Devices and methods for nucleic acid extraction

Abstract

Disclosed herein are methods and devices for preparing a sample of nucleic acid molecules from a biological sample. The methods and devices may perform similarly to or better than standard sample preparation methods. The nucleic acid molecules prepared using the methods and devices provided herein may be utilized for downstream applications, including polymerase chain reaction (PCR).

1 . An apparatus, comprising:
 (a) a housing;   (b) a sample input module defining an input reservoir configured to receive a biological sample, the biological sample containing a biological entity;   (c) a lysing and inactivation module disposed within the housing, the lysing and inactivation module including a heater and first flow member, the first flow member defining a volume configured to receive an input solution containing at least the biological sample and a lysis buffer, the heater coupled to the first flow member and configured to convey thermal energy into the volume to A) lyse at least a portion of the biological sample thereby releasing a plurality of nucleic acid molecules and B) inactivate an enzyme within the input solution when a volume of the input solution flows through the volume; and   (d) an amplification module disposed within the housing, the amplification module including a second flow member configured to receive the volume of the input solution from the lysing and inactivation module, the amplification module configured to amplify a nucleic acid molecule from the plurality of nucleic acid molecules within the volume of the input solution to produce an output containing a target amplicon.   
     
     
         2 . The apparatus of  claim 1 , wherein a wall of the lysing and inactivation module that defines the volume has a surface area, a ratio of the surface area to the volume being greater than about 10 cm −1 . 
     
     
         3 . The apparatus of  claim 11 , wherein
 the lysing and inactivation module defines a vent opening into the volume.   
     
     
         4 . The apparatus of  claim 3 , wherein the lysing and inactivation module includes a sensor disposed within the volume, the sensor configured to produce an electronic signal indicating the presence of the input solution within the volume, the heater activated in response to the electronic signal. 
     
     
         5 . The apparatus of  claim 1 , wherein:
 (a) the heater is a first heater;   (b) the second flow member defines an amplification flow path; and   (c) the amplification module includes a second heater different from the first heater, the second heater coupled to the second flow member and configured to convey thermal energy into the amplification flow path to amplify the nucleic acid molecule from the plurality of nucleic acid molecules.   
     
     
         6 . The apparatus of  claim 1 , further comprising:
 (a) a non-electronic sample actuator to produce a pressure within the sample input module to convey the biological sample from the sample input module towards the lysing and inactivation module; and   (b) a fluid pump disposed within the housing, the fluid pump configured to produce a flow of the input solution from the lysing and inactivation module to the amplification module.   
     
     
         7 . The apparatus of  claim 6 , wherein:
 (a) the flow of the input solution from the lysing and inactivation module to the amplification module is in a first direction; and   (b) the lysing and inactivation module includes a check valve to configured to prevent a flow of the input solution in a second direction.   
     
     
         8 . The apparatus of  claim 1 , wherein:
 (a) a first portion of the first flow member is heated to a first temperature zone;   (b) a second portion of the first flow member is heated to a second temperature zone; and   (c) lysing and inactivation occur as the input solution flows through the first flow member.   
     
     
         9 . A method of nucleic acid extraction, comprising:
 (a) conveying a biological sample into a sample input module of a molecular diagnostic test device; and   (b) actuating the molecular diagnostic test device to:
 (c) convey the biological sample from the sample input module to a lysing and inactivation module, the lysing and inactivation module including a heater and defining a reaction volume; 
 (d) maintain an input solution containing the biological sample and a lysis buffer within the reaction volume to lyse at least a portion of the biological sample thereby extracting a plurality of nucleic acid molecules; 
 (e) activate the heater to heat a portion of the lysing and inactivation module to produce an inactivation temperature zone within the reaction volume; and 
 (f) produce a flow of the input solution within the reaction volume such that a volume of the input solution is heated within the inactivation temperature zone to inactivate an enzyme within the input solution. 
   
     
     
         10 . The method of  claim 9 , wherein
 the lysing and inactivation module defines a vent opening into the reaction volume.   
     
     
         11 . The method of  claim 9 , wherein the portion of the lysing and inactivation module is a second portion, and wherein the actuating the molecular diagnostic test device further causes the molecular diagnostic test device to:
 (a) heat a first portion of the lysing and inactivation module to produce a lysing temperature zone within the reaction volume, the flow of the input solution within the reaction volume being such that the volume of the input solution is heated within the lysing temperature zone to lyse a biological entity within the volume of the input solution.   
     
     
         12 . The method of  claim 9 , wherein the actuating the molecular diagnostic test device includes moving a sample actuator to produce a pressure within the sample input module to convey the biological sample from the sample input module towards the lysing and inactivation module. 
     
     
         13 . The method of  claim 12 , wherein the actuating the molecular diagnostic test device further causes the molecular diagnostic test device to:
 (a) receive an electronic signal from a sensor within the lysing and inactivation module, the electronic signal indicating the presence of the input solution within the reaction volume; and   (b) activate the heater in response to the electronic signal.   
     
     
         14 . The method of  claim 9 , wherein the actuating the molecular diagnostic test device further causes the molecular diagnostic test device to:
 (a) heat a portion of an amplification module within the molecular diagnostic test device to amplify a nucleic acid from the plurality of nucleic acid molecules to produce an output containing a target amplicon; and   (b) convey the output to a detection module of the molecular diagnostic test device.   
     
     
         15 . The method of  claim 9 , wherein the molecular diagnostic test device is devoid of a filter. 
     
     
         16 . The method of  claim 9 , wherein:
 the molecular diagnostic test device further includes an amplification module and a detection module; and   the actuating the molecular diagnostic test device further causes the molecular diagnostic test device to:
 convey the input solution to the amplification module; 
 heat the input solution within the amplification module to amplify a nucleic acid from the plurality of nucleic acid molecules to produce an output containing a target amplicon; and 
 convey the output to the detection module of the molecular diagnostic test device to react the target amplicon with a detection reagent to produce a signal that indicates a presence of the target amplicon. 
   
     
     
         17 . The method of  claim 9 , wherein
 the reaction volume of the lysing and inactivation module includes a flow member, and   the portion of the lysing and inactivation module is a second portion of the flow member, and wherein the actuating the molecular diagnostic test device further causes the molecular diagnostic test device to:
 (a) heat a first portion of the flow member to a lysing temperature zone, and 
 (b) heat the second portion of the flow member to the inactivation temperature zone. 
   
     
     
         18 . The method of  claim 9 , wherein lysing and inactivation occur as the input solution flows through the flow member. 
     
     
         19 . A molecular diagnostic test device, comprising:
 a housing;   a flow path defined within the housing;   a sample input module within the flow path, the sample input module defining an input reservoir configured to receive a biological sample, the biological sample containing a biological entity;   a lysing module within the flow path, the lysing module including a heater and first flow member, the first flow member defining a volume configured to receive an input solution from the sample input module, the input solution containing at least the biological sample, the heater coupled to the first flow member and configured to convey thermal energy into the volume to lyse at least a portion of the biological sample thereby releasing a plurality of nucleic acid molecules; and   an amplification module disposed within the flow path, the amplification module including a second flow member fluidically coupled to the first flow member and configured to receive the input solution from the lysing module, the amplification module configured to amplify a nucleic acid molecule from the plurality of nucleic acid molecules within the input solution to produce an output containing a target amplicon.   
     
     
         20 . The molecular diagnostic test device of  claim 19 , wherein the molecular diagnostic test device is configured to inactivate an enzyme within the input solution when the input solution flows within the flow path from the lysing module towards the amplification module.