WO2011042426A1

WO2011042426A1 - Multifunctional rotor

Info

Publication number: WO2011042426A1
Application number: PCT/EP2010/064812
Authority: WO
Inventors: Lars Edvinsson; Magnus Molin
Original assignee: Alphahelix Molecular Diagnostics Ab (Publ)
Priority date: 2009-10-05
Filing date: 2010-10-05
Publication date: 2011-04-14

Abstract

A rotor capable of holding a plurality of vessels for subjecting samples to reactions involving thermal cycling in a thermal cycler, comprising a base element and an annular element for holding said plurality of vessels, wherein said annular element holds said plurality of vessels in a substantially horizontal position, and said base element comprises at least a processor, a transmitter and means for powering said processor and transmitter.

Description

Multifunctional rotor

Technical field

[0001 ] This description relates to the field of iaboratory equipment, and in particular to a rotor for use in an apparatus capable of subjecting a sample to repeated heating and cooling, while simultaneously subjecting the sample to a centrifugal force.

Background

[0002] Typically, increased temperature makes chemical reactions faster by speeding up key mechanisms like bringing molecules or molecule domains in contact with each other. Therefore it is common to heat reaction vessels, for example bringing them in contact with an open flame, hot gas, hot liquid, hot sand or a solid material. This procedure is often referred to as incubation.

[0003] One typical problem involved with incubation of fluid reaction mixtures is thermal heterogeneity, because the parts of the reaction mixture that are in close contact with the walls of the reaction vessel will become heated before the more central parts of the reaction mixture. In many cases there is a risk of part of the reaction mixture becoming overheated before other parts even reach the desired temperature. This leads to temperature gradients forming in the reaction mixture. Hot subsets of the reaction mixture has normally lower density than cold subsets which tends to generate temperature gradients or discrete layers of more or less isothermal bodies of liquid, so called thermoclines. Thus warm, less dense portions of the reaction mixture tend to find a position above cold, denser portions. Molecular motion and currents in the reaction mixture will eventually homogenize the reaction mixture with respect to temperature, a process referred to as temperation of the reaction mixture. The time it takes to temperate a reaction mixture may contribute substantially to the time required for the complete reaction.

[0004] However, time-consumption in itself is not the sole problem involved with temperation of chemical reaction mixtures. In certain incubation procedures such as the repetitive temperation involved in so called thermal cycling processes, e. g. for performing polymerase chain reactions, also known as PCR-reactions, long temperation periods also lead to unwanted side-reactions, sometimes causing severe quality problems with respect to the accuracy and specificity of the obtained PCR- product.

[0005] The Polymerase Chain Reaction, or PCR, is a technique to amplify a few copies of DNA into millions or more copies of a particular DNA sequence. The technique relies on thermal cycling, i.e. cycles of repeated heating and cooling, for the template DNA to melt and replicate. Replication occurs enzymatically through the action of a DNA polymerase. The use of primers, i.e. short stretches of DNA, which are complementary to the target region direct the DNA polymerase and enable selective and repeated amplification of the sequence/s of interest.

[0006] Today, PCR is widely used, and several commercial apparatuses are available for performing the PCR process. Using these apparatuses, a 40 cycle PCR run typically takes 1 - 3 hours, depending on instrumentation, with the actual PCR reaction itself taking only a small percentage of this time, represented by the so called 'hold times'. For most of the time, the samples are undergoing temperature transitions, which make up the major part of the total PCR run time.

[0007] Thus, it is possible to significantly shorten the total time of the PCR run by increasing temperature ramping rates. This must, however, be done in such a way that the thermal homogeneity is maintained, since temperature heterogeneity negatively affects PCR quality (specificity, sensitivity and yield). A common strategy to speed up PCR instruments has been to build faster Peltier element-based thermal cycling blocks; to scale down reaction volumes; and to increase the thermal conductivity of optimized reaction vessels (e.g. glass capillaries or 'ultra-thin walled' tubes). Nevertheless, current technology is still limited by the ramping rates of Peltier block based thermal cycles, due to inefficiencies of heat transfer from the block to the samples and vice versa; and the time it takes to homogenize the sample volume with respect to the target temperature.

[0008] There are essentially three ways to speed up a PCR process:

- Improve temperature ramp speed of the thermal cycler used for PCR.

- Modify PCR protocols to cut time from hold times. For example, amplicons used for fast PCR should be short, i.e. below 200 base pairs.

- Enhance enzyme functions by genetic alterations of the enzyme. For example, addition of a DNA binding domain to heat stable DNA polymerases increases processitivity as well as accuracy (Wang, 2004).

[0009] Wittwer and Garling ( 1 991 ) have shown that denaturation and annealing during a PCR occur almost instantaneously (within less than 1 s), why PCR cycle times are ultimately limited by the extension time, i.e. the time needed for the DNA polymerase to completely copy the template molecule/s. Certain DNA polymerases exhibit extension rates that are in the order of 1 kb/s. When used for fast PCR together with short amplicons, extension times need not be more than 1 -2 seconds. Thus, total hold time per cycle for fast PCR is in the order of less than about 5 seconds. This means, theoretically, that it should be possible to perform a 40 three- step cycles in less than about 3.3 min (5 s/cycle: 1 s; 1 s; 3 s) if there were no transition times. However, no commercially available PCR instrument does a 40 'three-step' cycle PCR in less than 40 minutes. Thus, ramp times alone amount to about 35 minutes or more, even for so called 'Fast' PCR instruments. In addition, when hold times are decreased to less than 1 5 s per hold step, it becomes critical that the PCR instrument - the thermal cycler - is engineered such that the sample reaches the specified temperature and remains at that temperature for the programmed time. In a conventional PCR instrument, 15 s or more may be required for the sample to actually reach the set temperature. As a consequence, fast PCR protocols run on conventional PCR instruments often exhibit unacceptable temperature variability across the sample blocks.

