US20160299132A1

US20160299132A1 - Systems and methods for bead-based assays in ferrofluids

Info

Publication number: US20160299132A1
Application number: US14/777,512
Authority: US
Inventors: Hur Koser
Original assignee: Ancera Inc
Current assignee: Arecna Holdings Inc; Ancera Inc
Priority date: 2013-03-15
Filing date: 2014-03-17
Publication date: 2016-10-13
Also published as: WO2014145765A1; US20170285060A1; US20220107311A1; US11204350B2

Abstract

Some embodiments of the present disclosure are directed to systems and methods for separating, directing, and/or extracting a target molecule from a mix of molecules and may comprise a plurality of non-magnetic beads suspended in a ferro fluid, where the non-magnetic beads may be functionalized with at least one predetermined first molecule configured to bind with a target particle. A microfluidic device may be included which may comprise at least one microfluidic channel, the device configured to dynamically and/or statically receive an amount of the mix. Magnetic field means may be included and may be configured to apply a magnetic field to at least a portion of the at least one channel to exert an indirect force on the non-magnetic beads in the ferro fluid mix, and separate the non-magnetic beads from the ferrofluid. The beads may then be directed to at least one receptor region. At least one outlet may be provided which is arranged to be in communication with the at least one microfluidic channel, the at least one outlet may be configured to receive and extract the separated non-magnetic beads from the ferrofluid.

Description

RELATED APPLICATIONS

This application claims benefit under 35 USC 119(e) of U.S. provisional patent application Nos. 61/798,087, filed Mar. 15, 2013, and entitled, “Bead-Based Assays in Biocompatible Ferrofluids” the entire disclosure of which is herein incorporated by reference in its entirety.

FIELD OF THE DISCLOSURE

The present disclosure relates to extraction and/or separation of particles in ferrofluids.

BACKGROUND OF THE DISCLOSURE

In immuno-magnetic separation, magnetic micro-beads covered with specific ligands are introduced into a complex biological sample to tag target particles in a mix (e.g., molecules, proteins, cells or other biological entities). Using an external magnetic field gradient, the tagged entities may be separated (e.g., focused, concentrated, precipitated), then extracted and purified for subsequent processing. These beads may also be used directly in biological assays (e.g., ELISA, PCR, gene sequencing, etc.) as they carry their target load to a sensor or a bio-functional surface.
A limitation of some magnetic bead separation systems is the wide distribution of the amount of magnetic content in each bead. This may be the case even for beads from the very same batch, and is a direct consequence of practicality in existing manufacturing methods. As a result, it may be impractical to attempt to distinguish bead tags based on the magnitude of the forces experienced by the magnetic beads from magnetic field, unless there is a considerable size difference between them (e.g., 1 micron vs. 10 micron beads).

SUMMARY OF THE DISCLOSURE

The teachings of this disclosure are a further application and development of a previous series of disclosures, including, for example PCT publication no. WO2011/071912 and WO2012/057878, the noted disclosures of which are all herein incorporated by reference in their entireties.
In some embodiments of the present disclosure, methods for extracting a target molecule from a mix of molecules are provided. Such methods may include suspending a plurality of non-magnetic beads in a ferrofluid, the non-magnetic beads being functionalized with at least one predetermined first molecule configured to bind with a target particle, and mixing or otherwise exposing the ferrofluid to a plurality of particles forming a mix, where target particles contained in the plurality of particles link with the first molecules functionalized on the non-magnetic particles. Such methods may further include flowing the mix through at least one microfluidic channel, applying a magnetic field to at least a portion of the at least one channel, where the magnetic field is configured to exert an indirect force on the non-magnetic beads to separate the non-magnetic beads from the ferrofluid, and extracting and/or otherwise separating the non-magnetic beads from the mix, wherein, as a result of the extraction, the target particles contained in the plurality of particles are separated from the mix.
Some embodiments provide a system for extracting a target molecule from a mix of molecules, and may comprise a plurality of non-magnetic beads suspended in a ferrofluid, the non-magnetic beads being functionalized with at least one predetermined first molecule configured to bind with a target particle, a plurality of particles, wherein the plurality of particles are mixed with the ferrofluid containing the non-magnetic beads resulting in a ferrofluid mix, and a microfluidic device comprising at least one microfluidic channel, where the device may be configured to dynamically and/or statically receive an amount of the mix. The magnetic field means may be configured to apply a magnetic field to at least a portion of the at least one channel to exert an indirect force on the non-magnetic beads in the ferrofluid mix, and separate the non-magnetic beads from the ferrofluid. The system may further include at least one outlet in communication with the at least one microfluidic channel, the at least one outlet configured to receive and extract the separated non-magnetic beads from the ferrofluid.
Some embodiments may further include one and/or another of the following additional features:

