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Jo S, Shin H, Joe SY, Baek D, Park C, Chun H. Recent progress in DNA data storage based on high-throughput DNA synthesis. Biomed Eng Lett 2024; 14:993-1009. [PMID: 39220021 PMCID: PMC11362454 DOI: 10.1007/s13534-024-00386-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Revised: 04/24/2024] [Accepted: 04/26/2024] [Indexed: 09/04/2024] Open
Abstract
DNA data storage has emerged as a solution for storing massive volumes of data by utilizing nucleic acids as a digital information medium. DNA offers exceptionally high storage density, long durability, and low maintenance costs compared to conventional storage media such as flash memory and hard disk drives. DNA data storage consists of the following steps: encoding, DNA synthesis (i.e., writing), preservation, retrieval, DNA sequencing (i.e., reading), and decoding. Out of these steps, DNA synthesis presents a bottleneck due to imperfect coupling efficiency, low throughput, and excessive use of organic solvents. Overcoming these challenges is essential to establish DNA as a viable data storage medium. In this review, we provide the overall process of DNA data storage, presenting the recent progress of each step. Next, we examine a detailed overview of DNA synthesis methods with an emphasis on their limitations. Lastly, we discuss the efforts to overcome the constraints of each method and their prospects.
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Affiliation(s)
- Seokwoo Jo
- Department of Biomedical Engineering, Korea University, 466 Hana Science Hall, Seoul, 02841 Korea
- Interdisciplinary Program in Precision Public Health, Korea University, 466 Hana Science Hall, Seoul, 02841 Korea
| | - Haewon Shin
- Department of Biomedical Engineering, Korea University, 466 Hana Science Hall, Seoul, 02841 Korea
- Interdisciplinary Program in Precision Public Health, Korea University, 466 Hana Science Hall, Seoul, 02841 Korea
| | - Sung-yune Joe
- Department of Biomedical Engineering, Korea University, 466 Hana Science Hall, Seoul, 02841 Korea
- Interdisciplinary Program in Precision Public Health, Korea University, 466 Hana Science Hall, Seoul, 02841 Korea
| | - David Baek
- Department of Biomedical Engineering, Korea University, 466 Hana Science Hall, Seoul, 02841 Korea
- Interdisciplinary Program in Precision Public Health, Korea University, 466 Hana Science Hall, Seoul, 02841 Korea
| | - Chaewon Park
- Department of Biomedical Engineering, Korea University, 466 Hana Science Hall, Seoul, 02841 Korea
- Interdisciplinary Program in Precision Public Health, Korea University, 466 Hana Science Hall, Seoul, 02841 Korea
| | - Honggu Chun
- Department of Biomedical Engineering, Korea University, 466 Hana Science Hall, Seoul, 02841 Korea
- Interdisciplinary Program in Precision Public Health, Korea University, 466 Hana Science Hall, Seoul, 02841 Korea
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2
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Kekić T, Milisavljević N, Troussier J, Tahir A, Debart F, Lietard J. Accelerated, high-quality photolithographic synthesis of RNA microarrays in situ. SCIENCE ADVANCES 2024; 10:eado6762. [PMID: 39083603 PMCID: PMC11290486 DOI: 10.1126/sciadv.ado6762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Accepted: 06/26/2024] [Indexed: 08/02/2024]
Abstract
Nucleic acid photolithography is the only microarray fabrication process that has demonstrated chemical versatility accommodating any type of nucleic acid. The current approach to RNA microarray synthesis requires long coupling and photolysis times and suffers from unavoidable degradation postsynthesis. In this study, we developed a series of RNA phosphoramidites with improved chemical and photochemical protection of the 2'- and 5'-OH functions. In so doing, we reduced the coupling time by more than half and the photolysis time by a factor of 4. Sequence libraries that would otherwise take over 6 hours to synthesize can now be prepared in half the time. Degradation is substantially lowered, and concomitantly, hybridization signals can reach over seven times those of the previous state of the art. Under those conditions, high-density RNA microarrays and RNA libraries can now be synthesized at greatly accelerated rates. We also synthesized fluorogenic RNA Mango aptamers on microarrays and investigated the effect of sequence mutations on their fluorogenic properties.