[001 0] WO 00/5801 3 discloses a device for thermal cycling of samples, said device comprising a rotor for holding reaction vessels, a motor, connected to said rotor, means such as a processor for controlling the speed of the rotor, and means for heating and cooling the contents of the reaction vessels, wherein the means for heating cover the apices of the reaction vessels for at least part of the rotational path of said vessels, and wherein the means for heating operate at a temperature significantly higher than the melting temperature of the reaction vessels.

[001 1 ] As explained in WO 00/58013, many important industrial processes as well as procedures applied in laboratories of various kinds are dependent on chemical reactions. Commonly the time consumed for completing a process or procedure is determined by the time it takes for some specific chemical reaction or reactions to reach equilibrium. This is often referred to as the kinetic properties of a chemical reaction or simply reaction kinetics. A host of variables influence the reaction kinetics in each case, for instance the concentrations of reactants, temperature, presence of catalytic agents etc.

[001 2] WO 98/49340 describes an apparatus and method for the amplification and real time detection of specific DNA fragments, using Polymerase Chain Reaction (PCR), Ligase Chain Reaction (LCR) or any other amplification or hybridization technology. The method of the present invention involves centrifugal loading of DNA samples and reagents into a rotor which is sealed to eliminate conlamination. This sealed rolor is then heated and or cooled, and detection means monitor the fluorescence of each sample during temperature transitions.

[001 3] US2008252905 discloses a centrifugal force based microfluidic system including: a microfluidic device including a rotatable platform and an optical path formed to extend horizontally in a straight line from a circumference of the platform; a motor rotating so as to control the microfluidic device; a light emitting unit emitting light towards the microfluidic device; a light receiving unit detecting the light emitted from the light emitting unit; and a controller determining a home position to be the position of the microfluidic device at a point of time when the light emitted from the light emitting unit is detected by the light receiving unit, wherein the light emitted from the light emitting unit passes through the optical path to be incident on the light receiving unit only when the microfluidic device is located in a predetermined position.

[0014] WO 2004/045771 presents the SuperConvection™ technology

(SuperConvection™ is a trademark of Alphahelix Molecular Diagnostics AB,

Uppsala, Sweden) and describes a method for rapid homogenization of reaction mixtures involving asymmetric heating and centrifugation, as well as reaction vessels designed for use in this method.

[001 5] DE 381 5449 presents a laboratory centrifuge where the identification of a rotor is carried out by means of a fixedly arranged sensor which has a bi-stable switching behavior and by means of which a bit pattern, arranged on a graduated circle of the rotor and rotating therewith, is sensed in a contactless fashion.

[001 6] It remains however to develop this technology and components for use in existing and future devices. It is desirable to make available less a costly, more efficient and yet accurate and reliable device for the thermal cycling of samples, in particular for faster PCR without compromising the specificity, sensitivity and yield of the PCR.

Summary

[001 7] The inventors make available a novel device and method, comprising several embodiments, the features of which can be freely combined.

[001 8] One embodiment of the invention comprises a rotor capable of holding a plurality of vessels for subjecting samples in said vessels to reactions involving thermal cycling, wherein said rotor comprises a base element and an annular element for holding said plurality of vessels, wherein

- said annular element holds said plurality of vessels in a substantially horizontal position, and

- said base element comprises at least a processor, a transmitter, and means for powering said processor and transmitter.

[001 9] The rotor preferably further comprises an insert having radial grooves for accommodating said vessels in said substantially horizontal position.

[0020] Said annular element preferably has an inner rim, wherein said insert rests on said rim. Further, said annular element preferably has pins engaging said base element. Preferably also said insert has pins engaging said annular element and/or said base element.

[0021 ] According to a preferred embodiment, freely combinable with any of the features listed herein, said annular element is shaped as a cylinder having a radius and a height, wherein said height is less than said radius. Preferably said annular element is shaped as a double walled cylinder having an outer and an inner wall.

[0022] According to one embodiment, said insert has a cut-out for receiving a probe for measuring a sample-related parameter. Said sample-related parameter can be any relevant sample related property, but is preferably the temperature in at least one of said plurality of vessels, Said sample temperature is measured for example using an in-tube temperature element, preferably a thermal resistor.

Preferably said probe, for example the above thermal resistor, connects to a component present on said base element.

[0023] In a rotor according to any of the embodiments listed herein, said components on said base element comprise at least a processor, a transmitter, and means for powering said processor and transmitter, and wherein said transmitter transmits information based on the measured sample-related parameter.

[0024] According to an embodiment, said rotor further comprises components for storing and transmitting information between the rotor and auxiliary equipment, for example information identifying said rotor. Other examples of information or data includes, but is not limited to data chosen from compatibility data, calibration data, data entered by the operator, data recorded or received during operation, and data for internal quality control.

[0025] Preferably said information or data is transmitted wirelessly to and from the rotor, in the form of wireless signaling, and said wireless signaling is preferably chosen from optica! and electromagnetic signaling, such as but not limited to IR- signaling, Bluetooth®, and WLAN.

[0026] According to a currently preferred embodiment of the rotor, freely combinable with any of the features listed herein, said base element substantially consists of a circuit board carrying at least a processor, a transmitter, and means for powering said transmitter. Said circuit board further preferably also comprises a receiver for receiving wireless signals. [0027] According to one embodiment, at least one conducting surface is arranged on a surface of said rotor, said conducting surface being capable of engaging a brush or collector shoe for receiving electric current.

[0028] Alternatively, or in addition to the above embodiment, the components on said circuit board are powered by a battery on said circuit board. Alternatively, or in combination with any of the features listed herein, the circuit board comprises an inductive coil.

[0029] The rotor is intended for use with conventional vessels, e.g. PCR- microtubes, or tubes specially designed for optimal fit to the rotor. According to an embodiment, said vessels are tubes having a volume in the interval 0.1 to 2.0 ml, preferably 0.2 to 0.6 ml.

[0030] The rotor is intended for use as a part of conventional handling of samples in a laboratory, and therefore the rotor is adapted to receive a number of tubes which is a multiple of twelve. Accordingly, in one embodiment, said annular element has thirteen openings for accommodating twelve microtubes and one probe. In another embodiment, said annular element has twenty-five openings for accommodating twenty-four microtubes and one probe. In another embodiment, said annular element has forty-nine openings for accommodating forty-eight microtubes and one probe. In yet another embodiment, said annular element has ninety-seven openings for accommodating ninety-six microtubes and one probe.

