Patent Application
20070081159
There are many use environments, the fields of medical research and pharmaceutical development being examples, where it is necessary to accurately acquire fluid samples with volumes that may be as small as a few nanoliters. In these same fields, it is also often desirable to measure optical characteristics of the acquired fluid samples. Such optical characteristics include, for example, the ability of a sample to absorb light.
For instance, UV-Visible Spectrophotometry may be used to characterize the chemical composition of a liquid sample (in solution or suspension phase) using the absorbed spectra of the sample. The light absorbance of a sample depends on the pathlength L of light passing through the sample, as well as on the concentration of light absorbers (e.g., biomolecules, cells, etc) in a sample solution and the wavelength (λ) of light being used to characterize the sample. The wavelengths of UV-Visible light span from 200 nm to 800 nm, while ultraviolet wavelengths range from 200 to 400 nm.
UV-Visible spectrophotometry provides a convenient analysis technique to determine the concentration, purity, and integrity of a biological sample without requiring additional sample preparation other than acquiring a sample. UV-Visible Spectrophotometry measurements depend on the light source (UV lamp), the sample and sampling technique. Most biological samples absorb electromagnetic radiation at wavelengths ranging from 200 nm to 800 nm, mostly 230, 260 and 280 nm. For a DNA and RNA samples in aqueous phase, one unit of absorbance, A, measured at a =260 nm and a pathlength of 10 mm corresponds to approximately 50 and 40 ng/μl concentration, respectively.
Most biological samples are highly concentrated for downstream processing (such as microarray spotting or protein sample preparation for mass spectrometers). The absorbance of such samples can be above the saturation limit for typical spectrophotometers if the pathlength is about 10 mm. While the sample concentration range can be extended by diluting the sample, diluting sample requires additional laboratory work and can result in errors. Other approaches are needed to extend the sample concentration range that can be evaluated by the instrument.
Sampling techniques used in conventional UV-Visible Spectrophotometers include utilizing a cuvette with an optical window and fixed optical pathlength that holds a sample in a semi-closed way, direct measurement of liquid ample in a sample container (e.g., a well) along with a real-time pathlength measurement, and using a cuvetteless sample held in semi-free space between optical fibers which define a light path from a light source to a detector.
The cuvette-based sampling technique is widely used in conventional UV-Visible spectrophotometers. Generally, a sample is pipetted into a cuvette that has either a 10 mm or 2 mm path length. This technique is very limited for most biological samples since cuvettes typically used generally require a minimum 200-1000 μl sample, which is problematic for valuable biological samples which may be present in limiting quantities, such as samples of protein or nucleic acids. A cuvette made of quartz or silica is expensive so it is typically reused after cleaning and drying. Further, adding 10 μl of sample with a pipette into a cuvette sometimes produces an air-bubble interface in the light path that can cause measurement error or void measurements. Additionally, a pathlength of 2 mm or 10 mm limits the sample concentration that may be measured to 1000 or 200 ng/μl, respectively, for DNA or RNA sample due to the limited dynamic range of absorbance of most spectrophotometers.
Direct UV-Visible spectrophotometry measurement of liquid samples in an open well also suffers from limitations, such as the need to determine pathlength and adjust sample concentration. In this case, the pathlength depends on the sample well dimensions and sample volume. The determination of pathlength requires use of instruments such as level detectors or position sensors. For a pathlength ranging from 2 mm to 10 mm or above, the workable range of sample concentration for a spectrophotometer measurement becomes limited. For an example, for a DNA sample, if the pathlength is 10 mm, one unit of absorbance is equal to 50 ng/μl concentration (OD), and the upper limit of detection is typically 250 ng/μl if the upper limit absorbance of the spectrophotometer is 5. In this case, sample dilution is required for a sample concentration greater than 250 ng/μl. Sample dilution for multiple well plate measurements can be a complex laboratory operation.
