Patent Application
20090325822
The present invention relates to increasing the hits or hit probability between bondable reaction partners which increases the number of bondable reaction partners or products while significantly shortening the reaction time.
The present invention is particularly directed toward shortening the required hybridization times in bioanalysis arrays, such as in DNA/RNA, protein or immunomicroarrays, while at the same time increasing the available fluorescence signals. This is achieved by agitating the hybridization solution with magnetic micro- or nanoparticles, which are moved in controlled manner through the hybridization solution to transport the target molecules to individual spots, i.e. bonding sites. This significantly increases and/or widens the effective range of the individual spots, which is diffusion-limited in conventional analysis methods.
The invention has the additional advantage that it can be readily combined with already existing bioanalysis array systems so that already existing reaction systems, particularly already existing bioanalysis systems, can be retrofitted.
New tools in molecular biology, such as DNA microarrays, for example, represent a true technology jump for the detection of genes and gene defects, gene expression analyses and acquiring a better understanding of gene functions.
A microbioarray or biochip conventionally has a chemically coated glass slide that contains up to a few thousand, microscopically small and differently functionalized points, so-called spots. In the case of DNA microarrays or chips, each individual spot consists of numerous copies of a clearly defined DNA section or gene. They function as “scavenger molecules” or probes for corresponding specific DNA or mRNA molecules, i.e. targets, that are present in the sample being analyzed. The target molecules are marked beforehand with fluorescence particles so that they can be detected with a fluorescence scanner after bonding of the corresponding chip probes.
Specificity and sensitivity play an important role in bio- and microarray analyses. Specificity essentially depends on the choice and sequence of DNA probes on the chip and the conditions under which the docking process or hybridization between targets and probes proceeds, such as, for example, the salt concentration of the hybridization buffer and the reaction temperature. Sensitivity essentially depends on the available amount of the corresponding target, the efficiency with which the target is fluorescence marked, and to a certain degree on the amount of DNA probe on the chip and the efficiency of the bond between the target and probe.
In conventional chip experiments, the transport of targets to the probes is controlled in an aqueous medium merely by diffusion. In practice an aqueous buffer solution with fluorescence-marked target molecules is applied to the chip with the DNA probes and a thin glass plate or cover glass is placed over it. A thin liquid film is thereby formed between the chip and cover glass, within which the target molecules move by free diffusion.
Up to now, different attempts have been made to increase the evaluable signals in DNA microarrays with different mixing or pumping devices, which can be divided into the following three categories:
Mechanical mixing by shaking or rotation of the chip on a device provided for this;
Pumping and recirculation of the hybridization solution on the chip by means of an external fluidic system; and
Mixing of the liquid on the chip itself.
Examples of the mentioned methods pursuant to the prior art are described below in order to better demonstrate the distinguishing features relative to the present invention.
Surface acoustic waves or acoustic surface waves are used by commercially available products which are available under the name “SlideBooster” from Advalytix AG, Eugen-Sänger-Strasse 53.0, D-85649 Brunnthal, www.advalytix.de, SlideBooster SB400, for mixing thin liquid films.
Active mixing of liquids was presented by R. H. Liu (R. H. Liu et al., Bubble-induced acoustic micromixing, Lab Chip, 2002, 2, 151-157). For implementing the mixing effect, acoustic microflows induced by small bubbles are used. They are preferably generated with a piezoelectric sound emitter. To increase the efficiency, microscopically small, mechanically produced pockets are incorporated in the mixing chamber, where gas bubbles form. This modification of the mixing chamber entails a considerable additional cost for producing biochips and its re-use is questionable due to contamination.
WO 94/28396 discloses a mixing device for biosensors in which the sample is homogenized with an agitator that generates mechanical waves from the outside in a chamber. The agitator produces movement in alternating directions normal to the surface of the sensor while the signals are measured.
Another patent, GB 876 070, generally describes the mixing of liquids with rotating grates.
WO 00/09991 A1 describes mixing a liquid being investigated near a border surface thereof. Here mixing occurs by moving magnetic spheres or by moving meshes. In the first case, the magnetic spheres are alternatingly pulled up and down in a liquid between two electromagnets.
Mixing of thin liquid layers that include a suspension of moving magnetic particles is described in EP 0 240 862 A1. The disclosed device also includes magnetic systems. This arrangement provides a gap for accommodating the liquid film with the permanent magnetic particles.
