Compositions and methods for nucleic acid-based data storage

Abstract

The present disclosure provides systems and methods for storing digital information into nucleic acid molecules in various ways. Digital information may be received as a sting of symbols, wherein each symbol in the string of symbols has a symbol value and a symbol position within the string of symbols. A first identifier nucleic acid molecule may be formed by depositing M selected component nucleic acid molecules into a compartment, the M selected component nucleic acid molecules being selected from a set of distinct component nucleic acid molecules that are separated into M different layers, and physically assembling the M selected component nucleic acid molecules. A plurality of identifier nucleic acid molecules may be formed, each corresponding to a respective symbol position. The identifier nucleic acid molecules may be formed in a pool having powder, liquid, or solid form.

1 . A method for storing digital information into nucleic acid molecules, the method comprising:
 (a) receiving the digital information as a string of symbols, wherein each symbol in the string of symbols has a symbol value and a symbol position within the string of symbols;   (b) forming a first identifier nucleic acid molecule by:
 (1) selecting, from a set of distinct component nucleic acid molecules that are separated into M different layers, one component nucleic acid molecule from each of the M layers; 
 (2) depositing the M selected component nucleic acid molecules into a compartment; 
 (3) physically assembling the M selected component nucleic acid molecules in (2) to form the first identifier nucleic acid molecule having first and second end molecules and a third molecule positioned between the first and second end molecules, such that the component nucleic acid molecules from first and second layers correspond to the first and second end molecules of the identifier nucleic acid molecule, and the component nucleic acid molecule in a third layer corresponds to the third molecule of the identifier nucleic acid molecule, to define a physical order of the M layers in the first identifier nucleic acid molecule; 
   (c) forming a plurality of additional identifier nucleic acid molecules, each (1) having first and second end molecules and a third molecule positioned between the first and second end molecules, and (2) corresponding to a respective symbol position, wherein at least one of the first end molecule, second end molecule, and third molecule of at least one additional identifier nucleic acid molecule is identical to a target molecule of the first identifier nucleic acid molecule in (b), so as to enable a probe to select at least two identifier nucleic acid molecules corresponding to respective symbols having contiguous symbol positions within the string of symbols, and   (d) collecting the identifier nucleic acid molecules in (b) and (c) in a pool having powder, liquid, or solid form.   
     
     
         2 . The method of  claim 1 , wherein at least one of the first and second end molecules of the at least one additional identifier nucleic acid molecule is identical to a target molecule of the first identifier nucleic acid molecule in (b). 
     
     
         3 . The method of  claim 1  wherein physically assembling the M selected component nucleic acid molecules comprises ligation of the component nucleic acid molecules. 
     
     
         4 . The method of  claim 1 , wherein the component nucleic acid molecules from each layer comprise at least one sticky end which is complementary to at least one sticky end of component nucleic acid molecules from another layer, so as to enable sticky end ligation for formation of the identifier nucleic acid molecules in (b) and (c). 
     
     
         5 . The method of  claim 1 , wherein the first molecule of the at least one additional identifier nucleic acid molecule in (c) is identical to the first end molecule of the identifier nucleic acid molecule in (b), and the second end molecule of the at least one additional identifier nucleic acid molecule in (c) is identical to the second end molecule of the identifier nucleic acid molecule in (b). 
     
     
         6 . The method of  claim 1 , further comprising using the probe to hybridize to the target molecule of at least some identifier nucleic acid molecules in the first identifier nucleic acid molecule and the plurality of additional identifier nucleic acid molecules to select identifier nucleic acid molecules corresponding to respective symbols having contiguous symbol positions. 
     
     
         7 . The method of  claim 1 , further comprising applying a single PCR reaction to amplify at least two identifier nucleic acid molecules corresponding to respective symbols having contiguous symbol positions. 
     
     
         8 . The method of  claim 7 , wherein the at least two identifier nucleic acid molecules corresponding to respective symbols having contiguous symbol positions are able to be further amplified by another PCR reaction that targets a specific component nucleic acid molecule in the third molecule of the identifier nucleic acid molecule. 
     
     
         9 . The method of  claim 1 , wherein the component nucleic acid molecules in each layer are structured with first and second end regions, and the first end region of each component nucleic acid molecule from one of the M layers is structured to bind to the second end region of any component nucleic acid molecule from another of the M layers. 
     
     
         10 . The method of  claim 1 , wherein M is greater than or equal to three. 
     
     
         11 . The method of  claim 1 , wherein each symbol position within the string of symbols has a corresponding different identifier nucleic acid molecule. 
     
     
         12 . The method of  claim 1 , wherein the identifier nucleic acid molecules in (b) and (c) are representative of a subset of a combinatorial space of possible identifier nucleic acid molecules, each including one component nucleic acid molecule from each of the M layers. 
     
     
         13 . The method of  claim 12 , wherein a presence or absence of an identifier nucleic acid molecule in the pool in (d) is representative of the symbol value of the corresponding respective symbol position within the string of symbols. 
     
     
         14 . The method of  claim 1 , wherein the symbols having contiguous symbol position encode similar digital information. 
     
     
         15 . The method of  claim 1 , wherein a distribution of numbers of component nucleic acid molecules in each of the M layers is non-uniform. 
     
     
         16 . The method of  claim 15 , wherein when the third layer includes more component nucleic acid molecules than either of the first layer or the second layer, a PCR query used to access the pool in (d) results in a larger pool of accessed identifier nucleic acid molecules than if the third layer included fewer component nucleic acid molecules than either of the first layer or the second layer. 
     
     
         17 . The method of  claim 16 , wherein when the third layer includes fewer component nucleic acid molecules than either of the first layer or the second layer, a PCR query used to access the pool in (d) results in a smaller pool of accessed identifier nucleic acid molecules than if the third layer included more component nucleic acid molecules than either of the first layer or the second layer, wherein the smaller pool of accessed identifier nucleic acid molecules corresponds to a higher resolution of access to the symbols in the string of symbols. 
     
     
         18 . The method of  claim 1  wherein the first layer has a highest priority, the second layer has a second highest priority, and the remaining M−2 layers have corresponding component nucleic acid molecules between the first and second end molecules. 
     
     
         19 . The method of  claim 18 , wherein the pool in (d) is able to be used to access all identifier nucleic acid molecules in the pool that have particular component nucleic acid molecules at the first and second end molecules, in one PCR reaction. 
     
     
         20 - 26 . (canceled) 
     
     
         27 . The method of  claim 1 , wherein physically assembling the M selected component nucleic acid molecules uses click chemistry. 
     
     
         28 . The method of  claim 1 , further comprising
 deleting at least some data collected in the pool by:   using sequence-specific probes to Dull-down select identifier nucleic acid molecules from the pool in (d) to selectively delete data;   obfuscating the identifier nucleic acid molecules in the pool in (d) to non-selectively delete data; or   using sonication, autoclaving, treatment with bleach, bases, acids, ethidium bromide or other DNA modification agents, irradiation, combustion, and non-specific nuclease digestion to degrade the identifier nucleic acid molecules from the pool in (d) to non-selectively delete data.   
     
     
         29 - 68 . (canceled)