# US 2019/0168215 A1 · Three-stage thermal convection apparatus and uses thereof > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 2019/0168215 A1 - Document ID: US20190168215A1 - Status: Published application - Kind: A1 - Application number: 16/108,547 - Filed: 2018-08-22 - Published: 2019-06-06 - Earliest claimed: 2010-01-12 - Assignees: Ahram Biosystems, Inc. - Applicants: Ahram Biosystems, Inc. - Inventors: Hyun Jin Hwang - Web page: https://patentgrep.com/patent/US20190168215A1 ## CPC - B01L 3/50851: {specially adapted for heating or cooling samples} - B01L 7/52: {with provision for submitting samples to a predetermined sequence of different temperatures, e.g. for treating nucleic acid samples} - B01L 3/50825: {Closing or opening means, corks, bungs} - B01L 2200/142: Preventing evaporation - B01L 2200/147: Employing temperature sensors - B01L 2300/042: Caps; Plugs - B01L 2300/0654: Lenses; Optical fibres - B01L 2300/0861: Configuration of multiple channels and/or chambers in a single devices - B01L 2300/1805: Conductive heating, heat from thermostatted solids is conducted to receptacles, e.g. heating plates, blocks - B01L 2300/1822: using Peltier elements - B01L 2300/1844: using fans - B01L 2300/1883: using thermal insulation - B01L 2400/0409: centrifugal forces - B01L 2400/0445: Natural or forced convection - B01L: CHEMICAL OR PHYSICAL LABORATORY APPARATUS FOR GENERAL USE ## Abstract Disclosed is a multi-stage thermal convection apparatus and uses thereof. In one embodiment, the invention features a three-stage thermal convection apparatus that includes a temperature shaping element for assisting a thermal convection mediated Polymerase Chain Reaction (PCR). The invention has a wide variety of applications including amplifying nucleic acid without cumbersome and expensive hardware associated with many prior devices. In a typical embodiment, the apparatus can fit in the palm of a user's hand for use as a portable, simple to operate, and low cost PCR amplification device. ## Claims ### Claim 1 An apparatus adapted to perform thermal convection PCR comprising: (a) a first heat source for heating or cooling a channel and comprising a top surface and a bottom surface, the channel being adapted to receive a reaction vessel for performing PCR, (b) a second heat source for heating or cooling the channel and comprising a top surface and a bottom surface, the bottom surface facing the top surface of the first heat source, (c) a third heat source for heating or cooling the channel and comprising a top surface and a bottom surface, the bottom surface facing the top surface of the second heat source, wherein the channel is defined by a bottom end contacting the first heat source and a through hole contiguous with the top surface of the third heat source, and further wherein center points between the bottom end and the through hole form a channel axis about which the channel is disposed, (d) at least one temperature shaping element such as at least one protrusion in at least one of the first, second and third heat sources, the protrusion being disposed about the channel axis and extending toward an adjacent heat source or away from the top or bottom surface of the heat source that comprises the protrusion; and (e) a receptor hole adapted to receive the channel within the first heat source. ### Claim 2 (depends on 1) The apparatus of claim 1, wherein the apparatus comprises a first insulator positioned between the top surface of the first heat source and the bottom surface of the second heat source. ### Claim 3 (depends on 2) The apparatus of claim 2, wherein the apparatus comprises a second insulator positioned between the top surface of the second heat source and the bottom surface of the third heat source. ### Claim at position 4 4-5. (canceled) ### Claim 6 (depends on 1) The apparatus of claim 1, wherein the apparatus comprises a first chamber disposed around the channel and within at least part of the first, second or third heat source, the first chamber comprising a chamber gap between the second or third heat source and the channel sufficient to reduce heat transfer between the second or third heat source and the channel. ### Claim 7 (depends on 6) The apparatus of claim 6, wherein the first chamber is positioned within the second heat source and comprises a first chamber top end facing a first chamber bottom end along the channel axis and at least one chamber wall disposed around the channel axis. ### Claim 8 (depends on 7) The apparatus of claim 7, wherein the apparatus further comprises