Patent Publication Number: US-2007116444-A1

Title: Heat blocks and heating

Description:
RELATED APPLICATIONS  
      This application claims priority to U.S. Provisional Patent Application Ser. No. 60/691,124, filed on Jun. 16, 2005, which is hereby incorporated by reference in its entirety. 
    
    
     FIELD  
      The embodiments disclosed herein relate to heating samples of biological material, and more particularly heating and thermal cycling of DNA samples to accomplish a polymerase chain reaction, a quantitative polymerase chain reaction, a reverse transcription-polymerase chain reaction, an immuno-polymerase chain reaction, or other nucleic acid amplification types of experiments.  
     BACKGROUND  
      Techniques for thermal cycling of DNA samples are known in the art. By performing a polymerase chain reaction, DNA can be amplified. It is desirable to cycle a specially constituted liquid biological reaction mixture through a specific duration and range of temperatures in order to successfully amplify the DNA in the liquid reaction mixture. Thermal cycling is the process of melting DNA, annealing short primers to the resulting single strands, and extending those primers to make new copies of double stranded DNA. The liquid reaction mixture is repeatedly put through this process of melting at high temperatures and annealing and extending at lower temperatures.  
      In a typical thermal cycler, a biological reaction mixture including DNA will be provided in a large number of sample wells on a thermal block assembly. It is desirable that the samples of DNA have temperatures throughout the thermal cycling process that are as uniform as reasonably possible. Even small variations in the temperature between one sample well and another sample well can cause a failure or undesirable outcome of the experiment. For instance, in quantitative PCR, one objective is to perform PCR amplification as precisely as possible by increasing the amount of DNA that generally doubles on every cycle; otherwise there can be an undesirable degree of disparity between the amount of resultant mixtures in the sample wells. If sufficiently uniform temperatures are not obtained by the sample wells, the desired doubling at each cycle may not occur. Although the theoretical doubling of DNA rarely occurs in practice, it is desired that the amplification occurs as efficiently as possible.  
      In addition, temperature errors can cause the reactions to improperly occur. For example, if the samples are not controlled to have the proper annealing temperatures, certain forms of DNA may not extend properly. This can result in the primers in the mixture annealing to the wrong DNA or not annealing at all. Moreover, by ensuring that all samples are uniformly heated, the dwell times at any temperature can be shortened, thereby speeding up the total PCR cycle time. By shortening this dwell time at certain temperatures, the lifetime and amplification efficiency of the enzyme are increased. Therefore, undesirable temperature errors and variations between the sample well temperatures should be decreased.  
      Prior art heat blocks composed of all metal can be expensive. In metal machined blocks or metal, thick base, electro-formed blocks, the primary heat transfer path, from the heating means to the well cavity, is limited by the wall area of the well. That is, the heat must move from the bottom of the block through the wall area of the well to heat the well cavity. To promote heat distribution the well wall is made as thin as possible to maximize the heating ramp rate of the well cavity.  
      In light of the foregoing, there is a need for a thermal cycling apparatus and method that enhances temperature uniformity of the sample wells to improve the efficiency or accuracy of processing samples. Thus, there is a need in the art for an apparatus and method for a non-metal block thermal system for thermal cycling a plurality of samples.  
     SUMMARY  
      In accordance with one aspect of the invention, an apparatus and method are provided for a non-metal block thermal system comprising a top plate having a non-metal material wherein the top plate comprises a plurality of heating wells, each heating well sized to accommodate a plurality of sample tubes containing samples. A bottom plate engages to the top plate to form a heat block. A plurality of heat transfer pins extend from the bottom plate to the top plate. The plurality of heat transfer pins deliver heat to the plurality of heating wells. The non-metal material of the top plate may be molded to engage the heat transfer pins and increase heating efficiency. The heat block may be used for efficient thermal cycling of biological samples.  
      One heat block in accordance with this aspect of the invention comprises a top plate comprising a non-metal material wherein the top plate comprises a plurality of heating wells for accepting a plurality of sample tubes; a bottom plate engaging the top plate; and a plurality of heat transfer pins extending from the bottom plate to the top plate to transfer heat from the bottom plate to the top plate.  
      One heat block in accordance with this aspect of the invention comprises a top plate comprising a non-metal core with a metal coating on an outer surface and a bottom plate comprising a metal.  
      The present invention also provides a method of thermal cycling samples comprises placing a plurality of sample tubes containing samples in a sample retainer, rotating a rotating heat assembly to position a top plate of a heat block below the sample retainer, the top plate comprising a plurality of heating wells; raising the rotating heat assembly to bring the plurality of heating wells of the top plate in thermal contact with the plurality of sample tubes; heating the heat block to a first temperature for a first time period to control a temperature of the samples in the plurality of sample tubes; and lowering the rotating heat assembly so the plurality of heating wells of the top plate are no longer in thermal contact with the plurality of sample tubes.  
      The present invention further provides a method for heating a plurality of heating wells comprises providing a heat block having a top plate comprising a non-metal material and a bottom plate with a plurality of heat transfer pins engaging a plurality of heating wells of the top plate; placing the plurality of heating wells in thermal contact with a plurality of sample tubes; heating the bottom plate of the heat block with a heater; and transferring heat from the bottom plate to the plurality of heating wells by the plurality of heat transfer pins.  
      In accordance with a second aspect of the invention, one or more thermally conductive materials are used to form at least one plate of a heat block. One heat block in accordance with this aspect comprises a thermal plate comprising a thermally conductive material, the thermal plate including a major upper surface having a substantially planar area and a plurality of heating wells for accepting a plurality of sample tubes; and a heating plate engaging the thermal plate and contacting the major upper surface of the thermal plate.  
      The thermally conductive material can be aluminum.  
      Additionally, the thermal plate can include a boss having a cavity defined therein to simulate a temperature response of a biological sample. Alternatively, or in addition, one heating well of the heat block can be used to measure a simulated biological fluid sample temperature.  