[0031 ] Another embodiment of the invention is a method involving the use of a rotor as described herein, according to any one of the embodiments or

combinations thereof, for performing reactions involving cyclic heating.

[0032] Another embodiment is a novel thermal cycling device having a rotor capable of holding a plurality of vessels for subjecting samples to thermal cycling, a base and an outer cover which can be opened, a motor coupled to said rotor, means For controlling the rotation of said rotor, and a heating element for heating said plurality of samples, wherein said rotor is movably enclosed in a housing, wherein said housing comprises of at least two parts movably arranged in relation to each other, and said heating element is arranged in at least one of said parts, wherein said rotor housing is arranged to be opened independently of the outer cover.

[0033] In this embodiment, said housing preferably comprises an upper and lower part, wherein the heating element is arranged in the upper part.

[0034] Further, said at least two parts, which together form the housing, in a closed state preferably define a hollow space which at least in part forms a reflector extending over an elongated heating element and part of the path taken by a sample vessel in the rotor during rotation.

[0035] Further said reflector preferably has an elliptic cross-section and two focal points, wherein said elongated heating element is centered approximately in one focal point, and the path taken by a sample vessel in the rotor during rotation intersects the other focal point.

[0036] Further, said reflector preferably has the shape of an arch, semicircle or circle, parallel to the circumference of the rotor.

[0037] According to an embodiment, said heating element is an IR-source, e.g. a resistance wire.

[0038] Preferably at least one the surfaces of the rotor housing adjacent to said rotor is/are manufactured of a material with low thermal absorption and/or low thermal conductivity. [0039] Further, according to another embodiment, said rotor housing preferably comprises a double-walled vacuum element at least in the portions adjacent to said rotor.

[0040] According to an embodiment, said rotor housing in a closed state defines an inner hollow space conforming closely to the shape of the rotor and minimizing the dead-space between the rotor and said rotor housing.

[0041 ] Another embodiment encompasses a thermal cycling device having a rotor capable of holding a plurality of samples, a base and an cover that can be opened, a rotor housing, a motor coupled to said rotor, means for controlling the rotation of said rotor, and a heating element for heating said plurality of samples, wherein said rotor is movably enclosed in said rotor housing comprising an upper and a lower part, wherein said heating element is arranged in the upper part of said housing, wherein said upper part can be moved in relation to said lower part during operation of the rotor, and said upper part has an aperture or valve for guiding ambient air towards the rotor. This has the advantage of maximizing the flow of ambient cooling air over the samples.

[0042] Preferably the degree of opening of said aperture or valve can be regulated from fully closed to fully open. Further, said aperture is preferably centered with the rotor axis. By purposefully designing the position and size of said aperture, the rotor will function as the impeller in a centrifugal pump, drawing ambient air into the rotor housing, cooling the samples, and expelling the air though the opening between the upper and lower parts of the rotor housing.

[0043] Another embodiment involves a thermal cycling device having a rotor capable of holding a plurality of samples, a base and an cover which can be opened, a rotor housing, a motor coupled to said rotor, means for controlling the rotation of said rotor, and a heating element for heating said plurality of samples, wherein said rotor is movably enclosed in said housing, said heating element is arranged in a part of said rotor housing, and said motor is a spindle motor, a brushless motor, or the like.

[0044] Preferably said motor operates at a constant rate in the interval from about 2000 rpm to about 1000 rpm, preferably from about 3000 to about 7200 rpm, most preferably at 3000 rpm or at a rate equal to or higher than 3000 rpm, and lower or equal to 7200 rpm.

[0045] Another embodiment involves a thermal cycling having a rotor capable of holding a plurality of samples, a base and an cover that can be opened, a rotor housing, a motor coupled to said rotor, means for controlling the rotation of said rotor, and a heating element for heating said plurality of samples, wherein said rotor is arranged in and capable of rotating within a space delimited by a rotor housing, wherein said rotor housing comprises a lower and an upper part, and wherein the surfaces of said lower and an upper part oriented towards the rotor comprise a thermal barrier.

[0046] Preferably said thermal barrier comprises a material having high thermal resistance, In any of the above embodiments, said material is preferably chosen from ceramic fibres, fiberglass, high-density fiberglass, thermoplastic foam, expanded thermoplast, aerogel, extruded glass, foam glass, mineral fibre sheets or similar.

[0047] Preferably said material is coated with a reflective metal coating. The reflective metal coating is preferably a coating suitable for reflecting IR, e.g. a gold or copper coating.

[0048] According to another embodiment, freely combinable with the above embodiments or features thereof, said thermal barrier preferably comprises an arrangement of a barrier layer and an evacuated space. Preferably said barrier layer is coated with a reflective metal coating, e.g. a gold or copper coating.

[0049] Another embodiment of the invention is a method for performing reactions involving cyclic heating of samples contained in sample vessels arranged in a rotor, said rotor enclosed in a rotor housing, and said rotor and rotor housing being covered by an outer cover, wherein the samples during a heating phase are heated by a heating element arranged in a part of said rotor housing, and wherein the samples during a cooling phase are cooled by opening said rotor housing without opening said outer cover.

[0050] In the above method, ambient air is preferably guided to enter between the sample containing vessels and the heating element when the rotor is in operation during the cooling phase.

[00 1 ] Further, ambient air is preferably guided to enter approximately at the center of the rotor and exit along the periphery of the rotor during the cooling phase.

[0052] Further, the heating element is preferably removed from operational contact with the sample containing vessels during the cooling phase.

[0053] Another embodiment of the invention is the use of a device as described herein for performing reactions involving cyclic heating.

[0054] Further embodiments of the invention include separate rotors constructed as defined herein, for example to be used as replacement rotors in a device for thermal cycling or PCR.

