Rapid thermal cycling for sample analyses and processing
10569273 ยท 2020-02-25
Assignee
Inventors
Cpc classification
B01L2200/06
PERFORMING OPERATIONS; TRANSPORTING
B01L7/02
PERFORMING OPERATIONS; TRANSPORTING
B01L2300/0627
PERFORMING OPERATIONS; TRANSPORTING
B01L3/5027
PERFORMING OPERATIONS; TRANSPORTING
B01L2200/025
PERFORMING OPERATIONS; TRANSPORTING
B01L9/06
PERFORMING OPERATIONS; TRANSPORTING
B01L2200/141
PERFORMING OPERATIONS; TRANSPORTING
B01L7/52
PERFORMING OPERATIONS; TRANSPORTING
B01L2300/12
PERFORMING OPERATIONS; TRANSPORTING
C12Q1/6848
CHEMISTRY; METALLURGY
B01L2300/1805
PERFORMING OPERATIONS; TRANSPORTING
B01L2300/1894
PERFORMING OPERATIONS; TRANSPORTING
B01F31/20
PERFORMING OPERATIONS; TRANSPORTING
B01L2300/0829
PERFORMING OPERATIONS; TRANSPORTING
B01L2300/0618
PERFORMING OPERATIONS; TRANSPORTING
B01L2200/147
PERFORMING OPERATIONS; TRANSPORTING
B01L2200/14
PERFORMING OPERATIONS; TRANSPORTING
B01L9/065
PERFORMING OPERATIONS; TRANSPORTING
B01L2200/08
PERFORMING OPERATIONS; TRANSPORTING
International classification
B01L7/00
PERFORMING OPERATIONS; TRANSPORTING
B01L9/06
PERFORMING OPERATIONS; TRANSPORTING
B01L3/00
PERFORMING OPERATIONS; TRANSPORTING
B01L9/00
PERFORMING OPERATIONS; TRANSPORTING
C12Q1/6848
CHEMISTRY; METALLURGY
G01N35/00
PHYSICS
Abstract
A method and an apparatus for thermal processing of nucleic acid in a thermal profile. The method employs at least a first bath and a second bath, the method further employing a reactor holder for holding reactor(s) accommodating reaction material containing the nucleic acid. The method includes maintaining bath mediums in the baths at two different temperatures; and alternately allowing the reactor(s) to be in the two baths in a plurality of thermal cycles to alternately attain a predetermined high target temperature T.sub.HT, and a predetermined low target temperature T.sub.LT, wherein the bath medium in at least one of the baths is a high thermal conductivity powder.
Claims
1. A method of thermal cycling for polymerase chain reaction (PCR) of nucleic acid, the method employing at least a first bath and a second bath, the method further employing a reactor holder for holding reactor(s) accommodating reaction material containing the nucleic acid and the reactor(s) being in a form of capillaries or tubes or wellplates or chips or cartridges, the method comprising: maintaining bath mediums in the baths at two different temperatures; and alternately allowing the reactor(s) to be in the two baths in a plurality of thermal cycles to alternately attain: a predetermined high target temperature T.sub.HT, and a predetermined low target temperature T.sub.LT, wherein the bath medium in at least one of the baths is a powder, wherein the powder comprises particles of substantially spherical shape with a diameter of 0.1 mm-1 mm.
2. The method according to claim 1, further comprising maintaining the T.sub.HT in the region 85-99 degree Celsius for denaturation of the nucleic acid; and maintaining the T.sub.LT in the region 45-75 degree Celsius for annealing of primers or probes onto the nucleic acid or for primer extension.
3. The method according to claim 2, further comprising: allowing the reactor(s) to be in a third bath to attain a predetermined medium target temperature T.sub.MT corresponding to the extension of primers in the nucleic acid or the annealing of primers or probes onto the nucleic acid.
4. The method according to claim 1, further comprising: during the thermal cycling, allowing the reactor(s) to be in an air zone for conducting fluorescence imaging or electrochemical detection of the nucleic acid.
5. The method according to claim 1, further comprising: employing a first optical fiber means for light transmission from an illumination light source into the reaction material; and employing a second optical fiber means for light transmission from the reaction material to a photodetector.
6. The method according to claim 1, wherein the reactor(s) are in the form of tubes or well plates with a feature of a metallic layer at a bottom tip of the reactor(s).