      One heat block in accordance with this second aspect includes a first plate having a substantially planar major upper surface and a plurality of heating wells defined in the major upper surface for accepting a plurality of sample tubes; and a second plate abutting the major upper surface of the first plate, the second plate being a heating plate having a body portion having a plurality of apertures formed therein, where the body portion can be substantially planar in shape; an insulative portion surrounding the plurality of apertures; and a heating element carried by the heating plate, arranged between insulative portions thereof.  
      The heating element can be a resistive heating element, or a tubular conduit for carrying heated fluid, and can be secured to a bottom surface of the second plate, for contacting the first plate, embedded in the second plate, or formed within in the second plate.  
      The insulative portion can be thermally insulative, or electrically insulative.  
      The heat block can also include connecting portions for connecting the heating element of the second plate to a heat energy source. The heat energy source can be an electrical energy source for providing an electrical current to the heating element, or can be an energy source that provides heated fluid to the heating element.  
      Preferably, the first plate comprises a metal material, and can include copper, aluminum, brass and combinations thereof. The metal material of the heat block can also include a first metal coated with a second metal.  
      The present invention also provides a method for heating a plurality of heating wells comprising; providing a heat block having a thermal plate comprising a thermally conductive material, the thermal plate including a major upper surface having a substantially planar area and a plurality of heating wells for accepting a plurality of sample tubes; and a heating plate engaging the thermal plate and contacting the major upper surface of the thermal plate; placing the plurality of heating wells in thermal contact with a plurality of sample tubes; heating the thermal plate of the heat block with the heating plate; and transferring heat from the thermal plate to the plurality of heating wells through conductive heat transfer.  
      In one embodiment, the thermal plate of the heat block is heated prior to the step of placing the plurality of heating wells in thermal contact with the plurality of sample tubes.  
      The present invention also provides a method of thermal cycling samples comprises placing a plurality of sample tubes containing samples in a sample retainer, rotating a rotating heat assembly to position a top plate of a heat block below the sample retainer, the top plate comprising a plurality of heating wells; raising the rotating heat assembly to bring the plurality of heating wells of the top plate in thermal contact with the plurality of sample tubes; heating the heat block to a first temperature for a first time period to control a temperature of the samples in the plurality of sample tubes; and lowering the rotating heat assembly so the plurality of heating wells of the top plate are no longer in thermal contact with the plurality of sample tubes, and wherein the heat block comprises a first plate having a substantially planar major upper surface and a plurality of heating wells defined in the major upper surface for accepting a plurality of sample tubes; and a second plate abutting the major upper surface of the first plate, the second plate being a heating plate having a body portion having a plurality of apertures formed therein; an insulative portion surrounding the plurality of apertures; and a heating element carried by the heating plate, arranged between insulative portions thereof.  
      The heat block improves heat transfer, efficiently processes samples, and allows for substantial cost savings through the use of a top plate comprising a non-metal material.  
    
    
     BRIEF DESCRIPTION OF THE DRAWINGS  
      The presently disclosed embodiments will be further explained with reference to the attached drawings, wherein like structures are referred to by like numerals throughout the several views. The drawings are not necessarily to scale, the emphasis having instead been generally placed upon illustrating the principles of the presently disclosed embodiments.  
       FIG. 1  shows an assembly view of a heat block wherein a top plate of the heat block is disengaged from a bottom plate of the heat block.  
       FIG. 2  shows a perspective view of a bottom plate of a heat block.  
       FIG. 3  shows a top perspective view of a top plate of a heat block.  
       FIG. 4  shows a bottom perspective view of a top plate of a heat block.  
       FIG. 5  shows a cut away view of a heat block wherein a top plate is engaged to a bottom plate.  
       FIG. 6  shows an alternative embodiment of the heat block.  
       FIG. 7  shows a view of a block heater of a heat block.  
       FIG. 8  shows a perspective view of a central tube of an embodiment wherein multiple heat blocks may engage the central tube.  
       FIG. 9  shows a perspective view of a rotating heat assembly wherein a plurality of heat blocks engage the central tube.  
       FIG. 10  is a top perspective view of a thermal plate in accordance with the invention.  
       FIG. 11  is a bottom perspective view of the thermal plate of  FIG. 10 .  
       FIG. 12  is a bottom perspective view of a heating plate in accordance with the invention.  
       FIG. 13  is top perspective view of a heat block assembly in accordance with the invention, illustrating the thermal plate of  FIGS. 10 and 11  and the heating plate of  FIG. 12  in an abutting configuration.  
       FIG. 14  is a perspective view of a rotating heat assembly including three heat block assemblies as shown in  FIG. 13 .  
       FIG. 15  shows a perspective view of a rotating heat assembly as part of a processing apparatus.  
       FIG. 16  shows a close up view of a rotating heat assembly as part of a processing apparatus.  
       FIG. 17  shows a perspective view of a rotating heat assembly as part of a processing apparatus. 
    
    
      While the above-identified drawings set forth presently disclosed embodiments, other embodiments are also contemplated, as noted in the discussion. This disclosure presents illustrative embodiments by way of representation and not limitation. Numerous other modifications and embodiments can be devised by those skilled in the art which fall within the scope and spirit of the principles of the presently disclosed embodiments.  
     DETAILED DESCRIPTION  
      A heat block is capable of delivering a desired amount of heat uniformly and efficiently to a plurality of samples. The heat block comprises a metal and/or a non-metal material to increase the efficiency of processing samples while reducing the cost of constructing the heat block.  
      Thermal cyclers are the programmable heating blocks that control and maintain the temperature of the sample through the three temperature-dependent stages that constitute a single cycle of PCR: template denaturation; primer annealing; and primer extension. These temperatures are cycled up to forty times or more to obtain amplification of the DNA target. Thermal cyclers use different technologies to effect temperature change including, but not limited to, peltier heating and cooling, resistance heating, and passive air or water heating.  