[0055] Further embodiments include separate base elements as defined herein, for example to be used as components of rotors, or as replacement parts for rotors, [0056] The invention also comprises a system comprising a rotor as defined herein. The invention also comprises a general method for performing reactions involving cyclic heating comprising the steps of placing a sample, and optionally reagents in a vessel, loading said vessel in a rotor as defined herein, and subjecting said sample to centrifugation and cyclic heating.

[0057] The invention also comprises a general method for performing reactions involving cyclic heating comprising subjecting a sample and optionally reagents to centrifugation and cyclic heating in a system as defined herein.

Short description of the drawings

[0058] The invention will be described in closer detail with reference to the enclosed, non-limiting drawings, in which

[0059] Fig. 1 schematically shows a partially exploded view of a thermal cycler.

[0060] Fig, 2 shows a schematic cross-section of a thermal cycler comprising a rotor according to an embodiment of the invention.

[0061 ] Fig. 3 shows a perspective view of a rotor according to an embodiment of the invention.

[0062] Fig. 4 shows a cross-section of a rotor, and a detail view of the connection between a probe and components on a base element.

[0063] Fig. 5 consists of four panels, showing a side view, a cross-section, a view from above, and a view from below, of an annular element.

[0064] Fig. 6 schematically illustrates an example of components or operational units preferably present on the base of a rotor according to the invention.

Description - -

[0065] Before the present device and method is described, it is to be understood that this invention is not limited to the particular configurations, method steps, and materials disclosed herein as such configurations, steps and materials may vary somewhat. It is also to be understood that the terminology employed herein is used for the purpose of describing particular embodiments only and is not intended to be limiting since the scope of the present invention will be limited only by the appended claims and equivalents thereof.

[ΟΟόό] It must also 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.

[0067] The term "about" when used in the context of numeric values denotes an interval of accuracy, familiar and acceptable to a person skilled in the art. Said interval can be ± 10 % or preferably ± 5 %.

[0068] When describing and claiming the present invention, the following terminology will be used in accordance with the definitions set out herein.

[0069] The term "sample" here means a volume of a liquid, solution or suspension, intended to be subjected to qualitative or quantitative determination of any of its properties, such as the presence or absence of a component, the concentration of a component, etc. The sample may be a sample taken from an organism, such as a mammal, preferably a human; or from the biosphere, such as a water sample, or an effluent; or from a technical, chemical or biological process, such as the production of medicaments, food, feed, or the like. The sample may be subjected to cyclic heating as such, or after suitable pre-treatment, such as concentration, dilution, purification, homogenization, sonication, filtering, sedimentation, centrifugation, heat-treatment etc. [0070] The term "sample vessel" or simply "vessel" is intended to encompass any vessel capable of containing a reaction mixture within a temperature range necessary for performing the desired reaction / reactions. Examples of reaction vessels suitable for use according to the invention include, but are not limited to, test tubes, so called micro tubes, PCR-tubes, Eppendorf-tubes and the like.

[0071 ] The term "reaction" is intended to encompass any reaction in which the reaction kinetics is influenced by temperature and where a faster, more efficient and homogenous temperature adjustment is desired. A non-exhaustive list of examples of reactions, suitable for the present device and method are chemical / biochemical reactions within the field of chemical synthesis, combinatorial chemistry, high throughput screening, assays, methods for the determination of the presence of or the concentration of a given substance, and biochemical reactions involving incubation or temperature adjustments, e.g. repeated temperature adjustments, cyclic temperature changes, including a polymerase chain reaction (PCR), a ligase chain reaction (LCR), a "gapped-LCR-reaction", a nucleic acid sequence-based amplification (NASBA), a self-sustained replication (3SR), a transcription mediated amplification (TMA), a stand displacement amplification (SDA), a target

amplification, a signal amplification, rolling-circle amplification (RCA), or a combination of any of the above.

[0072] According to one embodiment of the invention, the present inventors make available a rotor, and in particular a rotor for use in a thermal cycling device where the rotor is capable of holding a plurality of vessels for subjecting samples to reactions involving thermal cycling.

[0073] An example of a thermal cycler or thermal cycling device is given in Fig. 1 , schematically showing a thermal cycler comprising a base 1 , and an openable cover 2 also acting as an outer protective cover for a rotor (not shown) enclosed in a rotor housing 3. The thermal cycler further comprises an interface 4, here shown as a display with integrated or separate controls for entering information. The device preferably also has a communication interface for communicating with external equipment, e.g. a personal computer, a miniature computer, a hand-held computer, a mobile phone, a printer or storage medium, e.g. an external hard disk; either via an USB port or other wire-bound connection, or wirelessly, through optical or electromagnetic signaling, such as but not limited to IR, Bluetooth^®, WLAN etc.

[0074] Fig. 2 shows a schematic cross-section of a thermal cycler comprising a rotor 33 according to an embodiment of the invention, having an outer housing 10 and an outer cover 20, an inner rotor housing 30 comprising a first part 3 1 and a second part 32, a rotor 33, said rotor shown holding vessels 34 in a substantially horizontal position, and operated by a motor 35, control electronics 40 in connection with an interface 41 , said motor 35 and said means 50 for

manipulating the rotor housing 30 or parts thereof.

[0075] Further, a thermal cycler according to an embodiment of the invention, comprises a base 10 and an outer cover 20. This outer cover 20 is preferably always closed during operation of the device, except of course for the loading and removal of the rotor and samples. It is conceivable that the outer cover 20 also comprises a lock and a sensor, said sensor indicating when the cover is in closed and locked position. The control electronics 50 would then preferably comprise a function, ensuring that the motor engaging the rotor cannot be turned on, unless the cover is in a closed and locked position.