7. The method according to claim 1, further comprising: attaining the target temperatures based on a real-time temperature as sensed by a reactor temperature sensor during thermal cycling.
8. The method according to claim 1, further comprising: attaining the target temperatures based on time-periods for which the reactor(s) are allowed to be in the baths.
9. An apparatus of thermal cycling for polymerase chain reaction (PCR) of nucleic acid, the apparatus employing a reactor holder for holding reactor(s) to accommodate reaction material containing the nucleic acid and the reactor(s) being in any form such as capillaries or tube(s) or wellplate(s) or chip(s) or cartridge(s), the apparatus comprising: a first bath; a second bath, bath mediums in the baths being respectively maintainable at two different temperatures, and a transfer means for allowing the reactor(s) to be in the two baths in a plurality of thermal cycles to alternately attain: a predetermined high target temperature T.sub.HT, and a predetermined low target temperature T.sub.LT; and an amount of powder to serve as the bath medium in at least one of the baths, wherein the powder comprises particles of substantially spherical shape with a diameter of 0.1 mm-1 mm.
10. The method according to claim 1, wherein the powder is selected from the group consisting of: i) ceramic powder, ii) glass powder, iii) metal powder, iv) copper powder, v) any of the above dispersed in a liquid, and vi) mixture of any of the above.
11. The method according to claim 1, wherein the powder has a thermal conductivity more than 0.3 watts per meter-kelvin (W/m.Math.K).
12. The apparatus according to claim 9, wherein the powder is at least one selected from the group consisting of: i) ceramic powder, ii) glass powder, iii) metal powder, and iv) copper powder.
13. The apparatus according to claim 9, wherein the powder has a thermal conductivity that is more than 0.3 watts per meter-kelvin (W/mK).
14. The method according to claim 1, wherein the powder is ceramic powder.
15. The apparatus according to claim 9, wherein the powder is ceramic powder.
16. The apparatus according to claim 9, wherein the transfer means is further adapted to shaking the reactors when the reactors are inside at least one of the first bath or the second bath, the shaking being of a high speed reciprocating motion.
17. The apparatus according to claim 16, wherein the reciprocating motion is in a vertical direction or a depth direction of the first bath or the second bath.
18. The apparatus according to claim 16, wherein the reciprocating motion or the shaking is at a speed that is higher than 100 mm per second.
19. The apparatus according to claim 16, wherein the reciprocating motion or the shaking is at a speed that is higher than 500 mm per second.
20. A method of thermal cycling for polymerase chain reaction (PCR) of nucleic acid, the method employing at least a first bath and a second bath, the method further employing a reactor holder for holding reactor(s) accommodating reaction material containing the nucleic acid and the reactor(s) being in a form of capillaries or tubes or wellplates or chips or cartridges, the method comprising: maintaining bath mediums in the baths at two different temperatures; and alternately allowing the reactor(s) to be in the two baths in a plurality of thermal cycles to alternately attain: a predetermined high target temperature T.sub.HT, and a predetermined low target temperature T.sub.LT, wherein the bath medium in at least one of the baths is a powder and employing a reactor guard to partially confine the reactor(s) to prevent the reactor(s) from getting deformed under resistive forces of the bath medium and the T.sub.HT when the reactor(s) is/are received in the powder.
21. An apparatus of thermal cycling for polymerase chain reaction (PCR) of nucleic acid, the apparatus employing a reactor holder for holding reactor(s) to accommodate reaction material containing the nucleic acid and the reactor(s) being in any form such as capillaries or tube(s) or wellplate(s) or chip(s) or cartridge(s), the apparatus comprising: a first bath; a second bath, bath mediums in the baths being respectively maintainable at two different temperatures, and a transfer means for allowing the reactor(s) to be in the two baths in a plurality of thermal cycles to alternately attain: a predetermined high target temperature T.sub.HT, and a predetermined low target temperature T.sub.LT; and an amount of powder to serve as the bath medium in at least one of the baths and a reactor guard, wherein the reactor guard comprises a confining means to partially confine the reactor(s) to prevent the reactor(s) from getting deformed under resistive forces of the bath medium and the T.sub.HT when the reactor(s) is/are received in the bath medium comprising the powder.