      Thermal cycling of DNA can accomplish a polymerase chain reaction (PCR), a quantitative polymerase chain reaction (qPCR), a reverse transcription-polymerase chain reaction (RT-PCR), a reverse transcription-quantitative polymerase chain reaction (RT-qPCR), immuno-polymerase chain reaction (I-PCR), or other nucleic acid amplification types of experiments.  
      A heat block is shown generally at  67  in  FIG. 1 . The heat block  67  comprises a top plate  83  and a bottom plate  75 . In this embodiment, the top plate  83  comprises a non-metal material. The top plate  83  may be composed of any plastic material which may be molded and has physical properties sufficient to satisfy the structural and temperature requirements. The top plate  83  comprises a high-temperature moldable plastic. The top plate  83  may comprise polyphenylene sulfide (PPS), polyetherimide (PEI) or other similar materials known to those skilled in the art.  
      In certain embodiments, the top plate  83  comprises a metal coating over a non-metal material. The metal coating is on an outer surface of the top plate  83 . The metal coating acts as a wear surface and permits easy cleaning of the top plate  83 . The metal coating also promotes the sensitivity of the instrument, when used to obtain quantitative data, by providing a more optically reflective surface as compared to the molded plastic surface. The metal coating or plating may comprise copper, nickel, chromium, gold, or a combination of multiple metals or other metals known to those skilled in the art. The metal coating may be applied using coating methods known in the art including, but not limited to, bath plating, physical, chemical, or ion vapor deposition, or other coating methods known in the art.  
      The bottom plate  75  comprises a conductive material, preferably a metal. The bottom plate  75  may be prepared by casting, machining, forging, metal injection molding or other methods known in the art. In an embodiment, the bottom plate  75  comprises aluminum. The bottom plate  75  may comprise copper, silver, aluminum alloy, other castable alloys or other similar materials known to those skilled in the art. The bottom plate  75  may comprise a plurality of metals. Those skilled in the art will recognize that the bottom plate may comprise a variety of conductive materials and be within the spirit and scope of the presently disclosed embodiments.  
      The design of the top plate  83  in relation to the bottom plate  75  allows for heat to be more evenly distributed throughout a sample which leads to more uniform, efficient and reliable results as compared to those obtained through the use of prior art heat blocks. The use of a non-metal material for the top plate  83  is cost effective. Processing a large number of samples often requires the use of a large number of heat blocks which increases expenses. The presently disclosed embodiments allow for substantial cost savings by using heat blocks that can have a non-metal top plate. As such, the presently disclosed embodiments provide both cost savings and improved results.  
       FIG. 1  shows an assembly view of a heat block wherein the top plate  83  of the heat block  67  is disengaged from the bottom plate  75  of the heat block  67 . A plurality of heat transfer pins  77  extend from the bottom plate  75 . The plurality of heat transfer pins  77  may be formed with the bottom plate  75 . Alternatively, the plurality of heat transfer pins  77  may be added to the separate bottom plate  75 . The plurality of heat transfer pins  77  may be composed from a different material than the bottom plate  75 . The plurality of heat transfer pins  77  may be different shapes including, but not limited to, square, rectangular, circular, oval, and other shapes. The plurality of heat transfer pins  77  may be etched, roughened, grooved, notched or formed with any other surface effect such that the surface area for each pin is increased. This may be useful to promote a mechanical connection with a plurality of ribs  87  of the top plate  83 .  
      The plurality of heat transfer pins  77  deliver heat to a plurality of heating wells  85 . The plurality of heat transfer pins  77  distribute heat evenly to each individual sample. The plurality of heat transfer pins  77  transfer heat to the sides of the plurality of heating wells  85  that contain the plurality of sample tubes  39 . The plurality of heat transfer pins  77  act as an interface to deliver heat along the entire length of the sample tube  39 . Delivering heat to the sides of the heating well  85  distributes heat in a sample better than delivering heat to the sample exclusively through the bottom of the heating well  85 . The heating well  85  is molded so that the heating well  85  better engages the heat transfer pins  77  and therefore allows for heat to be efficiently delivered to the heating well  85  from the sides of the heating well  85  through thermal conduction. The flexibility and moldability of the non-metal material of the top plate  83  to engage the heat transfer pins  77  provides uniform heating to the sample and increases processing efficiency. The heating well  85  may have the plurality of ribs  87  to engage the plurality of heat transfer pins  77  and promote uniform heat distribution.  
      The heating ramp rate is important as a user feature since it impacts the speed at which a user can conduct a biological experiment. As the heating well wall thickness is reduced, to reduce the amount of heated mass, the area for the heat path is reduced as well. As the heating well wall thickness is reduced, the temperature gradient within a single heating well cavity increases. This single well temperature gradient may become as great or greater than the temperature gradient across the entire sample block for thin well walls. The plurality of heat transfer pins  77  combined with the top plate  83  allows the heat transfer path to enter the heating well  85  from the sides of the heating well  85 . The heat travels from the plurality of heat transfer pins  77  through the plurality of ribs  87  which engage the heating well  85  on the underside of the top plate  83 . In an embodiment, the heating well  85  has four ribs  87 . More or less ribs, or ribs with other shapes and orientations may be used to transfer the heat to the heating well in alternative embodiments, given fabrication and cost considerations. The presently disclosed embodiments provide a significant increase in the heat transfer area from the heating means to the heating well.  
      The geometry of the plurality of ribs  87  contained in the top plate  83  and the plurality of heat transfer pins  77  in the bottom plate  75  may be optimized to promote both single well temperature uniformity and also complete heat block temperature uniformity. The optimization is obtained by the size and orientation of the rib draft angle, rib thickness versus heating well position, pin size, pin draft angle, and other design dimensions and characteristics.  
