Deoxyribonucleic acid-based data storage

Abstract

A method for deoxyribonucleic acid (DNA)-based data storage. The method includes receiving a binary data sequence, dividing the binary data sequence to a plurality of data chunks, encoding each of the plurality of data chunks to a respective DNA sequence of a plurality of DNA sequences, and mapping each of the plurality of DNA sequences to a respective genome segment of a plurality of genome segments. Each of the plurality of data chunks includes a predefined number of bits. The plurality of genome segments are stored in a genome bank.

Description

DEOXYRIBONUCLEIC ACID-BASED DATA STORAGETECHNICAL FIELD

[0001] The present disclosure generally relates to biological data processing, and particularly, to biological data storage.BACKGROUND ART

[0002] Deoxyribonucleic acid (DNA)-based data storage has a rich history rooted in early discoveries of its molecular structure and potential for information encoding, dating back to the 1960s. As researchers began to understand DNA’s capacity to store vast amounts of biological data, the idea of repurposing it for digital data storage emerged. Recent advances in sequencing and synthesis technologies have reignited interest, as today’s rapid data generation demands storage solutions beyond the capabilities of conventional methods. DNA offers a promising alternative due to its unparalleled density and longevity. A single gram of DNA may theoretically store over 200 petabytes of data. This compact nature, combined with its ability to last thousands of years under optimal conditions, positions DNA as a revolutionary solution for long-term data storage.

[0003] DNA-based data storage typically involves encoding digital information into nucleotide sequences — the building blocks of DNA, represented by A, T, C, and G. This data is then stored synthetically in vitro, where it can remain stable for extensive periods. Advanced encoding and error-correction methods have been developed to ensure data integrity, mitigating the effects of sequencing errors. Additionally, techniques such as polymerase chain reaction (PCR) and nanopore sequencing are used to retrieve data when needed. Research is also advancing on random access techniques that would allow for targeted retrieval of specific data segments, thereby enhancing DNA’s usability as a storage medium.

[0004] Despite its potential, DNA-based data storage faces challenges. Error rates during sequencing can impact data accuracy, and the cost of DNA synthesis and sequencing remains a significant barrier to large-scale application. Moreover, DNA-based data storage may require processing a vast amount of data that needs to be encoded into DNA sequences, stored, and accurately retrieved. There is, therefore, a need for a method for a cost-efficient DNA-based data storage that may accurately process large amounts of DNA data.SUMMARY OF THE DISCLOSURE

[0005] This summary is intended to provide an overview of the subject matter of this patent, and is not intended to identify essential elements or key elements of the subject matter, nor is it intended to be used to determine the scope of the claimed implementations. The proper scope of this patent may be ascertained from the claims set forth below in view of the detailed description below and the drawings.

[0006] In one general aspect, the present disclosure describes an exemplary method for deoxyribonucleic acid (DNA)-based data storage. An exemplary method may include receiving a binary data sequence, dividing the binary data sequence to a plurality of data chunks, encoding each of the plurality of data chunks to a respective DNA sequence of a plurality of DNA sequences, and mapping each of the plurality of DNA sequences to a respective genome segment of a plurality of genome segments. In an exemplary embodiment, each of the plurality of data chunks may include a predefined number of bits. An exemplary plurality of genome segments may be stored in a genome bank.

[0007] An exemplary method may further include preparing the genome bank. In an exemplary embodiment, preparing the genome bank may include providing the genome bank from a living organism, searching for a respective genome segment of the plurality of genome segments in the genome bank, determining uniqueness of the respective genome segment in the genome bank responsive to finding the respective genome segment in the genome bank, saving information of the respective genome segment responsive to the uniqueness of the respective genome segment being determined, determining a uniqueness of at least one of a preceding genome segment of the respective genome segment and a succeeding genome segment of the respective genome segment in the genome bank responsive to the uniqueness of the respective genome segment not being determined, saving the information of the respective genome segment responsive to the uniqueness of at least one of the preceding genome segment and the succeeding genome segment being determined, and adding the respective genome segment to the genome bank responsive to the respective genome segment not being found in the genome bank or the uniqueness of at least one of the preceding genome segment and the succeeding genome segment not being determined. An exemplary respective genome segment may correspond to the respective DNA sequence.

[0008] In an exemplary embodiment, providing the genome bank from a living organism may include extracting a genome from the living organism, dividing the genome into the pluralityof genome segments, placing each of the plurality of genome segments in a respective droplet of a plurality of droplets, and storing each respective droplet of the plurality of droplets in a respective reservoir of a plurality of reservoirs. In an exemplary embodiment, extracting the genome from the living organism may include extracting the genome from a human being. An exemplary method may further include dispensing the plurality of droplets on respective electrodes of an electrowetting on dielectric (EWOD) device according to a predetermined order.

[0009] An exemplary method may further include reading the binary data sequence. In an exemplary embodiment, reading the binary data sequence may include reading each respective chunk of the plurality of data chunks and merging the plurality of data chunks into the binary data sequence. In an exemplary embodiment, reading each respective chunk of the plurality of data chunks may include accessing a respective droplet of the plurality of droplets according to the predetermined order. An exemplary respective droplet may contain a respective genome segment of the plurality of genome segments. An exemplary respective genome segment may correspond to the respective DNA sequence. In an exemplary embodiment, reading each respective chunk of the plurality of data chunks may further include mapping the respective genome segment to the respective DNA sequence and decoding the respective DNA sequence to a respective data chunk of the plurality of data chunks.

