Title of Invention

METHOD AND APPARATUS FOR THE DETECTION OF LABELING ELEMENTS IN A SAMPLE

Abstract The invention relates to a method and an apparatus for the detection of occupied binding sites (15) in a sample (10), preferably for the detection of a fluorescent labeling element bound to probes on a solid surface. The method comprises the scanning of said sample (10) with a spot (26) of laser light (22) and the detection of target specific responses, e.g. fluorescent light (32), with a detection unit (30). The size of the scanning spot (26) is chosen small enough such that only one occupied binding site (15) is irradiated at the same time. A location (11) is classified as an occupied binding site (15) if a target specific response is observed in repeated scans of said location. Such repeated scans particularly allow to discriminate between specific and nonspecific binding.
Full Text

Method and apparatus for the detection of labeling elements in a sample
The invention relates to a method and an apparatus for the detection of occupied binding sites in a sample that contain at least one labeling element.
The US 6 327 G31 Bl discloses an optical apparatus derived from a Compact Disc (CD) reading and writing device that is adapted to examine biological, chemical or biochemical samples on a rotating disc. The device detects target specific responses of opaque, reflecting or fluorescent spots of a target substance distributed on said disc that are generated when said spots are irradiated with a beam of laser light. The disc may farther carry a code on its surface that allows to (re-)locate specific positions on the disc.
In general, the purpose of a biosensor is to detect the presence and;or concentration of a target substance in an analyte. This detection is based on a specific binding to a "binding site" or capture probe which is immobilized on a substrate. In order to make this binding detectable a label element (or short "label") is attached to the target. The signal of the label needs to be detected with the highest possible sensitivity. There are different approaches to build such an assembly of capture probe - target -label (e.g. one can first attach the label to the target and then let that couple bind to the capture probe or one can first bind the target to the capture probe and in a second step label the immobilized targets). This is relevant if one wants to measure while the binding reaction is still going on. or for the problem of background signal from the solution and the required washing steps to remove non-specifically bound targets and/or labels. Though the presence of labels is measured, one is only interested in the labels which are attached to a target which is immobilized by a capture probe on a substrate.
Based on this situation it was an object of the present invention to provide means for the detection and quantification of a target substance or a labeling element in a sample with a hish sensitivity and reliability.

This object is achieved by a method according to claim 1 and an apparatus according to claim 10. Preferred embodiments are disclosed in the dependent claims.
The method according to the present invention allows the detection of occupied binding sites in a sample, wherein the 'occupation" of a binding site by definition means that the binding site contains at least one labeling element (for example a certain fluorescent molecule). In the most simple case, a "binding site" may just be a certain location in the sample, the "binding" being the presence of a labeling element at said location. Other examples of (occupied) binding sites will be discussed in connection with preferred embodiments of the invention. The method comprises the following steps:
d) The scanning of said sample with a spot of (preferably
electromagnetic) radiation, wherein the effective extension of the spot and the effective scanning speed of the spot are such that nearly always maximally one occupied binding site is present within the currently examined spot area during the corresponding examination duration.
The spot of radiation may for example be the focus of a (laser) light beam produced by an optical pickup unit (OPU) which is scanned above the sample without mechanical contact to the sample. The "extension of the spot" has to be defined reasonably with respect to the shape of the spot for example as the maximal or the mean diameter of the spot (corresponding to the usual diameter in case of a simply circular spot). Similarly, the "scanning speed" has to be defined reasonably with respect to the particular method of scanning, for example as the average spatial velocity (in m/s) with which the spot moves through the sample. Finally, the "corresponding examination duration" of a spot area in the sample is defined as the (average) time for which points of this area are irradiated by the spot without interruption. If for example a spot of radiation moves stepwise through the sample, the "corresponding examination duration" is the time between two jumps. If the spot moves continuously, the "corresponding examination duration" can be defined as the mean irradiation

time of a spot area in the sample (i.e. the average over all its points).
The postulated condition for spot extension and scanning speed means that almost alw ays . in more than 90°/of preferably more than 99% of the time) none or at most one occupied binding site is irradiated by the spot at a time, wherein the consideration of scanning speed takes into account that the appearance of occupied binding sites may be a dynamic process. The proposed scanning may thus be called "digital" because there are effectively only two possible outcomes of a measurement ai a location in the sample, i.e. "empty" or "single occupied".
The postulated condition is fulfilled irrespectively of scanning speed in the special case in which the effective extension of the spot is (e.g. by a factor of about 10"1 to 10"5) smaller than the mean distance between occupied binding sites. This corresponds to the situation of a sparse distribution of isolated occupied binding sires, in which - apart from seldom exceptions - maximally one occupied binding site is irradiated by the spot at a time.
b) The memorization of each location, which was examined by the aforementioned spot of radiation, as a "candidate" for an occupied binding site if a target specific response was observed from said location. The concrete definition of a "target specific response" depends on the kind of binding sites and labeling elements that are examined. If the labeling element comprises for example metal particles, a target specific response to the radiation of the spot may be the reflection of the scanning light. In case of a fluorescent labeling element, the specific response may be the stimulated emission of fluorescent light, and in case of chemiluminescence, the target specific response may be spontaneously produced light observed in the spot area.
c) The at least one times repeated scarrning of locations of the aforementioned candidates. This means that each location of a candidate is measured at least two times such that a temporal development of a potential binding site can be observed. Between repeated scans certain treatments, like washing steps and/or temperature changes may be carried out for instance as stringency test to better discriminate between specific and non-specific binding.
d) The classification of a candidate as a "detected" (or "real")

