Nucleic acid classification

Abstract

A method and system for classifying a target nucleic acid includes exposing, in a test system, one or more capture probes to the target nucleic acid. The one or more capture probes is attached to a surface. A first hybridization condition is established in the test system. A first degree of hybridization of the one or more capture probes with the target nucleic acid under the first hybridization condition is determined. A second hybridization condition in the test system is established. A second degree of hybridization of the one or more capture probes with the target nucleic acid under the second hybridization condition is determined and the target nucleic acid is classified by comparing the first and the second degrees of hybridization.

What is claimed is: 
     
         1 . A method for classifying a target nucleic acid, the method comprising:
 exposing, in a test system, one or more capture probes to the target nucleic acid, the one or more capture probes being attached to a surface;   establishing a first hybridization condition in the test system;   determining a first degree of hybridization of the one or more capture probes with the target nucleic acid under the first hybridization condition;   establishing a second hybridization condition in the test system;   determining a second degree of hybridization of the one or more capture probes with the target nucleic acid under the second hybridization condition; and   classifying the target nucleic acid by comparing the first and the second degrees of hybridization.   
     
     
         2 . The method of  claim 1 , wherein:
 the test system comprises one or more sensors on the surface configured to measure hybridization of the one or more capture probes with the target nucleic acid.   
     
     
         3 . The method of  claim 2 , wherein:
 the sensor is a resonator array configured to measure a mass of an object on at least one surface of the resonator array;   the one or more captures probes are attached to the surface of the resonator system; and   determining the first and second degrees of hybridization of the one or more capture probes with the target nucleic acid comprises measuring the mass on the surface of the resonator array.   
     
     
         4 . The method of  claim 1 , wherein:
 exposing the one or more capture probes to the target nucleic acid comprises contacting the one or more capture probes with a solution containing the target nucleic acid;   establishing the first hybridization condition comprises adjusting a temperature of the solution to a first temperature; and   establishing the second hybridization condition comprises adjusting the temperature of the solution to a second temperature.   
     
     
         5 . The method of  claim 1 , wherein the first hybridization condition is selected to minimize hybridization between a target nucleic acid and the one or more capture probes, and wherein the second hybridization condition is selected to favor hybridization between the target nucleic acid and the one or more capture probes. 
     
     
         6 . The method of  claim 1 , wherein classifying the target nucleic acid comprises:
 progressively adjusting one or more hybridization conditions of the test system to favor hybridization between a target nucleic acid and the one or more capture probes;   after each adjustment, determining a degree of hybridization of the one or more capture probes with the target nucleic acid; and   continuing to adjust the hybridization conditions until the degree of hybridization reaches a threshold degree of hybridization.   
     
     
         7 . The method of  claim 1 , wherein the test system comprises one or more first capture probes at a first location and one or more second capture probes at a second location, and wherein classifying the target nucleic acid comprises:
 progressively adjusting one or more hybridization conditions of the test system;   after each adjustment, determining a respective degree of hybridization for each of the first and second locations; and   determining whether the degree of hybridization at the first location reaches a threshold degree of hybridization prior to or after the degree of hybridization at the second location reaches the threshold degree of hybridization.   
     
     
         8 . The method of  claim 1 , further comprising calibrating the test system prior to exposing the one or more capture probes to the target nucleic acid, including:
 attaching one or more double stranded nucleic acid capture probes to a surface of the test system;   contacting the one or more double stranded nucleic acid capture probes with a solution;   progressively adjusting one or more hybridization conditions of the test system until a degree of dissociation of the double stranded nucleic acid capture probes is reached, so that the solution contains single stranded nucleic acid and single stranded nucleic acid capture probes remain on the surface; recording the one or more hybridization conditions at which the degree of dissociation of a first double stranded nucleic acid capture probes is reached, generating a single stranded nucleic acid; and   removing the single stranded nucleic acid from the test system.   
     
     
         9 . The method of  claim 8 , further comprising calibrating the test system prior to exposing the one or more capture probes to the target nucleic acid, including:
 measuring a first set of nucleic acid capture probes attached to the surface of the test system;   progressively adjusting the one or more hybridization conditions of the test system until the recorded hybridization condition is passed;   measuring a second set of nucleic acid capture probes attached to the surface of the test system; and   determining changes to the single stranded nucleic acid capture probes based on the first set of nucleic acid capture probes and the second set of nucleic acid capture probes.   
     
     
         10 . A method for determining an optimal density of capture probes, the method comprising:
 classifying a target nucleic acid; and   determining the optimal density of capture probes on a test system, wherein determining comprises:   exposing, in a test system, at a hybridization condition, a first set of capture probes to the target nucleic acid, the first set of capture probes being attached to a first surface;   determining a first association rate at the first surface;   exposing, in the test system, at the hybridization condition, a second set of capture probes to the target nucleic acid, the second set of capture probes being attached to a second surface and having a density different from first set of capture probes at the first surface;   determining a second association rate at the second surface; and   comparing the first association rate with the second association rate.   
     
     
         11 . The method of  claim 10 , wherein the optimal density of capture probes is related to a sequence length of the capture probe. 
     
     
         12 . The method of  claim 10 , wherein the test system comprises a plurality of attachment surfaces, each of the plurality of attachment surfaces comprising a plurality of capture probes. 
     
     
         13 . The method of  claim 12 , wherein each of the plurality of capture probes, comprised by one of the plurality of attachment surfaces, comprises an identical sequence. 
     
     
         14 . The method of  claim 13 , wherein a first of the plurality of attachment surfaces comprises a first plurality of capture probes and a second of the plurality of attachment surfaces comprises a second plurality of capture probes different from the first plurality of capture probes, the first and the second of the plurality of attachment surfaces having different optimal densities of capture probes. 
     