[0010] An exemplary method may further include charging each respective droplet of the plurality of droplets utilizing a polymerase chain reaction (PCR) method. An exemplary method may further include storing a binary data string utilizing ribonucleic acids (RNAs) of the genome.

[0011] Other exemplary systems, methods, features and advantages of the implementations will be, or will become, apparent to one of ordinary skill in the art upon examination of the following figures and detailed description. It is intended that all such additional systems, methods, features and advantages be included within this description and this summary, be within the scope of the implementations, and be protected by the claims herein.BRIEF DESCRIPTION OF THE DRAWINGS

[0012] The drawing figures depict one or more implementations in accord with the present teachings, by way of example only, not by way of limitation. In the figures, like reference numerals refer to the same or similar elements.

[0013] FIG. 1A shows a flowchart of a method for deoxyribonucleic acid (DNA)-based data storage, consistent with one or more exemplary embodiments of the present disclosure.

[0014] FIG. IB shows a flowchart for preparing a genome bank, consistent with one or more exemplary embodiments of the present disclosure.

[0015] FIG. 1C shows a flowchart for reading a binary data sequence, consistent with one or more exemplary embodiments of the present disclosure.

[0016] FIG. ID shows a flowchart for storing a binary data string utilizing ribonucleic acids (RNAs), consistent with one or more exemplary embodiments of the present disclosure.

[0017] FIG. IE shows a flowchart for reading a binary data string, consistent with one or more exemplary embodiments of the present disclosure.

[0018] FIG. 2 shows a schematic of implementing a method for DNA-based data storage, consistent with one or more exemplary embodiments of the present disclosure.

[0019] FIG. 3A shows a schematic of an electrowetting on dielectric (EWOD) device, consistent with one or more exemplary embodiments of the present disclosure.

[0020] FIG. 3B shows a schematic of placement of a guide ribonucleic acid (gRNA) array on an EWOD device, consistent with one or more exemplary embodiments of the present disclosure.

[0021] FIG. 4A shows a schematic of moving a droplet utilizing an EWOD device, consistent with one or more exemplary embodiments of the present disclosure.

[0022] FIG. 4B shows a schematic of splitting a droplet utilizing an EWOD device, consistent with one or more exemplary embodiments of the present disclosure.

[0023] FIG. 5 shows a high-level functional block diagram of a computer system, consistent with one or more exemplary embodiments of the present disclosure.DESCRIPTION OF EMBODIMENTS

[0024] In the following detailed description, numerous specific details are set forth by way of examples in order to provide a thorough understanding of the relevant teachings. However, it should be apparent that the present teachings may be practiced without such details. In other instances, well known methods, procedures, components, and / or circuitry have been described at a relatively high-level, without detail, in order to avoid unnecessarily obscuring aspects of the present teachings.

[0025] The following detailed description is presented to enable a person skilled in the art to make and use the methods and devices disclosed in exemplary embodiments of the present disclosure . For purposes of explanation, specific nomenclature is set forth to provide a thorough understanding of the present disclosure. However, it will be apparent to one skilled in the art that these specific details are not required to practice the disclosed exemplary embodiments. Descriptions of specific exemplary embodiments are provided only as representative examples. Various modifications to the exemplary implementations will be readily apparent to one skilled in the art, and the general principles defined herein may be applied to other implementations and applications without departing from the scope of the present disclosure. The present disclosure is not intended to be limited to the implementations shown, but is to be accorded the widest possible scope consistent with the principles and features disclosed herein.

[0026] Herein is disclosed an exemplary method for deoxyribonucleic acid (DNA)-based data storage. An exemplary method may include encoding a sequence of binary data to DNA sequences. Exemplary DNA sequences may be obtained by searching a genome bank that may be obtained from a genome of a living organism. An exemplary genome may be divided into a large number of genome segments that may be stored in droplets. Exemplary genome segments containing DNA sequences may be dispensed on corresponding electrodes of an electrode array. An exemplary method may further include storing a binary data string utilizing ribonucleic acids (RNAs) of an exemplary genome. Different bits of an exemplary binary data string may be stored by inserting a corresponding guide RNA into an exemplary droplet. An exemplary stored data may be read by expressing guide RNAs stored in an exemplary droplet. As a result, large amounts of binary data may be mapped to DNA and RNA data that may be obtained from existing genomes of living organisms, thereby facilitating fast and cost-efficient data storage in a large scale.

[0027] FIG. 1A shows a flowchart of a method for DNA-based data storage, consistent with one or more exemplary embodiments of the present disclosure. An exemplary method 100 may include receiving a binary data sequence (step 102), dividing the binary data sequence to a plurality of data chunks (step 104), encoding each of the plurality of data chunks to a respective DNA sequence of a plurality of DNA sequences (step 106), and mapping each of the plurality of DNA sequences to a respective genome segment of a plurality of genome segments (step 108).