22. The apparatus according to claim 21, wherein the reactor guard is made up of materials comprising metal or glass or high temperature plastics or ceramics.
23. The apparatus according to claim 21, wherein the reactor guard is an extension of the reactor holder.
Description
BRIEF DESCRIPTION OF THE DRAWINGS
(1) In the following drawings, same reference numbers generally refer to the same parts throughout. The drawings are not to scale, instead the emphasis is on describing the concept.
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DETAILED DESCRIPTION
(12) The following description presents several preferred embodiments of the present invention in sufficient detail such that those skilled in the art can make and use the invention.
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(14) In another embodiment (not shown) of thermal cycling, in between the baths 50 and 51, the reactor 15 with the monitoring unit 34 may be inserted into a 3rd bath containing bath medium at a medium target temperature or positioned in hot air for a period of time required for annealing and or extension. Herein the thermal cycling is performed in three-steps by inserting the reactor 15 into the three baths within each thermal cycle.
(15) According to yet another embodiment (not shown) a fourth bath is maintained at a predetermined temperature T.sub.AP and before the thermal cycling, the reactor 15 with the temperature monitoring unit 34 is inserted in the fourth bath to allow at least one additional process from the group consisting reverse transcription-polymerase chain reaction (RT-PCR) and isothermal amplification reaction. The RT-PCR is carried out prior to the thermal cycling for nucleic acid amplification.
(16) A temperature guided motion controlling means (TeGMCM) (not shown) may preferably be employed in the apparatus for allowing the reactor(s) 15 to remain in the bath(s) 50 to 54 until the corresponding target temperature is attained, in order to maintain better accuracy of the predetermined target temperatures attained by the reactor(s) 15. The TeGMCM may be provided with advance signals when the reactor(s) 15 are about to reach the target temperatures as sensed by the temperature monitoring unit 34 in order to avoid over heating or over cooling of the reactor(s) 15. The thermal cycling with this method provides higher accuracy and needs no user calibration though is at a higher cost and complexity of the apparatus due to requirement of very fast temperature sampling and signal processing electronics, fast data communication with the reactor transfer mechanism, and very responsive mechanical motion components such as motors and actuators in the reactor transfer mechanism. Alternately, a time guided motion controlling means (TiGMCM) may be used that is operable based on the time-periods for which the reactor(s) are allowed to be in the baths. The TiGMCM may be user calibrated for the time-periods. This embodiment requires lower complexity of the apparatus as it operates by time-duration hence does not require highly responsive set-up though needs user calibration.
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(25) Different bath may contain different bath medium 75 for specific advantages as desired. The reactors 15 may be made up of plastics, elastomer, glass, metal, ceramic and their combinations, in which the plastics include polypropylene and polycarbonate. The glass reactor 15 can be made in a form of a glass capillary of small diameters such as 0.1 mm-3 mm OD and 0.02 mm-2 mm ID, and the metal can be aluminum in form of thin film, thin cavity, and capillary. Reactor materials can be made from non-biological active substances with chemical or biological stability. At least a portion of the reactor 15 is preferred to be transparent. In another embodiment, the reactors 15 can be in a form of a reactor array chip or a microfluidic reactor chip or arrayed chip. For example, the reactors 15 can be in a form of wells or channels of a substrate plate and optionally covered with a solid layer of material to form closed reaction chambers, in which the reaction fluid or reaction system is situated. The reaction material 21 in all the reactors 15 in the reactor holder 33 may not be identical. Simultaneous PCR can be advantageously conducted for different materials 21 if the bath temperatures are suitable. At least part of the reactor wall may be made of metal sheet of thickness 1 m-2 mm. This feature enhances the rate of heat transfer between the bath and the reaction material 21. At least part of the reactor wall may be made of plastic or glass sheet of thickness 0.5 m-500 m. At least a part of the reactor wall is made of transparent material so as to enable the imaging and detection process. When using the above described apparatus for nucleic acid analysis and processing, the reaction material 21 comprises reaction constituents including at least one enzyme, nucleic acid and/or particle containing at least one nucleic acid, primers for PCR, primers for isothermal amplifications, primers for other nucleic acid amplifications and processing, dNTP, Mg.sup.2+, fluorescent dyes and probes, control DNA, control RNA, control cells, control micro-organisms, and other reagents required for nucleic acid amplification, processing, and analysis. The particle containing