occupied binding site if it shows a predetermined response behavior in the aforementioned repeated scans. A candidate may for example be classified as a detected occupied binding site if it shows the target specific response in all or e.g. in more than 90% of the repeated scans. As will be discussed in more detail in connection with preferred embodiments of the invention, such a classification allows a discrimination between specific and nonspecific binding in a (bio-)chemical sample.
The method described above provides a very sensitive and reliable determination of occupied binding sites within a sample because only one binding site is measured at a time and because the classification of a location as detected occupied binding site is based on repeated measurements. It should be noted that the method optionally comprises the detection of more than one kind of occupied binding site, for example of binding sites containing different labeling elements (e.g. two different fluorophores).
The sample in which the measurements are made may be (approximately) two-dimensional or three-dimensional.
It may preferably comprise a solid surface on which probes are distributed as "binding sites" that are capable to bind directly or indirectly the at least one labeling element. The solid surface may for example be realized by a polymer carrier to which (biological) capture molecules are attached with a surface density of typically between 1 and 106 per m\ preferably between 10 and 104 per m2. wherein said molecules specifically bind a labeling element that shall be detected. An indirect binding of labeling elements may particularly take place via a prior specific binding of a target substance. Said target substance may for example consist of biological molecules of interest in a solution. These biological molecules axe then immobilized on the solid surface by capturing them with the probes. To see if the capturing has occurred, a signal from the presence of the targets is needed. This is achieved by attaching a label element (e.g. a fluorescent molecule) to each occupied binding site. The sensitivity of the measurement then depends on the label element (in the case of fluorescence on the number of dye molecules in the label; the more dye molecules, the higher the signal). The biological binding of the target substance to the probes can be due to hybridization of a strand of cDNA, or by recognition of a protein to an antibody.

etc. The label element may be bound 10 the target by a similar biological interaction between specific molecules attached to the real label (e.g. on the surface of a PS sphere containing fluorescent dye molecules). The labeling of a target substance can be carried out in solution before binding to the probes (by mixing in the label elements and incubating) or in a separate step after binding of the target molecules to the probes (by applying a solution containing the labels to the solid surface where target molecules have already bound). The labels may also be included in the target substance, for instance if the target substance is the product of a PCR (multiplication of single DNA strands) in which nucleic acids are supplied with an attached dye molecule. In the latter case, the compound of labels and target substance can formally considered as a "labeling element" in the sense of the present invention.
According to a further development of the aforementioned embodiment, the solid surface of the sample is exposed to a solution that potentially contains the at least one target substance and-or labeling element before or while the samole is scanned with the spot of radiation. The term "target substance" shall comprise in a broad sense any material object one is interested in. for example atoms, ions, molecules, complexes or biological systems like cells or microbial organisms. The target substance and/or labeling element may leave the solution and bind to the probes on the solid surface, thereby being fixed to a certain location for the subsequent measurements. Additional , washing and labeling steps (in a sandwich type of assay) can be carried out to improve the specificity of the biological binding.
In the aforementioned method it is particularly possible to determine the concentration of the at least one target substance and/or of the labeling elements in said solution from the measured distribution of detected occupied binding sites on the solid surface of the sample. Thus it is not only possible to detect the mere presence of a target substance and/or labeling element, but also to quantify its amount and spatial distribution. This quantification is based on the effect that the binding of the solved target substance and/or labeling elements to the probes on the solid surface is either a kinetic process or a thermodynamic equilibrium according to which the density of occupied binding sites at a certain time is proportional to the concentration of the target substance and/or labeling elements in the solution. Therefore, the detected density or distribution of occupied binding sites allows inferring the concentration of the target

substance and/or labeling elements in the solution. As the proposed method is very sensitive and based on the detection of single occupied binding sites, it is possible to measure extremely low concentrations (typically fM) in this way. The lower detection limit isr among other, determined by the area of the surface covered with capture probes - the larger the surface, the higher the probability to find a single target - at the expense of scanning time. It is an important advantage of this approach, to be able to increase the surface area and thus detection limit without affecting the noise or background.
The labeling elements may in principle be any entity that is capable to bind to a binding site mechanically, electrically, chemically or otherwise. Preferably, the labeling elements comprise a single molecule (particularly a protein or single strand DNA). a collection of a plurality of (identical or different) molecules, preferably a collection of between 10 to 10 molecules, and/or a semi-conducting particle. If the labeling element is a collection of several molecules, a correspondingly stronger response to the irradiation and a better signal-to-noise ratio can be achieved.
The target specific response may in principle be any event or process at the location of the spot that can be detected with appropriate means. In a preferred embodiment, the target specific response comprises the emission of fluorescent light that is stimulated by the radiation of the spot and/or of light generated by chemiluminescence. In this case both the radiation of the scanning spot and the response of light from fluorescence or chemiluminescence can be processed by an optical system without mechanical contact to the sample. Another advantage of the described method is that it does not require the absolute measurement of light intensity from fluorescence or cherniluminescence but only the detection if said intensity is above or below a given threshold. wrhich discriminates the response of occupied binding sites from background. The fluorescence may for example originate from the probes that bind a labeling element, from the labeling element, or from fluorescent markers attached to the labeling element. Moreover, the fluorescence may be the "normal" behavior of a probe that is suppressed or reduced when a labeling element is bound. In this case, the target specific response is the observed reduction in fluorescence. When chemiluminescence is observed, the production of light is chemically induced, and the spot of radiation is only.needed to determine the coordinates of the currently examined location.

