Heated nanowells for polynucleotide synthesis

Abstract

Devices for the manufacturing of high-quality building blocks, such as oligonucleotides, are described herein. Nano-scale devices allow for selective control over reaction conditions. Further, methods and devices described herein allow for the rapid construction of large libraries of highly accurate nucleic acids.

What is claimed is: 
     
         1 . A device for polynucleotide synthesis comprising:
 a. a solid support comprising a surface;   b. a plurality of structures for polynucleotide extension located on the surface, wherein each structure has a width of about 10 nm to about 1000 nm, wherein each structure is in contact with a heating unit, and wherein the heating unit comprises at least one electrode; and   c. a solvent distributed across the surface, wherein the solvent is a polar solvent.   
     
     
         2 . A device for polynucleotide synthesis comprising:
 a. a solid support comprising a surface;   b. a plurality of structures for polynucleotide extension located on the surface, wherein each structure has a width of about 10 nm to about 1000 nm, wherein each structure is in contact with a heating unit, and wherein the heating unit comprises at least one electrode; and   c. a solvent distributed across the surface, wherein the solvent has a melting temperature of no more than about 18 degrees C.   
     
     
         3 . A device for polynucleotide synthesis comprising:
 a. a solid support comprising a surface;   b. a plurality of structures for polynucleotide extension located on the surface, wherein each structure has a width of about 10 nm to about 1000 nm, wherein each structure is in contact with a heating unit, and wherein the heating unit comprises at least one electrode; and   c. a solvent distributed across the surface, wherein the solvent has a boiling temperature no more than about 82 degrees C.   
     
     
         4 . The device of any one of  claims 1  to  3 , wherein the surface comprises at least 30,000 loci for nucleic acid synthesis. 
     
     
         5 . The device of  claim 1 , wherein the surface comprises at least 50,000 loci for nucleic acid synthesis. 
     
     
         6 . The device of any one of  claims 1  to  3 , wherein the surface comprises at least 100,000 loci for nucleic acid synthesis. 
     
     
         7 . The device of any one of  claims 1  to  3 , wherein the surface comprises at least 200,000 loci for nucleic acid synthesis. 
     
     
         8 . The device of any one of  claims 1  to  3 , wherein the surface comprises at least 1,000,000 loci for nucleic acid synthesis. 
     
     
         9 . The device of any one of  claims 1  to  3 , wherein the one or more electrodes are addressable electrodes that heats one or more individual loci. 
     
     
         10 . The device of any one of  claims 1  to  3 , wherein the solid support further comprises a cooling unit. 
     
     
         11 . The device of any one of  claims 1  to  3 , wherein the distance between the centers of any two structures is about 10 nm to about 1000 nm. 
     
     
         12 . The device of any one of  claims 1  to  3 , wherein the distance between the centers of any two structures is about 100 nm to about 500 nm. 
     
     
         13 . The device of  claim 1 , wherein the distance between the centers of any two structures is about 20 nm to about 300 nm. 
     
     
         14 . The device of any one of  claims 1  to  3 , wherein the distance between the centers of any two structures is about 100 nm. 
     
     
         15 . The device of any one of  claims 1  to  3 , wherein the distance between the centers of any two structures is about 200 nm. 
     
     
         16 . The device of any one of  claims 1  to  3 , wherein the distance between the centers of any two structures is about 500 nm. 
     
     
         17 . The device of any one of the preceding claims, wherein each structure comprises a 3-dimensional structure, wherein the 3-dimensional structure is a nanowell, a nanowire, a nanopost, or a nanorod. 
     
     
         18 . The device of  claim 2 , wherein the solvent is a polar solvent. 
     
     
         19 . The device of  claim 1  or  2 , wherein the solvent comprises a nitrile group. 
     
     
         20 . The device of  claim 1 , wherein the solvent is trimethylacetonitrile. 
     
     
         21 . The device of  claim 1  or  2 , wherein the solvent has a melting temperature between 5 degrees C. to 18 degrees C. 
     
     
         22 . The device of  claim 1 , wherein the solvent has a melting temperature of between 10 degrees C. to 18 degrees C. 
     
     
         23 . The device of  claim 1  or  2 , wherein the solvent has a melting temperature of between 15 degrees C. to 18 degrees C. 
     
     
         24 . The device of  claim 1 , wherein the solvent has a melting temperature of between 5 degrees C. to 30 degrees C. 
     
     
         25 . The device of  claim 3 , wherein the solvent has a boiling temperature of between 0 degrees C. to 82 degrees C. 
     
     
         26 . The device of  claim 3 , wherein the solvent has a boiling temperature of between 30 degrees C. to 82 degrees C. 
     
     
         27 . The device of  claim 3 , wherein the solvent has a boiling temperature of between 55 degrees C. to 82 degrees C. 
     
     
         28 . The device of any one of  claims 1  to  3 , wherein the solvent has a density of between 0.5 and 1.5 g/mL. 
     