[0028] For further detail with respect to method 100, FIG. 2 shows a schematic of implementing a method for DNA-based data storage, consistent with one or more exemplary embodiments of the present disclosure. An exemplary schematic 200 illustrates implementation of different steps of method 100, as described below.

[0029] Referring to FIGs. 1A and 2, in an exemplary embodiment, step 102 may include receiving a binary data sequence 202. In an exemplary embodiment, a “binary data sequence” may refer to a sequence of bits (each bit having a value of “0” or “1 ”) that may be streamed in real-time. In an exemplary embodiment, binary data sequence 202 may be streamed by a communication device and may be received by one or more processors.

[0030] In an exemplary embodiment, step 104 may include dividing binary data sequence 202 to a plurality of data chunks 204. In an exemplary embodiment, each of plurality of data chunks 204 may include a predefined number of bits. In an exemplary embodiment, the predefined number of bits may be set to about 26-30.

[0031] In an exemplary embodiment, step 106 may include encoding each of plurality of data chunks 204 to a respective DNA sequence of a plurality of DNA sequences 206. For example, a data chunk 208 may be encoded to a DNA sequence 210 in step 106. In an exemplary embodiment, a joint source -channel coding method may be used for encoding plurality of data chunks 204. In an exemplary embodiment, a “DNA sequence” may refer to a sequence of four types of bases in a DNA molecule, including adenine (referred to as “A” in a DNA sequence), cytosine (referred to as “C” in a DNA sequence), guanine (referred to as “G” in a DNA sequence), and thymine (referred to as “T” in a DNA sequence). In an exemplary embodiment, each two successive bits of data chunk 208 may be encoded to a corresponding base of four bases A, C, G, and T, starting from a first bit in data chunk 208. For example, bits “00” may be encoded to “A”, “01” may be encoded to “C”, “10” may be encoded to “G”, and “11” may be encoded to “T”.

[0032] In an exemplary embodiment, step 108 may include mapping each of plurality of DNA sequences 206 to a respective genome segment of a plurality of genome segments 212. For example, DNA sequence 210 may be mapped to a genome segment 214 in step 108. In an exemplary embodiment, plurality of genome segments 212 may be stored in a genome bank 216 that may be represented by a lookup table 218. To distinguish different genome segments in genome bank 216, each exemplary genome segment may be represented by a row number (between 1 and Z) and a starting point (between 1 and L) in lookup table 218. An exemplaryrow number may refer to a row in lookup table 218 that may include a representation of an exemplary genome segment. An exemplary starting point may refer to a position in an exemplary row of lookup table 218 that may include a representation of a first base in an exemplary genome segment. For example, genome segment 214 may be represented by a row number 1 and a starting point 1000000, which means that a representation of genome segment 214 may be positioned in a 1strow and a first base of genome segment 214 is located at a 1000000thspot of the 1strow of lookup table 218.

[0033] FIG. IB shows a flowchart for preparing a genome bank, consistent with one or more exemplary embodiments of the present disclosure. In an exemplary embodiment, method 100 may further include a step 110 for preparing genome bank 216. In an exemplary embodiment, preparing genome bank 216 may include providing genome bank 216 from a living organism (step 112). In an exemplary embodiment, providing genome bank 216 from a living organism may include extracting a genome from the living organism. In an exemplary embodiment, the living organism may include a human being. Due to the diversity of DNA sequences in the human genome, an exemplary human genome may form a rich genome bank. An exemplary human genome may be easily obtained from human saliva.

[0034] In an exemplary embodiment, providing genome bank 216 may further include dividing the genome into plurality of genome segments 212. In an exemplary embodiment, each genome segment of plurality of genome segments 212 may include about 15 bases. To divide an exemplary genome to plurality of genome segments 212, an exemplary window with a fixed length (for example, 15) of bases may be slidely moved on an exemplary genome. An exemplary string of bases that may be covered by the window may be selected as a genome segment. An exemplary window may then move forward for a length of one base through an exemplary genome to cover the next genome segment. For example, for an exemplary genome including “ATCAGTCCGGAAGAGTAGCTCGG...”, a first genome segment may be a first string of bases in the genome with a length of 15 bases from the first base to the fifteenth base of the genome, i.e., “ATCAGTCCGGAAGAG”, and a second genome segment may include a string of the second base to the sixteenth base of the genome, i.e., “TCAGTCCGGAAGAGT”. An exemplary genome may have a length of about 3 gigabase (Gb). Therefore, in an exemplary embodiment, about 3 billion genome segments may be obtained by dividing the genome into plurality of genome segments 212. In an exemplary embodiment, strings that may have three or more similar successive bases (for example, “GGG”) may be excluded from plurality ofgenome segments 212. In an exemplary embodiment, about 250 million useful genome segments with a length of 15 bases may obtained by dividing an exemplary human genome into plurality of genome segments 212. As a result plurality of data chunks 204 with a length of about 26-27 bits for each data chunk may be uniquely mapped to plurality of genome segments 212.

[0035] In an exemplary embodiment, providing genome bank 216 may further include placing each of plurality of genome segments 212 in a respective droplet of a plurality of droplets 220. For example, genome segment 214 may be placed in a droplet 222 of plurality of droplets 220.