nucleic acid mentioned above comprises at least one cell virus, white blood cell and stromal cell, circulating tumor cell, embryo cell. One application may be to use the apparatus to test different kinds of reaction materials 21 against the same set of primer and probes, such as test more than one sample. For such application, different kinds of reaction material 21 containing no target primers and/or probes are each loaded into one reactor 15 in a reactor array, with all the reactors 15 being pre-loaded with the same set or the same sets of PCR primers and/or probes. For the same application, different kinds of reaction materials 21 pre-mixed with respective PCR target primers and/or probes are each loaded into one reactor 15 in a reactor array, with all the reactors 15 being not pre-loaded with the same set of PCR primers and or probes. The reaction materials 21 can include control genes and/or cells and corresponding fluorescent dyes or probes. In the above situations, the different probes emit light of different wavelengths. Another application of the methods and devices are used to test the same reaction material 21 against different sets of primer and probes. One example of such an application is to test one type of sample for more than one purpose. For this application, a single reaction material 21 is added into the reactors 15 each loaded with at least one different set PCR primers and or probes. The reaction material 21 can include control genes and/or cells and corresponding fluorescent dyes or probes. In the above situations, the different probes emit light of different wavelengths. The above reaction material 21 is used in polymerase chain reaction, reverse transcription-PCR, end-point PCR, ligase chain reaction, pre-amplification or target enrichment of nucleic acid sequencing or variations of polymerase chain reaction (PCR), isothermal amplification, linear amplification, library preparations for sequencing, bridge amplification used in sequencing. The variation of the polymerase chain reaction mentioned above comprises reverse transcription-PCR, real-time fluorescent quantitative polymerase chain amplification reaction and real-time fluorescent quantitative reverse transcription polymerase chain amplification reaction, inverse polymerase chain amplification reaction, anchored polymerase chain amplification reaction, asymmetric polymerase chain amplification reaction, multiplex PCR, colour complementation polymerase chain amplification reaction, immune polymerase chain amplification reaction, nested polymerase chain amplification reaction, the target enrichment of pre-amplification or nucleic acid sequencing, ELISA-PCR
(26) The powder may be metallic like copper, or may be ceramic or glass or the powder may be dispersed in a liquid such as oil or glycerol or water or any mixture thereof. The liquid fills up the voids between the particles in the powder and liquids have much higher thermal conductivity and heat capacity than air. The liquid also reduces the frictional resistance to the movement of the reactors in the bath. The liquid however adheres to the surfaces of the reactors when taken out of the baths.
(27) The particles in the powder may be of substantially spherical shape to lower the frictional resistance to the movement of the reactors in the bath. The powder may advantageously be of particle size in the range of 1 m to 5 mm. A particle size of 0.1 to 1.0 mm may be optimum as finer particle sizes may cause health hazards upon inhalation and larger particle sizes tend to have more voids that deteriorate the heat transfer to the reactors.
(28) Ceramic powder is known to have high thermal conductivity and the described particle size is found to have low frictional resistance for commercially available reactors with diameters 0.1 mm-5 mm. The particle sizes within the bath may be selected so as to optimize between the ease of insertion of the reactor(s) and the rate of heat transfer. Ceramic powder has the advantage of not oxidising with time unlike copper powder thereby reducing the thermal conductivity of the powder. Ceramic powder particles as manufactured have a shape that is more spherical than copper powder particles. Besides, the surface finish of ceramic particles is such that the inter-particle surface friction is much lower than that with metal particles. In the bath, these features of shape and surface finish advantageously reduce the frictional resistance to the movement of the reactors including glass capillaries.
(29) Copper being electrically a good conductor, any spillage of the powder outside the baths may potentially cause short-circuits in the electrical components of the apparatus. Advantageously this is not the case with ceramic powder.
(30) The powder described herein preferably has a thermal conductivity that is more than 0.3 watts per meter-kelvin (W/m.Math.K), that is higher than the thermal conductivity of materials like plastics, wood or rubber. Higher the thermal conductivity of the powder, advantageously, lower is the duration of the thermal cycling.
(31) From the foregoing description it will be understood by those skilled in the art that many variations or modifications in details of design, construction and operation may be made without departing from the present invention as defined in the claims.