[0076] Fig. 2 further illustrates how a rotor housing 30 can comprise a first part 3 1 and a second part 32, surrounding a rotor 33, holding vessels 34 and operated by a motor 35, control electronics 40 in connection with an interface 41 , the motor 35 and means 50 for manipulating the rotor housing or parts thereof. It is schematically shown how the upper and lower parts of the housing confirm closely to the size and shape of the rotor with samples, thus minimizing dead space. [0077] The construction outlined above has several advantages. The feature that the rotor housing 3 can be opened separately from the outer cover 2, during operation of the rotor, makes it possible to rapidly cool the samples simply by opening the upper part of the rotor housing while the rotor rotates with high speed. Minimizing dead space around the vessels and rotor when the rotor housing is closed, reduces the energy requirements for heating the samples, and makes it possible to both heat and cool the samples rapidly. Minimized accumulation of heat not only reduces the time and energy required to heat the samples, it also reduces the time and energy required to cool the samples, both important advantages of the embodiments of the invention.

[0078] The control electronics 40, may comprise components for storing information, such as one or more programs for operating the device, components for reading said stored information and translating the information into signals for controlling components of the device, as well as components capable of receiving signals from sensors present in a sample, sensors present in or on the rotor, from sensors within the device etc. The signals preferably concern parameters such as speed of rotation, sample temperature, ambient temperature, and optionally also the temperature within the device, e.g. within the rotor housing. The sample temperature is preferably measured in-tube, using one or more thermal resistors.

[0079] One embodiment of the invention is a rotor 300 capable of holding a plurality of vessels 330 for subjecting samples in said vessels to reactions involving thermal cycling, said rotor comprising a base element 320 and an annular element 3 1 0 for holding said plurality of vessels, wherein said annular element holds said plurality of vessels in a substantially horizontal position, and said base element comprises at least a processor, a transmitter, and means for powering said processor and transmitter. - -

[0080] Preferably said rotor 300 further comprises an insert 340 having radial grooves 341 for accommodating said vessels 330 in said substantially horizontal position. Said radial grooves 341 may further have a notch or slot (not shown) the shape of which corresponds to the shape of a feature on the vessel 330 to guide the vessel and to make certain that each vessel is inserted in the rotor in exactly the same orientation. One such feature may be the hinge for the cap in a microtube. One advantage of this arrangement is that the influence of any variations in wall thickness or shape of the vessels is minimized, as all vessels are oriented in identical fashion.

[0081 ] Preferably said annular element 3 1 0 has an inner rim 650, and said insert 340 rests on said rim 650 when in position. Between said insert 340 and the base element 320 a space is formed, accommodating components present on the base element 320. Although the electronic components present on, or integrated into the base element, require very little space, it is an advantage that a space is formed, protecting the components.

[0082] In Fig. 3 and 4, the insert 340 is shown having an opening corresponding to the opening 350 in the base element 320. It is conceived that the axel or spindle of the motor 35 ends in a hub engaging only the base element 320, in which case the insert 340 would not have any opening. It is however preferred that the connection between the motor and the base element is visible from above, which has the advantage that proper attachment can be inspected visually. Alternatively, an opening in the insert 340 makes it possible to access a possible locking mechanism on the hub engaging the base element, for example when releasing the rotor,

[0083] According to an embodiment, said components on said base element (320) comprise at least a processor, a transmitter, and means for powering said - -

processor and transmitter, and wherein said transmitter transmits information based on the measured sample-related parameter.

[0084] Preferably said annular element 3 1 0 has pins 620 engaging said base element 320. Preferably also said insert 340 has pins (not shown) engaging said annular element 31 0 and/or said base element 320. Said pins extending downwards from the insert 340 may engage openings 670 provided in the annular element 3 1 0 and optionally also extend through said openings 670 and engage the base element 320. This construction makes the rotor very stable.

[0085] Preferably said annular element 3 10 is shaped as a cylinder having a radius and a height, wherein said height is less than said radius. This design has the advantage of providing a compact, space saving yet stable and durable rotor.

[0086] Preferably said annular element 3 1 0 is shaped as a double walled cylinder having an outer 630 and an inner 640 wall. The vessels 330 fit Into opening 610 in the outer 630 and inner 640 walls, and are well supported. The design makes the rotor significantly lighter without compromising stability and strength. Further, the double wal!ed annular element has a lower mass and therefore heats and cools more rapidly, which also constitutes an important advantage.

[0087] The rotor is schematically shown in Fig. 3 which shows a perspective view of a rotor 300 comprising an annular element 3 1 0, a base element 320, where said annular element 3 10 here is shown holding 24 sample containers 330, illustrated as PCR-tubes, and one probe 331 , preferably a temperature sensor. The base element 320 has an opening 350 for engaging with the shaft of a motor (not shown) . Further, inside the annular element 310, an insert 340 can be seen. The insert 340 has indentations or groves 341 accommodating the sample containers 330. [0088] When the sample containers or vessels 330 are in place, inserted into the openings 610 in the annular element 3 10, each vessels held in an opening 610, which holds it in a substantially horizontal position, and simultaneously rests in a grove 341 of the insert 340. Thereby the insert, which rests on a rim 650 of the annular element 310, is effectively held in place by twelve, twenty-four or more vessels. This gives stability to the construction, and makes it possible to simplify the construction of the insert.

[0089] The rotor is intended For use with conventional vessels, e.g. PCR- microtubes, or tubes specially designed for optimal fit to the rotor. According to an embodiment, said vessels are tubes having a volume in the interval 0.1 to 2.0 ml, preferably 0.2 to Ο.ό ml.

[0090] The rotor is also intended for use as a part of conventional handling of samples in a laboratory, and therefore the rotor is adapted to receive a number of tubes which is a multiple of twelve. This has among other things the advantage that samples can be transferred from a conventional format, e.g. a micro-titer plate, into a series of vessels which can be simultaneously subjected to PCR.

[0091 ] Thus, according to one embodiment, said vessels 330 are tubes having a volume in the interval 0. 1 to 2.0 ml, preferably 0.2 to 0.6 ml. Further, said annular element 3 1 0 may have thirteen openings 610 for accommodating twelve microtubes 330 and one probe 331 . Alternatively, said annular element 310 may have twenty-five openings 61 0 for accommodating twenty-four microtubes 330 and one probe 331 . Alternatively, said annular element 3 1 0 may have forty-nine openings 610 for accommodating forty-eight microtubes 330 and one probe 33 1 . Alternatively, said annular element 3 1 0 may have ninety-seven openings 610 for accommodating ninety-six microtubes 330 and one probe 33 1 . [0092] In the central opening 350 further elements can be provided to engage the rotor to the motor shaft, such as threads, coupling means, locking means etc.