      The amount of pin  77  to rib  87  contact area versus well position forms a design configuration for excellent temperature uniformity across the heat block. In an embodiment, for internal wells, four pins  77  contact each heating well rib  87  and the four pins  77  share contact with two heating well ribs  87  each. In an embodiment, for edge wells, four pins  77  contact each heating well rib  87 , but only three pins  77  share contact with two heating well ribs  87  each. The fourth pin  77  does not share contact with another well and therefore more heat from the fourth pin  77  is available for the edge heating wells  85  to help counteract the inherently cooler edge temperature of a heated rectangular body. The corner heating wells  85  benefit from four pins  77  which contact each heating well rib  87 . Only two of the pins  77  share contact with another heating well. The other two pins  77  do not share contact with another well and even more heat is available for the corner wells to counteract the inherently cooler corner temperature of a heated rectangular body. Those skilled in the art will recognize the number of pins and ribs may vary and still be within the spirit and scope of the presently disclosed embodiments.  
      As shown in  FIG. 1 , the bottom plate  75  comprises a plurality of recesses  78 . The plurality of recesses  78  have varying depths and are symmetrical about the bottom plate.  10  Each recess  78  is designed to promote the temperature uniformity across the heat block when engaged with the top plate  83 . The plurality of recesses  78  form an efficient way to promote temperature uniformity since they are efficiently formed via machining, casting, or other fabrication methods known in the art. Other shapes and patterns of recesses, or no recesses, may be used in alternative embodiments.  FIG. 2  shows a perspective view of the bottom plate  75  of the heat block  67 .  FIG. 3  shows a top perspective view of a top plate of a heat block  67 .  FIG. 4  shows a bottom perspective view of the top plate  83  of the heat block  67 .  
      As shown in  FIG. 5 , the top plate  83  engages the bottom plate  75  to form the heat block  67 . The top plate  83  may be connected to the bottom plate  75  by any mechanical engagement known in the art including, but not limited to glue, welding, snap fit, shrink fit, press fit, epoxy, adhesives and other mechanical fasteners known in the art and be within the spirit and scope of the presently disclosed embodiments. An alternative configuration could utilize a process where the bottom plate is used as a mold insert. In this way, the top plate could be molded and attached to the bottom plate during the molding process.  
      In addition to the top plate of the heat block having ninety-six heating wells shown in  FIGS. 1-5 , the heat block may have one or more dedicated wells  97  for measuring a simulated biological fluid sample temperature. The heat block may have one, two, three, four or more dedicated wells  97  for measuring a simulated biological fluid sample temperature. In an embodiment, the dedicated wells  97  for measuring a simulated biological fluid sample temperature are located along the edges of the heat block  67 . Those skilled in the art will recognize that the dedicated wells  97  for measuring a simulated biological fluid sample temperature could be located along the edges, in the middle or at other locations in the top plate  83  of the heat block  67 . A control system where a simulated biological fluid temperature measurement is used to make accurate transitions between biological sample fluid temperatures may also be used.  
      Although  FIGS. 1-5  show the heat block  67  with a  96  well configuration, those skilled in the art will recognize that  48  well,  384  well,  1536  well, and other multiple well heat blocks are within the spirit and scope of the presently disclosed embodiments.  
       FIG. 6  shows an alternative embodiment of the heat block  67  for use with  384  well plates. The top plate  83 , which can be made of a non-metal material may be molded in a variety of forms to best match commercially available sample container sizes and configurations. The  384  well format is often used for higher throughput of DNA samples. The bottom plate  75  may be cast or otherwise formed to support a variety of configurations.  
       FIG. 7  shows a view of a block heater  107  for heating the heat block  67 . The heater  107  is positioned below the bottom plate  75  of the heat block  67 . Heat is generated by the heater  107  and transferred to the bottom plate  75 . The heat transfer pins  77  of the bottom plate  75  then transfer the heat to the heating wells  85  in the top plate  83  that hold the sample tubes containing samples. Placing the heater  107  below the bottom plate  75  provides an efficient and uniform transfer of heat to the samples. The heater  107  may heat the samples by resistance heating, peltier heating and cooling passive air or water heating and other heating and cooling methods known in the art and be within the spirit and scope of the presently disclosed embodiments.  
      The heat block  67  may be used in a variety of ways. The heat block  67  may be used in isolation to process a plurality of samples. Alternatively, the heat block  67  may be used with a plurality of additional heat blocks  67  in order to perform various processes (i.e., a first heat block delivers heat to the samples for a first time period, a second heat block delivers heat to the samples for a second time period, a third heat block delivers heat to the samples for a third time period, etc.).  
      The following discussion illustrates one use of the heat block  67 . The following discussion is in no way meant to limit the use of the heat block of the presently disclosed embodiments. Those skilled in the art will recognize that various uses of the heat block are within the spirit and scope of the presently disclosed embodiments.  
      A plurality of heat blocks  67  may be used in conjunction to process a plurality of samples. The plurality of heat blocks may be utilized in a single process wherein each heat block may be operated at a different temperature. The plurality of heat blocks may be engaged to a central tube thereby creating a rotating heat assembly. The rotating heat assembly may be engaged to a processing apparatus. The rotating heat assembly may be rotated so that any of the heat blocks engaged to the rotating heat assembly may be positioned parallel to a plurality of sample tubes containing samples. The rotating heat assembly may be moved up and down in order to bring either heat block into thermal contact with the plurality of sample tubes. The presently disclosed embodiments include a method of improving PCR efficiency by using the apparatus of the presently disclosed embodiments to rapidly bring a plurality of heat blocks into and out of thermal contact with the plurality of sample tubes and avoiding the problems of raising and lowering the temperature of a single heat source.  
       FIG. 8  shows a perspective view of an embodiment wherein multiple heat blocks may engage a central tube  103 . The central tube  103  comprises a cylindrical geometry. A first heat block, a second heat block, and a third heat block may engage the central tube  103 . Those skilled in the art will recognize that the central tube  103  may have any of a variety of shapes and geometries and be within the spirit and scope of the presently disclosed embodiments.  