In the aforementioned embodiment, the sensitivity of the whole method depends on the capability to detect the fluorescent light and to discriminate it from background radiation. In order to produce a strong fluorescence signal without bleaching the fluorescent substance excessively: it is therefore preferred to adjust the parameters of the examination, particularly the intensity* of the radiation in the scanning spot such that about 10 % to 90 %, preferably about 30 % to 80 %. of the saturation level of the fluorescence is produced. Said saturation level is defined as the maximum achievable intensity of fluorescence which cannot be increased by a higher intensity of exciting radiation. As the spot of scanning light is typically very small in the proposed method (because single binding sites shall be detected), it is generally no problem to produce the required high intensity that stimulates the desired amount of fluorescence.
According to a farther development of the invention, the definition of a "target specific response" is adapted based on the measured responses from scanned locations. In case of the embodiment using fluorescent light, the definition of a target specific fluorescent response typically comprises the setting of a threshold of measured intensity' above which a response is classified as "target specific". The optimal value of this threshold depends on the level of background radiation that is present and that has to be discriminated from a proper response of an occupied binding site. It is therefore preferred that the intensity coming from "empty" locations without an occupied binding site is continuously measured and taken as an indication of the level of background radiation.
The proposed method allows to draw conclusions about a sample based on the detection (or absence) of as few as one single binding site. In order to improve the reliability and the statistics of a measurement however, it is preferred to design a measurement such that about 100 to 1000 occupied binding sites will be detected in a sample during the whole examination duration. A preferred parameter that can be adjusted to achieve these numbers is the size of the sample, e.g. the area of surface covered with capture probes. If for example the concentration of a labeling element in a solution and the density of probes on a solid surface are given, a certain number of occupied binding sites per unit area of the surface and unit time results after a contact
*
between the surface and the solution. In order to achieve the desired numbers of occupied binding sites in a measurement, the (scanned) area of the solid surface has

therefore to be chosen appropriately.
The invention further relates to an apparatus for the detection of
occupied binding sites in a sample, wherein said occupied binding sites contain at least
one labeling element comprising:
A scanning unit that is adapted to scan the sample with a spot of radiation, wherein the extension and the scanning speed of the spot can be adjusted such that approximately always at most one occupied binding site is present within the currently examined spot area during the corresponding examination duration. The scanning unit may particularly comprise a laser for generating a light beam and focusing it to a circular spot of about 0.1 to 10 urn diameter.
A detection unit that is adapted to detect a target specific response from locations in the sample examined by the aforementioned spot. The detection unit may particularly comprise an optical system for collecting (reflected, transmitted, luminescent, ...) light emerging from the sample and a detector to measure its intensity. The detection unit and the scanning unit are preferably integrated in an optical pickup unit (OPU) which is scanned over the sample. Moreover, the units typically include means for focusing and tracking the light beam that produces the spot of radiation (structures on the sample and appropriate signal processing and control, like in a optical pick-up unit, but preferably with not rotating sample).
An evaluation unit that is adapted to memorize locations from which a target specific response was observed as candidates for an occupied binding site and to classify such a candidate as detected occupied binding site if it shows a predetermined response behavior in repeated scans. The evaluation unit may particularly comprise a data processing unit with the usual components (microprocessor, memory, I/O interfaces etc.) and with appropriate software to execute the required processing steps.
The aforementioned apparatus is able to execute all the steps of a method
of the kind described above. Therefore, reference is made to the preceding description
for more information on the details, advantages and improvements of that apparatus.
Particular embodiments of the apparatus will also be described in more detail below

with reference to the Figures.
The apparatus may especially be derived from a Compact Disc player/writer. Moreover, it may comprise a specific carrier for the sample that allows to identify locations in the sample with sufficient spatial resolution and reproducibility. Such a carrier may for example resemble a conventional Compact Disc (CD, including derivates like DVD and the like), i.e. use similar features as found on a DVD and also a similar light path. In contrast to a CD/DVD, the carrier would preferably not be rotated and not be circular (particularly not with a diameter of about 12 cm), but rather have a credit card format with pregrooves (and wobble) for position information and auto focusing of the beam.
For the scanning of a sample with a spot it is possible to move the scanning unit or a part of it with respect to a stationary sample, to move the sample with respect to a stationary scanning unit, to move both sample and scanning unit (for example in transverse directions), to guide a light beam across a sample by moving/rotating polygon mirrors, or the like.
These and other aspects of the invention will be apparent from and elucidated with reference to the embodiment(s) described hereinafter.
In the following the invention is described by way of example with the help of the accompanying drawings in which:
Fig. 1 schematically shows a perspective view of an apparatus for detecting occupied binding sites in a sample;
Fig. 2 shows an enlarged perspective view* of the surface of a sample comprising pre-grooves for tracking a laser beam;
Fig. 3 shows a section across line Ul-in of Figure 2;
Fig. 4 shows the optics of a confocal measurement.
The embodiment of the invention that will be described now in more detail relates to the challenge of a quantitative and sensitive measurement of the concentration of a biological component (the "target substance") in a liquid mixture.

