Measuring Liquid Volumes in Sub-nanoliter Wells

Transcription

1 Measuring Liquid Volumes in Sub-nanoliter Wells Ian T. Young *1, Kari T. Hjelt 2, Richard van den Doel 1, Michiel J. Vellekoop 2, Lucas J. van Vliet 1 1 Pattern Recognition Group, Faculty of Applied Sciences, Lorentzweg 1, 2 Lab. for Electronic Instrumentation, Faculty of Information Technology and Systems, Mekelweg 4 Delft University of Technology, NL-2628 CJ Delft, The Netherlands ABSTRACT We are developing a method for high-throughput screening using arrays of nanowells built into a silicon substrate. These wells can serve as bioreactors for studying a variety of biochemical reactions such as the enzymatic activity that occurs in yeast metabolism. For a variety of studies it is important to know the volume of liquid that has been deposited in a given well and/or to monitor the evaporation of the liquid. Using silicon as our substrate means that we can take advantage of the ability to build microelectronics into the wells in order to develop smart wells. The wells are manufactured on silicon wafers using conventional photolithography and etching techniques and typical wells measure µm 3 which is a volume of 800 pl. Aluminum electrodes are patterned on the floor of the wells. The floor as well as the electrodes are then covered by an electrical insulation layer. The complex impedance measured through the electrodes is then related to the volume of liquid in the wells. Using fluorescence microscopy as well as interference microscopy to calibrate our system, we can measure liquid volumes with an accuracy of about 5% and a resolution better than 1 pl. Real-time monitoring of fluid volumes in a collection of wells is possible by additional on-chip microelectronics which permits multiplexing the measurements over the bioreactor array. Keywords: microarrays, picoliter, evaporation, volume detection, quantitative microscopy, interference fringe analysis 1 INTRODUCTION For the past three years we have been developing a system for the analysis of nanowells built into a silicon substrate. These wells, whose volume can range from 60 pl ( µm 3 ) to 1500 pl ( µm 3 ) depending upon design, offer the opportunity to analyze a large number of samples on a relatively small chip. An array of wells can fit within a surface area of 2 2 cm 2. and each well uses a tiny fraction, 10 6, of the amount of material that is commonly used in a 96-well microtiter plate. This can lead to the advantages of smaller sample requirements, lower sample costs, and faster measurements. One of the side effects of working with such tiny amounts of fluid is the rapid evaporation of sample from the wells. The physical processes associated with the liquid evaporation of small volumes are not yet fully understood and have recently been the subject of much study 1-3. A water-based solution takes less than 30 seconds to evaporate from a 1 nl well. Mixing the sample with a high-viscous fluid such as glycol or glycerol can significantly retard the evaporation process stretching the time to 20 minutes or more 4. As it is important in a variety of applications to know the volume of liquid that has been deposited in a given well, to monitor the evaporation of a liquid, and/or to monitor the dynamics of a biochemical reaction, we have developed a method to build microelectronics into the wells in order to implement smart wells. In this paper we describe the microelectronics, the measurement technique, and the calibration process. 2 MICROELECTRONICS The basic concept for the liquid volume measurement is that the presence of a liquid alters the electrical impedance between planar electrodes. This impedance change can be correlated to the volume of the liquid layer above the electrodes. The utilization of planar electrodes enables us to use conventional silicon fabrication techniques. This opens up the possibility to integrate the volume measurement sensor with electronics on the same chip that contains the nanowells. Figure 1a shows a 5 5 mm 2 silicon array of 12 different wells, the sizes of which vary from µm 3 to µm 3, * Correspondence young@ph.tn.tudelft.nl WWW: Telephone: ; Fax:

2 corresponding to volumes from 60 pl to 1500 pl, respectively. The wells are formed on a silicon wafer covered by a 2 µm layer of SiO 2. The 300 nm thick aluminum electrodes are patterned on this SiO 2 layer and covered by a 500 nm thick Si x N y layer for electrical insulation. The wells are then formed in either 6 µm thick (deep) SiO 2 or in 20 µm thick photoresist (SU- 8). A schematic representation of this is shown in Figure 1b. SiO 2 or polymer SixNy Liquid Si SiO 2 Aluminum electrodes Figure 1: Pico-liter array with integrated electrodes Cross section of a well ANSYS simulations were used to study the penetration of an electric field into a non-conducting liquid and thus to determine an effective configuration for the electrodes. According to the simulation results, for a non-conductive liquid the maximum measurable fluid thickness is about 25% of the separation between the electrodes. With a 40 µm distance between electrodes, this means that the maximum fluid depth that can be measured is about 10 µm. The predicted capacitance for our 6 µm deep, 60 pl well varied between 2 ff (empty) and 10 ff (filled) for watery liquids. These data influenced our well design as indicated in Table 1. Well volume (pl) Well size (µm) Electrode size (µm) Electrode separation (µm) Table 1: Design parameters for wells based upon ANSYS simulations 3 MEASUREMENT TECHNIQUE The complex impedance of the system, Z x, was determined by using a floating impedance measurement technique which minimizes the influence of parasitic components. The measurement set-up is shown in Figure 2. A 20 khz voltage source was used for steering and a current-to-voltage converter was used to determine the current. The impedance magnitude Z x in our measurement was on the order of 100 MΩ with a current of about 100 na. The impedance is determined by the capacitive and resistive components which are, in turn, dependent on the well geometry, the material conductivity, and the dielectric constant of the fluid. The measurement system was tuned to give an output voltage V o of 20 mv/mω with a resolution of about 1 mv. R C p Z x + + C p V o Figure 2: Impedance measurement configuration Figure 3 shows the measurement results for a 60 pl well and a 540 pl well. In both measurements the wells were filled with a glycol/water (90% / 10%, v/v) mixture. The filling procedure and the initial calibration procedure have been described in