a second chamber positioned in the second heat source. ### Claim at position 8 9-16. (canceled) ### Claim 17 (depends on 2) The apparatus of claim 2, wherein the first insulator comprises a solid or a gas. ### Claim 18 (depends on 3) The apparatus of claim 3, wherein the second insulator comprises a solid or a gas. ### Claim 19 (depends on 6) The apparatus of claim 6, wherein the first chamber comprises a solid or a gas. ### Claim 20 (canceled) ### Claim 21 (depends on 17, 18, 19) The apparatus of any of claims 17-19, wherein the gas is air. ### Claim at position 14 22-40. (canceled) ### Claim 41 (depends on 6) The apparatus of claim 6, wherein the first chamber is disposed essentially symmetrically about the channel along a plane perpendicular to the channel axis. ### Claim 42 (depends on 6) The apparatus of claim 6, wherein at least part of the first chamber is disposed asymmetrically about the channel along a plane perpendicular to the channel axis. ### Claim at position 17 43-54. (canceled) ### Claim 55 (depends on 8) The apparatus of claim 8, wherein the first chamber is spaced from the second chamber by a length (l) along the channel axis. ### Claim 56 (depends on 55) The apparatus of claim 55, wherein the first chamber, the second chamber, and the second heat source define a first thermal brake contacting the channel between the first and second chambers with an area and a thickness (or a volume) sufficient to reduce heat transfer from the first heat source or to the third heat source. ### Claim at position 20 57-58. (canceled) ### Claim 59 (depends on 7) The apparatus of claim 7, wherein the apparatus comprises a first insulator positioned between the top surface of the first heat source and the bottom surface of the second heat source, and the first chamber and the first insulator define a first thermal brake contacting the channel between the first chamber and the first insulator with an area and a thickness (or a volume) sufficient to reduce heat transfer from the first heat source. ### Claim 60 (depends on 59) The apparatus of claim 59, wherein the first thermal brake comprises a top surface and a bottom surface and the bottom surface of the first thermal brake is located at about the same height as the bottom surface of the second heat source. ### Claim at position 23 61-78. (canceled) ### Claim 79 (depends on 1) The apparatus of claim 1, wherein the second heat source comprises at least one protrusion extending away from the second heat source toward the first or third heat source. ### Claim at position 25 80-86. (canceled) ### Claim 87 (depends on 1) The apparatus of claim 1, wherein the first heat source comprises at least one protrusion extending away from the first heat source toward the second heat source or away from the bottom surface of the first heat source. ### Claim at position 27 88-92. (canceled) ### Claim 93 (depends on 1) The apparatus of claim 1, wherein the third heat source comprises at least one protrusion extending away from the third heat source toward the second heat source or away from the top surface of the third heat source. ### Claim at position 29 94-98. (canceled) ### Claim 99 (depends on 1) The apparatus of claim 1, wherein the apparatus is adapted so that the channel axis is tilted with respect to the direction of gravity. ### Claim 100 (depends on 99) The apparatus of claim 99, wherein the channel axis is perpendicular to the top or bottom surface of any of the first, second, and third heat sources, and the apparatus is tilted. ### Claim 101 (depends on 99) The apparatus of claim 99, wherein the channel axis is tilted from a direction perpendicular to the top or bottom surface of any of the first, second, and third heat sources. ### Claim at position 33 102-180. (canceled) ### Claim 181 (depends on 1) The apparatus of claim 1, wherein the apparatus is adapted to generate a centrifugal force inside the channel so as to modulate the convection PCR. ### Claim at position 35 182-192. (canceled) ### Claim 193 (depends on 181) A PCR centrifuge adapted to perform a polymerase chain reaction (PCR) under centrifugation conditions, the PCR centrifuge comprising the apparatus featured in claim 181. ### Claim 194 A method for performing a polymerase chain reaction (PCR) by thermal convection, the method comprising at least one and preferably all of the following steps: (a) maintaining a first heat source comprising a receptor hole at a temperature range suitable for denaturing a double-stranded nucleic acid molecule and forming a single-stranded