In another patent, WO 97/02357 A1, a mixing device for use with DNA chips is considered. Acoustic and magnetic mixing are mentioned and produced by alternating currents in electromagnets.
An electromagnetic chip or biochip is known from U.S. Pat. No. 6,806,050 B2. It employs a matrix of individually feedable microelectromagnetic units on the surface of which probe molecules are immobilized. Magnet units move molecules bonded to small magnetic particles essentially in the plane of the biochip to increase the number of bonds that is achieved.
The device of the present invention seeks to increase the effectiveness of the individual bonding sites such as, for example, DNA spots, by adding magnetic micro- or nanoparticles to the hybridization solution. The particles are moved by an externally generated magnetic field which, for example, guides the DNA targets to the probes of the individual spots in much more targeted manner. The DNA targets are moved by or with the magnetic particle or particles in a microflow and are transported in this manner.
It is an object of the present invention to provide a device that increases the contact rate or frequency between two reaction partners capable of bonding with each other. The contacts are preferably between an analyzer molecule, or a part of such a molecule, and an analyte molecule, or part of such a molecule, to increase bonding effectiveness and to reduce the bonding times required for detection in bioanalysis arrays according to the preamble of claim 1. The device has the features mentioned in the characterizing portion of this claim.
In particular, the combination of a matrix-like arrangement of micro- or millimagnetic coils with only one opposite central magnetic coil permits a targeted and accurate movement of the magnetic particles in the reaction liquid, especially a hybridization liquid film for the controlled guiding of target DNA to the immobilized probes on the DNA biochip.
The special arrangement of micro- or millicoils, and the “pattern” for feeding the magnetizing current to them, prevent an accumulation of magnetic particles and therefore represent a significant advantage relative to the known mixing devices mentioned above that move magnetic particles. The use of magnetic fields further facilitates a simple combination with a sample chamber in which moisture and temperature are controlled which makes a higher degree of system integration possible.
The matrix-like or array-like arrangement of the millimagnetic coils with or without magnetic cores that are located, for example, beneath the DNA chip, and the use of only one magnetic coil above the DNA chip enable a very targeted movement of the magnetic particles.
The individual magnetic coil above the chip causes the magnetic particles to move in an upward direction. When this coil is no longer magnetic because the current has been switched off, the magnetic particles begin to descend again. Descent along the same path as the rising path is prevented by magnetizing the micromagnetic coils of the micromagnetic matrix beneath the chip, for example, in a wave-like manner. The magnetic particles are therefore shifted sideways during their descent and ultimately an oblique flow is induced in the reaction liquid. This enhances the movement of the target molecules so that more probe molecules are supplied as well.
The present invention therefore moves the particles laterally towards the center of the appropriately switched micromagnetic matrix. By varying the duration and relative intensity of the pulses of adjacent micromagnetic coils and the magnetic coil arranged above the chip, any desired movement pattern can be programmed for a targeted lateral and vertical transport of the target molecules dissolved in the hybridization liquid film.
In contrast to the earlier discussed prior art arrangements, which deal with undirected or, at most, with a one-directional mixing of liquid films, the arrangement of the present invention permits a pre-programmed and very targeted movement of the micromagnetic particles. In contrast to the prior art, the device of the present invention prevents the agglomeration and/or collection of magnetic particles in particular.
The present invention further provides the advantage that it can be readily combined with existing bioanalysis arrays. In addition, by integrating the magnetic coil on a support, the temperature at the interface to the biochip can be precisely set with an integrated cooling/heating loop as is further discussed below.
The device of the present invention therefore differs from arrangements that exclusively employ process steps in an integrated microfluidic biochip, which cannot be used for retrofitting existing DNA microarrays.
To demonstrate the effectiveness of the device of the present invention, hybridization experiments were conducted on equivalent DNA biochips with the device of the present invention and, parallel thereto, in the conventional manner. Constant temperature conditions (65° C.), hybridization times (25 minutes) and evaluation methods were maintained in the experiments. When using the device of the present invention over all experiments, an average signal gain of about 150%
was obtained over all experiments relative to what is attainable with conventional hybridization.
An advantageous variant embodiment of the invention provides a control device for the micromagnetic coils, on the one hand, and for the individual magnetic coil, on the other hand, in accordance with claim 2, by means of which each micromagnetic coil can be controlled individually and by means of which each time-dependent magnetization pattern can be impressed on the magnetic matrix surface.
In another embodiment for an interference-free optical control, the individual magnetic coil of the device without a core, i.e. with an exposed center recess according to claim 3, provides a clear view of the reaction event, especially on the bioanalysis chip or array.
