Detecting target molecules in a sample

Abstract

The invention relates to detection the presence of a target molecule in a sample, wherein the sample is contacted with a substrate, the substrate subsequently being washed in a wash step. In particular, the invention relates to a method of detecting the presence of a target molecule in a sample, the method comprising: (a) contacting the sample (37) with a substrate having immobilized thereon probe molecules that specifically binds to the target molecule; (b) washing the substrate (38) in a wash step by a wash fluid in order to remove or dilute unbound target molecules; (c) detect the presence of resultant binding complexes (39) on the substrate to determine whether the target molecule is present in the sampleThe wash fluid being substantially refractive index matched to the substrate.

Claims

1. An apparatus for preparing an assay, the apparatus comprising: a handler arranged to receive a substrate, wherein the substrate has a first side and a second side, wherein the second side is opposite to the first side, wherein probe molecules are immobilized upon the substrate, wherein the probe molecules specifically bind to a target molecule, and wherein the handler is arranged to contact a sample with the substrate; and a washer arranged to press a wash fluid through the substrate by introducing a stream of the wash fluid under pressure at the first side of the substrate, the stream of the wash fluid passing through the substrate and out of the second side of the substrate, and wherein the wash fluid has a refractive index substantially matched to a refractive index of the substrate.

2. The apparatus of claim 1, wherein the refractive index of the wash fluid is within a range of the refractive index of the substrate, and wherein the range is a range of plus and minus 10% to the refractive index of the substrate.

3. The apparatus of claim 1, wherein the handler is arranged to flow the sample through the substrate by introducing a stream of the sample to the first side of the substrate, the stream of the sample passing through and out of the second side of the substrate forming binding complexes that are bound throughout the substrate while leaving unbound luminescently labeled target molecules.

4. An apparatus for preparing an assay, the apparatus comprising: a handler arranged to receive a substrate, the substrate having probe molecules immobilized thereon, the probe molecules specifically bind to a target molecule, wherein the substrate has a first side and a second side, wherein the second side is opposite to the first side, wherein the handler is arranged to contact a sample with the substrate, wherein the handler is arranged to flow the sample through the substrate by introducing a stream of the sample to the first side of the substrate, the stream of the sample passing through and out of the second side of the substrate forming binding complexes that are bound throughout the substrate while leaving unbound luminescently labeled target molecules; and a washer arranged to perform washing on the substrate using a wash fluid, the wash fluid having a refractive index substantially matched to a refractive index of the substrate.

5. The apparatus of claim 4, wherein the refractive index of the wash fluid is within a range of the refractive index of the substrate, and wherein the range is a range of plus and minus 10% to the refractive index of the substrate.

Description

BRIEF DESCRIPTION OF THE DRAWINGS

(1) Embodiments of the invention will be described, by way of example only, with reference to the drawings, in which

(2) FIGS. 1A and 1B schematically illustrate two general embodiments of the optical setup;

(3) FIG. 2 illustrates spectral characteristics for the setup of FIG. 1B together with the spectra of the Cy5 dye;

(4) FIGS. 3A, 3B and 3C illustrate an embodiment of a method of detecting the presence of a target molecule in a sample;

(5) FIG. 4 shows a graph of the index of refraction, n, of aqueous sucrose solutions, as a function of the weight percent, p.

DESCRIPTION OF EMBODIMENTS

(6) In biological research and medical diagnostics many biomarkers are detected with the aid of an attached fluorescent label. The apparatus generally used is a fluorescent scanner or microscope, but for specific applications dedicated equipment is made based on the same detection principles.

(7) In a general embodiment of the present invention, an optical setup is used where at least two spectral filters are applied. FIG. 1 schematically illustrates two general embodiments. FIG. 1A shows a schematic illustration of a fluorescence detection device in a transmission mode where the resultant beam is transmitted through the substrate, whereas FIG. 1B shows a schematic illustration of a fluorescence detection device in a reflection mode where the resultant beam is reflected from the substrate. In FIGS. 1A and 1B a light beam 1A, 1B is emitted towards a substrate 3. In order to separate the resultant fluorescent light beam form the illuminating non-fluorescent light spectral filters are applied.

(8) The spectral filter function consists of two steps: a first radiation filter 2 (called the excitation filter) being introduced in the beam path between the radiation (light) source and the substrate. The excitation filter preferably transmits the rays with a wavelength overlapping with the excitation spectrum of the label and blocks all rays with a wavelength that is inside the spectrum of the detection window. A second radiation filter 4 (called the emitter filter or alternatively a detection filter) is introduced in the beam path, the emitter filter preferably blocks or at least substantially suppresses the illumination light and transmits only the fluorescent rays. The attenuation (blocking power) of a typical filter set is better than 10.sup.6.