Cuvetteless sampling also suffers from drawbacks. For example, in cuvetteless sampling, typically a narrow beam of light is directed to a sample stage that consists of a 1-2 μl liquid droplet suspended between two multi-mode optical fibers, one source-side fiber which provides light from a light source to the droplet and a detection-side fiber that guides light from the droplet to appropriate detection optics. The close proximity between the source-side and detection-side fibers allows enough of the light cone emanating from the source-side fiber to be collected by the detection-side fiber after passing through a liquid sample.
Cuvetteless instruments typically require a clamping surface that can be wetted with sample to avoid an air-bubble interface. Carry-over contamination is not completely removed with a simple wiping-off of the clamping surface. Adding a small amount of sample (1 μl) to the center of the clamping surface is also a complicated lab technique.
In summary, existing sampling techniques used in the conventional UV-Visible Spectrophotometers generally require too much sample, provide insufficient confidence in the sample application technique, may result in carry-over contamination, and may require pathlength determination and/or dilution of sample, over a range of solution concentrations.
In one aspect, the invention provides an apparatus for acquiring and holding a volume of a liquid sample whose optical properties may be detected, monitored and/or quantitated for the sample and/or apparatus in which the sample is placed.
In one embodiment, the apparatus includes a body having a first opening located at a first end, a second opening located at a second end. An inner space within the body connects the first opening and the second opening and provides a passage from the first opening to the second opening. In another aspect, the passage or a portion of the passage constitutes a measurement region of the device. In one aspect, the pathlength of a light passing through a measurement region of the apparatus is predetermined.
At least a portion of the body is made of material semi-transparent or transparent to electromagnetic radiation in some wavelength range that is detectable by a detection system being used.
In another aspect, the invention provides an adaptor or is adapted for providing a substantially gastight connection to a device for aspirating fluid (e.g., such as a Pipetman®, a Gilson®, Rainin®, Eppendorf® or Finnipipette® pipette) or a fluid-dispensing device. In one aspect, the adaptor is configured in the shape of a pipette tip.
In another embodiment, the invention provides a holder that includes a housing capable of receiving the apparatus body. In one aspect, the holder housing has two or more openings that are substantially aligned to define a light transmission path for electromagnetic radiation when the hollow body is held in the housing.
For a better understanding of the present invention, reference is made to the accompanying drawings and detailed description and its scope will be pointed out in the appended claims.
a, 1b, 1c and 1d are views of a schematic representation of an embodiment of the apparatus of this invention;
a, 2b and 2c are views of a schematic representation of an embodiment of an adaptor of this invention;
a, 3b, 3c, 3d and 3e are views of a schematic representation of another embodiment of the apparatus of this invention;
a, 4b and 4c are views of a schematic representation of yet another embodiment of the apparatus of this invention;
a, 6b, 6c, 6d are schematic block diagram representations of embodiments of the measurement system of this invention.
Before describing the present invention in detail, it is to be understood that this invention is not limited to specific apparatuses, method steps, or equipment, as such may vary. It is also to be understood that the terminology used herein is for the purpose of describing particular embodiments only, and is not intended to be limiting. Methods described herein may be carried out in any order of the recited steps that is logically possible. Furthermore, where a range of values is provided, it is understood that every intervening value, between the upper and lower limit of that range and any other stated or intervening value in that stated range is encompassed within the invention. Also, it is contemplated that any optional feature of the inventive embodiments and aspects described herein may be set forth and claimed independently, or in combination with any one or more of the features described herein, or may be specifically excluded.
Unless defined otherwise below, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Still, certain terms are defined herein for the sake of clarity.
The publications discussed herein are provided solely for their disclosure prior to the filing date of the present application. Nothing herein is to be construed as an admission that the present invention is not entitled to antedate such publication by virtue of prior invention. Further, the dates of publication provided may be different from the actual publication dates, which may need to be independently confirmed. All publications mentioned herein are incorporated herein by reference to disclose and describe the methods and/or materials in connection with which the publications are cited.
It must be noted that, as used in this specification and the appended claims, the singular forms “a”, “an” and “the” include plural referents unless the context clearly dictates otherwise. Thus, for example, reference to “a biopolymer” includes more than one biopolymer, and the like.