The characterizing features of claim 4 can be used to increase the effectiveness of the arrangement of the micromagnetic coils of the magnet coil matrix.
Moreover arranging the analysis device in a climatized chamber according to claim 5 is also preferred, especially when stable environmental conditions must be precisely maintained.
claim 6 concerns a specific arrangement of the components of the device of the present invention.
Finally, claim 7 is directed to a preferred embodiment of the device that has a receiving chamber for the reaction vessel, which is particularly useful for the bioanalysis array microchip.
a shows the signal increase during use of the new device in comparison; and
b is a diagram which shows the signal increase as a function of hybridization time and also in comparison with the prior art.
The perspective view of
A bioanalysis array 6 with regularly applied small spots of respective probe molecules or biochips 6 is arranged on a glass slide 4 beneath a cover glass 5. The reaction liquid, especially a hybridization liquid with the target molecules, and the micromagnetic particles provided for agitation of the liquid are situated between slide 4 and cover glass 5.
A large number of micromagnetic coils 2 that have coil cores 21 are individually supplied with a magnetization current. The coils 2 are preferably arranged in a hexagonal matrix 20 beneath and in the vicinity of biochip 6 beneath slide 4.
The schematic of
A control device 8 schematically shown in
A central control unit (PC control) 81 is connected to a control device, for example a D/A card 82, which is connected, on the one hand, to a power supply 83 (power supply 1) for micromagnetic coil matrix 20 and, on the other hand, to a power supply 84 (power supply 2) for the individual magnetic coil 3.
Power supply 83 (power supply 1) is connected to a relay matrix unit 85 that is itself directly connected to D/A card 82. The D/A card in turn individually supplies power, which is variable as a function of time, to each individual micromagnetic coil 2 of magnetic matrix 20 connected to it in accordance with a program provided by central control unit 81.
The probe includes a temperature control. For this, a temperature control unit (thermocontrol) 86 is directly connected to the central control unit 81 and supplies the control unit with actual temperature data from thermosensors (not shown here) arranged in the probe area or in the vicinity of the magnets 2, 20 and 3.
As is apparent from
b illustrates the arrangement and orientation of the cooling/heating medium channels 22, 22′. Their intakes and discharges are indicated by arrows. Openings generated during the production of the channels in the block 21 are closed with plugs or stoppers.
The top of aluminum block 21 is covered with a thin film 23. Rubber rings or loops 26, 27 are arranged around the periphery of the block, the inside of which forms a space 230 for placing the sample.
Cover unit II shown in
A center opening 34′ extends through aluminum block 31, exposes and permits viewing of the sample, and is sealed on the bottom with a glass plate 33.
Temperature control occurs by means of thermocouples 300 which send current temperature data to the previously mentioned thermocontrol unit.
d provides a top view of the arrangement and orientation of the cooling/heating medium channels 32 in aluminum block 31 of cover unit II.
a and 6b show signal increases achieved with the device of the present invention as a function of the concentration of magnetic particles after hybridization.
The ordinate of the diagram of
The signal values shown in square form were achieved with the above-described device; those depicted with crosses were achieved conventionally. It shows a higher average signal gain. The reference signals of the DNA probe of Ec. faecium 2 are shown in
The use of the new device for all experiments shows that the average signal gain was about 150% as compared to conventional hybridization. The signals for the DNA probe Ec. faecium 2 were arithmetically averaged for different bead concentrations.
b shows (with otherwise constant equivalent designations) a comparison of the intensities I of the fluorescence signals obtained with the device of the present invention to the intensities of the signals obtained in a conventional manner as a function of hybridization time.
The hybridization time is plotted on the abscissa in minutes, and the concentration of micromagnetic particles or beads M-PVA 13 bead 5-8 μm is kept constant at 1.8 μg/μL.
After only 5 minutes a very large signal gain is encountered when using the device of the present invention.
| Number | Date | Country | Kind |
|---|---|---|---|
| A 648/2006 | Apr 2006 | AT | national |
This application claims the priorities of Austrian Patent Application No. A648/2006 filed Apr. 13, 2006 and of International Application No. PCT/AT2007/000160 filed Apr. 11, 2007, the disclosures of which are incorporated herein by reference.
| Filing Document | Filing Date | Country | Kind | 371c Date |
|---|---|---|---|---|
| PCT/AT07/00160 | 4/11/2007 | WO | 00 | 8/21/2009 |