       FIG. 9  shows a perspective view of a rotating heat assembly  65  in which the plurality of heat blocks engage the central tube  103 . In  FIG. 9 , a first heat block  67 , a second heat block  69 , and a third heat block  71  engage the central tube  103  to produce the rotating heat block assembly  65 . The rotating heat block assembly  65  may comprise two, three, four or more heat blocks and be within the spirit and scope of the presently disclosed embodiments. Those skilled in the art will recognize that that various methods of engaging the heat blocks  67 ,  69 ,  71  to central tube  103  may be within the spirit and scope of the presently disclosed embodiments.  
      The rotating heat block assembly  65  may engage to a processing apparatus  100 . The use of the rotating heat block assembly  65 , comprising the plurality of heat blocks  67 ,  69 ,  71 , allows for a plurality of samples to be processed rapidly and efficiently. Those skilled in the art will recognize that various types of processing assemblies are within the spirit and scope of the presently disclosed embodiments.  
      Reference will now be made to the embodiment illustrated in  FIGS. 10-14 , unless otherwise noted.  FIGS. 10-14  illustrate an alternate embodiment of a first plate  200 , a second heat block plate, which is a heating plate  300  and a complete heat block assembly  400 , in accordance with the invention. The first plate  200  can be configured to be made of a thermally conductive material, can include a major upper surface having a substantially planar area and a plurality of well cavities or “heating wells”  285  for accepting a plurality of sample tubes defined therein. The term major upper surface is intended to mean an upper surface which constitutes a portion of an upper surface of the first plate  200 . For example, since wells  285  are formed in the first plate  200 , and interrupt the otherwise substantially planar upper surface, the space between the wells  285  is referred to as a major upper surface  283 . The purpose of the first plate is consistent with that of the top plate, such as top plate  83  of  FIG. 1 , described above. However, as is apparent, the configuration thereof is somewhat different.  
      The first plate  200 , in accordance with this embodiment is preferably made of a heat-conducting material such as a metal. However, metal-coated materials can be utilized, including, but not limited to metal-coated polymers, or metal-plated metals. Metals such as copper, nickel, chromium, gold, other suitable materials and combinations thereof can be used. In certain embodiments, the first plate  200  comprises a metal coating over a metal material. The metal coating is on an outer surface of the first plate  200 . The metal coating acts as a wear surface and permits easy cleaning of the first plate  200 . The metal coating also promotes the sensitivity of the instrument, when used to obtain quantitative data, by providing a more optically reflective surface as compared to the first plate surface (which may also be optically reflective). The metal coating or plating may comprise copper, nickel, chromium, gold, or a combination of multiple metals or other metals known to those skilled in the art. The metal coating may be applied using coating methods known in the art including, but not limited to, bath plating, physical, chemical, or ion vapor deposition, or other coating methods known in the art.  
      While shown in the accompanying figures as having  96  heating wells  285 , first plate  200  may include  48  well,  384  well,  1536  well, and other multiple well configurations. In addition, while shown as being substantially circular in cross section, the heating wells  285  may be of any shape suitable to the use of first plate  200  in thermal cycling.  
      The second plate  300  is configured to serve as a heating plate, and is configured to abut the major upper surface  283  of the first plate  200 , and/or to engage the first plate. The second plat preferably includes a plurality of apertures  310 , defined therein, which correspond to respective wells  285  of the first plate  200 . The second plate can further include a heating element  320 , carried by the plate  300 . Optionally, insulative portions  330  are provided between the heating element  320  and the edge of each aperture  310 . The purpose of such insulation is twofold. Firstly, the insulation serves to distribute the heat from the heating element  320 , allowing the edge of the aperture  310 , and anything in contact therewith to change temperature more gradually than the heating element  320  itself. Further, since the insulation is slower to transfer heat, the insulation moderates any temperature fluctuations of the heating element  320 , or the second plate  300  in general. When the heating element  320  is a resistive electrical heating element, the insulation also helps electrically insulate the edge of the apertures  310 , through which test tubes will normally pass, from the electrical current running through the heating element  320 .  
      This embodiment of first and second plates  200 ,  300 , and the combined heat block assembly  400  differ from the foregoing embodiments, and typical heat blocks, in that the second plate  300 , which is the heating plate, is in contact with an upper surface of the first plate. This provides certain advantages over typical heat blocks. Specifically, since the well walls  295  of heating wells  285  taper toward the bottom end  297  of each well, the cross-section of each well  285  is greater near the top of the well  285 , which is in direct thermal communication with the major upper surface  283  of the first plate  200 . Therefore, the upper portion of the well walls can conduct more heat than the bottom portion of the well walls. As configured in this embodiment, since heat will be applied via the second plate, which is in contact with the major upper surface  283  of the first plate  200 , heat will more effectively flow to the far end of the heating well  285 , which is the bottom end  297  thereof, than if heat were to flow in the opposite direction, that is, from the bottom  297  of the heating well to the top thereof, near the major upper surface  283 . As embodied, improved intra-well thermal uniformity is achieved.  
      A further advantage of this embodiment over certain typical heating blocks, is that a negative draft angle in forming for the first plate is not needed. Some typical thermal plates, which serve a similar purpose to that of the present first plate  200 , include a heating well bottom wall that is wider than the top, in order to better contact a heating element arranged on the bottom surface thereof. The present invention obviates such negative draft angle, and the cumbersome manufacturing processes needed to manufacture such components.  
      Still a further advantage of the embodiment of  FIGS. 10-14  is that in use, convective heat losses are reduced. Since many typical heating blocks provide a heating element arranged on a bottom of the heating block, heat can be lost through convection with the surrounding environment. The second plate  300  of the present heat block  400 , in use, will be situated between the first tray  200 , which is intentionally heated, and a cover of a processing apparatus, such as processing apparatus  100  in  FIG. 16 . Accordingly, little or no portion of the second plate  300  is exposed to the surrounding environment or subject to substantial convective heat loss. As a result, the temperature uniformity among wells  285  in the first plate  200  and the heating block  400  as a whole, is improved, as compared with a heating block having an exposed heating element.  