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Affiliation(s)
- Tadija Kekić
- Institute of Inorganic Chemistry, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
| | | | - Joris Troussier
- IBMM, University of Montpellier, CNRS, ENSCM, Montpellier, France
| | - Amina Tahir
- IBMM, University of Montpellier, CNRS, ENSCM, Montpellier, France
| | - Françoise Debart
- IBMM, University of Montpellier, CNRS, ENSCM, Montpellier, France
| | - Jory Lietard
- Institute of Inorganic Chemistry, University of Vienna, Josef-Holaubek-Platz 2, 1090 Vienna, Austria
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3
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Kim JW, Jeong J, Kwak HY, No JS. Design of DNA Storage Coding Scheme With LDPC Codes and Interleaving. IEEE Trans Nanobioscience 2024; 23:447-457. [PMID: 38512749 DOI: 10.1109/tnb.2024.3379976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2024]
Abstract
In this paper, we propose a new coding scheme for DNA storage using low-density parity-check (LDPC) codes and interleaving techniques. While conventional coding schemes generally employ error correcting codes in both inter and intra-oligo directions, we show that inter-oligo LDPC codes, optimized by differential evolution, are sufficient in ensuring the reliability of DNA storage due to the powerful soft decoding of LDPC codes. In addition, we apply interleaving techniques for handling non-uniform error characteristics of DNA storage to enhance the decoding performance. Consequently, the proposed coding scheme reduces the required number of oligo reads for perfect recovery by 26.25% ~ 38.5% compared to existing state-of-the-art coding schemes. Moreover, we develop an analytical DNA channel model in terms of non-uniform binary symmetric channels. This mathematical model allows us to demonstrate the superiority of the proposed coding scheme while isolating the experimental variation, as well as confirm the independent effects of LDPC codes and interleaving techniques.
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Tong Y, Sun J, Chen Y, Yi C, Wang H, Li C, Dai N, Yang G. POSoligo software for in vitro gene synthesis. Sci Rep 2024; 14:11117. [PMID: 38750104 PMCID: PMC11096389 DOI: 10.1038/s41598-024-59497-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Accepted: 04/11/2024] [Indexed: 05/18/2024] Open
Abstract
Oligonucleotide synthesis is vital for molecular experiments. Bioinformatics has been employed to create various algorithmic tools for the in vitro synthesis of nucleotides. The main approach to synthesizing long-chain DNA molecules involves linking short-chain oligonucleotides through ligase chain reaction (LCR) and polymerase chain reaction (PCR). Short-chain DNA molecules have low mutation rates, while LCR requires complementary interfaces at both ends of the two nucleic acid molecules or may alter the conformation of the nucleotide chain, leading to termination of amplification. Therefore, molecular melting temperature, length, and specificity must be considered during experimental design. POSoligo is a specialized offline tool for nucleotide fragment synthesis. It optimizes the oligonucleotide length and specificity based on input single-stranded DNA, producing multiple contiguous long strands (COS) and short patch strands (POS) with complementary ends. This process ensures free 5'- and 3'-ends during oligonucleotide synthesis, preventing secondary structure formation and ensuring specific binding between COS and POS without relying on stabilizing the complementary strands based on Tm values. POSoligo was used to synthesize the linear RBD sequence of SARS-CoV-2 using only one DNA strand, several POSs for LCR ligation, and two pairs of primers for PCR amplification in a time- and cost-effective manner.
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Affiliation(s)
- Yingying Tong
- International Research Center for Biological Sciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China
- National Aquatic Animal Pathogen Collection Center, Shanghai Ocean University, Shanghai, 201306, China
- Aquatic Animal Genetics and Breeding Center, Shanghai Ocean University, Shanghai, 201306, China
| | - Jie Sun
- International Research Center for Biological Sciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China
- National Aquatic Animal Pathogen Collection Center, Shanghai Ocean University, Shanghai, 201306, China
- Aquatic Animal Genetics and Breeding Center, Shanghai Ocean University, Shanghai, 201306, China
| | - Yang Chen
- International Research Center for Biological Sciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China
- National Aquatic Animal Pathogen Collection Center, Shanghai Ocean University, Shanghai, 201306, China
- Aquatic Animal Genetics and Breeding Center, Shanghai Ocean University, Shanghai, 201306, China
| | - Changhua Yi
- International Research Center for Biological Sciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China
- National Aquatic Animal Pathogen Collection Center, Shanghai Ocean University, Shanghai, 201306, China
- Aquatic Animal Genetics and Breeding Center, Shanghai Ocean University, Shanghai, 201306, China
| | - Hua Wang
- Shanghai Telebio Biomedical Technology Co., LTD, Shanghai, China
| | - Caixin Li
- Shanghai Telebio Biomedical Technology Co., LTD, Shanghai, China
| | - Nana Dai
- Anhui Health College, Chizhou, 247100, Anhui, China
| | - Guanghua Yang
- International Research Center for Biological Sciences, Ministry of Science and Technology, Shanghai Ocean University, Shanghai, 201306, China.
- National Aquatic Animal Pathogen Collection Center, Shanghai Ocean University, Shanghai, 201306, China.