It will also be appreciated that throughout the present application, words such as “upper”, “lower” are used in a relative sense only.
The following definitions are provided for specific terms that are used in the following written description.
A “biopolymer” is a polymer of one or more types of repeating units. Biopolymers are typically found in biological systems and particularly include polysaccharides (such as carbohydrates), peptides (which term is used to include polypeptides and proteins, such as antibodies or antigen-binding proteins), glycans, proteoglycans, lipids, sphingolipids, and polynucleotides as well as their analogs such as those compounds composed of or containing amino acid analogs or non-amino acid groups, or nucleotide analogs or non-nucleotide groups. Biopolymers may be heterogeneous in backbone composition thereby containing any possible combination of polymer units linked together such as peptide-nucleic acids (which have amino acids linked to nucleic acids and have enhanced stability).
Polynucleotides include single or multiple stranded configurations, where one or more of the strands may or may not be completely aligned with another. A “nucleotide” refers to a sub-unit of a nucleic acid and has a phosphate group, a 5 carbon sugar and a nitrogen containing base, as well as functional analogs (whether synthetic or naturally occurring) of such sub-units which in the polymer form (as a polynucleotide) can hybridize with naturally occurring polynucleotides in a sequence specific manner analogous to that of two naturally occurring polynucleotides. Biopolymers include DNA (including cDNA), RNA, oligonucleotides, PNA, LNA and other polynucleotides as described in U.S. Pat. No. 5,948,902 and references cited therein, regardless of the source.
“Communicating information” refers to transmitting the data representing that information as signals (e.g., electrical, optical, radio, magnetic, etc) over a suitable communication channel (e.g., a private or public network).
As used herein, a component of a system which is “in communication with” or “communicates with” another component of a system receives input from that component and/or provides an output to that component to implement a system function. A component which is “in communication with” or which “communicates with” another component may be, but is not necessarily, physically connected to the other component. For example, there may be a structural, functional, mechanical, optical, or fluidic relationship between two or more components or elements, or some combination thereof. As such, the fact that one component is said to communicate with a second component is not intended to exclude the possibility that additional components may be present between, and/or operatively associated or engaged with, the first and second components.
The term “assessing” and “evaluating” are used interchangeably to refer to any form of measurement, and includes determining if an element is present or not. The terms “determining,” “measuring,” and “assessing,” and “assaying” are used interchangeably and include both quantitative and qualitative determinations. Assessing may be relative or absolute. “Assessing the presence of” includes determining the amount of something present, as well as determining whether it is present or absent.
The term “using” has its conventional meaning, and, as such, means employing, e.g. putting into service, a method or composition to attain an end.
An apparatus for holding volume liquid samples is described hereinbelow.
In one embodiment, the apparatus includes a body having a first opening located at a first end, a second opening located at a second end.
An inner space of the body connects the first opening and the second opening and comprises a passage from the first opening to the second opening whose walls are formed by the inner surfaces of the hollow body. In one aspect, the two of the inner surfaces are parallel for at least a portion of their length, forming a measurement region. In one embodiment the measurement region is polygonal in cross-section (e.g., square or rectangular). The measurement region of the device comprises a portion of a first inner surface and its corresponding outer surface, a portion of a second inner surface and its corresponding outer surface, and a passage between them for holding a liquid sample.
An embodiment of the apparatus 110 of this invention is shown in
In one aspect, at least one inner surface 157, 167 and its corresponding parallel outer surface 155, 165 is at least partially transparent. In another aspect, at least two inner surfaces 157, 167 and their corresponding parallel outer surfaces 155, 165 are at least partially transparent. An “at least partially transparent” material, as used herein, refers to a material that transmits sufficient light that may be detected by a detection device in an optical instrument (e.g., such as a spectrophotometer). In one aspect, an “at least partially transparent material has at least about 50% transmittance of electromagnetic radiation.