      Two boss extensions  287 , which extend away from the major upper surface  283 , along the long edge  282  of the heat block, are used for heat block retention in a supporting frame. These bosses  287  interface with cutouts  455  in a heat block retainer  450  ( FIG. 14 ), to capture and partially locate the heat block  400  in a heat block assembly  500 . Along one or both short edges  284  of the first plate, one or more bosses  289 , which can include a cavity  288  define therein, can be used to interface with a temperature sensor for simulating the temperature response of a biological sample mixture in contact with the heating wells  285 , albeit if through a vial or test tube wall. While the embodiment of  FIGS. 10-14  includes two such bosses  289  and cavities  288 , fewer than or more than two may be provided. Moreover, the precise location of these cavities can be altered given other system design considerations, and such temperature sensors can alternatively be provided in one or more of the wells  285  of the first tray  200 , as described above in connection with  FIGS. 1-5 .  
       FIG. 11  illustrates an underside of the first tray  200 , in accordance with this embodiment of the invention. As can be seen, substantially cylindrical recesses  293  are provided in the bottom surface  291  of the first plate  200 , opposite of the major upper surface  283 . These recesses  293  promote heat block temperature uniformity in the horizontal plane by distributing the heat block mass in the horizontal plane. Such distribution can be modified by selecting appropriate diameter, location, depth or other aspects, or other attributes to the recess  293 , including use of other shapes, such as polygonal shapes such as square, hexagonal and the like, or a hyperbolic shape, such as region  321  of the heating element of the second plate  300 , as will be described hereinbelow.  
      The second plate  300 , which acts as a heating plate for the subject heating block  400 , is best illustrated in  FIG. 12 . This heater contains apertures  310  defined therein, which correspond to the heating wells  285  provided in the first plate  200 . As such, in use, a sample tube, such as a vial or test tube can pass through one of the apertures  310 , and into a well  285 . Insulation  330  is provided around the apertures  310 , and a heating element  320  passes between rows of apertures  310  and insulation  330  in a substantially serpentine manner. As can be seen, the heating element  320  begins at each end at a connecting portion  340   a,    340   b.  from there, the heating element follows a path that passes between each row of apertures  310 , until reaching the opposite end. This configuration helps promote temperature uniformity throughout the second plate  300 , and the heating block  400  as a whole.  
      Insulating materials that can be used in conjunction with this second plate  300  include, but are not limited to silicone rubber, polyimide (PI), mica, polyester, nomex, and other similar materials. Such materials are described in U.S. Pat. No. 6,878,905, which is hereby incorporated by reference in its entirety. The insulating materials can be electrically insulative, thermally insulative or both electrically and thermally insulative.  
      The heating element  320  can include an electric resistive heating material, or can be another suitable type of heating element. A warm side of a Peltier junction can be configured to be in contact with the major upper surface  283  of the first tray  200 . Alternatively, a fluid-carrying conduit can be provided, to interface with an external source for heated or cooled fluid, such as a heat pump or a hot water supply.  
      The heating element  320 , as illustrated, includes expanded-width regions at points located between four apertures  310 , such regions having a substantially hyperbola-shaped border. Accordingly, heat is provided more evenly to regions near the circumference of the apertures  310  and heating wells  285 . Connection portions  340   a,    340   b  are provided to enable electrical connection of the heating element  320  of the second plate  300  to an electrical source.  
      If desired, the heating element can be substituted for an element that can provide heat or remove heat, or alternatively still, only remove heat, depending on the desired capability of the heating block. For example, a cool side of a Peltier junction can be used in place of a resistive heating element  320 . Alternatively still, if a tubular element is provided to conduct conditioning fluid, that is, heating or cooling fluid, then a cold fluid, such as chilled liquid or refrigerant can be used. If a heat pump system is utilized, then a user need only select the desired temperature, and the system will heat or cool the heating block as necessary.  
      The heating element  320  and/or cooling element, if so embodied, can be applied to a surface of the second plate  300 , or can be embedded therein. For example, fluid-carrying tubes can be provided on or in the second plate  300 . The heating/cooling elements  320  and insulation  330  can both be carried by a substrate, or can be mutually joined without a substrate, such that the second plate  300  is consistent in composition throughout cross-sections taken parallel to the substantially planar top and bottom surfaces thereof.  
      The first plate  200  and the second plate  300  can be joined in any suitable manner, such as those set forth above. That is, the first plate  200  can be connected to the second plate  300  by any mechanical engagement known in the art including, but not limited to glue, welding, snap fit, shrink fit, press fit, epoxy, adhesives and other mechanical fasteners known in the art and be within the spirit and scope of the presently disclosed embodiments. An alternative configuration could utilize a process where the plates are integrally formed, for example, in casting or molding.  
       FIG. 14  illustrates a perspective view of a rotating heat block assembly  500 , in which the plurality of heat blocks  400  engage a central tube  103 , similarly to the embodiment of  FIG. 9 . The rotating heat block assembly  500  can include two, three, four or more heat blocks and be within the spirit and scope of the presently disclosed embodiments. Those skilled in the art will recognize that that various methods of engaging the heat blocks  410   a,    410   b,    410   c  to central tube  103  may be within the spirit and scope of the presently disclosed embodiments.  
      The rotating heat block assembly  500  can engage to a processing apparatus  100  (See  FIG. 15 , for example). The use of the rotating heat block assembly  500  comprising the plurality of heat blocks  410   a - 410   c  allows for a plurality of samples to be processed rapidly and efficiently. Those skilled in the art will recognize that various types of processing assemblies are within the spirit and scope of the presently disclosed embodiments.  FIG. 15 ,  FIG. 16  and  FIG. 17  show various views of an embodiment of the processing apparatus  100 .  FIG. 15  shows a perspective view of the rotating heat assembly  65  as part of the processing apparatus  100 . In  FIG. 15 , a tube cover  13  is in an open position. The tube cover  13  comprises a tube cover handle  11  for moving the tube cover  13  from an open position to a closed position. The tube cover  13  may include a tube cover heater  15 . A sample retainer  43  contains a plurality of sample wells  38  for receiving a plurality of sample tubes  39 . The plurality of sample tubes  39  are placed in the plurality of sample wells  38 . The sample wells  38  provide a means to accommodate a variety of sample tube  39  formats commonly used for biological experiments. Some of these sample tube  39  formats include, but are not limited to, strips of eight tubes, flange connected plates of  96  tubes, single tubes, and other tube configurations known in the art. A sample carrier  45  supports the sample retainer  43 .  