template, (b) maintaining a third heat source at a temperature range suitable for annealing at least one oligonucleotide primer to the single-stranded template, (c) maintaining a second heat source at a temperature suitable for supporting polymerization of the primer along the single-stranded template; and (d) producing thermal convection between the receptor hole and the third heat source under conditions sufficient to produce the primer extension product, wherein a channel that is adapted to receive a reaction vessel for performing the PCR is defined by a bottom end of the receptor hole contacting the first heat source and a through hole contiguous with the top surface of the third heat source, and further wherein center points between the bottom end of the receptor hole and the through hole form a channel axis about which the channel is disposed; and wherein the method further comprising a step of providing at least one protrusion in at least one of the first, second and third heat sources, the protrusion being disposed about the channel axis and extending toward an adjacent heat source or away from the top or bottom surface of the heat source that comprises the protrusion. ### Claim 195 (depends on 194) The method of claim 194, wherein the method further comprises a step of providing the reaction vessel comprising the double-stranded nucleic acid molecule and the oligonucleotide primer in aqueous solution, and a DNA polymerase in aqueous solution or an immobilized DNA polymerase. ### Claim at position 39 196-197. (canceled) ### Claim 198 (depends on 195) The method of claim 195, wherein the method further comprises a step of contacting the reaction vessel to the receptor hole and at least one temperature shaping element such as a chamber disposed within at least one of the first, second or third heat source, the contacting being sufficient to support the thermal convection within the reaction vessel. ### Claim 199 (depends on 198) The method of claim 198, wherein the method further comprises a step of contacting the reaction vessel to a first insulator between the first and second heat sources and a second insulator between the second and third heat sources. ### Claim at position 42 200-201. (canceled) ### Claim 202 (depends on 195) The method of claim 195, wherein the method further comprises a step of producing a fluid flow within the reaction vessel that is essentially symmetric about the channel axis. ### Claim 203 (depends on 195) The method of claim 195, wherein the method further comprises a step of producing a fluid flow within the reaction vessel that is asymmetric about the channel axis. ### Claim 204 (depends on 195) The method of claim 195, wherein at least steps (a)-(c) consume less than about 1 W of power per reaction vessel to produce the primer extension product. ### Claim at position 46 205-208. (canceled) ### Claim 209 (depends on 194) The method of claim 194, wherein the method further comprises a step of applying a centrifugal force to the reaction vessel conducive to performing the PCR. ### Claim 210 (depends on 1) A method for performing a polymerase chain reaction (PCR) by thermal convection, the method comprising the steps of adding an oligonucleotide primer, nucleic acid template, DNA polymerase, and buffer to a reaction vessel received by the apparatus of claim 1 under conditions sufficient to produce a primer extension product. ### Claim 211 (canceled) ### Claim 212 (depends on 193) A method for performing a polymerase chain reaction (PCR) by thermal convection, the method comprising the steps of adding an oligonucleotide primer, nucleic acid template, DNA polymerase, and buffer to a reaction vessel received by the PCR centrifuge of claim 193 and applying a centrifugal force to the reaction vessel under conditions sufficient to produce a primer extension product. ### Claim at position 51 213-238. (canceled) ### Claim 239 (depends on 1, 181) The apparatus of any of claims 1 and 181 further comprising at least one optical detection unit. ### Claim 240 (depends on 193) The PCR centrifuge of claim 193, further comprising at least one optical detection unit. ### Claim 241 (depends on 194, 209) The method of any one of claims 194 and 209, further comprising the step of detecting the primer extension product in real-time by using at least one optical detection unit. ### Claim 242 (depends on 210, 212) The method of any one of claims 210 and 212, further comprising the step of detecting the primer extension product in real-time by using at least one optical detection unit.