In a further aspect, shown in
Materials used to form the at least partially transparent portion(s) of the body may vary and may include any at least partially transparent material, for example, a polymeric material such as polyimide, polycarbonate, polystyrene, polyolefin, fluoropolymer, polyester, a nonaromatic hydrocarbon, polyvinylidene chloride, polyhalocarbon, such as polycholortrifluoroethylene. Polyolefins may include polyethylenes, polymethylpentenes and polypropylenes, and fluoropolymers may include polyvinyl fluorides. Other materials glass, quartz, fused silica, silicon rubber, such as crosslinked dimethyldisiloxane, or materials used in optical crystals, such as sapphire or garnet (e.g., undoped Yttrium Aluminum Garnet). In certain aspects, the material transmits light with a range of about 200-1100 nm, from about 180-1000 nm, and/or transmits light of a wavelength greater than about 900 nm. The apparatus of this invention can be manufactured by casting or molding or other methods routine in the art.
In certain aspects, materials and dimensions are selected to ensure that a measured signal relating to a sample within the measurement area of the body remains within the limit of the linear range for measurements by a particular detection device with which the apparatus of this invention is used (e.g., such as a spectrophotometer, photometer, spectrofluorometer, and the like).
In another aspect, the sample holding dimensions are chosen to allow a substantial part of an optical beam (originating at a source in an instrument) to pass through the aperture of the sample measurement part of the sample holder without being obstructed or severely refracted by the sample holder.
In one aspect, the body comprises an outer coating or clad 160. In certain aspects, the outer coating reduces stray light (light other than from a light source being using by the optical detector) during optical measurement. In one aspect, the coating comprises a UV absorber.
However, in another aspect, at least a portion of the body is not coated to provide an optical window or aperture 140. In one aspect, a clad is stripped at one section to form the optical window 140. In another aspect, to reduce surface scattering during the optical measurement, the outer surface of the aperture window is smooth. Portions of the surface may be removed to create the desired smooth surface (e.g., by laser machining) or materials may be added to create a smooth surface (e.g., an at least partially transparent coating may be provided).
In embodiments in which the optical window-containing portion of the body is directly dipped into a liquid sample, a portion of the surface area of the body 110 may, in one embodiment, be coated by a hydrophobic coating to eliminate/prevent any liquid sample residue remaining on the outer surface of the body 110. In one aspect, the coating is less than about 1 μm in thickness. In another aspect, the coating is transparent or semi-transparent to electromagnetic radiation. An exemplary embodiment of a hydrophobic coating material comprises a siloxane, for example, the coating may be polydimethylsiloxane silicon rubber, PTFE (e.g., Teflon®), a polyacrylate, and the like but this invention is not limited to only these exemplary embodiments.
In one aspect, the passage connecting the first and second openings comprises a channel. Channel characteristic dimensions may be, but are not limited to, in the order of up to about 2.5 mm. In certain aspects, the passage comprises varying channel dimensions at one or more sections through the length of the body. In another embodiment, over a portion of the channel including the measurement region, the channel dimensions vary approximately (substantially) monotonically from one end to another end (such as, for example, the embodiment shown in
In one embodiment, the outer coating 160 can be, but is not limited to, a polymeric material such as polyamide. The outer coating 160 can also be an at least partially UV transparent material.
In one aspect, at least a portion of the body 110 is comprised of a material capable of allowing transmission of electromagnetic radiation of sufficient intensity to enable performance of an optical measurement (e.g., the material is a semi-transparent or a transparent material). The portion of the body 110 comprised of a material capable of allowing transmission of electromagnetic radiation of sufficient intensity to enable performance of an optical measurement is referred to hereinbelow as the measurement region. In one embodiment, at least the optical window is comprised of a semi-transparent or a transparent material.