- the first molecule comprises a ligand;
- the target particle comprises a biological particle, where the biological particle may comprise at least one of an organic molecule, of a cell, a bacteria, a virus, DNA, RNA, a carbohydrate, a protein, a biomarker, a hormone, kinase, enzyme, cytokine, toxin, and any fragments thereof;
- the magnetic field source includes at least one of planar electrodes, electromagnets or a magnet array;
- detecting the target particles after at least one of separation and extraction via detection means, where the detecting comprises a flow cytometer and/or the like;
- the detection means includes any of an optical scanner/detector, and/or other detecting means, optical or otherwise, familiar to those of skill in the art, including, for example those found in any one and/or another of U.S. Pat. No. 4,448,534, WO2013/155525, WO2008/042003, U.S. Pat. No. 8,364,409, WO1991/001381, and WO2013/054311;
- the ferrofluid includes a plurality of magnetic nanoparticles and the magnetic field is configured to drive the magnetic nanoparticles in a first direction opposite a direction in which the non-magnetic beads are driven; and
- the separated non-magnetic beads flow into at least one outlet port in communication with the at least one microfluidic channel, such that the non-magnetic beads may be extracted or otherwise collected therefrom.

The above-noted embodiments, as well as other embodiments, will become even more evident with reference to the following detailed description and associated drawing, a brief description of which is provided below.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is a schematic of a bead-based assay for a ferrofluid, according to some embodiments of the present disclosure.

FIG. 2 shows a bead-based bioassay in a ferrofluid according to some embodiments of the present disclosure.

DETAILED DESCRIPTION OF SOME OF THE EMBODIMENTS

Magnetic bead based approaches have positively impacted the speed, throughput and simplicity of biological assays and protocols. Instead of using a standard buffer with magnetic microbeads to extract and work with target entities, embodiments of the present disclosure present systems and methods using non-magnetic functionalized beads suspended in a ferrofluid (e.g., a biocompatible ferrofluid). Since non-magnetic items placed in a ferrofluid medium feel repulsive forces (i.e., an indirect force) in the presence of externally applied magnetic field gradients, they can be used to capture, enrich, collect and detect molecular and cellular entities (i.e., at least biological entities) within biocompatible ferrofluids. This is a direct extension of earlier systems and methods disclosed in WO2011/071912 and WO2012/057878, where cells can be any one or more of manipulated, captured, detected and quantified in a ferrofluid without any labels. While micro-sized cells can be generally be manipulated in a label-free fashion inside ferrofluids without the need for any labels, smaller biological particles like viruses, DNA, RNA, proteins and other biological molecules may be too small to respond to the indirect/repulsive magnetic forces in ferrofluids within reasonable times. Thus, in some embodiments, using bead-based assays as opposed to label-free approaches extends the high utility of ferrofluid concentration/separation systems/methods from strictly cell assays to other molecular assays as well.
Thus, in some embodiments, instead of using magnetic beads in a standard, clear biological buffer, some embodiments of the present disclosure use non-magnetic beads in a ferrofluid to run bead-based extraction, purification and/or ultimate detection of target moieties. Thus, in some embodiments, it becomes possible to conduct virtually all biological assays in ferrofluids. Aside from being the dual opposite of immuno-magnetic assays, embodiments of the present disclosure are also different in at least several aspects. First, the magnetic force on the beads suspended in ferrofluid is repulsive/indirect (as opposed to attractive as in standard immuno-magnetic methods). The repulsive force enables much better localization, manipulation and/or focusing of the non-magnetic beads towards, for example, a bio-functional surface, thereby inherently increasing the sensitivity of a bead-based assay. Second, while bead manufacturing technology enables high precision bead diameters, there is typically much less control on the volume of the magnetic phase integrated inside a magnetic bead. As a result, magnetic forces acting on tagging beads is much more uniform in bead-based assays conducted in ferrofluids, enabling, in some embodiments, higher precision, repeatability, and reliability in final results.
FIG. 1 illustrates a bead-based assay utilizing a ferrofluid according to some embodiments. As shown, an initial sample containing a mixture of particles (e.g., moieties 2, including target moieties) and functionalized beads is mixed with a biocompatible ferrofluid 3 in a reservoir 1. After an incubation period in which target moieties bind with the molecules functionalized onto the beads, an external force, such as a pressure source, e.g., a pump 4, introduces the overall mixture into a channel inlet 8 that is connected to fluidic channel 5 that sits atop a magnetic field source 6. The magnetic field source 6, which is configured to apply a force, either directly or indirectly to particles/beads of the mix (e.g., on non-magnetic particles/beads), such that the functionalized beads are forced upward and focused. The magnetic source may comprise at least one of a planar electrode(s), an electromagnet(s) and a permanent magnet(s), each of which may be arranged in an array. In some embodiments, the beads (along with target particles/moieties bound to the functionalized molecules), move along the channel ceiling (e.g., roll) and interact serially with receptor regions 7 on that surface. Specific interactions between the particles 2 on the surface of the beads and the receptor regions 7 result in the temporary, and in some embodiments permanent, capture of beads. In some embodiments, detecting means, such as an optical scanner 10, may be provided and configured to detect the target particles captured and/or moving along the receptor regions 7. The mixture flows through to the channel outlet 9, in some embodiments, to waste or back to the reservoir 1.
FIG. 2 illustrates some embodiments, where a simple bead-based bioassay in a biocompatible ferrofluid is presented. Initially, the complex sample is incubated with bead tags 21, which are then sorted inside a bio-ferrofluidic device based on size. A plurality of non-magnetic beads 21 with at least one predetermined first molecule, in one embodiment, a ligand, binds with target particles 20 in the ferrofluid. Applying magnetic field gradients from below, the bead tags 21 are rapidly pushed and concentrated towards a corresponding capture surface 22. The capture surface 22, in one embodiment, includes receptors 23 to capture the target particles 20. The main role of the ferrofluid here is to accelerate mass manipulation and transport toward surfaces.
When using non-magnetic beads in ferrofluids, the force on each bead is proportional to the volume of ferrofluid that they displace. Hence, bead populations with limited size distributions may be easily distinguished from each other. For example, beads above about 1 micrometer in diameter may be easily separated and sorted from each other based on a size difference of just 1 micron (PNAS 106 (51), p 21478, 2009). Hence bead populations of various sizes may be used to multiplex bio-assays without the need to use any chromophores.
Accordingly, in some embodiments, the ability to push/force (either directly or indirectly) the beads instead of attracting (i.e., pulling) them may allow the user to:

- selectively focus, separate, sort, concentrate and/or capture them; and
- count the beads (e.g., one at a time), as they pass through a detection region (e.g., flow cytometry), which, in some embodiments, may obviate the need to use hydrodynamic focusing in such applications.

In some embodiments, one can use a combination of magnetic and non-magnetic beads to increase separation efficiency in an assay. Accordingly, using a ferrofluid medium, magnetic beads may be configured such that they could be manipulated in the opposite direction of non-magnetic beads/particles.
Thus, in some embodiments, bead-based assays in ferrofluids can be used to quantify concentrations of any of proteins, molecular biomarkers, hormones, kinases, enzymes, cytokines, toxins, viruses and DNA/RNA fragments. Moreover, systems according to some embodiments may also be used as an enrichment step prior to traditional techniques, such as culture, ELISA, and PCR.
In some embodiments, captured beads and entities can be released and collected at an outlet port by destabilizing the colloidal suspension of the ferrofluid (via changes in pH and/or salt or other additives).
Some embodiments of this disclosure may be used, for example, simultaneously with label-free assays in the same ferrofluid. In such a combined approach, cellular assays may be run simultaneously with biomolecular assays. Some embodiments may also be used as a pathogen detection panel and configured for detecting and/or quantifying bacterial pathogens in a label-free fashion while detecting viruses or other smaller antigens using non-magnetic beads as labels.
Some embodiments of this disclosure may be used, for example, in the context of drug discovery. In such approaches, bead-based assays may be used to at least one of detect, identify and quantify binding between a candidate drug molecule and a number of ligand targets.
Any and all references to publications or other documents, including but not limited to, patents, patent applications, articles, webpages, books, etc., presented in the present application, are herein incorporated by reference in their entirety.
Example embodiments of the devices, systems and methods have been described herein. As noted elsewhere, these embodiments have been described for illustrative purposes only and are not limiting. Other embodiments are possible and are covered by the disclosure, which will be apparent from the teachings contained herein. Thus, the breadth and scope of the disclosure should not be limited by any of the above-described embodiments but should be defined only in accordance with claims supported by the present disclosure and their equivalents. Moreover, embodiments of the subject disclosure may include methods, systems and devices which may further include any and all elements from any other disclosed methods, systems, and devices, including any and all elements corresponding to bead assays. In other words, elements from one or another disclosed embodiments may be interchangeable with elements from other disclosed embodiments. In addition, one or more features/elements of disclosed embodiments may be removed and still result in patentable subject matter (and thus, resulting in yet more embodiments of the subject disclosure). Correspondingly, some embodiments of the present disclosure may be patentably distinct from one and/or another reference by specifically lacking one or more elements/features. In other words, claims to certain embodiments may contain negative limitation to specifically exclude one or more elements/features resulting in embodiments which are patentably distinct from the prior art which include such features/elements.