       FIG. 15  shows the rotating heat assembly  65  engaged with the processing apparatus  100 . The rotating heat assembly  65  comprises a plurality of heat blocks. In  FIG. 15 , the rotating heat assembly  65  comprises three heat blocks: a first heat block  67 , a second heat block  69  and a third heat block  71 .  
      The first heat block  67  is capable of reaching and maintaining a first temperature, the second heat block  69  is capable of reaching and maintaining a second temperature, and the third heat block  71  is capable of reaching and maintaining a third temperature. The first temperature, the second temperature and the third temperature can be the same or distinct from one another. In some embodiments, only the first temperature and the second temperature are distinct, and the third temperature is the same as the first temperature or the second temperature. Those skilled in the art will recognize that each heat block may reach and maintain any temperature and be within the spirit and scope of the presently disclosed embodiments.  
      As shown in  FIG. 15 , the plurality of heat blocks  67 ,  69 ,  71  are engaged to the central tube  103  wherein the central tube  103  runs from a first slide  37  to a second slide  53  and the central axis of the central tube  103  is substantially horizontal.  
      The plurality of heat blocks  67 ,  69 ,  71  each have the top plate  83  with a plurality of heating wells  85 . While the figures show the heat blocks  67 ,  69 ,  71  with the top plate  83  having  96  heating wells  85 , those skilled in the art will recognize that the heat block may have  48  wells,  384  wells,  1536  wells, and other numbers of wells and be within the spirit and scope of the presently disclosed embodiments. The number of heating wells  85  in the top plate  83  corresponds to the number of sample wells  38  in the sample retainer  43 .  
      As shown in  FIG. 15 , the central tube  103  is rotated by a rotation motor  49  that is mechanically connected to the central tube  103 . The central tube  103  is rotated so the top plate  83  of the heat block  67 ,  69  or  71  is below, aligned with and substantially parallel to the sample retainer  43 . Each sample well  38  of the sample retainer  43  is positioned above the heating well  85  of the top plate  83  of the heat block  67 ,  69  or  71 . As will be discussed in greater detail below, the rotating heat assembly  65  may be raised and lowered, allowing the plurality of sample tubes  39  supported in the plurality of sample wells  38  to be received by respective ones of the plurality of heating wells  85 . The plurality of sample tubes  39  are thus in thermal contact with the plurality of heating wells  85  of the top plate  83 .  
      The rotating heat assembly  65  may be raised and lowered to any desired vertical position. The rotating heat assembly  65  may be raised and/or lowered manually or automatically using a motor  25 . Those skilled in the art will recognize that various mechanisms and/or motors may be utilized to raise and lower the heat block  67  of the rotating heat assembly  65  and be within the spirit and scope of the presently disclosed embodiments.  
       FIG. 16  shows a close up view of the rotating heat assembly  65  as part of the processing apparatus  100 .  FIG. 16  shows a view from below the sample retainer  43 . The rotating heat assembly  65  is engaged to the processing apparatus  100 . The top plate  83  of the second heat block  69  is below, aligned with and substantially parallel to the sample retainer  43 . The plurality of heating wells  85  of the second heat block  69  are positioned beneath the plurality of sample tubes  39 . The plurality of sample tubes  39  are located within the plurality of sample wells  38  of the sample retainer  43 . A sample fluid sensor  57  or a plurality of sample fluid sensors  57  are operatively connected to the sample retainer  43 .  
      The rotating heat assembly  65  may be rotated to a desired position. As shown in  FIG. 16 , a rotational position sensor  63  is in communication with the rotating heat assembly  65 . The rotational position sensor  63  controls and/or indicates the current rotational position of the rotating heat assembly  65 . The rotating heat assembly  65  may be raised or lowered to a desired vertical position. A vertical position sensor  59  is in communication with the top plate  83  of the heat block  67 . The vertical position sensor  59  controls and/or indicates the current vertical position of the rotating heat assembly  65 . The position sensors  59 ,  63  provide a repeatable position signal. The position sensors  59 ,  63  are selected to support a position resolution sufficient for reliable motion. In an embodiment, the position sensors  59 ,  63  comprise multiple terminals for wire harness connection. Those skilled in the art will recognize that various rotational and/or vertical position sensors known in the art may be within the spirit and scope of the presently disclosed embodiments.  
       FIG. 17  shows a perspective view of the rotating heat assembly  65  as part of the processing apparatus  100 . In  FIG. 17 , the tube cover  13  has been lowered to a closed position to cover the sample retainer  43  and the plurality of sample tubes  39 . The tube cover  13  comprises the tube cover heater  15  (shown in  FIG. 15 ). Closing the tube cover  13  and activating the tube cover heater  15  heats the plurality of sample tubes  39 . The tube cover heater  15  provides heat to the plurality of sample tubes  39  to provide a desired temperature profile. The tube cover heater  15  may provide a constant temperature or a variable temperature during processing of the plurality of sample tubes  39 . The tube cover heater  15  may be used in conjunction with the rotating heat assembly  65  to achieve a desired temperature profile of the plurality of sample tubes  39 . Those skilled in the art will recognize that various temperature profiles are within the spirit and scope of the presently disclosed embodiments.  
      The tube cover  13  comprises a temperature sensor to sense a cover temperature so that this temperature may be actively controlled. The temperature sensor may be a thermistor engaged to the tube cover  13 . The thermistor has multiple lead wires that exit the tube cover  13  and are operatively connected to the thermal system.  