(9) In FIG. 1B a beamsplitter 5 is moreover applied, the beamsplitter may e.g. be applied in a situation where the substrate is not transparent. In an alternative embodiment a dichroic mirror may be applied instead of a beamsplitter, a dichroic mirror reflects excitation light below a certain wavelength and transmits light above this wavelength. A dichroic mirror may therefore also act as an emitter filter 4, a separate emitter filter may still be used for increased performed, but it may not be necessary.

(10) In an embodiment, the substrate may be illuminated by a number of high power LEDs, such as 2 to 10 red LEDs, a dark field setup may be applied. The resulting light being detected by a CCD camera (not shown) with the emitter filter mounted in front of the camera. As an example of a fluorophore, the dye Cy5 may be used.

(11) The substrate 3 may be prepared in any suitable way of preparing a substrate, such as a bio-array substrate for use in a bio-assay. One typical array assay method involves immobilizing probe molecules in discrete locations on the substrate. A solution containing target molecules that bind with the attached probes is placed in contact with the bound probes under conditions sufficient to promote binding of targets in the solution to the complementary probes on the substrate to form a binding complex that is bound to the surface of the substrate. The bio-array may have a dimension in the micrometer range or even in the millimeter range. The number of different spots with distinct hybridization characteristics on the bio-array may vary from around 1 to 1000 per mm.sup.2 on current arrays, and even higher, e.g. up to 10.sup.6 spots per mm.sup.2. Within a spot on the array typically identical probe molecules are immobilized.

(12) FIG. 2 illustrates an embodiment of possible involved spectral characteristics for the setup of FIG. 1B together with the spectra of the Cy5 dye. FIG. 2 is generated by use of the Curv-o-matic online application, accessible from the Omega Optical website (www.omegafilters.com). FIG. 2 shows the transmission, T, in percent as a function of the wavelength, , in nanometers of the involved spectra, for the Omega filter set XF110-2.

(13) FIG. 2 shows the excitation spectrum 20 of Cy5 having an excitation peak at 649 nm together with the corresponding emission spectrum 21 having an emission peak at 670 nm. The difference between illumination wavelength and fluorescent wavelength, per photon, is called the Stokes shift. The Stokes shift of Cy5 is 21 nm.

(14) The excitation filter is an Omega 630AF50 excitation filter exhibiting the spectrum denoted by 22 (bandwidth 50 nm, center at 630 nm). The emitter filter is an Omega 695AF55 emitter filter exhibiting the spectrum denoted by 23 (bandwidth 55 nm, center at 695 nm). The dichroic mirror is chosen so that the spectrum of the mirror, as denoted by 24, is such that it reflects incident light at the wavelength of the excitation radiation, whereas it transmits the resulting Stoke shifted light. The specific filter set and dichroic mirror are provided as an example, and may not necessarily be applied in a all embodiments. For example, as mentioned in connection with FIG. 1B, an emitter filter may be dispensed when using a dichroic mirror.

(15) Table 1 shows the results of an experiment, in which the optical properties were measured of porous Nylon substrates (Nytran N and Nytran SPC) 3. The experiment was performed by irradiating the substrate at the incident wavelength of 650 nm and subsequently detecting the resulting beam from the substrate. Two types of experiments were performed, one with a dry substrate, and one which have been exposed to water in a wash step.

(16) TABLE-US-00001 TABLE 1 Wet Dry Nytran N Transmittance 31.1% 4.2% Reflectance 68.7% 95.3% Absorbance 0.1% 0.5% Nytran SPC Transmittance 33.8% 5.3% Reflectance 65.4% 94.4% Absorbance 0.8% 0.4%

(17) As can be seen in Table 1, the substrate has a very high reflectivity, especially when dry. The cause for this high reflectivity is scattering due to the high porosity of the substrate. The amount of scattering depends on the difference between the index of refraction of air and substrate. Compared to air, the index of water is much closer to the index of the substrate. This is the reason why a wet substrate has a lower reflection than a dry substrate.

(18) In accordance with the present invention, a substantially index matching fluid is applied during the wash step of the assay, and thereby the reflectivity of the substrate can be greatly reduced, down to a typical value of 5% reflectivity.