Claims

1. A method for extracting a target particle from a mix of particles, comprising:

suspending a plurality of non-magnetic beads in a ferrofluid, the non-magnetic beads being functionalized with at least one predetermined first molecule configured to bind with a target particle;

mixing or otherwise exposing the ferrofluid to a plurality of particles forming a mix, wherein target particles contained in the plurality of particles bind with the first molecules functionalized on the non-magnetic beads;

flowing the mix through at least one micro fluidic channel; and

applying a magnetic field to at least a portion of the at least one channel, wherein the magnetic field is configured to exert an indirect force on the non-magnetic beads to separate the non-magnetic beads from the ferrofluid.

2. The method of claim 1, further comprising flowing the separated non-magnetic beads over at least one receptor region provided along the at least one channel, wherein the target particles bind to the molecules of the receptor region.

3. The method of claim 1, further comprising extracting the non-magnetic beads from the mix.

4. The method of claim 1, wherein the first molecule comprises a ligand.

5. The method of claim 1, wherein the target particle comprises a biological particle.

6. The method of claim 5, wherein the biological particle comprises at least one of an organic molecule, a cell, a bacteria, a virus, DNA, RNA, a carbohydrate, a protein, a biomarker, a hormone, kinase, enzyme, cytokine, toxin, and any fragments thereof.

7. The method of claim 1, wherein a source of the magnetic field includes at least one of planar electrodes, electromagnets or a magnet array.

8. The method of claim 1, further comprising detecting the target particles via detection means after at least one of: separation of the non-magnetic beads from the ferrofluid and extraction of the non-magnetic beads from the mix.

9. The method of claim 8, wherein the detection means includes an optical scanner.

10. The method of claim 8, wherein the detection means comprises a flow cytometer.

11. The method of claim 1, wherein the ferrofluid includes a plurality of magnetic nanoparticles and the magnetic field is configured to drive the magnetic nanoparticles in a first direction opposite a direction in which the non-magnetic beads are driven.

12. The method of claim 1, wherein the separated non-magnetic beads flow into at least one outlet port in communication with the at least one microfluidic channel, such that the non-magnetic beads may be extracted or otherwise collected therefrom.

13. A system for extracting a target molecule from a mix of molecules, comprising:

a plurality of non-magnetic beads suspended in a ferrofiuid, the non-magnetic beads being functionalized with at least one predetermined first molecule configured to bind with a target particle;

a plurality of particles, wherein the plurality of particles are mixed with the ferrofluid containing the non-magnetic beads resulting in a ferrofluid mix;

a microfluidic device comprising at least one microfluidic channel, the device configured to dynamically and/or statically receive an amount of the mix;

magnetic field means configured to:

apply a magnetic field to at least a portion of the at least one channel to exert an indirect force on the non-magnetic beads in the ferrofluid mix,

separate the non-magnetic beads from the ferrofluid;

direct the non-magnetic beads to at least one receptor region.

14. The system of claim 13, further comprising at least one outlet in communication with the at least one microfluidic channel, the at least one outlet configured to receive and extract the separated non-magnetic beads from the ferrofluid.

15. The system of claim 13, wherein the first molecule comprises a ligand.

16. The system of claim 13, wherein the target particle comprise a biological particle.

17. The system of claim 16, wherein the biological particle comprises at least one of an organic molecule, a cell, a bacteria, a virus, DNA, RNA, a carbohydrate, a protein, a biomarker, a hormone, kinase, enzyme, cytokine, toxin, and any fragments thereof.

18. The system of claim 13, wherein the magnetic field means includes at least one of planar electrodes, electromagnets or a magnet array.

19. The system of claim 14, further comprising detection means configured to detect the target particles after at least one of: separation of the non-magnetic beads from the ferrofluid and extraction of the separated non-magnetic beads from the ferrofluid.

20. The system of claim 19, where the detection means includes an optical scanner.

21. The system of claim 19, wherein detection means comprises a flow cytometer.

22. The system of claim 13, wherein the ferrofluid includes a plurality of magnetic beads and the magnetic field is configured to drive the magnetic beads in a first direction opposite a direction in which the non-magnetic particles are driven.

23. The system of claim 13, wherein the separated non-magnetic beads flow into at least one outlet port in communication with the at least one microfluidic channel, such that the non-magnetic beads may be extracted or otherwise collected therefrom.