      A temperature sensor may be positioned in a sample container within a sample well  38  of the sample retainer  43  to measure the temperature of the heat block  67 . The temperature data from the temperature sensor is sent to a controller which will then adjust the amount of heat provided by the heat source. The temperature sensor may be a thermistor. The thermistor accurately controls the components involved in a temperature transition. Those skilled in the art will recognize that thermocouples, resistance temperature detectors (RTD) or other temperature sensors known in the art are within the spirit and scope of the presently disclosed embodiments.  
      The presently disclosed embodiments provides a method of performing thermal cycling comprising placing at least one sample tube  39  in at least one sample well  38  of the sample retainer  43  engaged to a main frame of the processing assembly  100 . The rotating heat assembly  65  is rotated so the top plate  83  of the first heat block  67  is positioned below the sample retainer  43 . The top plate  83  comprises at least one heating well  85 . The rotating heat assembly  65  is raised to bring the heating well  85  into thermal contact with the plurality of sample tubes  39  and allow the heating wells  85  remain in thermal contact with the plurality of sample tubes  39  for a first time period at a first temperature. The rotating heat assembly  65  is lowered to separate the plurality of heating wells  85  from the plurality of sample tubes  39  so the heating wells  85  and sample tubes  39  are no longer in thermal contact.  
      The second heat block  69  is heated to a second temperature and the second heat block  69  is rotated into a position below the sample retainer  43 . The rotating heat assembly  65  is raised to bring the second heat block  69  into thermal contact with the plurality of sample tubes  39 . The plurality of heating wells  85  remain in thermal contact with the plurality of sample tubes  39  for a second time period at a second temperature so the samples in the plurality of sample tubes  39  attain a desired temperature profile. The rotating heat assembly  65  is lowered after the second heat block  69  has heated the plurality of sample tubes  39  for a sufficient time period. The rotating heat assembly  65  is lowered to separate the plurality of heating wells  85  from the plurality of sample tubes  39  so the heating wells  85  and sample tubes  39  are no longer in thermal contact.  
      The third heat block  71  is heated to a third temperature and the third heat block  71  is rotated into a position below the sample retainer  43 . The rotating heat assembly  65  is raised to bring the third heat block  71  into thermal contact with the plurality of sample tubes  39 . The plurality of heating wells  85  remain in thermal contact with the plurality of sample tubes  39  for a third time period at a third temperature so the samples in the plurality of sample tubes  39  attain a desired temperature profile. The rotating heat assembly  65  is lowered after the third heat block  71  has heated the plurality of sample tubes  39  for a sufficient time period. The rotating heat assembly  65  is lowered to separate the plurality of heating wells  85  from the plurality of sample tubes  39  so the heating wells  85  and sample tubes  39  are no longer in thermal contact.  
      The method may be repeated for multiple heat blocks. The heat blocks may operate at a constant temperature or a variable temperature while in thermal communication with the plurality of sample tubes. The heat blocks of the rotating heat assembly may operate at varying temperature and for varying time periods for the samples to reach a desired temperature profile.  
      Other sample holding structures such as slides, partitions, beads, channels, reaction chambers, vessels, surfaces, or any other suitable device for holding a sample can be used with the presently disclosed embodiments. The samples to be placed in the sample holding structure are not limited to biological reaction mixtures. Samples could include any type of product for which it is desired to heat and/or cool, such as cells, tissues, microorganisms or non-biological product.  
      Each sample tube  39  can have a corresponding cap for maintaining the biological reaction mixture in the sample tube. The caps are typically inserted inside the top cylindrical surface of the sample tube. The caps are relatively clear so that light can be transmitted through the cap. Similar to the sample tubes, the caps are typically made of molded polypropylene, however, other suitable materials are acceptable. Each cap has a thin, flat, plastic optical window on the top surface of the cap. The optical window in each cap allows radiation such as excitation light to be transmitted to the DNA samples and emitted fluorescent light from the DNA to be transmitted back to an optical detection system during cycling.  
      Heat blocks in accordance with the invention can be used with thermal cyclers of various makes and models, and is not limited to use in a thermal cycler as exemplified in  FIGS. 8, 9  and  14 - 17 . Other thermal cycler systems and methods of detecting the fluorescence from a PCR reaction could also benefit from a heat block of the presently disclosed embodiments. For example, the heat block could be used with the apparatus for thermally cycling samples of biological material described in assignee&#39;s U.S. Pat. No. 6,657,169, and the entirety of this patent is hereby incorporated herein by reference. The heat block can also be used with the Mx3000P Real-Time PCR System and the Mx4000 Multiplex Quantitative PCR System (commercially available from Stratagene Calif. in La Jolla, Calif.) using a tungsten halogen bulb that sequentially probes each sample, detected with a photomultiplier tube. In addition, the heat block could be used with thermal cyclers incorporating any or all of the following: a tungsten halogen bulb that sequentially probes each sample; a scanning optical module; stationary light emitting diodes (LEDs) for each well and the same detector for all wells; stationary samples, light sources, and detectors; stationary LEDs and a detector to probe spinning samples sequentially; a tungsten halogen bulb to illuminate the entire plate and a charge-coupled device detection of the entire plate; a stationary light source and multiple detectors sampling spinning capillaries sequentially; a stationary laser and detector that sequentially probes stationary samples using independent fiber optics collecting light from each sample; a tungsten halogen bulb to illuminate the entire plate and charge-coupled device detection of the entire plate, and other thermal cyclers known in the art.  
      All patents, patent applications, and published references cited herein are hereby incorporated by reference in their entirety. It will be appreciated that various of the above-disclosed and other features and functions, or alternatives thereof, may be desirably combined into many other different systems or applications. Various presently unforeseen or unanticipated alternatives, modifications, variations, or improvements therein may be subsequently made by those skilled in the art which are also intended to be encompassed by the following claims.