[0093] According to an embodiment of the invention, freely combinable with the other features presented herein, said insert 340 has a cut-out όόθ for receiving a probe 33 1 for measuring a sample-related parameter. Preferably said sample- related parameter is the temperature in at least one of said plurality of vessels. Most preferably said sample temperature is measured using an in-tube temperature element, preferably a thermal resistor. Measuring a parameter, e.g. the

temperature, inside a tube, has the advantage of being more representative of the conditions in the remaining tubes, as the sensor is subjected to the same conditions as the remaining tubes.

[0094] Fig. 4 shows a cross-section of the rotor 300, comprising the annual element 3 10 and the base element 320, as well as an insert 340. The sample containers 330 as well as the probe 33 1 are shown held in substantially horizontal position. The detail view schematically shows how a probe 33 1 can be arranged in a tube and connected to a socket on the base element.

[0095] Fig. 5 consists of four panels, where panel A shows a side view of an annular element 310, having openings 61 0 for receiving / holding sample vessels and the probe, as well as one or more pins 620 for engaging the base.

[0096] Panel B shows a cross-section of the annular element 31 0, with the openings 610 and pins 620, and additionally illustrating how the annular element preferably has a double side, consisting of two walls 630 and 640. Further, the annular element 310 preferably has an inner rim 650 or similar abutment, on which the insert (not shown] rests when in place.

[0097] Panel C shows the annular element 310 from above, showing the double side walls 630 and 640, the inner rim 650, and also a cut-out 660 for accommodating the connection between the probe and the components on the base. Holes 670 for accommodating corresponding pins on the insert are also shown.

[0098] Panel D shows the annular element 310 from below, showing the pins 620 and the holes 670, as well as the cut-out 660.

[0099] The rotor is preferably made of a light-weight metal or a thermoplastic, capable of withstanding the temperatures generated by the heating element.

[001 00] As described above, the base element 320 carries functional components, and these preferably also comprise components for storing and transmitting information or data relating to or identifying said rotor. Said information or data preferably comprises data chosen from compatibility data, calibration data, data entered by the operator, data recorded or received during operation, and data for internal quality control. This has the advantage of minimizing user errors, mix-up of batches, etc.

[001 01 ] Said components on the base element are preferably electronic

components on or within a circuit board. Thus, according to one embodiment of the invention, said base element 320 substantially consists of a circuit board carrying at least a processor, a transmitter for transmitting wireless signals, and means for powering said transmitter. Preferably said circuit board further comprises a receiver for receiving wireless signals. Preferably said wireless signals are chosen from optical signals or electromagnetic signals, such as IR-signaling, Bluetooth®, and WLAN.

[001 02] Fig. 6 schematically illustrates an example of the components or operational units preferably present on the base of rotor according to the invention; a storage and processing unit 700 for storing information and processing information and instructions, a measurement unit or sensor 71 0, preferably detachable from the base as illustrated by the contact 71 1 , a sender 720, and receiver 730, Further, a power source 740 is included, optionally having a component 750 capable of receiving energy from outside the rotor.

[001 03] This embodiment has an advantage in that the supply of power to the rotor while in operation is less sensitive to interruptions or discontinuity than the

transmission of signals. Preferably, the incoming current is filtered to remove disturbance or interference that could influence the function of the one or more sensors, sender and receiver in the circuits on the base of the rotor. In its most simple form, such filter can comprise a capacitor. Alternatively, the power supplied through the brushes or collector shoes can be stored in a battery or used to recharge a battery on the base of the rotor.

[00104] Alternatively, the components on said circuit board are powered by a battery on said circuit board. Said battery may also function as a buffer,

compensating for interruptions in the supply of power to the rotor.

[001 05] Alternatively the energy necessary to power the components present on the base is generated through induction . Thus the rotation of the rotor is utilized for generating energy, for example by a suitable arrangement of a stationary permanent magnet arranged in operational contact and a coil, arranged on the base.

[0010ό] Another embodiment of the invention is a method involving the use of a rotor as described herein, according to any one of the embodiments or

combinations thereof, for performing reactions involving cyclic heating.

[001 07] Another embodiment is a novel thermal cycling device having a rotor capable of holding a plurality of vessels for subjecting samples to thermal cycling, a base and an outer cover, a motor coupled to said rotor, means for controlling the rotation of said rotor, and a heating element for heating said plurality of samples, wherein said rotor is movably enclosed in a housing, wherein said housing comprises of at least two parts movably arranged in relation to each other, and said heating element is arranged in at least one of said parts, wherein said rotor housing is arranged to be opened independently of the outer cover,

[001 08] This is illustrated in Fig. 1 and 2, described above. In this embodiment, said housing 3 preferably comprises an upper 30 and lower part 32, wherein the heating element is arranged in the upper part.

[001 09] Further, said at least two parts 30 and 32, which together form the housing 3, in a closed state preferably define a hollow space which at least in part forms a reflector extending over an elongated heating element and part of the path taken by a sample vessel in the rotor during rotation.

[001 1 0] Further said reflector preferably has an elliptic cross-section and two focal points, wherein said elongated heating element is centered approximately in one focal point, and the path taken by a sample vessel in the rotor during rotation intersects the other focal point.

[001 1 1 ] Further, said reflector preferably has the shape of an arch, semicircle or circle, parallel to the circumference of the rotor.

[001 1 2] According to an embodiment, said heating element is an IR-source, e.g. a resistance wire.

[001 1 3] Preferably at least one the surfaces of the rotor housing adjacent to said rotor is/are manufactured of a material with low thermal absorption and/or low thermal conductivity.

[001 1 ] Further, according to another embodiment, said rotor housing 3 preferably comprises a double-walled vacuum element at least in the portions adjacent to said rotor. - -

[001 1 5] According lo an embodiment, said rotor housing in a closed state defines an inner hollow space conforming closely to the shape of the rotor and minimizing the dead-space between the rotor and said rotor housing. This is schematically shown in Fig. 2.