In one embodiment, the invention provides an adaptor 190 (
An example of such an adaptor for use with a device for aspirating fluid, a pipette in the embodiment shown, is shown in
In another embodiment of the apparatus of this invention, the first opening is adapted so that is capable of operatively connecting to a device for aspirating fluid.
a-3e show another embodiment 210 of an apparatus of this invention in which a body 210 comprises at least two sections. In this embodiment, the body 210 has two ends 220, 230, each end having an opening 295, 250. The first end 220 with opening 295 is capable of connecting to a device for aspirating fluid, a conventional pipette in the embodiment shown, for aspiration and dispensing, while the second end 230 with opening 250 is capable of being dipped into a liquid well for aspirating liquid. In one embodiment, the body 210 also has two passageways, shown in the Figure as flow channel sections 240 and 260, each having different dimensions. Both of the flow channel sections 240, 260 have parallel inner and outer surfaces which are substantially planar, forming a flow channel 250, 270, with different dimensions L1 and L2 flow channel length H1 and H2, and flow width (aperture width) W1 and W2. In one aspect, the flow channels are rectangular. In another aspect, at least one of the flow channels has an aspect ratio less than 1.
In one aspect, the two flow channels are joined by a taper transition area 280, which has an internal rectangular flow channel. In one embodiment, the upper section 210, which includes the first end 220 with opening 295, generally has a round taper shape 295 in order to fit a conventional pipette. In one aspect, the openings 250 are co-centered and the flow channels share the same longitudinal axis. In another aspect, at least one of the flow channels comprises dimensions (for example, but not limited to, cross sectional area, ratio of cross sectional area to circumference) that are suitable for holding a liquid sample within the flow channel by capillary action. In a further aspect, at least one of the flow channels comprises dimensions that are not suitable for holding a liquid sample within the measurement region of the flow channel by capillary action. (It should be noted that, if the dimensions are not suitable for holding a liquid sample by capillary action, the dimensions are also not suitable for aspirating a liquid sample by capillary action.)
The dimensions of sections of the body may vary and are not limiting features of the invention. However, in certain aspects, L, ranges from about 0.05 to about 5 mm, L2 ranges from about 0.05 to about 10 mm, H1 ranges from about 0.25 to about 50 mm, H2 ranges from about 0.25 to about 50 mm, W, ranges from about 0.25 to 25 mm, and W2 ranges from about 0.25 to about 25 mm.
In one aspect, flow channel 150 (
In another embodiment, shown in
In another embodiment, the openings 325, 335, 327, 337 are capable of receiving portions (e.g., such as ends) of optical waveguides such as fiber optic connectors. In that embodiment, which is shown in
The center of the optical window of the body may be co-centered with the axes of a collimated source of electromagnetic radiation or with the longitudinal axes of optical waveguides. In one embodiment, a planar square surface of an optical window may be provided which is perpendicular to excitation light from a light source. The bottom face of the housing is not necessary closed, but in one aspect, a closed bottom reduces the stray light (e.g., non-source light) getting into the sample pathlength in order to improve the sensitivity of optical measurement. In certain aspects, an adaptor 340 may be used to interface the top face of the housing with the body of the apparatus to reduce stray light.
In one embodiment, the housing 310 can seat the body 110 (or at least one measurement region of the body) at a position that aligns the optical window of the body 110 with a light path defined by source-side and detection side optical fibers, such that sufficient light from the source-side fiber passes through the window to the detection-side optical fiber to be detected by a detector and distinguished from background signal (e.g., a signal produced by a blank, that is a body without a sample).
In certain embodiments in which the body 210 comprises at least two measurement regions (such as the embodiments shown in
The apparatus may be positioned within the housing by manually pressing frictional or mechanical detents or by providing an automatic and/or motor-assisted element that can move in an appropriate direction (e.g., see, 360 in
In one aspect, during operation, the apparatus of this invention is fitted to a device for aspirating fluid, such as a pipette (a pipette or pipettor, as used herein, unless otherwise specified, refers to that aspiration-causing portion of a pipette or pipettor, such as a Pipetman®, a Gilson®, Rainin®, Eppendorf® or Finnipipette® pipette), by a substantially gas-tight fitting, either directly, as in embodiment 210, or indirectly, e.g., using an adaptor 190.