[0036] In an exemplary embodiment, providing genome bank 216 may further include storing each respective droplet of plurality of droplets 220 in a respective reservoir of a plurality of reservoirs. Each exemplary droplet may be stored in a reservoir (for example, a vial) with a capacity of at least about 1.5 microliters. For example, droplet 222 may be stored in a reservoir 224. An exemplary droplet of a size less than about 1 microliter may store about 1 million successive genome segments of plurality of genome segments 212.

[0037] Referring to FIGs. IB and 2, in an exemplary embodiment, preparing genome bank 216 in step 110 may further include searching for a respective genome segment of plurality of genome segments 212 in genome bank 216 (step 114). An exemplary respective genome segment may correspond to the respective DNA sequence. For example, step 114 may include searching for genome segment 214 corresponding to DNA sequence 210 in genome bank 216.

[0038] In an exemplary embodiment, preparing genome bank 216 in step 110 may further include determining uniqueness of the respective genome segment in genome bank 216 responsive to finding the respective genome segment in genome bank 216 (step 116, yes). For example, if genome segment 214 is found in genome bank 216, other genome segments in genome bank 216 may be checked to determine whether genome segment 214 is unique in genome bank 216.

[0039] In an exemplary embodiment, preparing genome bank 216 in step 110 may further include saving information of the respective genome segment (step 118) responsive to the uniqueness of the respective genome segment being determined (step 120, yes). For example, if genome segment 214 is determined to be unique in genome bank 216, the information of genome segment 214 may be saved. In an exemplary embodiment, the information of genome segment 214 may include the genome number (corresponding to the row number “1” in lookup table 218) and the starting point (1000000) of genome segment 214 in genome bank 216.

[0040] In an exemplary embodiment, preparing genome bank 216 in step 110 may further include determining a uniqueness of at least one of a preceding genome segment of the respective genome segment and a succeeding genome segment of the respective genome segment in genome bank 216 responsive to the uniqueness of the respective genome segment not being determined (step 120, no). For example, if genome segment 214 is not unique in genome bank 216, a preceding genome segment of genome segment 214 and a succeeding genome segment of genome segment 214 may be checked to determine whether either of the preceding genome segment or the succeeding genome segment is unique in genome bank 216.

[0041] In an exemplary embodiment, preparing genome bank 216 in step 110 may further include saving the information of the respective genome segment (step 118) responsive to the uniqueness of at least one of a preceding genome segment of the respective genome segment and a succeeding genome segment of the respective genome segment being determined (step 122, yes). For example, if either the preceding genome segment of genome segment 214 or the succeeding genome segment of genome segment 214 is determined to be unique in genome bank 216, the information of genome segment 214 may be saved.

[0042] In an exemplary embodiment, preparing genome bank 216 in step 110 may further include adding the respective genome segment to genome bank 216 responsive to the respective genome segment not being found in genome bank 216 (step 116, no) or the uniqueness of at least one of the preceding genome segment and the succeeding genome segment not being determined (step 122, no). For example, if genome segment 214 is not found in genome bank 216, the information of genome segment 214 may be saved. Similarly, in an exemplary embodiment, if neither the preceding genome segment of genome segment 214 nor the succeeding genome segment of genome segment 214 is unique, the information of genome segment 214 may be saved.

[0043] FIG. 3A shows a schematic of an electrowetting on dielectric (EWOD) device, consistent with one or more exemplary embodiments of the present disclosure. An exemplary EWOD device 300 may include a plurality of electrodes 302. In an exemplary embodiment, method 100 may further include dispensing plurality of droplets 220 on electrodes 302 of EWOD device 300 according to a predetermined order. In an exemplary embodiment, an “EWOD device” may refer to a microfluidic system that may use electric fields to control the movement, manipulation, and mixing of small droplets (smaller than about 1 mm3) of fluid. An exemplary predetermined order may be the order of electrode arrangement of EWODdevice 300. In an exemplary embodiment, electrodes 302 of EWOD device 300 may be numbered according to the arrangement of electrodes 302 on EWOD device 300. Each exemplary droplet that contains an exemplary genome segment of genome bank 216 may be placed on an exemplary electrode of EWOD device 300 that may correspond to a position of an exemplary DNA sequence mapped to the exemplary genome segment. For example, droplet 222 that contains genome segment 214 (corresponding to DNA sequence 210 that is the first DNA sequence of plurality of DNA sequences 206) may be placed on a first electrode 304 of EWOD device 300.

[0044] FIG. 1C shows a flowchart for reading a binary data sequence, consistent with one or more exemplary embodiments of the present disclosure. In an exemplary embodiment, method 100 may further include a step 126 for reading binary data sequence 202. In an exemplary embodiment, reading binary data sequence 202 in step 126 may include reading each respective chunk of the plurality of data chunks (step 128) and merging the plurality of data chunks into the binary data sequence (step 130).