     
         15 . A test system for classifying a target nucleic acid, the test system comprising:
 one or more capture probes;   a detector configured to determine a degree of hybridization of the one or more capture probes with the target nucleic acid;   a non-transitory computer readable medium storing instructions that, when executed by a control system, causes the control system to perform operations comprising:
 establishing a first hybridization condition in the test system; 
 determining, using the detector, a first degree of hybridization of the one or more capture probes with the target nucleic acid under the first hybridization condition; 
 establishing a second hybridization condition in the test system; 
 determining, using the detector, a second degree of hybridization of the one or more capture probes with the target nucleic acid under the second hybridization condition; and 
 classifying the target nucleic acid by comparing the first and the second degrees of hybridization. 
   
     
     
         16 . The system of  claim 15 , wherein the detector comprises a resonator array. 
     
     
         17 . The system of  claim 15 , wherein:
 exposing the one or more capture probes to the target nucleic acid comprises contacting the one or more capture probes with a solution containing the target nucleic acid;   establishing the first hybridization condition comprises adjusting a temperature of the solution to a first temperature; and   establishing the second hybridization condition comprises adjusting the temperature of the solution to a second temperature.   
     
     
         18 . The system of  claim 15 , wherein the first hybridization condition is selected to reduce hybridization between a target nucleic acid and the one or more capture probes, and wherein the second hybridization condition is selected to favor hybridization between the target nucleic acid and the one or more capture probes. 
     
     
         19 . The system of  claim 15 , wherein the control system comprises a processor and a conditioning system configured to adjust one or more hybridization conditions in the test system. 
     
     
         20 . The system of  claim 19 , wherein the conditioning system comprises a heating element or a cooling element or both. 
     
     
         21 . A method for classifying a target nucleic acid, the method comprising:
 exposing, in a test system, one or more capture probes to the target nucleic acid, the one or more capture probes being attached to a detector;   measuring a first mass of the target nucleic acid hybridized with the one or more capture probes;   modifying the target nucleic acid to generate a second mass;   measuring the second mass of the target nucleic acid hybridized with the one or more capture probes; and   classifying the target nucleic acid based on comparing the first mass with the second mass.   
     
     
         22 . The method of  claim 20 , wherein the detector comprises a resonator array. 
     
     
         23 . The method of  claim 20 , wherein modifying comprises adding a non-metallic mass reporter to the target nucleic acid. 
     
     
         24 . The method of  claim 20 , wherein the second mass is substantially larger than the first mass. 
     
     
         25 . The method of  claim 20 , wherein modifying comprises a covalent bond. 
     
     
         26 . The method of  claim 20 , wherein modifying comprises a non-covalent bond. 
     
     
         27 . The method of  claim 20  wherein the modified target nucleic acid comprises one or more unpaired regions configured to modify the target nucleic acid for generating a third mass. 
     
     
         28 . The method of  claim 26 , wherein the one or more unpaired regions comprise biotin binding sites. 
     
     
         29 . The method of  claim 26 , wherein mixing leads to dissociation of low stability hybrids. 
     
     
         30 . A method for performing sequence analysis on a target nucleic acid, the method comprising:
 exposing, in a test system, the target nucleic acid to a polymerase that includes a target nucleotide targeted to a target nucleobase on the target nucleic acid, the target nucleic acid being attached to a surface; and   determining a mass shift of the target nucleic acid resulting from the exposure of the target nucleic acid to the polymerase.   
     
     
         31 . The method of  claim 30 , further comprising determining, based on the mass shift, a characteristic of the target nucleic acid regarding the target nucleobase. 
     
     
         32 . The method of  claim 31 , wherein determining the characteristic comprises determining a position of the target nucleobase in the target nucleic acid or a number of positions occupied by the target nucleobase in the target nucleic acid. 
     
     
         33 . The method of  claim 30 , wherein the test system comprises a resonator array configured to measure a mass of an object on the surface; and determining the mass shift comprises measuring the mass of the target nucleic acid on the surface prior to exposing the target nucleic acid to the polymerase and measuring the mass of the target nucleic acid on the surface after exposing the target nucleic acid to the polymerase and determining a difference between the two measured masses. 
     
     
         34 . The method of  claim 30 , wherein the target nucleotide is targeted to the target nucleobase by being configured to optimally hybridize with the target nucleobase. 
     
     
         35 . The method of  claim 30 , wherein the target nucleotide includes a functional group that reversibly reduces growth of the target nucleic acid. 
     
     
         36 . The method of  claim 35 , wherein exposing the target nucleic acid to the polymerase comprises exposing the target nucleic acid to the polymerase sequentially or as a mixture. 
     
     
         37 . The method of  claim 35 , further comprising removing the functional group that reversibly reduces growth of the target nucleic acid, thereby permitting growth of the target nucleic acid. 
     
     
         38 . The method of  claim 37 , wherein exposing the target nucleic acid to the polymerase comprises contacting the target nucleic acid with the polymerase in a microfluidic solution, and wherein the method further comprises repeating determining the mass shift and removing the functional group that reversibly reduces growth of the target nucleic acid, and between the repeating, flushing the microfluidic solution with new material. 
     
     
         39 . The method of  claim 37 , wherein exposing the target nucleic acid to the polymerase comprises contacting the target nucleic acid with the polymerase in a microfluidic solution, and wherein the method further comprises repeating determining the mass shift and removing the functional group that reversibly reduces growth of the target nucleic acid, and between the repeating, allowing the microfluidic solution to remain undisturbed.