This is usually done by detecting the occurrence of a selective binding of the target to a capture probe, which is attached to a solid surface. The occurrence of the binding is detected by the presence of a label element (or simply "label"), which is attached to the target, or is present on a second (or third) probe that selectively binds to the bound target (or target-probe complex). The gold standards in this type of analysis are fluorescence- which is stimulated by irradiation of the label with light, and chemiluminescence. which is stimulated by a chemical or enzymatic reaction. One of the prime challenges is to have a very low detection limit. This detection limit of a certain test is determined by the affinity and selectivity of the biological interaction (cross-reactivity, non-specific adsorption, binding constant, etc.) as well as by the sensitivity of the sensor or detector (how many events are required to give a significant signal). Typically, the detector is measuring the fluorescent intensity, which is emitted from a surface, while being irradiated by the excitation beam (for instance by the evanescent field of a light guide to Which the biomolecular Drobes are attachedV This intensity can be measured by a diode or in case the biomolecules are attached in a patterned fashion (multiplexed) by a CCD camera. For a low concentration of the target molecules in the sample, the density of labels indicating occupied binding sites on the surface is low so that the measured intensity is affected by other sources, like fluorescence of the substrate and all other materials in the light path. The lower detection limit is determined by the accuracy of the background measurement and its subtraction. A significant background signal can be expected from the non-specific binding of labels to the surface or the presence of such labels in close vicinity7 of the surface. The latter makes it difficult to measure "real time", meaning while the binding reaction is occurring rather than after completion of the reaction step and stringency washing.
Normally, only the integral of the bound labels is detected (as intensity per unit area or integrated optical density, i.e. intensity per unit area multiplied by the area). In this way no differentiation is possible between local variations, specific vs. non-specific binding, and the calibration is difficult as it depends on many parameters, which together determine the background signal. This is overcome by "digital detection" of single events as described below. The invention also provides a very convenient and cost effective detection technology. Implementations are given with a

scanning laser beam resembling an optical pick-up unit as it is used for optical data storaee systems. Such an arrangement allows the measurement of the number and the coordinates of bound labels (occupied binding sites). In this way die background subtraction is not critical anymore and the lifetime of the binding events allows the distinction between specific and non-specific binding and in this way yields much more accurate and detailed information about the biochemical reaction goinh on at a conditioned surface. It also allows the measurement of the binding and dissociation constants simultaneously, which is very important for the characterization of biochemical assays.
Existing solutions make use of surface selective illumination of labels to increase selectivity. This is done by evanescent field illumination (e.g. WO 2004/023143 A2, Duveneck et al. Proc. SPIE, vol. 2928 (1996)). The achievable intensities of these methods are far below the saturation limits of the dye molecules. Other existing solutions make use of confocal scanning beams for illumination.. In this way the illuminated area is limited and consequently the background radiation and cross-talk is reduced. High spatial resolution and sensitive measurement lead to very long "scanning" times. As an alternative the use of arrays of lightpaths (including source, optical elements and detectors) has been proposed in the US 6 437 345 Bl. This, however, is a relatively expensive solution and requires a precise alignment of the cartridge with the reader.
■Another method to reduce background fluorescence from the substrate or other components is the use of electrical, chemical or enzymatic triggers to stimulate emission of light. These processes are called electroluminescence or chemi-luminescence and do not require stimulation with an irradiating light beam. Instead at least one substrate is added that can cause a reaction that leads to the generation of light.
The fundamentally different approach which is proposed here is based on the detection of single events or "occupied binding sites" and the coordinates of each event rather than detecting the (integral/average) luminescent intensity. The basis for detection of single binding events is a sufficiently strong signal, which can be distinguished unambiguously from the background intensity. By scanning a surface on which binding events are very rare (less than 1 ppm depending on the scanning speed