[0045] Referring to FIGs. 1C and 2, in an exemplary embodiment, step 128 may include reading each respective chunk of plurality of data chunks 204. For example, data chunk 208 may be read in step 128. In an exemplary embodiment, reading data chunk 208 may include accessing a respective droplet of plurality of droplets 220 according to the predetermined order. An exemplary respective droplet may contain a respective genome segment of plurality of genome segments 212. An exemplary respective genome segment may correspond to a respective DNA sequence. For example, droplet 222 that contains genome segment 214 (corresponding to DNA sequence 210) may be accessed to read data chunk 208 in step 128.

[0046] Referring again to FIG. 3A, in an exemplary embodiment, accessing droplet 222 may require “copying” contents of droplet 222 by utilizing EWOD device 300. For this purpose, in an exemplary embodiment, droplet 222 may be first “moved” to a new location (for example, an electrode 306) that may be appropriate for the copying process. Next, in an exemplary embodiment, droplet 222 may be “split” into two new droplets 22A and 222B. In an exemplary embodiment, each of droplets 22A and 222B may contain a copy of the contents of droplet 222 (including genome segment 214). In an exemplary embodiment, droplet 222 A may be used for reading data chunk 208 and droplet 222B may be moved back to be placed on electrode 304 as a replacement of droplet 222.

[0047] FIG. 4A shows a schematic 400A of moving a droplet utilizing an EWOD device, consistent with one or more exemplary embodiments of the present disclosure. In an exemplary embodiment, transport of information chunks stored in droplets may be achieved through precise electrical control of electrodes of EWOD device 300 that may be positioned beneath a dielectric layer. When an exemplary electrode 402 is turned on, an exemplary electric field may be generated, causing a contact angle of an exemplary droplet 404 to decrease on activated electrode 402 side due to electro wetting. Simultaneously, an exemplary contact angle may increase on an exemplary adjacent deactivated electrode 406. In an exemplary embodiment, this difference in surface tension may propel droplet 404 toward the activated electrode. By sequentially switching exemplary electrodes on and off, droplet 404 may be transported across the surface of EWOD device 300 with high precision. Such electrode-based manipulation may enable complex exemplary operations that may be critical to processing workflows. For instance, after completing each step in a multiplexing process, droplet 404 may be moved to a next electrode to initiate a subsequent operation.

[0048] FIG. 4B shows a schematic 400B of splitting a droplet utilizing an EWOD device, consistent with one or more exemplary embodiments of the present disclosure. Information chunk splitting may be achieved by dynamically controlling activation and deactivation of exemplary electrodes. For example, a droplet 408 containing an information chunk may be initially positioned on an electrode 410 in a linear array of three electrodes. Initially, in an exemplary embodiment, all three electrodes 410, 412, and 414 may be activated simultaneously, causing droplet 408 to spread uniformly across the array due to a uniform reduction in surface tension. Subsequently, in an exemplary embodiment, selective activation may be applied: electrodes 412 and 414 may remain on and electrode 410 may be turned off This strategic activation pattern may create surface tension gradients that may divide original droplet 408 into two equally sized segments, localized on electrodes 412 and 414.

[0049] In an exemplary embodiment, the splitting mechanism may enable critical operations in information processing workflows. For example, splitting may allow for quality control of copied and read information, enabling precise analysis to verify accuracy and fidelity. Furthermore, new information samples may be drawn from a reservoir of material, ensuring seamless integration into a processing pipeline.

[0050] Referring again to FIG. 2, exemplary split segments of copied information may be directed to recharge genome bank 216, ensuring sufficient reserves for future applications.

[0051] In an exemplary embodiment, method 100 may further include charging each respective droplet (such as droplet 222) of plurality of droplets 220 utilizing a polymerase chain reaction (PCR) method. In an exemplary embodiment, a “PCR method” may refer to a laboratory technique for producing numerous copies of a specific segment (such as genome segment 214) of a genome. In an exemplary embodiment, recharging plurality of droplets 220 may ensure that the concentration of genome segments in plurality of droplets 220 may remain above a required level for accessing each genome segment during a process of reading stored data.

[0052] Referring again to FIGs. 1C and 2, in an exemplary embodiment, step 128 may further include mapping a respective genome segment to a respective DNA sequence. For example, genome segment 214 may be mapped to DNA sequence 210. In an exemplary embodiment, step 128 may further include decoding a respective DNA sequence to a respective data chunk of plurality of data chunks 204. For example, DNA sequence 210 may be decoded to data chunk 208. In an exemplary embodiment, the decoding process of step 128 may be an inverse of the encoding process of step 106. In other words, every exemplary DNA sequence corresponding to an exemplary data chunk in the encoding process of step 106 may be mapped to the same exemplary data chunk in step 128.

[0053] In an exemplary embodiment, step 130 may include merging plurality of data chunks 204 into binary data sequence 202. For this purpose, in an exemplary embodiment, plurality of data chunks 204 may be arranged together according to the predetermined order (i.e., the arrangement of genome segments corresponding to plurality of data chunks 204 on electrodes of EWOD device 300).

[0054] FIG. ID shows a flowchart for storing a binary data string utilizing ribonucleic acids (RNAs), consistent with one or more exemplary embodiments of the present disclosure. In an exemplary embodiment, method 100 may further include a step 132 for storing a binary data string utilizing RNAs of the genome. In an exemplary embodiment, step 132 may include receiving a binary data string (step 134). An exemplary binary data string may include a plurality of bits. In an exemplary embodiment, each of the plurality of bits may be an active bit (for example, logic 1) or a non-active bit (for example, logic 0).