[001 1 6] Another embodiment encompasses a thermal cycling device 1 having a rotor 33 capable of holding a plurality of samples, a base 1 , 1 0 and an cover 2, 20 a rotor housing 3, 30, a motor 35 coupled to said rotor, means for controlling the rotation of said rotor, and a heating element for heating said plurality of samples, wherein said rotor is movably enclosed in said rotor housing comprising an upper 30 and a lower part 32 , wherein said heating element is arranged in the upper part of said housing, wherein said upper part can be moved in relation to said lower part during operation of the rotor, and said upper part has an aperture or valve for guiding ambient air towards the rotor.

[001 1 7] Preferably the degree of opening of said aperture or valve can be regulated from fully closed to fully open. Further, said aperture is preferably centered with the rotor axis.

[001 1 8] Another embodiment involves a thermal cycling device having a rotor capable of holding a plurality of samples, a base 1 , 10 and an outer cover 2, 20 a rotor housing 3, 30, a motor 35 coupled to said rotor 33, means for controlling the rotation of said rotor, and a heating element for heating said plurality of samples, wherein said rotor is movably enclosed in said housing, said heating element is arranged in a part of said rotor housing, and said motor is a spindle motor, a brushless motor, or the like.

[001 1 9] Preferably said motor operates at a constant rate in the interval from about 2000 rpm to about 1 000 rpm, preferably from about 3000 to about 7200 rpm, most preferably at 3000 rpm or at a rate equal to or higher than 3000 rpm, and lower or equal to 7200 rpm.

[001 20] Another embodiment involves a thermal cycling having a rotor capable of holding a plurality of samples, a base 1 , 10 and an outer cover 2, 20, a rotor housing 3, 30, a motor 35 coupled to said rotor, means for controlling the rotation of said rotor, and a heating element for heating said plurality of samples, wherein said rotor is arranged in and capable of rotating within a space delimited by a rotor housing, wherein said rotor housing comprises a lower 32 and an upper part 30, and wherein the surfaces of said lower and an upper part oriented towards the rotor comprise a thermal barrier 3 1 .

[001 21 ] Preferably said thermal barrier 31 comprises a material having high thermal resistance, in any of the above embodiments, said material is preferably chosen from ceramic fibres, fiberglass, high-density fiberglass, thermoplastic foam, expanded thermoplast, aerogel, extruded glass, foam glass, mineral fibre sheets or similar, This arrangement has the advantage of minimizing the dissipation and absorption of heat, thus reducing in particular the time and energy required for heating the samples.

[001 22] Preferably said materia! is coated with a reflective metal coating. The reflective metal coating is preferably a coating suitable for reflecting IR, e.g. a gold or copper coating. This has the advantage of increasing the reflection and minimizing the absorption of heat, thus reducing both the time and energy required for heating and cooling the samples.

[001 23] According to another embodiment, freely combinable with the above embodiments or features thereof, said thermal barrier preferably comprises an arrangement of a barrier layer and an evacuated space. Preferably said barrier layer is coated with a reflective metal coating, e.g. a gold or copper coating. [001 24] Another embodiment of the invention is a method for performing reactions involving cyclic heating of samples contained in sample vessels arranged in a rotor, said rotor enclosed in a rotor housing, and said rotor and rotor housing being covered by an outer cover, wherein the samples during a heating phase are heated by a heating element arranged in a part of said rotor housing, and wherein the samples during a cooling phase are cooled by opening said rotor housing without opening said outer cover.

[001 25] In the above method, ambient air is preferably guided to enter between the sample containing vessels and the heating element when the rotor is in operation during the cooling phase.

[001 26] Further, ambient air is preferably guided to enter approximately at the center of the rotor and exit along the periphery of the rotor during the cooling phase.

[001 27] Further, the heating element is preferably removed from operational contact with the sample containing vessels during the cooling phase,

[001 28] Another embodiment of the invention is the use of a device as described herein for performing reactions involving cyclic heating.

[00129] Further embodiments of the invention include separate rotors constructed as defined herein, for example to be used as replacement rotors in a device for thermal cycling or PCR.

[001 30] Further embodiments include separate base elements as defined herein, for example to be used as components of rotors, or as replacement parts for rotors.

[001 31 ] The invention also comprises a system comprising a rotor as defined herein, The invention also comprises a general method for performing reactions involving cyclic heating comprising the steps of placing a sample, and optionally reagents in a vessel, loading said vessel in a rotor as defined herein, and subjecting said sample to centrifugation and cyclic heating.

[001 32] The invention also comprises a general method for performing reactions involving cyclic heating comprising subjecting a sample and optionally reagents to centrifugation and cyclic heating in a system as defined herein.

[001 33] Further problems, solved by the device according to embodiments of the invention, as well as further advantages associated with the device, will become evident to a skilled person upon study of the present description, claims, and the non-limiting drawings which are intended to illustrate various embodiments of the invention.

Examples

Example 1 .

[001 34] A rotor was assembled from the following parts: a base consisting of an integrated circuit in the shape of a disk having a diameter of 95 mm, and the thickness of about 2 mm; an annular element machined in aluminum, having a diameter of 95 mm and a height of 1 6 mm; and an insert made of injection-molded thermoplastic polymer material. The annular element engages the base though pins positioned around the periphery of the annular element, corresponding to holes in the base element. Further, also the insert has pins, corresponding to and engaging with holes in the disk. As the insert also rests on an inner rim of the annular element, the insert helps securing the annular element to the base.

[001 35] The weight of the annular element was about 40 g, the weight of the base together with the components thereon was about 1 0 g, and the weight of the insert was about 5 g. Depending on the choice of materials and material thickness, the weight of the assembled rotor can be about 40 g to about 60 g, which is a surprisingly low weight. In operation, the total weight of the rotor will be that of the rotor and its components, plus that of the vessels holding the samples and reagents. For a rotor accommodating 24 PCR-tubes, then this will amount to about 24 to 48 g. The total weight of the rotor will thus remain comparatively very low.