and the spot diameter) one can determine the signal level of the background very accurately because the vast majority of measurements is background. Most of the noise sources do not have a high spatial or timely variation. Only when the signal is above a certain threshold value it is identified as a (potential) binding event and the coordinates of that point are recorded as a candidate of an occupied binding site. In this way a map can be constructed of the potential occupied binding sites and the scanning can be repeated. By continuously comparing the maps, the lifetime of bound sites can be determined and the long-lived can be identified as the specific binding events or occupied binding sites. Short-lived sites can be discarded as noise or unspecific binding. This approach thus provides much more information and more certainty of the measured binding. This is achieved by the adjustment of the size of the scanning spot and the brightness of the illuminated label. Scanning speed and label size are related and can be optimized for each application.
One embodiment of an apparatus-using the principles discussed above is based on a DVD optical pickup unit and is schematically shown in Figure 1. It is adapted to detect fluorescence coming from occupied binding sites 15 in a "two-dimensional" sample 10 (of which only a small fraction is shown).
The apparatus comprises a scanning unit 20 with a laser source 21, a first lens 23 (wherein the term "lens" here and in the following also comprises optical systems with several individual lenses) that collimates a laser beam 22 emerging from the laser source 21 to a parallel light bundle, a dichroic beam splitter 24 that reflects the laser beam 22 in a right angle towards the surface of the sample 10, and a second lens 25 (objective) that focuses the laser beam 22 to a spot 26 in the sample 10.
For the detection of fluorescent light coming from the sample 10. the apparatus comprises* a detection unit 30 with the following components: the already mentioned lens 25 that collects fluorescent light emerging from the sample 10 and collimates it to a parallel beam which is sent through the beam splitter 24; a third lens 33 that focuses the beam 32 on a detector 31 which is adapted to measure the intensity of incident (fluorescent) light and to produce a corresponding electrical signal.
Finally, the apparatus comprises an evaluation unit 40 that may for example be realized by a conventional computer. The evaluation unit 40 executes all the required processing of the measured data which is described in more detail below.

Moreover, the evaluation unit 40 may be adapted to control the apparatus, i.e. to command measurements in certain locations and;or with certain parameters.
A numerical aperture (NA) of the objective 25 of 0.2 at 650 nm excitation may for example be used to obtain a spot 26 with a surface area of-10 μm2 (corresponding to a diameter d of die spot of about 3.6 am). If every partition of the sample with an area of 0.1x0.1 mm" is statistically labeled with one label, it may be divided in 1000 virtual sub-partitions 11, 12, ... of 3.3x3.3 urn" that can separately be scanned by the aforementioned laser spot 26. For a concentration of 1 pM of target molecules (e.g. proteins) the calculated effective binding rate or "hit rate" is 10 : events per μm2 and per second. During a period of 1000 s on average 1 specific binding event will then be measured if one sub-partition per second is scanned.
The sensitivity of the method and the apparatus described above does not depend on the number of events (i.e. detected occupied binding sites) but on the certainty with w:hich a single event can be identi5ed as such. There is no lower limit for the concentration which can be detected except for the reasonable timescale of the duration of the measurement. For a certain optical arrangement it will even be possible to measure during the binding reaction while the unbound labels are still present in the solution above the sensing surface. These aspects will now be explained in more detail.
The basis of the proposed approach is the single event detection in a scanning optical arrangement. Single event detection requires a certain minimum power and energy of the emitted radiation to be detected by a sensor. As a first aspect in this respect, the fluorescent saturation intensity and power shall be considered. The average fluorescence lifetime Tf\UOT of fluorophores is of the order of 2 ns (cf. S.W. Hell and J. Wichmann. Opt Lett. 19, 780 (1994)). Typical values of the cross sections for the absorption abs of these specimens range between 10-16 and 10-17 cm". The saturated fluorescent excitation intensity7 is

with h the Planck's constant, c the speed of light, and X the wavelength of the absorbed light. A saturated fluorescent excitation intensity Is of 1.5 MW/cm or 15 kW/mm2is found for λ is 650 nm, σabs is 10"16 cm2, and Tfiuor is 2 ns (MA. Kramer, W.R. Tompkin, R.W. Boyd: Phys. Rev. A 34,-2026 (1986)). Labeled biological

specimens should be excited ciose to. but below the saturation level to obtain optimal fluorescence emission and thus an optimal signal-to-noise ratio (SNR). A save excitation level would be at 60 % to 70% of the saturation level. An optimal excitation power for biological specimens of 2 mW, 100 mW5 and 10 kW is found on a 0.2 μm2, 10 μm2 and 1 mm" surface area, respectively, wherein a surface area of 0.2 urn2 corresponds with an optical spot size of a DVD optical pickup unit (0.6 NA. 650 run). In a fluorescent multilayer storage technology assessment (cf. WO 01/06501 A2) an excitation power of 2 mW has been used to optimize the fluorescent emission from dye molecules using a DVD optical pickup unit (0.6 NA, 650 run).
The maximum SNR is obtained and increasing the laser power does not improve the SNR anymore. It should be noted that the maximum number of excitation cycles for an organic fluorophore is on average 105 before it will be bleached. The average total lifetime of an organic fluorophore is

he
T = TN =
N
(2)
with Arthe maximum number of excitation cycles, TEXCthe lifetime of one excitation cycle at an excitation intensity /. The lifetime of one excitation cycle is inversely proportional to the excitation intensity and equals the fluorescent lifetime at saturated intensities . The average total lifetime of an organic
fluorophore at saturation levels is 0.2 ms for an average fluorescence lifetime Tfmor of fluorophores of the order of 2 ns.
Typical dyes are those from the xanthene and cyanine families, having excitation and emission properties spanning the visible spectrum. These dyes are traded under several names, such as Bodipy. Alexa and Cy-dyes (the applied trade name depends on the exact chemical composition of the dye). Dyes especially suited for laser excitation are known as well. For example, Oregon green 488 and 514 can be excited at 488 and 514 run, respectively, and are exceptionally photo-stable.
Quantum efficiencies of many commercial dyes are between 0.1 and 1. However, many unsubstituted fluoresceines and rhodamines (e.g. Texas Red) bleach relatively fast (for Texas Red 1% in 10 s at saturation intensity). Substituted dyes, such as tetramethyl rhodamine (TMR) have a higher photo stability, but the fluorescent quantum yield of TMR is lower as compared to the fluorescein conjugates.

