approximately 1 micrometer.
As discussed above, the concentrator system 190 may be formed into a microfluidic chip and the chambers 192 and channels 98 may be pre-etched into the chip, for example, with microlithographic manufacturing techniques. Similarly, a shallow depth region 160 may also be pre-etched into the chip.
It should be appreciated that although there are no parallel channels illustrated in the embodiment of
In some embodiments, systems and methods of transferring and concentrating a sample are provided to maintain the band integrity of the sample after the sample collects on a membrane 24. For example, as shown in
In this embodiment, a channel 600 is opposing the sample contacting surface of the membrane 24. In this particular embodiment, the channel 600 is substantially perpendicular to the chamber 22. In other embodiments, the channel 60 may have other angular orientations with respect to the chamber 22, such as, but not limited to approximately 30°, approximately 45°, or approximately 60°. As shown in
This squeezing process may be repeated to further compress the sample. In one embodiment, the squeezing process may be repeated so that the portion of the sample 12 at each end is compressed inwardly toward the center of the sample. Then, when the sample is moved, the sample 12 is less dispersed and may be more likely to move in a uniform band. It is contemplated that the more the squeezing process is repeated, the greater the sample concentration. The squeezing process may be repeated until a desired sample concentration is reached. Once the squeezing process is completed, the sample 12 may be moved down either end of the chamber 22 or out through the channel 60.
It is also contemplated that the geometry of the chamber may be configured to maintain the band integrity of the sample. As shown in
As illustrated, the concentrator system 300 is arranged to minimize the distance between the membrane 304 and the downstream component 320. It may be desirable to minimize this distance to maintain the concentration of the sample after the sample leaves the membrane 304. In one embodiment, the distance D between the membrane 304 and the downstream component 320 is between approximately 0.5-1.0 mm, and may for example be less than 1 mm. In another embodiment, the distance D is between 1 mm-5 mm, and may for example be approximately 2.5 mm.
Although the size and shape of the channel 302 may vary, in one embodiment, the channel is pre-etched within a microfluidic chip and the depth of the channel 302 may be approximately 20 μm. In one embodiment, the adjacent downstream component 320 may be pre-etched within the chip and the depth of the downstream component 320 may be approximately 2 μm. In one embodiment, the location of the membrane 302 is pre-etched within a chip with a depth of approximately 1 μm.
In one embodiment, the electric field may oscillate between concentrator systems 340, 360 to more evenly distribute the sample across the two membranes 304. In other words, the electric field may be configured such that the sample first travels towards the membrane in the first system 340. The electric field may then switch to be configured such that the sample travels towards the membrane in the second system 360. This oscillating process may be repeated until the entire sample has been transferred to one of the two membranes 304. It should be appreciated that the oscillation rate may be adjusted to control the amount of the sample at each membrane. For example, if the oscillation rate is 50:50, the sample should be split approximately equally between the two membranes.
Thereafter, the sample on the membrane 304 in the first system 340 may be transferred to the membrane 304 in the second system 360. This process may be beneficial when the sample enters the two concentrator systems 340, 360 having been separated by sample size where it is desirable to recombine the various sample sizes back together. For example, in one embodiment, an upstream component may separate a nucleic acid sample such that the longer nucleic acids are clustered together and shorter nucleic acids are clustered together. By splitting up the sample onto the two membranes and thereafter combining the sample together, one may recombine the longer and shorter nucleic acids back together in a more evenly distributed mixture.
As mentioned above, it may be desirable to minimize the distance D between the membrane 304 and the downstream component 350. In one embodiment, the distance D is between approximately 0.5-5.0 mm, and may for example be approximately 2.5 mm.
Turning now to
Once the sample has collected on the first membrane 522, an electrode assembly is provided to transfer the sample back through the switch valve 510 and onto a second sample contacting surface of a second membrane 532 positioned within a second chamber 530 which is in selective fluid communication with the first chamber. The assembly is also configured to move a sample at least partially through the second chamber from an intermediate position to the second sample contacting surface. In particular, the assembly includes an electrode assembly configured to selectively create an electric field across the second membrane to move a sample to the second sample contacting surface. In one embodiment, the current used to move the sample from the first membrane 522 to the second membrane 532 is approximately 25 uA.
The membranes 502, 522, 532 may be made and formed using any of the above-described materials and methods. In one embodiment, the reaction chamber membrane 502 and the first membrane 522 are made of a cellulose membrane and the second membrane 532 is made of a polyacrylamide gel.
Also, as discussed above, in certain embodiments, the area of the first sample contacting surface of the first membrane 522 is greater than the area of the second sample contacting surface of the second membrane 532. For example, in one embodiment, the area of the first sample contacting surface of the first membrane 522 is approximately 10 mm2 and the area of the second sample contacting surface of the second membrane 532 is approximately 0.4 mm2, such that the ratio between the two surfaces is approximately 25. In one embodiment, the sample contacting surface of the reaction chamber membrane 502 is approximately 100 mm2, such that the ratio between this surface and the downstream first sample contacting surface of the first membrane 522 is approximately 10.