[0055] FIG. 3B shows a schematic of placement of a guide ribonucleic acid (gRNA) array on an EWOD device, consistent with one or more exemplary embodiments of the present disclosure. An exemplary gRNA array 308 may be placed on electrodes 309 of EWOD device 300. Referring to FIGs. ID and 3B, in an exemplary embodiment, step 132 may further includemapping each respective bit of the plurality of bits to a respective gRNA of a gRNA array 308 (step 136). For example, after receiving the binary data string, a bit of the plurality of bits may be mapped to a gRNA 310 of gRNA array 308. In an exemplary embodiment, a gRNA may refer to a short sequence of RNA that may function as a guide for the Cas9 endonuclease or other Cas-proteins that cut a double-stranded DNA and thereby can be used for gene editing. For an exemplary binary data string with a length of 10 bits, there may be 10 different gRNAs, each corresponding to a different bit in the binary data string.

[0056] In an exemplary embodiment, step 132 may further include placing the respective gRNA in a respective droplet responsive to mapping an active bit of the plurality of bits to a respective gRNA (step 138). For example, if an active bit is mapped to gRNA 310, gRNA 310 may be placed in a droplet 312. In an exemplary embodiment, droplet 312 may be similar to or the same as droplet 222. In an exemplary embodiment, if 5 bits out of 10 bits of a 10-bit binary data string are logic 1, 5 different gRNAs, each corresponding to a different active bit, may be placed in droplet 312.

[0057] FIG. IE shows a flowchart for reading a binary data string, consistent with one or more exemplary embodiments of the present disclosure. In an exemplary embodiment, method 100 may further include a step 140 for reading the binary data string. In an exemplary embodiment, step 140 may include expressing a respective gRNA in a respective droplet utilizing a clustered regularly interspaced short palindromic repeats (CRISPR) system (step 142). An exemplary CRISPR system may express every gRNA that may be present in droplet 312. In an exemplary embodiment, other exemplary variants of a CRISPR system may also be utilized for expressing gRNAs. For example, a clustered regularly interspaced short palindromic repeats activation (CRISPRa) system may be utilized for expression of specific genes without altering an underlying DNA sequence. In an exemplary embodiment, clustered regularly interspaced short palindromic repeats interference (CRISPRi) system may be utilized for sequence-specific repression of gene expression in prokaryotic and eukaryotic cells.

[0058] In an exemplary embodiment, step 140 may include mapping a respective gRNA to a respective bit of the plurality of bits in the binary data string utilizing a quantitative polymerase chain reaction (qPCR) method. In an exemplary embodiment, existence of a gRNA expression in droplet 312 may indicate activeness of a corresponding bit in the binary data string.

[0059] FIG. 5 shows an example computer system 500 in which an embodiment of the present invention, or portions thereof, may be implemented as computer-readable code, consistent withexemplary embodiments of the present disclosure. For example, method 100 may be implemented in computer system 500 using hardware, software, firmware, tangible computer readable media having instructions stored thereon, or a combination thereof and may be implemented in one or more computer systems or other processing systems. Hardware, software, or any combination of such may embody any of the modules and components in FIGs. 1A-4B.

[0060] If programmable logic is used, such logic may execute on a commercially available processing platform or a special purpose device. One ordinary skill in the art may appreciate that an embodiment of the disclosed subject matter can be practiced with various computer system configurations, including multi-core multiprocessor systems, minicomputers, mainframe computers, computers linked or clustered with distributed functions, as well as pervasive or miniature computers that may be embedded into virtually any device.

[0061] For instance, a computing device having at least one processor device and a memory may be used to implement the above-described embodiments. A processor device may be a single processor, a plurality of processors, or combinations thereof. Processor devices may have one or more processor “cores.”

[0062] An embodiment of the invention is described in terms of this example computer system 500. After reading this description, it will become apparent to a person skilled in the relevant art how to implement the invention using other computer systems and / or computer architectures. Although operations may be described as a sequential process, some of the operations may in fact be performed in parallel, concurrently, and / or in a distributed environment, and with program code stored locally or remotely for access by single or multiprocessor machines. In addition, in some embodiments the order of operations may be rearranged without departing from the spirit of the disclosed subject matter.

[0063] Processor device 504 may be a special purpose (e.g., a graphical processing unit) or a general -purpose processor device. As will be appreciated by persons skilled in the relevant art, processor device 504 may also be a single processor in a multi-core / multiprocessor system, such system operating alone, or in a cluster of computing devices operating in a cluster or server farm. Processor device 504 may be connected to a communication infrastructure 506, for example, a bus, message queue, network, or multi-core message-passing scheme.

