Enrichment and detection of nucleic acids with ultra-high sensitivity

Abstract

Methods, systems, and devices are disclosed for enrichment and detection of molecules of a target biomarker. In one aspect, In one aspect, a biosensor device for enriching and detecting biomarker molecules include a substrate, and a microarray of hydrophilic islands disposed on the substrate. A sensing area on each of the microarray hydrophilic islands is structured to anchor bio-molecular probes of at least one type for detecting molecules of a target biomarker and to attract an array of nanodroplets of a biomarker solution that includes the target biomarker molecules. A hydrophobic surface disposed to surround the microarray of hydrophilic islands.

What is claimed is: 
     
         1 . A biosensor device for enriching and detecting biomarker molecules, the biosensor device comprising:
 a substrate;   a microarray of hydrophilic islands disposed on the substrate;   sensing areas disposed on the microarray hydrophilic islands, the sensing areas structured to anchor bio-molecular probes of at least one type for detecting molecules of a target biomarker and to attract an array of droplets of a biomarker solution that includes the target biomarker molecules; and   a hydrophobic surface surrounding the microarray of hydrophilic islands, the hydrophobic surface including nanostructures having rough surfaces to enrich the target biomarker molecules on the sensing area by enhancing evaporation of the array of droplets leading to an enriched array of droplets with an increased concentration of the target biomarker molecules compared to before evaporation;   wherein the sensing areas are structured to receive a layer of water-immiscible-liquid over the enriched array of droplets to form water-immiscible-liquid encapsulated reaction chambers for controlling a reaction between the target biomarker molecules and the bio-molecular probes.   
     
     
         2 . The biosensor device of  claim 1 , wherein the sensing areas include a layer of a hydrophilic material. 
     
     
         3 . The biosensor device of  claim 2 , wherein the hydrophilic material of the sensing areas includes a dielectric material. 
     
     
         4 . The biosensor device of  claim 2 , wherein the hydrophilic material of the sensing areas includes silicon oxide (SiO 2 ). 
     
     
         5 . The biosensor device of  claim 1 , wherein the nanostructures of the hydrophobic surface includes nanopillars. 
     
     
         6 . The biosensor device of  claim 1 , wherein the sensing areas structured to receive a labeling material to label target biomarker molecules that reacted with the bio-molecular probes. 
     
     
         7 . The biosensor device of  claim 3 , wherein the labeling material includes quantum dots. 
     
     
         8 . The biosensor device of  claim 1 , wherein the hydrophilic property of the sensing areas causes the array of droplets to be self-aligned with the sensing areas. 
     
     
         9 . The biosensor device of  claim 1 , wherein the sensing areas covered microarray of hydrophilic islands and the nanostructures of the hydrophobic surface are disposed to have a height difference that reduces adhesion of target biomolecules to a sidewall of the sensing areas covered microarray of hydrophilic islands during evaporation. 
     
     
         10 . The biosensor device of  claim 1 , wherein the hydrophobic surface includes black silicon. 
     
     
         11 . The biosensor device of  claim 1 , wherein the bio-molecular probes of at least one kind include DNA probes and the target biomarker molecules include target nucleic acids. 
     
     
         12 . The biosensor device of  claim 1 , wherein the sensing areas of the microarray of hydrophilic islands are structured to enrich and detect different types of target biomarker molecules. 
     
     
         13 . The biosensor device of  claim 1 , wherein the biosensor device is configured to detect the target biomarker molecules of approximately 1 femtomolar (fM) concentration. 
     
     
         14 . The biosensor device of  claim 1 , wherein the biosensor device is configured to detect the target biomarker molecules of approximately 0.5 fM concentration. 
     
     
         15 . The biosensor device of  claim 1 , wherein the biosensor device is configured to enrich and detect multiple biomarker molecule types in parallel. 
     
     
         16 . The biosensor device of  claim 11 , wherein the multiple types of biomarker molecules includes RNA and DNA markers. 
     
     
         17 . The biosensor device of  claim 1 , wherein each droplet is nanoliter or less. 
     
     
         18 . The biosensor device of  claim 1 , wherein the water-immiscible-liquid includes oil. 
     
     
         19 . A method performed by a biosensor device to enrich and detect biomarker molecules, the method comprising:
 receiving, by a biosensor device including a microarray of hydrophilic islands having sensing areas and surrounded by hydrophobic nanostructures, bio-molecular probes of at least one type for detecting molecules of a target biomarker to functionalize the sensing areas of the microarray of hydrophilic islands;   receiving, over the functionalized sensing areas of the microarray of hydrophilic islands, droplets of a biomarker solution that includes the biomarker molecules to form an array of droplets of the biomarker solutions on the functionalized sensing areas;   receiving over the array of droplets of the biomarker solutions a layer of water-immiscible-liquid to encapsulate the array of droplets of the biomarker solutions to form water-immiscible-liquid encapsulated reaction chambers for controlling a reaction between the target biomarker molecules and the bio-molecular probes.   
     
     
         20 . The method of  claim 19 , wherein the bio-molecular probes of at least one type include DNA probes, and the molecules of biomarkers include nucleic acids. 
     
     
         21 . The method of  claim 20 , wherein the DNA probes include DNA oligonucleotides. 
     
     
         22 . The method of  claim 20 , wherein receiving the layer of water-immiscible-liquid to encapsulate the array of droplets of the biomarker solutions to form water-immiscible-liquid encapsulated reaction chambers for controlling a reaction between the target biomarker molecules and the bio-molecular probes include facilitating hybridization of the biomarker molecules with the DNA probes within the nano-chambers. 
     