Once the sample is transferred to the second membrane 532, the sample may be transferred with the electrode assembly to downstream locations. For example, in one embodiment, the sample may be transferred to chamber 540 for further processing which may, for example, include stretching the sample.
As shown in
It should be appreciated that in some embodiments the system 450,460 may be used primarily to transfer a sample. In other embodiments, the system 450, 460 may be used to transfer and concentrate the sample. Accordingly, many of the features described above with respect to concentrator systems may be interchangeably used with a transferor systems 450, 460, as the invention is not limited in this respect.
In one embodiment, one or more of the above-mentioned systems for transferring and/or concentrating a sample may be used to perform a reaction on the sample, in the absence or presence of transferring or concentrating. A reaction, as used herein, is a covalent or non-covalent modification of a sample, or more usually components of a sample. A covalent modification means that a covalent bond is broken and/or formed. A non-covalent modification means any other type of modification. The reaction may be a chemical or biological reaction. In one embodiment, the reaction is performed on a nucleic acid sample.
In one embodiment, a reaction may be performed by placing a sample within the first chamber of one of the above-mentioned systems. The sample may comprise a nucleic acid and/or other biological material. When the sample is negatively charged, such as with a nucleic acid sample, an electric field is created with the electrode assembly across the first membrane such that a charged component of the sample moves to the first sample contacting surface. It should be appreciated that the sample as a whole may not be negatively charged. One or more reagents are placed within the first chamber and a reaction is performed between the sample and the one or more reagents. It should also be appreciated that similar reactions may be performed in the second chamber on the second membrane, as the invention is not limited in this respect.
The reaction may be performed in a variety of ways. In one embodiment, the reaction may be performed by creating an electric field with the electrode assembly across the first membrane such that the reagent(s) moves to the first sample contacting surface to react with the sample. In another embodiment, the reaction may be performed by hydrodynamically moving the reagent(s) to the first sample contacting surface to react with the sample. After the reaction, excess reagent(s) may be flushed out of the chamber by flowing a buffer solution across the surface of the membrane. In one embodiment, a plurality of reactions may be performed on the membrane. Once the series of one or more of the reactions is complete, the electric field may be reversed to transfer the sample to a downstream component for further processing of the sample.
A reaction may be performed with various types of reagents. The reagent may include at least one of fluorescent intercalating dyes, bisPNA tags, restriction endonucleases, and DNA-binding reagents. For example, in one embodiment, the reagent may be an intercalating dye and the sample may be a DNA sample and the reaction may facilitate fluorescent detection of the DNA molecule in a subsequent step.
Turning now to
According to one particular method, the first end 206 of the pipette 200 is placed in contact with a negatively charged nucleic acid sample contained within a reservoir 250. An electric field is created through the passageway 204 of the pipette 200 between the positive and negative electrodes 230, 232. Under the electric field, a first portion 252 of the negatively charged nucleic acid sample 254 is drawn into the first end 206 of the pipette body 202 to concentrate the first portion of the sample in the pipette 200, where the concentration of nucleic acid of the first portion 252 is greater than the concentration of nucleic acid of the reservoir nucleic acid sample 254.
The negative electrode 232 may be positioned proximate to the first end 206 of the body. In one embodiment, the negative electrode 232 may be adjacent to or within the reservoir 250. The pipette 200 may be used to withdraw a small sample 252 from a larger volume of the sample 254 contained within the reservoir 250. Once drawn into the pipette 200, the sample may concentrate against the membrane 220 as discussed above. It should be recognized that when the negative electrode 232 is within the reservoir 250, a physical barrier (not shown) may be provided between the electrode 232 and the sample to prevent direct contact but still permit electrical contact, as direct contact may cause a detrimental electro-chemical reaction.
The pipette 200 may also be used to separate a charged sample from a non-charged or oppositely charged material. When the electric field is created through the pipette 200, the charged sample may be attracted into the pipette 200, leaving the non-charged or oppositely charged material outside of the pipette.
The pipette 200 may be used to transfer a sample between two locations that are not in fluid communication with each other (i.e. remote), for example, between two spaced apart reservoirs. For example, in one particular embodiment, a first portion 252 of a negatively charged sample 254 is drawn up into the pipette 200 from a reservoir 250 due to the electric charge. Thereafter, the first portion 252 of the sample may be dispensed into another reservoir (not shown) by either moving the first end 206 of the pipette 200 to a second reservoir or by moving a second reservoir over to the pipette 200.