3 our previous publications 4,5. The experiments show that the volume of both wells can be measured with a high resolution which is currently about 1 pl. Voltage (V) Volume (pl) Voltage (V) Volume (pl) Figure 3: Measured output voltage as a function of the liquid volume in 60 pl well and 540 pl well The sub-nanoliter volume measurement device can be used to monitor (unwanted) evaporation in wells. Two consecutive measurements shown in Figure 4 demonstrate the reproducibility of the electrical measurements. The measurements were conducted as a function of time as the glycol/water mixture (90% / 10% water v/v in this case) evaporated from the well. Voltage (V) 2 meas meas Time (s) Figure 4: Measured output voltage as a function of time in a 424 pl well. To illustrate reproducibility, two consecutive measurements are shown. As the evaporation takes place, the liquid is pinned to the corners of the well. The middle part of the well will dry first producing a rupturing of the liquid film. This is illustrated in Figure 5 where we have added a fluorescent dye (rhodamine) to the glycol/water mixture to enable us to record a fluorescence image using a KAF 1400 Photometrics Series 200 CCD camera system and a Zeiss Axioskop epi-illumination fluorescent microscope system. The rupture of the film causes an easily identifiable moment in the volume measurement: the voltage drops suddenly because of the rapid increase of the impedance and a concomitant fall in the measured voltage. This phenomenon can be used in automated systems as a measure for excess evaporation. 4 CALIBRATION To provide an accurate measurement system for liquid volume in a nanowell an independent procedure for calibration is most appropriate. We have observed that interference fringes appear in images of the images and that these fringe patterns change in time as the fluid in the well evaporates. The explanation for this phenomenon is straightforward.

4 Fluorescent image Display of fluorescence as a 3D surface time 0 min. 8.5 min min. Figure 5: Evaporation in a µm well as a function of time With the bottom of the well acting as a reflecting mirror, the fringe patterns are caused by interference between the direct path and the reflected path of an incident plane wave (reflected from the bottom of the well.) The optical path difference (OPD) between the direct and the reflected wave is proportional to the distance to the reflecting bottom surface of the well. Evaporation decreases the OPD at the meniscus level and causes alternating constructive and destructive interference of the incident light resulting in an interferogram. Imaging of the space-varying OPD yields a fringe pattern in which the isophotes correspond to isoheight curves of the meniscus. When the bottom is flat, the interference pattern allows monitoring of the liquid meniscus as a function of time during evaporation. This illustrated in Figure 6. Confocal x-z image of well Display of fringes time 53 s 97 s 164 s Figure 6: Evaporation of fluid from a well produces fringe patterns on the surface of the liquid as observed with an epiillumination microscope. (top) Confocal image in x-z display that shows decrease of meniscus height. (middle) Fringe pattern observed in x-y display of conventional microscope. (bottom) Time of observation in seconds with the flat meniscus point being considered as t = 0. There is a phase difference that corresponds to each value of the OPD which implies that the height of the meniscus can be retrieved if the absolute phase difference can be measured. This leads directly to the concept of using a temporal phase as opposed to a spatial phase unwrapping algorithm to retrieve the OPD and thus the meniscus height. The details of our algorithm can be found in Doel et al. 6 The acquired interferograms can be described by the sum of a space and time varying background, the cosine of the wrapped phase map modulated in amplitude, and an additive noise term. The unwrapped phase map is related to the height of the meniscus level as previously explained. The goal of the unwrapping algorithm is first to estimate the wrapped phase map from the interferogram and second to unwrap the wrapped phase map. This results in the height profile of the meniscus as a function of space and time. The two steps together are known as an unwrapping algorithm.