[0064] In an exemplary embodiment, computer system 500 may include a display interface 502, for example a video connector, to transfer data to a display unit 530, for example, amonitor. Computer system 500 may also include a main memory 508, for example, random access memory (RAM), and may also include a secondary memory 510. Secondary memory 510 may include, for example, a hard disk drive 512, and a removable storage drive 514.Removable storage drive 514 may include a floppy disk drive, a magnetic tape drive, an optical disk drive, a flash memory, or the like. Removable storage drive 514 may read from and / or write to a removable storage unit 518 in a well-known manner. Removable storage unit 518 may include a floppy disk, a magnetic tape, an optical disk, etc., which may be read by and written to by removable storage drive 514. As will be appreciated by persons skilled in the relevant art, removable storage unit 518 may include a computer usable storage medium having stored therein computer software and / or data.

[0065] In alternative implementations, secondary memory 510 may include other similar means for allowing computer programs or other instructions to be loaded into computer system 500. Such means may include, for example, a removable storage unit 522 and an interface 520.Examples of such means may include a program cartridge and cartridge interface (such as that found in video game devices), a removable memory chip (such as an EPROM, or PROM) and associated socket, and other removable storage units 522 and interfaces 520 which allow software and data to be transferred from removable storage unit 522 to computer system 500.

[0066] Computer system 500 may also include a communications interface 524.Communications interface 524 allows software and data to be transferred between computer system 500 and external devices. Communications interface 524 may include a modem, a network interface (such as an Ethernet card), a communications port, a PCMCIA slot and card, or the like. Software and data transferred via communications interface 524 may be in the form of signals, which may be electronic, electromagnetic, optical, or other signals capable of being received by communications interface 524. These signals may be provided to communications interface 524 via a communications path 526. Communications path 526 carries signals and may be implemented using wire or cable, fiber optics, a phone line, a cellular phone link, an RF link or other communications channels.

[0067] In this document, the terms “computer program medium” and “computer usable medium” are used to generally refer to media such as removable storage unit 518, removable storage unit 522, and a hard disk installed in hard disk drive 512. Computer program medium and computer usable medium may also refer to memories, such as main memory 508 and secondary memory 510, which may be memory semiconductors (e.g. DRAMs, etc.).

[0068] Computer programs (also called computer control logic) are stored in main memory 508 and / or secondary memory 510. Computer programs may also be received via communications interface 524. Such computer programs, when executed, enable computer system 500 to implement different embodiments of the present disclosure as discussed herein. In particular, the computer programs, when executed, enable processor device 504 to implement the processes of the present disclosure, such as the operations of such as the operations in method 100 illustrated by flowchart 100 of FIG. 1A and flowchart 126 of FIG.1C discussed above. Accordingly, such computer programs represent controllers of computer system 500. Where an exemplary embodiment of method 100 is implemented using software, the software may be stored in a computer program product and loaded into computer system 500 using removable storage drive 514, interface 520, and hard disk drive 512, or communications interface 524.

[0069] Embodiments of the present disclosure also may be directed to computer program products including software stored on any computer useable medium. Such software, when executed in one or more data processing device, causes a data processing device to operate as described herein. An embodiment of the present disclosure may employ any computer useable or readable medium. Examples of computer useable mediums include, but are not limited to, primary storage devices (e.g., any type of random access memory), secondary storage devices (e.g., hard drives, floppy disks, CD ROMS, ZIP disks, tapes, magnetic storage devices, and optical storage devices, MEMS, nanotechnological storage device, etc.).

[0070] The embodiments have been described above with the aid of functional building blocks illustrating the implementation of specified functions and relationships thereof. The boundaries of these functional building blocks have been arbitrarily defined herein for the convenience of the description. Alternate boundaries can be defined so long as the specified functions and relationships thereof are appropriately performed.

[0071] While the foregoing has described what are considered to be the best mode and / or other examples, it is understood that various modifications may be made therein and that the subject matter disclosed herein may be implemented in various forms and examples, and that the teachings may be applied in numerous applications, only some of which have been described herein. It is intended by the following claims to claim any and all applications, modifications, and variations that fall within the true scope of the present teachings.

[0072] Unless otherwise stated, all measurements, values, ratings, positions, magnitudes, sizes, and other specifications that are set forth in this specification, including in the claims that follow, are approximate, not exact. They are intended to have a reasonable range that is consistent with the functions to which they relate and with what is customary in the art to which they pertain.

[0073] The scope of protection is limited solely by the claims that now follow. That scope is intended and should be interpreted to be as broad as is consistent with the ordinary meaning of the language that is used in the claims when interpreted in light of this specification and the prosecution history that follows and to encompass all structural and functional equivalents.

[0074] Except as stated immediately above, nothing that has been stated or illustrated is intended or should be interpreted to cause a dedication of any component, step, feature, object, benefit, advantage, or equivalent to the public, regardless of whether it is or is not recited in the claims.

[0075] It will be understood that the terms and expressions used herein have the ordinary meaning as is accorded to such terms and expressions with respect to their corresponding respective areas of inquiry and study except where specific meanings have otherwise been set forth herein. Relational terms such as first and second and the like may be used solely to distinguish one entity or action from another without necessarily requiring or implying any actual such relationship or order between such entities or actions. The terms “comprises,” “comprising,” or any other variation thereof, are intended to cover a non-exclusive inclusion, such that a process, method, article, or apparatus that comprises a list of elements does not include only those elements but may include other elements not expressly listed or inherent to such process, method, article, or apparatus. An element proceeded by “a” or “an” does not, without further constraints, preclude the existence of additional identical elements in the process, method, article, or apparatus that comprises the element.