Sometimes phosphorescent emission may be preferred (for example to reduce background fluorescent emission). Typical dyes with a relatively late emission are eosins and erythrosines. The quantum yield of these phosphorophores are lower, typically 10 % - 20 % of those of the fluoresceines.
Other suitable dyes contain metal complexes, such as those from En, Pt. Cu, Zn, Tb, Dy. Sm. Yb, Nd5 Er, Ho. Gd and Ce. Also lanthanide complexes such as based on Ru, Os, Ir, Pd, Re have suitable emission properties.
An increase of fluorescent emission can also be achieved when using fluorescent beads of a certain size. These beads usually consist of a polymer in which fluorophores are dispersed or chemically linked. Typical polymers applied are polystyrene and dextran. These beads show high photo stability. It is also possible to select different dyes such that excitation can be performed at the same wavelength, but emission occurs at a chosen wavelength. By careful selection of the dyes one can use fluorescence resonance energy transfer (FRET) between the dyes to obtain the desired wavelengths. Bead sizes range from 20 nm to several microns. Typically polystyrene beads of 20 nm contain about 180 low molecular weight fluorophores; 200 nm beads about 1.1x10" fluorophores and 1 micron beads about 1.3x10' fluorophores. High signal amplification can in principle be obtained.
Small semi-conducting particles ("Quantum dots and rods") are also suitable labels because they can withstand high laser powers before bleaching occurs. Quantum dot sizes are typically between 1-5 nm (diameter). The emitted wavelength is a function of the particle size (blue to red with increasing diameter), while the absorption spectrum does not change much. Typical materials for Quantum dots are: CdSe, CdTe, etc. Core shell type Quantum dots have also been described, e.g. particles with a CdSe core and ZnS shell. Quantum dots may also be excited electrically or chemically. Quantum rods may be of especial interest as they can emit linear polarized light when their spatial and/or rotational motion is disrupted (e.g. upon binding).
Concerning the size of the laser spot 26, the targeted concentration range of the application is important. For a concentration of 1 pM of target molecules (e.g. proteins) one can expect that the effective binding rate/hit rate will be less than 10 events (occupied binding sites) per urn and per second. For a reasonable assay accuracy one would like to have 100-1000 events (for reliable statistics and dynamic

range). With a sensor area of 100x100 microns, a measuring rate of one event per second seams to be reasonable. This means that after 100-1000 s the assay would be finished. 100-1000 bound labels need to be detected then on an area of 104 μrn2, which corresponds with a density of 0.01-0.1 per μrn". This means that with a beam area of 1 ΜM2 the limit of statistically single events in the beam is reached. The power of this approach is that it can be easily extended to lower concentrations or shorter times. Due to the single event sensitivity it is possible to measure already 1 fM on the same surface area in the same time (this corresponds to 1 binding event on 104 ΜM2 in 1000s).
For an increased detection limit larger areas can be covered with receptors. In this way the time for 1000 events is reduced proportionally. The scanning time will increase. This can be compensated by an increase in the spot size and power of the spot. Therefore the speed of detection will not be affected and neither will be the sensitivity of the read-out.
Conventional fluorescent-based biosensors illuminate the whole sample surface, e.g. 1 mm", using propagating wave excitation or evanescent wave excitation. The maximal SNR for propagation wave and evanescent wave excitation is obtained using an excitation power of-10 kW and ~2 W. respectively. These required powers are not feasible in a commercial biosensor, thus much lower excitation powers are used resulting in a lower potential sensitivity of the biosensor.
Concerning the scanning aspect, numerous optical scanning solutions exist in the optical recording technology. As an example a continuous groove can be present in the substrate surface which is in contact with the mixture to analyze. The groove contains information about the position (a so-called "wobble"). The scanning is achieved either by moving the stage on which the cartridge is mounted in which the (bio-)chemical reaction of a liquid or gaseous mixture and the receptor surface takes place, or alternatively by moving the optical pick-up unit (containing light source, optical elements and detector, as described above). The latter can be achieved by a 2D translation stage or alternatively by an actuated mirror and a stationary light source and detector. The movement can be a linear scanning, like reading a page, or a continuous trace, like in a Compact Disc. Movement of the light beam is preferred over movement of the cartridge as in the latter case acceleration and deceleration wall affect the fluid movement inside the sensor.