In one embodiment, the portion 252 of the sample is also dispensed from the pipette 200 using an electric field. For example, the negatively charged sample may be dispensed from the pipette by reversing the electric field (i.e., an electric field is created between a negative electrode positioned at the second end 208 of the body and a positive electrode is positioned proximate the first end 206 of the body). In another embodiment, the portion 252 of the sample may be dispensed from the pipette 200 hydrodynamically using mechanical approaches such as using a pump. It should be appreciated that in embodiments where the sample is more fragile, such as, for example, when the sample is a nucleic acid sample which includes long DNA segments, dispensing the sample with an electric field may be desirable to prevent damaging the sample due to shear forces. In one embodiment, a first portion 252 of the sample is drawn into and dispensed from the pipette 200 without substantially shearing the nucleic acids.
The semi-permeable membrane 220 is conductive, such that an electric field may travel through the membrane. The membrane may be porous, but the membrane is configured such that the sample, such as a nucleic acid sample, cannot easily pass completely through the membrane 220. In one embodiment, the membrane 220 is substantially resistant to the flow of nucleic acids through the membrane 220. As discussed further below, the membrane 220 may be configured such that a sample, such as a nucleic acid sample, may pass partially into but not completely through the membrane. In one embodiment, the membrane 220 may be formed from a semi-solid material, and may for example, be made from a dense polymer matrix. In one embodiment, the membrane 220 is formed from a 20% solution of acrylimide which acts as a plug within the passageway to substantially limit the flow of a sample from the first end 206 to the second end 208.
The membrane 220 may also be formed in a variety of ways. In one embodiment, a membrane is a semi-permeable polymer membrane formed from a material such as a gel matrix plug. For example, the gel matrix plug may be formed with an acrylimide gel or agarose gel which may be formed within the pipette passageway 204 using one of the methods and techniques described above. In yet other embodiments, the membrane may be formed by a regenerated cellulose material. As discussed above, in some embodiments, joule heating caused by the electric field may affect a membrane formed from a gel. In some embodiments, a membrane formed from regenerated cellulose filter paper may be less affected by joule heating.
The pipette body 202 may be made of a variety of materials, as the invention is not limited in this respect. In one particular embodiment, the pipette body 202 is made from a plastic or glass, and the body 202 may include a surface treatment to change the surface from a polar to a non-polar surface. The dimensions of the pipette 200 may vary according to different applications, as the invention is not so limited. However, in one embodiment, the pipette 200 has a height of between approximately 4-5 inches, with a diameter of approximately 0.5 inches. The tip of the pipette at the first end 206 may taper down such that the diameter at the first end 206 is within approximately 0.5 mm.
The pipette 200 may include a layer 260 positioned within the passageway 204 adjacent the semi-permeable membrane 220 and proximate the first end 206 of the body. In this embodiment, a sample 252 drawn into the first end 206 of the pipette will collect and concentrate on the layer 260 and may not directly contact the membrane 220. This additional layer 260 is conductive, such that an electric field may travel through the layer, and the layer 260 may act as a cushion as the sample 252 is drawn into the pipette 200. The layer 260 may prevent the sample from becoming embedded within the membrane 220. The layer 260 may be less dense than the buffer solution such that the layer 260 floats up and/or remains adjacent to the membrane 220. In one embodiment, the layer 260 includes an electrically conductive solvent layer which forms a separate phase when mixed with a fluid, such as water. In one embodiment, the layer 260 is an organic solvent layer, and may for example be made of butanol. The thickness of the layer 260 may be between approximately 5 mm-1 cm. When the layer 260 is too thin, in some embodiments, the sample 252 may tend to get trapped within the membrane 220, and when the layer is too thick, the resistance within the passageway of the pipette may build up due to joule heating. It should be recognized that although this layer 260 is shown with respect to the pipette 200 that in other embodiments, the layer 260 may be provided adjacent a membrane in any one of the above-described systems, as the invention is not limited in this respect.
In one particular embodiment, a pipette 200 is able to concentrate a nucleic acid sample which includes elongated DNA segments having a length of between approximately 100 kilobase and 1 megabase. Such samples my be concentrated within the pipette 200 up to 10 times or even 20 times the sample concentration within the reservoir 250 without substantially shearing and thus damaging the sample.
It should be appreciated that in one embodiment, the pipette 200 may be used individually, while it is also contemplated that a plurality of pipettes 200 may be used simulataneously, as the invention is not so limited.
Having thus described several aspects of at least one embodiment of this invention, it is to be appreciated various alterations, modifications, and improvements will readily occur to those skilled in the art. Such alterations, modifications, and improvements are intended to be part of this disclosure, and are intended to be within the spirit and scope of the invention. Accordingly, the foregoing description and drawings are by way of example only.
This invention was made with Government support under U.S. Department of Homeland Security, Science & Technology Directorate contract HSHQPA-05-9-0019. The Government has certain rights to this invention.
| Filing Document | Filing Date | Country | Kind | 371c Date |
|---|---|---|---|---|
| PCT/US08/08530 | 7/11/2008 | WO | 00 | 7/21/2010 |
| Number | Date | Country | |
|---|---|---|---|
| 60959302 | Jul 2007 | US |