[0076] The Abstract of the Disclosure is provided to allow the reader to quickly ascertain the nature of the technical disclosure. It is submitted with the understanding that it will not be used to interpret or limit the scope or meaning of the claims. In addition, in the foregoing Detailed Description, it can be seen that various features are grouped together in various implementations. This is for purposes of streamlining the disclosure, and is not to be interpreted as reflecting an intention that the claimed implementations require more features than are expressly recited in each claim. Rather, as the following claims reflect, inventive subject matterlies in less than all features of a single disclosed implementation. Thus, the following claims are hereby incorporated into the Detailed Description, with each claim standing on its own as a separately claimed subject matter.

[0077] While various implementations have been described, the description is intended to be exemplary, rather than limiting and it will be apparent to those of ordinary skill in the art that many more implementations and implementations are possible that are within the scope of the implementations. Although many possible combinations of features are shown in the accompanying figures and discussed in this detailed description, many other combinations of the disclosed features are possible. Any feature of any implementation may be used in combination with or substituted for any other feature or element in any other implementation unless specifically restricted. Therefore, it will be understood that any of the features shown and / or discussed in the present disclosure may be implemented together in any suitable combination. Accordingly, the implementations are not to be restricted except in light of the attached claims and their equivalents. Also, various modifications and changes may be made within the scope of the attached claims.

Claims

What is claimed is:

1. A method for deoxyribonucleic acid (DNA)-based data storage, comprising:receiving, utilizing one or more processors, a binary data sequence;dividing, utilizing the one or more processors, the binary data sequence to a plurality of data chunks, each of the plurality of data chunks comprising a predefined number of bits;encoding, utilizing the one or more processors, each of the plurality of data chunks to a respective DNA sequence of a plurality of DNA sequences; andmapping, utilizing the one or more processors, each of the plurality of DNA sequences to a respective genome segment of a plurality of genome segments stored in a genome bank.

2. The method of claim 1, further comprising:preparing the genome bank, comprising:providing the genome bank from a living organism;searching, utilizing the one or more processors, for a respective genome segment of the plurality of genome segments in the genome bank, the respective genome segment corresponding to the respective DNA sequence;responsive to finding the respective genome segment in the genome bank, determining uniqueness of the respective genome segment in the genome bank;responsive to the uniqueness of the respective genome segment being determined, saving information of the respective genome segment;responsive to the uniqueness of the respective genome segment not being determined, determining a uniqueness of at least one of a preceding genome segment of the respective genome segment and a succeeding genome segment of the respective genome segment in the genome bank;responsive to the uniqueness of at least one of the preceding genome segment and the succeeding genome segment being determined, saving the information of the respective genome segment; andadding the respective genome segment to the genome bank responsive to at least one of:the respective genome segment not being found in the genome bank; and the uniqueness of at least one of the preceding genome segment and the succeeding genome segment not being determined.

3. The method of claim 2, wherein providing the genome bank from a living organism comprises:extracting a genome from the living organism;dividing the genome into the plurality of genome segments;placing each of the plurality of genome segments in a respective droplet of a plurality of droplets; andstoring each respective droplet of the plurality of droplets in a respective reservoir of a plurality of reservoirs.

4. The method of claim 3, wherein extracting the genome from the living organism comprises extracting the genome from a human being.

5. The method of claim 3, further comprising:dispensing the plurality of droplets on respective electrodes of an electrowetting on dielectric (EWOD) device according to a predetermined order.

6. The method of claim 5, further comprising reading the binary data sequence, comprising:reading each respective chunk of the plurality of data chunks, comprising:accessing, utilizing the EWOD device, a respective droplet of the plurality of droplets according to the predetermined order, the respective droplet containing a respective genome segment of the plurality of genome segments, the respective genome segment corresponding to the respective DNA sequence;mapping, utilizing a next generation sequencing method, the respective genome segment to the respective DNA sequence; anddecoding, utilizing the one or more processors, the respective DNA sequence to a respective data chunk of the plurality of data chunks; andmerging, utilizing the one or more processors, the plurality of data chunks into the binary data sequence.

7. The method of claim 6, further comprising storing a binary data string utilizing ribonucleic acids (RNAs) of the genome.

8. The method of claim 6, further comprising:receiving, utilizing one or more processors, a binary data string comprising a plurality of bits, each of the plurality of bits comprising one of an active bit or a non-active bit;mapping, utilizing the one or more processors, each respective bit of the plurality of bits to a respective guide ribonucleic acid (gRNA) of a gRNA array; andresponsive to mapping an active bit of the plurality of bits to the respective gRNA, placing the respective gRNA in the respective droplet.

9. The method of claim 8, further comprising reading the binary data string, comprising: expressing, utilizing a clustered regularly interspaced short palindromic repeats (CRISPR) system, the respective gRNA in the respective droplet;mapping, utilizing a quantitative polymerase chain reaction (qPCR) method, the respective gRNA to a respective bit of the plurality of bits in the binary data string.

10. The method of claim 4, further comprising:charging, utilizing a polymerase chain reaction (PCR) method, each respective droplet of the plurality of droplets.

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