In the embodiment of the proposed scanning fluorescent biosensor based on a DVD optical pickup unit shown in Figure 1, pre-grooves in the sample can be used to guide the spot 26 using the conventional servo-techniques as used in a DVD player for focusing and tracking. Figures 2 and 3 show such pre-grooves 16 for tracking in an enlarged perspective view and a section, respectively. The sample 10 consists of a lower layer 13. which contains the occupied binding sites 15, and an upper layer 14. which comprises the pre-grooves 16. The pre-grooves 16 should be transparent for the excitation and fluorescent light. The depth of the grooves should be tuned to optimize the focus and tracking signals.
For pM concentration during a period of 1000 s on average 1 specific binding event will typically occur within a spot 26 with a size of 10 μm2-. The scanned spot allows the local detection of one specific binding (occupied binding site). Furthermore, the long lifetime of the specific binding of several days allows fast scanning of the optical spot, along the 10" sub-partitions II, 12. enabling not only localized measurements, but also time-resolved measurements. For example, the whole sample 10 of Fig. 1 could be scanned 100 times during a total measuring period of 1000 s. This corresponds with a scan speed of 0.3 m/s (the speed of a lxDVD is 4.8 m/s). The time-resolution can be used to discriminate between specific binding events, with a lifetime of several days, and non-specific binding events, with much shorter lifetimes in the order of minutes. A higher SNR and sensitivity is obtained due to the localized and time-resolved measurements. The background contribution from sub-partitions 12, ... where no binding event occurred can be subtracted from the measurement. This background reduction due to the localized measurement improves the SNR. The background contribution from non-specific or random events can also be distinguished from the measurement. This background reduction due to the time-resolved measurement further improves the sensitivity of the analysis and provides additional information on the binding kinetics. The maximal SNR is obtained using an excitation power of ~ 100 mW, which is a feasible power requirement for a commercial biosensor (650 nm DVD recording laser diodes have power between 20-200 mW). The power requirement for the proposed scanning fluorescent biosensor is therefore much smaller compared to the prior art biosensors based on propagation wave and evanescent wave excitation.

During the binding reaction also the fluorescence of the unbound labels in the solution will be measured and the measurement is obtained after binding reaction. However, for a confocal optical arrangement it will even be possible to measure during the binding reaction wrhile the unbound labels are still present in the solution below the sensing surface. Figure 4 shows the optics of a modification of the scanning fluorescent biosensor of Figure 1, said modification being based on a confocal DVD optical pickup unit. A pinhole 34 in front of the detector 31 is used to block the light from the out-of-focus area 17. Only the light from the in-focus plane 18 passes through the pinhole resulting in a smaller focal depth or optical depth resolution. Even with a small penetration of the detected volume labels in the liquid will move fast (due to Browmian motion, diffusion or convection). In a repeated scanning their co-ordinates will be different. By correlating different scans they can be eliminated as unbound.
Further modifications of the embodiment of a scanning fluorescent biosensor described above are for example;
While above a NA of 0.2 was used for the excitation and collection of the fluorescent light it is also possible to use a much larger NA to collect the fluorescent light, e.g. 0.85 NA.,and a lower NA, e.g. 0.2 NA, for the excitation using the same lens. An improvement of the fluorescent collection
(0 9?
efficiency with a factor = 20 results in a further improvement of the
lo.2y
SNR and thus the sensitivity of the biosensor. More details on this approach may be found in the WO 2004 023459 A2 which is incorporated into this application by reference.
In the described embodiment the whole OPU is scanned above the fixed sample. A scanning fluorescent biosensor without translating components can be obtained by using a non-translated tilting mirror, e.g. galvano mirror, while the OPU and the sample are fixed.
Pulsed operation of the laser can be used to decrease bleaching effects and to measure at the same frequency, thereby filtering processes that occur at other frequencies.
Measurement in reflection can be done by illuminating through the sample and applying a reflector (e.g. Au) on the receptor surface. The Au

reflector can be used directly for the quenching of the fluorescence (molecular beacons). Otherwise any other inactive metal or dielectric surface can be used. To increase the dynamic range of a sensor, different spot sizes can be used on the same chip.
Smart fluorescent probes can be used with an on-off triggering of fluorescence upon binding (e.g. molecular beacons).
Probes can be used that show fluorescence alone or if a certain label is bound, and that stop or reduce fluorescence after binding of a target substance. In this case, the target specific response to be detected is a "hole" of fluorescence in a generally fluorescent sample.
The scanning fluorescent biosensor proposed here has the following advantages:
SNR improves compared to prior-art biosensors, due to the optimal fluorescent excitation of the biological specimens close to the saturation levels, due to the localized measurements of the specific binding events, and due to the time- (and place) resolved measurements of the specific and non-specific binding events.
The method allows detection of binding kinetics. The method allows for a/'simple" and cheap read-out system (DVD instead of expensive confocal scanners).
Important applications of the described apparatus and method may be in the areas of molecular diagnostics (clinical diagnostics, point-of-care diagnostics), biosensors, DNA and protein arrays (e.g. detection of proteins or gene sequences for molecular diagnostics or screening), cell analysis, drug screening, environmental sensors, food quality sensors, etc., especially where a very high sensitivity and throughput are required.
Finally it is pointed out that in the present application the term "comprising" does not exclude other elements or steps, that "a" or "an" does not exclude a plurality, and that a single processor or other unit may fulfill the functions of several means. Moreover, reference signs in the claims shall not be construed as limiting their scope.