[001 36] At the same time, the construction of the rotor makes it very stabile. Not only is the annular element fastened to the base by pins of the annular element engaging holes in the base, also the insert helps to secure the annular element. Further, the insert is additionally held in place by the sample containers or PCR- tubes, which when inserted in the openings in the annular element, also bear down on the insert, where they fit into groves which secure their position and correct insertion. Practical stress testing of rotor prototypes at extreme rpm has shown that the rotor is well balanced and very durable.

[001 37] Further, a light weight is an advantage in a process involving cyclic heating, as the rotor itself stores only little heat. In particular the embodiment where the annular element has double walls allows heat to dissipate very quickly from the rotor,

[001 38] Further still, a light and stable rotor allows the construction of a lighter thermocycler, requiring less energy for rotating the rotor, less energy for heating the samples, and less mass for stabilizing the apparatus and protecting the user.

[001 39] Although the invention has been described with regard to its preferred embodiments, which constitute the best mode presently known to the inventors, it should be understood that various changes and modifications as would be obvious to one having the ordinary skill in this art may be made without departing from the scope of the invention as set forth in the claims appended hereto. References

Wang, Y., et al., A novel strategy to engineer DNA polymerases for enhanced processivity and improved performance in vitro. Nucleic Acids Res, 2004. 32(3): p. 1 1 97-207.

Wittwer, C.T. and D.J . Garling, Rapid cycle DNA amplification: time and

temperature optimization. Biotechniques, 1 991 . 1 0( 1 ): p. 76-83.

Claims

1 . A rotor (300) capable of holding a plurality of vessels (330) for subjecting

samples in said vessels to reactions involving thermal cycling, said rotor comprising a base element (320) and an annular element (31 0) for holding said plurality of vessels, characterized in that

2. The rotor according to claim 1 , wherein said rotor (300) further comprises an insert (340) having radial grooves (341 ) for accommodating said vessels (330) in said substantially horizontal position.

3. The rotor according to claim 2, wherein said annular element (3 1 0) has an inner rim (650), and wherein said insert (340) rests on said rim (650).

4. The rotor according to claim 2, wherein said annular element (3 1 0) has pins (620) engaging said base element (320) .

5. The rotor according to claim 2, wherein said insert (340) has pins engaging said annular element (3 1 0) and/or said base element (320) .

6. The rotor according to claim 1 , wherein said annular element (3 1 0) is shaped as a cylinder having a radius and a height, wherein said height is less than said radius,

7. The rotor according to claim 1 , wherein said annular element ( 10) is shaped as a double walled cylinder having an outer (630) and an inner (640) wall.

8. The rotor according to claim 2, wherein said insert (340) has a cut-out (όόθ) for receiving a probe (331 ) for measuring a sample-related parameter.

9. The rotor according to claim 8, wherein said sample-related parameter is the temperature in at least one of said plurality of vessels.

1 0. The rotor according to claim 8 or 9, wherein said probe (33 1 ) connects to a component present on said base element.

1 1 . The rotor according to claim 1 0, wherein said components on said base element

(320) comprise at least a processor, a transmitter, and means for powering said processor and transmitter, and wherein said transmitter transmits information based on the measured sample-related parameter.

1 2. The rotor according to claim 9, wherein said sample temperature is measured using an in-tube temperature element, preferably a thermal resistor.

1 3. The rotor according to claim 1 , wherein said rotor (300) further comprises

components for storing and transmitting information identifying said rotor.

1 4. The rotor according to claim 1 3, wherein said information comprises data

chosen from compatibility data, calibration data, data entered by the operator, data recorded or received during operation, and data for internal qual ity control .

1 5. The rotor according to claim 1 , wherein said base element (320) substantially consists of a circuit board carrying at least a processor, a transmitter, and means for powering said transmitter.

1 ό- The rotor according to claim 1 5 , wherein said circuit board further comprises a receiver for receiving wireless signals.

1 7. The rotor according to claim 1 or 1 5 , wherein at least one conducting surface is arranged on a surface of said rotor (300), and capable of engaging a brush or collector shoe for receiving electric current.

1 8. The rotor according to claim 1 or 1 5, wherein the components on said circuit board are powered by a battery on said circuit board.

1 9. The rotor according to claim 1 or 1 , wherein the circuit board comprises an inductive coil .

20. The rotor according to any one of claims 1 1 to 1 6, wherein said wireless

transmission is chosen from optical and electromag netic signaling.

21 .The rotor according to claim 1 , wherein said vessels (330) are tubes having a volume in the interval 0.1 to 2.0 ml, preferably 0.2 to 0.6 ml.

22. The rotor according to claim 1 , wherein said annular element (3 1 0) has 1 3

openings (610) for accommodating 1 2 microtubes (330) and 1 probe (331 ).

23. The rotor according to claim 1 , wherein said annular element ( 1 0) has 25

openings (610) for accommodating 24 microtubes (330) and 1 probe (331 ).

24. The rotor according to claim 1 , wherein said annular element (3 1 0) has 49

openings (610) for accommodating 48 microtubes (330) and 1 probe (331 ).

25. The rotor according to claim 1 , wherein said annular element (3 1 0) has 97

openings (610) for accommodating 96 microtubes (330) and 1 probe (331 ).

2ό. The use of a rotor (300) according to any one of claims 1 to 25 for performing reactions involving cyclic heating.

27. An annular element (310) for use in a rotor according to any one of claims 1 to 25.

28. A base element (320) for use in a rotor according to any one of claims 1 to 25.

29. A system comprising a rotor according to any one of claims 1 to 25.

30. A method for performing reactions involving cyclic heating comprising the steps of placing a sample, and optionally reagents in a vessel, loading said vessel in a rotor according to any one of claims 1 to 25, and subjecting said sample to centrifugation and cyclic heating.

31 . A method for performing reactions involving cyclic heating comprising subjecting a sample and optionally reagents to centrifugation and cyclic heating in a system according to claim 29.