(19) The improvement in excitation intensity may be at least factor of 3 as compared to water as the washing fluid, but can be as high as 20 compared to a dry substrate.

(20) The improvement in the ratio of excitation and fluorescence radiation may be at least 14 as compared to water and can be as high as 19 as compared to a dry substrate.

(21) FIG. 3 illustrates an embodiment of a method of detecting the presence of a target molecule in a sample in accordance with the present invention, where a bio-array is prepared using as a wash-step. FIG. 3A to 3C illustrates at least some of the involved steps.

(22) In steps prior to the step of FIG. 3A, a sample fluid has been prepared with target bio-molecules conjugated to fluorophores. In the step 37 of FIG. 3A the sample 6 is contacted with the substrate 30 by flowing the sample fluid through the substrate 30, causing the target bio-molecules with fluorophores to attach to specific binding locations on the substrate. It is to be understood that target molecules may be contacted to the substrate in alternative ways, e.g. by the application of drop deposition from pulsejets, or by other suitable means.

(23) During the preparation steps not all fluorophores can be expected to bind to a probe molecule. This means that in addition to fluorophores that have bound to the substrate 30, there are also unbound fluorophores that are not attached to the substrate, but are still present. A wash step 38 is applied to remove or at least dilute any unbound fluorophore-conjugates, leaving only bound fluorophore-conjugates behind on the substrate, as illustrated in FIG. 3B. During this step a washing liquid 7 is pressed through the substrate 31. In the current invention, the washing liquid 7 is chosen such, that it has the index of refraction of the wash fluid substantially match the index of refraction of the substrate 31.

(24) FIG. 3C illustrate a detection step 39 in order to detect the presence of resultant binding complexes on the substrate, the detection step has been described in connection with FIG. 1. Because a substantially index matching fluid was used during the washing step (FIG. 3B), the reflectivity of the substrate 32 has been reduced considerably, improving the sensitivity of the detection step. The detection is typically applied in direct continuation of the wash step so that the substrate is still wet.

(25) In different embodiments of the present invention different index matching fluids that can be used. In one embodiment an oils may be used, as an example of a suitable oil; Zeiss Immersol 518F, with n=1.518 at 23 C. may be used. In other embodiments, aqueous solutions of dense materials may be applied. In a specific embodiment an aqueous solution of sugar is used. It may be advantageous to use a solution of 60% to 70% sugar (sucrose, etc.), thereby achieving an index of refraction of 1.45 (see FIG. 4 illustrating the index of refraction, n, of aqueous sucrose solutions, as a function of the weight percent, p). Aqueous sucrose solutions may be a preferred index matching fluid, because fluorophore-conjugates dissolve easily in such a fluid, making the fluid suitable for both the washing step and the detection step.

(26) It is to be understood that in alternative embodiment, additional washing steps may be applied. Such additional washing steps may be applied with different of same wash fluids, in the situation were different wash fluids are used for different wash steps, at least the last wash step is conducted using a wash fluid being substantially refractive index matched to the substrate.

(27) The steps of FIG. 3 and possible additional steps may be performed, possibly in an automated or semi-automated manner, in an apparatus for preparing an assay and/or an optical detection system. Such apparatuses and systems may include a handling unit 33 for receiving a substrate, and a wash unit 34 for performing a wash step on the substrate. The handling unit and the wash unit may be embodied in the same unit, or the sample may be moved between units. Embodiments of optical detection systems also comprise a radiation source 36 such as one or more laser diodes and a radiation detector 35, such as a CCD.

(28) Kits for use in target detection assays are also provided. The kits at least include a wash fluid, the wash fluid being substantially index matched to a substrate and instructions for using the wash fluid. The kits may further include one or more additional components to be used when carrying out a target detection assay, such as one or more substrates, sample preparation reagents, buffers, labels, etc. The instructions for use may be provided in paper format, be recorded on a suitable recording medium, be provided in the form of directions as how to access the instructions via a remote source, e.g. the Internet, etc.

(29) Although the present invention has been described in connection with the specified embodiments, it is not intended to be limited to the specific form set forth herein. Rather, the scope of the present invention is limited only by the accompanying claims. In the claims, the term comprising does not exclude the presence of other elements or steps. Additionally, although individual features may be included in different claims, these may possibly be advantageously combined, and the inclusion in different claims does not imply that a combination of features is not feasible and/or advantageous. In addition, singular references do not exclude a plurality. Thus, references to a, an, first, second etc. do not preclude a plurality. Furthermore, reference signs in the claims shall not be construed as limiting the scope.