CLAIMS:
1. A method for the detection of occupied binding sites (15), which contain
at least one labeling element, in a sample (10), the method comprising the steps of
a) scanning the sample (10) with a spot (26) of radiation, wherein the extension (d) and the scanning speed of the spot (26) are such that approximately always maximally one occupied binding site (15) is present within the currently examined spot area during the corresponding examination duration;
b) memorizing each location (13) examined by the spot (26) of radiation as a candidate for an occupied binding site (15) if a target specific response is observed from that location;
c) scanning the locations (11) of said candidates at least one more times;
d) classifying a candidate as detected occupied binding site (15) if it shows a predetermined response behavior in the repeated scanning.

2. The method according to claim 1, characterized in that the sample (10) comprises a solid surface with distributed probes on it that are able to bind labeling elements directly or indirectly, preferably via a prior binding of a target substance.
3. The method according to claim 2, characterized in that said surface of the sample (10) is exposed before or during the scanning procedure to a solution containing labeling elements and/or target substance.
4. The method according to claim 3, characterized in that the concentration of the labeling elements and/or target substance in said solution is determined from the distribution of detected occupied binding sites (15) on said surface of the sample (10).

5. The method according to claim 1. characterized in that at least one of the labeling elements is a single molecule, a collection of a plurality of molecules, preferably a plurality of between 10 and 10 molecules, and/or a semi-conducting particle.
6. The method according to claim L characterized in that the target specific response comprises the emission of light due to fluorescence or chemiluminescence.
7. The method according to claim 6, characterized in that the intensity of the radiation of the scanning spot (26) corresponds to about 10 % to 90 % of the saturation level of the fluorescence label, preferably to about 30 % to 80 %.
8. The method according to claim 1, characterized in that the definition of
the target specific response is adapted based on the measured responses of scanned
locations (11, 12).
9. The method according to claim L characterized in that the size of the
scanned sample (10) and the whole examination duration are chosen such that about
100 to 1000 occupied binding sites (15) are detected.
10. An apparatus for the detection of occupied binding sites (15), which
contain at least one labeling element, in a sample (10), the apparatus comprising
- a scanning unit (20) that is adapted to scan the sample (10) with a spot (26) of
radiation, wherein the extension (d) and the scanning speed of the spot (26) are such
that approximately always at most one occupied binding site (15) is present within the
currently examined spot area during the corresponding examination duration;
- a detection unit (30) that is adapted to detect a target specific response from
locations (11) examined by a spot (26) of radiation generated by the scanning unit;
- an evaluation unit (40) that is adapted to memorize locations (11) with a target
specific response as candidates for an occupied binding site (15) and to classify such a
candidate as detected occupied binding site (15) if it shows a predetermined response
behavior in two or more scans.


Documents:

1355-CHENP-2007 AMENDED CLAIMS 21-04-2011.pdf

1355-chenp-2007 form-3 21-04-2011.pdf

1355-CHENP-2007 OTHER PATENT DOCUMENT 21-04-2011.pdf

1355-CHENP-2007 POWER OF ATTORNEY 21-04-2011.pdf

1355-CHENP-2007 CORRESPONDENCE OTHERS 04-06-2010.pdf

1355-CHENP-2007 EXAMINATION REPORT REPLY RECEIVED 21-04-2011.pdf

1355-chenp-2007-abstract.pdf

1355-chenp-2007-claims.pdf

1355-chenp-2007-correspondnece-others.pdf

1355-chenp-2007-description(complete).pdf

1355-chenp-2007-drawings.pdf

1355-chenp-2007-form 1.pdf

1355-chenp-2007-form 26.pdf

1355-chenp-2007-form 3.pdf

1355-chenp-2007-form 5.pdf

1355-chenp-2007-pct.pdf


Patent Number 247609
Indian Patent Application Number 1355/CHENP/2007
PG Journal Number 17/2011
Publication Date 29-Apr-2011
Grant Date 27-Apr-2011
Date of Filing 02-Apr-2007
Name of Patentee KONINKLIJKE PHILIPS ELECTRONICS N. V.
Applicant Address Groenewoudseweg 1, NL-5621 BA Eindhoven
Inventors:
# Inventor's Name Inventor's Address
1 WIMBERGER-FRIEDL, Reinhold c/o Philips Intellectual Property & Standards GmbH, Weisshausstr. 2, 52066 Aachen
2 BALISTRERI, Marcello c/o Philips Intellectual Property & Standards GmbH, Weisshausstr. 2, 52066 Aachen
3 STAPERT, Hendrik c/o Philips Intellectual Property & Standards GmbH, Weisshausstr. 2, 52066 Aachen
PCT International Classification Number C12Q 1/68
PCT International Application Number PCT/IB2005/053168
PCT International Filing date 2005-09-26
PCT Conventions:
# PCT Application Number Date of Convention Priority Country
1 04104834.9 2004-10-01 EUROPEAN UNION