5 We unwrap the interferograms in time point-by-point. This means that there is no spatial correlation between the measured heights of the meniscus at any given time. The first step to compute the temporal phase map is to subtract the time-varying background from the interferogram. This is done by low-pass filtering the interferogram with a Gaussian kernel with a very large standard deviation. The phase of a data point at a certain moment in time is estimated by applying an FFT to a properly windowed part of the data around this point. The phase follows then as the phase of the bin with the maximum amplitude in the frequency domain. For typical signal-to-noise ratios of 10 (Amplitude of cosine / standard deviation of noise), the phase estimation is very precise; the standard deviation for this SNR is rad. The phase estimation has good performance down to a SNR equal to one. The final step of the algorithm is to unwrap the measured relative phases. This computation is based on an unwrapping operator in the literature 7. A typical result of this algorithm is shown in Figure 7. With this data the volume of fluid under the meniscus can be determined by simple numerical integration. sidewall of vial sidewall of vial Figure 7: Meniscus profile for one quarter of a µm 2 well as measured by the temporal phase unwrapping algorithm. 0 centerpart of vial When this procedure is applied to a well containing two electrodes, their height profiles at the bottom of the well are clearly visible. This is observed at the time point (t = 0) where the meniscus is flat, that is, in between 53 s and 97 s as shown in Figure 6. The result is shown in Figure 8. Figure 8: Image taken at t = 0 when the meniscus was flat and there are no fringes. The electrodes are clearly visible on the left and right sides of the image. Measured height difference between the bottom of the well and the electrodes on both sides of the well. The phase unwrapping yields electrode heights of 273 nm relative to the floor of the well. The seeming noisiness in Figure 8b can be reduced by median filtering which leaves the edges relatively intact and yields the results for the standard deviation of the measurements given in Table 2. The axial resolution of our interferometric system is about 20 nm which corresponds to about 70 molecules of water! 5 SUMMARY AND CONCLUSIONS The optical, interferometric methods which we have just described are not suitable for production systems, systems providing on-line information about liquid volume and evaporation dynamics. But the optical approach can be used to provide excellent calibration of the impedance approach to measuring the liquid volume.

6 Region Raw data Filtered data σ of height (nm) σ of height (nm) well bottom left electrode right electrode Table 2: Precision of height measurement based on raw data and after filtering with a 3 3 median filter. This electrical measurement procedure is suitable for high speed measurement. Further, the fabrication of the integrated volume detection system presented in the previous section is fully compatible with standard CMOS technology. For fast readout, we can apply multiplexing. Figure 9a shows a schematic presentation of an array of individually addressable wells. We have fabricated an array of wells with integrated electronics and a photograph of this chip is shown in Figure 9b. The device is currently under test. Co lumn _s elec t Row_select A A Signal detection circ uit A Figure 9: Schematic presentation of an array of Column_select individually addressable wells Photograph of the silicon chip containing sub-nanoliter wells provided with a CMOS liquid volume sensor. The chip measures 5x5 mm 2. ACKNOWLEDGMENTS This work was partially supported by the Rolling Grants program of the Foundation for Fundamental Research in Matter (FOM) and the Delft Inter-Faculty Research Center Intelligent Molecular Diagnostic Systems (DIOC-IMDS). We gratefully acknowledge the cooperation of Unilever Research Laboratories in Vlaardingen, The Netherlands for allowing us to make the confocal measurements with their facilities. REFERENCES 1 R. Deegan, O. Bakajin, T. Dupont et al., Capillary flow as the cause of ring stains from dried liquid drops, Nature, 389, pp , G. Mayer and J.M. Köhler, Micromechanical compartments for biotechnological applications: fabrication and investigation of liquid evaporation, Sensors and Actuators A, 60, pp , K. Hisatake, S. Tanaka, and Y. Aizawa, Evaporation rate of water in a vessel, Journal of Applied Physics, 73:11, pp , L.R. van den Doel, M.E. Vellekoop, P.M. Sarro et al., Fluorescence Detection in (sub-)nanoliter microarrays, presented at the Micro- and Nanofabricated Structures and Devices for Biomedical and Environmental Applications II, San Jose, California, M. Ferrari ed., Vol. 3606, pp , Publisher SPIE - The International Society for Optical Engineering, K.T. Hjelt, P. Szczaurski, L.R. van den Doel et al., Measurement of liquid volumes in sub-nanoliter microreactors, presented at the Transducers '99, Sendai, Japan, pp , L.R. van den Doel, L.J. van Vliet, K.T. Hjelt et al., Nanometer-scale height measurements in micro-machined picoliter vials based on interference fringe analysis, presented at the 15th ICPR, Barcelona Spain, A. Sanfeliu, J.J. Villanueva, M. Vanrell et al. ed., Vol. 3, pp , Publisher IEEE Computer Society, J. Strand, T. Taxt, and A.K. Jain, Two-dimensional phase unwrapping using a block least-squares method, IEEE Transactions on Image Processing, 8, pp , 1999.