     
         29 . The device of any one of the preceding claims, wherein the device is used for polynucleotide synthesis, wherein polynucleotide synthesis comprises a plurality of elongation steps. 
     
     
         30 . The device of  claim 29 , wherein the solvent is not removed during an elongation step. 
     
     
         31 . A method for polynucleotide synthesis using the device of any one of  claims 1 - 29 . 
     
     
         32 . A method for polynucleotide synthesis, the method comprising:
 a. providing predetermined sequences for a library of polynucleotides;   b. providing a substrate comprising a surface;   c. synthesizing the library of polynucleotides extending from the surface, wherein a solvent in the solid phase prevents deblocking of at least one polynucleotide extending from the at least one region of the surface, wherein the solvent has a melting temperature of no more than about 18 degrees C.   
     
     
         33 . The method of  claim 32 , wherein synthesizing the library of polynucleotides extending from the surface comprises contacting the surface with a first nucleotide phosphoramidite. 
     
     
         34 . The method of  claim 33 , wherein synthesizing the library of polynucleotides extending from the surface further comprises contacting the surface with a second nucleotide phosphoramidite, wherein the solvent is not removed between contact with the first nucleotide phosphoramidite and the second nucleotide phosphoramidite. 
     
     
         35 . The method of any one of  claims 32 - 34 , wherein synthesizing the library of polynucleotides extending from the surface further comprises melting the solvent present at the at least one region of the surface, and deblocking at least one extended polynucleotide extending from the surface in the at least one region. 
     
     
         36 . The method of any one of  claims 32 - 35 , wherein the solvent has a melting temperature of no more than about 15 degrees C. 
     
     
         37 . The method of any one of  claims 32 - 36 , wherein the solvent has a melting temperature of no more than about 10 degrees C. 
     
     
         38 . The method of any one of  claims 32 - 35 , wherein the solvent has a melting temperature between 5 degrees C. to 18 degrees C. 
     
     
         39 . The method of any one of  claims 32 - 35 , wherein the solvent has a melting temperature of between 10 degrees C. to 18 degrees C. 
     
     
         40 . The method of any one of  claims 32 - 35 , wherein the solvent has a melting temperature of between 15 degrees C. to 18 degrees C. 
     
     
         41 . The method of any one of  claims 32 - 35 , wherein the solvent has a melting temperature of between 5 degrees C. to 30 degrees C. 
     
     
         42 . A method for polynucleotide synthesis, the method comprising:
 d. providing predetermined sequences for a library of polynucleotides;   e. providing a substrate comprising a surface;   f. synthesizing the library of polynucleotides extending from the surface, wherein a solvent in the gas phase prevents deblocking of at least one polynucleotide extending from the at least one region of the surface, wherein the solvent has a boiling temperature no more than about 82 degrees C.   
     
     
         43 . The method of  claim 42 , wherein synthesizing the library of polynucleotides extending from the surface comprises contacting the surface with a first nucleotide phosphoramidite. 
     
     
         44 . The method of  claim 43 , wherein synthesizing the library of polynucleotides extending from the surface further comprises contacting the surface with a second nucleotide phosphoramidite, wherein the solvent is not removed between contact with the first nucleotide phosphoramidite and the second nucleotide phosphoramidite. 
     
     
         45 . The method of any one of  claims 42 - 44 , wherein synthesizing the library of polynucleotides extending from the surface further comprises condensing the solvent present at the at least one region of the surface, and deblocking at least one extended polynucleotide extending from the surface in the at least one region. 
     
     
         46 . The method of any one of  claims 42 - 45 , wherein the solvent has a boiling temperature no more than about 75 degrees C. 
     
     
         47 . The method of any one of  claims 42 - 46 , wherein the solvent has a boiling temperature no more than about 65 degrees C. 
     
     
         48 . The method of any one of  claims 42 - 47 , wherein the solvent has a boiling temperature of between 0 degrees C. to 82 degrees C. 
     
     
         49 . The method of any one of  claims 42 - 47 , wherein the solvent has a boiling temperature of between 30 degrees C. to 82 degrees C. 
     
     
         50 . The method of any one of  claims 42 - 47 , wherein the solvent has a boiling temperature of between 55 degrees C. to 82 degrees C. 
     
     
         51 . The method of any one of  claims 32  to  50 , wherein the surface comprises at least 30,000 loci for nucleic acid synthesis. 
     
     
         52 . The method of any one of  claims 32  to  51 , wherein the surface comprises at least 50,000 loci for nucleic acid synthesis. 
     
     
         53 . The method of any one of  claims 32  to  52 , wherein the surface comprises at least 100,000 loci for nucleic acid synthesis. 
     
     
         54 . The method of any one of  claims 32  to  53 , wherein the surface comprises at least 200,000 loci for nucleic acid synthesis. 
     
     
         55 . The method of any one of  claims 32  to  54 , wherein the surface comprises at least 1,000,000 loci for nucleic acid synthesis.