In one aspect, the device for aspirating fluid, such as a pipette, is used to aspirate a liquid sample, for example, a biological sample comprising a biopolymer such as a nucleic acid, peptide, polypeptide and/or protein, into the body (110 or 210) of the apparatus. After a sufficient amount of sample (for example, but not limited to, 1-20 μl) is aspirated into the body (110 or 210) to fill a measurement area (e.g., such as an entire optical window channel region), the body is placed into a housing 310, as shown in
Atotal=2Abody wall+Asample>Asample
Where 2Abody wall refers to the signal contributed by a first and second parallel walls of the apparatus body which define the measurement area (each wall comprising an inner and outer side) and Asample refers to the signal contributed by a sample held between the walls.
Since a blank measurement is generally required before the sample measurement, the actual measurement reading would still be Asample (i.e., the signal from the body walls would be subtracted). Hence, the optical signal produced by a wall of the apparatus will not affect the measurement of an optical signal from the sample.
A measurement system capable of measuring a sample held by an embodiment of the apparatus of this invention is shown in
In one embodiment, the holding component 430 is the holder shown in
In one embodiment, the optical component 420 includes a beam separating component (such as, but not limited to, a beam splitter) and may include optical components for delivering each beam to the apparatus 440 containing the sample. (In one embodiment, the optical components include components to couple each beam to an optical fiber and components to couple the beam from the fiber to the apparatus 440 containing the sample. In another embodiment, the optical components enabled the propagation of each beam to the apparatus 440 and the coupling of each beam to the apparatus 440.)
In one instance, each beam propagates through the apparatus 440 and the sample contained therein and, after propagation, strikes a reflecting component (such as, but not limited to, a mirror) 460, 450. Each reflecting component for 450, 460 is positioned such that the reflecting component 450, 460 redirects the propagation of each beam goers a beam selecting component 470. (There are many different possible embodiments of the beam selecting component 470 including, but not limited to, a galvo double mirror, a pair of deflecting elements and corner mirrors and beam selecting elements.) The selected beam(s) propagates towards the detecting components 480, 490.
In one embodiment, shown in
In another instance, the embodiment of the apparatus of this invention shown in
The invention also provides methods for detecting, monitoring (e.g., determining a change in) and/or quantitating an optical property of a sample.
In one aspect, the method comprises placing the measurement region of an apparatus according to the invention in a positional relationship to a light source and detector of an optical detection device (e.g., a spectrophotometer, photometer, spectrofluorometer, and the like) such that a light path is provided from the light source through the measurement area, to the optical detection device. In certain aspects, the light path is at least partially defined by an optical waveguide, for example a source-side optical fiber and/or a detection-side optical fiber. In certain other aspects, other optical elements may be used to further define the light path. In one aspect, a sample, such as a liquid sample, is held in the measurement region and the detector detects, monitors and/or quantitatively identifies an optical property of the sample (e.g., such as absorption, emission, or scattering of light). In one aspect, the concentration of a component (e.g., a nucleic acid, polypeptide, peptide, or protein) in a sample can be determined by comparing light transmission by a sample without the component to light transmission by a sample with the component. A standard curve may be used in certain cases to correlate optical properties (e.g., such as absorbance) with characteristics of the sample (e.g., such as concentration of a biomolecule within the sample).
In one embodiment, a liquid sample is placed within the measurement region of the apparatus by interfacing the apparatus body with a device for aspirating fluid, such as, but not limited to, a pipette or pipettor, either directly or indirectly using an adaptor as described above, and aspirating a sample from a sample source into the measurement area. In certain aspects, the apparatus may be placed into a sample holder-receiving area of an optical device (such as a spectrophotometer) or into a cartridge for receiving such a sample holder, which may be placed in the device. In one aspect, the ejector of the device for aspirating fluid can be used to place the apparatus into the sample holder-receiving area or cartridge. In another aspect, the body can remain connected to the device for aspirating fluid while the measurement is performed.
Although embodiments of the invention have been described with respect to applications to specific liquid samples (analytes) and specific optical equipment, it should be noted that these are not limitations of this invention and are only presented for exemplary purposes.
Although the invention has been described with respect to various embodiments, it should be realized this invention is also capable of a wide variety of further and other embodiments within the spirit and scope of the appended claims.