     
         23 . The method of  claim 19 , comprising:
 receiving labeling materials to within the reaction chambers to label bio-molecular probe attached biomarker molecules formed responsive to the controlled reaction.   
     
     
         24 . The method of  claim 23 , wherein the labeling materials include quantum-dots. 
     
     
         25 . The method of  claim 20 , wherein the nucleic acids include DNA, RNA or miRNA-based nucleic acids. 
     
     
         26 . The method of  claim 19 , wherein the sensing areas include a layer of silicon oxide (SiO 2 ). 
     
     
         27 . The method of  claim 19 , wherein the hydrophobic surface includes black silicon. 
     
     
         28 . The method of  claim 19 , wherein the target biomarker molecules includes fluorescently labeled biomarker molecules to determine a concentration of the target biomarker molecules based on an fluorescent intensity of the fluorescently labeled biomarker molecules that react with bio-molecular probes. 
     
     
         29 . The method of  claim 19 , wherein each droplet is nanoliter or less. 
     
     
         30 . The method of  claim 19 , wherein the water-immiscible-liquid includes oil. 
     
     
         31 . A method performed by a biosensor device for enriching biomarker molecules to facilitate ultra-sensitive detection and quantification of the biomarker molecules, the method comprising:
 receiving, by a biosensor device including an microarray of hydrophilic islands having sensing areas and surrounded by a hydrophobic structure, bio-molecular probes of at least one type for detecting molecules of a target biomarker to functionalize the sensing areas of the microarray of hydrophilic islands;   receiving, over the functionalized sensing areas of the microarray of hydrophilic islands, droplets of a biomarker solution that includes the biomarker molecules to form droplets of the biomarker molecules that cover the sensing areas of the microarray of hydrophilic islands;   allowing the biomarker solution to evaporate over the microarray of hydrophilic islands to concentrate the biomarker molecules onto the sensing areas of the microarray of hydrophilic islands;   receiving, over the functionalized sensing areas of the microarray of hydrophilic islands containing the concentrated biomarker molecules, a liquid in a controlled time to form an array of self-assembled droplets to resuspend the concentrated biomarker molecules in the droplets over the functionalized sensing areas;   receiving, over the array of self-assembled droplets of the biomarker solutions, a layer of water-immiscible-liquid to encapsulate the array of self-assembled droplets to form water-immiscible-liquid encapsulated reaction chambers for controlling a reaction between the target biomarker molecules and the bio-molecular probes; and   allowing a reaction between the target biomarker molecules and the bio-molecular probes to form hybridized target biomarker molecules.   
     
     
         32 . The method of  claim 31 , wherein the liquid includes one of:
 a hybridization buffer containing a labeling material for labeling the target biomarker molecules that have reacted with the bio-molecular probes; or   water.   
     
     
         33 . The method  claim 32 , wherein the labeling material includes quantum-dots linked reporting DNAs. 
     
     
         34 . The method  claim 31 , wherein the microarray of hydrophilic islands are separated by a grid of hydrophobic nanostructures. 
     
     
         35 . The method  claim 34 , wherein nanostructures include nanopillars. 
     
     
         36 . The method of  claim 34 , wherein the grid of hydrophobic nanostructures include Teflon-coated grids. 
     
     
         37 . The method  claim 31 , wherein the biomarker solution includes a hybridization buffer of the biomarker molecules. 
     
     
         38 . The method of  claim 31 , wherein the biomarker containing solution includes miRNA containing RNAse-free deionized water. 
     
     
         39 . The method of  claim 31 , wherein the target biomarker includes DNAs, RNAs, miRNAs, synthetic miR-205 DNA mimic, or other nucleic acids. 
     
     
         40 . The method of  claim 31 , wherein the biosensor device includes a lab-on-a-chip device. 
     
     
         41 . The method of  claim 31 , wherein the hydrophobic structure includes a nanopillar structure made of black silicon. 
     
     
         42 . The method of  claim 31 , wherein the sensing areas of the microarray of hydrophilic islands includes a layer of SiO 2 . 
     
     
         43 . The method of  claim 31 , wherein each of the microarray of hydrophilic islands is configured to detect and quantify a different typical of target biomarker. 
     
     
         44 . The method of  claim 31 , wherein the biosensor device is configured to perform parallel operation with a large number of target biomarkers. 
     
     
         45 . The method of  claim 31 , wherein the biosensor device is configured to detect a target biomarker with a detection sensitivity of approximately 0.05 femtomolar (fM). 
     
     
         46 . The method of  claim 31 , wherein the controlled time is approximately 1 second. 
     
     
         47 . The method of  claim 31 , wherein after the completion of the hybridization, the method further includes receiving, at the functionalized sensing areas, a cleaning liquid to remove the layer of oil and liquid to expose the hybridized target biomarker and the bio-molecular probes. 
     
     
         48 . The method of  claim 31 , wherein allowing the biomarker solution to evaporate over the microarray of hydrophilic islands to concentrate the biomarker molecules includes allowing the liquid in the biomarker solution to completely dry. 
     
     
         49 . The method of  claim 31 , wherein allowing the biomarker solution to evaporate over the microarray of hydrophilic islands to concentrate the biomarker molecules includes allowing the biomarker solution to concentrate to a predetermined thickness. 
     
     
         50 . The method of  claim 48 , wherein the predetermined thickness is approximately 20 μm. 
     
     
         51 . The method of  claim 31 , wherein each droplet is nanoliter or less. 
     
     
         52 . The method of  claim 31 , wherein the water-immiscible-liquid includes oil.