- Aquatic Animal Genetics and Breeding Center, Shanghai Ocean University, Shanghai, 201306, China.
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5
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Yu M, Tang X, Li Z, Wang W, Wang S, Li M, Yu Q, Xie S, Zuo X, Chen C. High-throughput DNA synthesis for data storage. Chem Soc Rev 2024; 53:4463-4489. [PMID: 38498347 DOI: 10.1039/d3cs00469d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
With the explosion of digital world, the dramatically increasing data volume is expected to reach 175 ZB (1 ZB = 1012 GB) in 2025. Storing such huge global data would consume tons of resources. Fortunately, it has been found that the deoxyribonucleic acid (DNA) molecule is the most compact and durable information storage medium in the world so far. Its high coding density and long-term preservation properties make itself one of the best data storage carriers for the future. High-throughput DNA synthesis is a key technology for "DNA data storage", which encodes binary data stream (0/1) into quaternary long DNA sequences consisting of four bases (A/G/C/T). In this review, the workflow of DNA data storage and the basic methods of artificial DNA synthesis technology are outlined first. Then, the technical characteristics of different synthesis methods and the state-of-the-art of representative commercial companies, with a primary focus on silicon chip microarray-based synthesis and novel enzymatic DNA synthesis are presented. Finally, the recent status of DNA storage and new opportunities for future development in the field of high-throughput, large-scale DNA synthesis technology are summarized.
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Affiliation(s)
- Meng Yu
- Institute of Medical Chips, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
- School of Microelectronics, Shanghai University, 201800, Shanghai, China
- Shanghai Industrial μTechnology Research Institute, 201800, Shanghai, China
| | - Xiaohui Tang
- Institute of Medical Chips, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
- Shanghai Industrial μTechnology Research Institute, 201800, Shanghai, China
| | - Zhenhua Li
- Institute of Medical Chips, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
- Shanghai Industrial μTechnology Research Institute, 201800, Shanghai, China
| | - Weidong Wang
- Shanghai Industrial μTechnology Research Institute, 201800, Shanghai, China
| | - Shaopeng Wang
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China.
| | - Min Li
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China.
| | - Qiuliyang Yu
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Sijia Xie
- Institute of Medical Chips, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
- School of Microelectronics, Shanghai University, 201800, Shanghai, China
- Shanghai Industrial μTechnology Research Institute, 201800, Shanghai, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China.
| | - Chang Chen
- Institute of Medical Chips, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
- School of Microelectronics, Shanghai University, 201800, Shanghai, China
- Shanghai Industrial μTechnology Research Institute, 201800, Shanghai, China
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 200050, Shanghai, China
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6
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Preuss I, Rosenberg M, Yakhini Z, Anavy L. Efficient DNA-based data storage using shortmer combinatorial encoding. Sci Rep 2024; 14:7731. [PMID: 38565928 PMCID: PMC11369284 DOI: 10.1038/s41598-024-58386-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 03/28/2024] [Indexed: 04/04/2024] Open
Abstract
Data storage in DNA has recently emerged as a promising archival solution, offering space-efficient and long-lasting digital storage solutions. Recent studies suggest leveraging the inherent redundancy of synthesis and sequencing technologies by using composite DNA alphabets. A major challenge of this approach involves the noisy inference process, obstructing large composite alphabets. This paper introduces a novel approach for DNA-based data storage, offering, in some implementations, a 6.5-fold increase in logical density over standard DNA-based storage systems, with near-zero reconstruction error. Combinatorial DNA encoding uses a set of clearly distinguishable DNA shortmers to construct large combinatorial alphabets, where each letter consists of a subset of shortmers. We formally define various combinatorial encoding schemes and investigate their theoretical properties. These include information density and reconstruction probabilities, as well as required synthesis and sequencing multiplicities. We then propose an end-to-end design for a combinatorial DNA-based data storage system, including encoding schemes, two-dimensional (2D) error correction codes, and reconstruction algorithms, under different error regimes. We performed simulations and show, for example, that the use of 2D Reed-Solomon error correction has significantly improved reconstruction rates. We validated our approach by constructing two combinatorial sequences using Gibson assembly, imitating a 4-cycle combinatorial synthesis process. We confirmed the successful reconstruction, and established the robustness of our approach for different error types. Subsampling experiments supported the important role of sampling rate and its effect on the overall performance. Our work demonstrates the potential of combinatorial shortmer encoding for DNA-based data storage and describes some theoretical research questions and technical challenges. Combining combinatorial principles with error-correcting strategies, and investing in the development of DNA synthesis technologies that efficiently support combinatorial synthesis, can pave the way to efficient, error-resilient DNA-based storage solutions.
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Affiliation(s)
- Inbal Preuss
- School of Computer Science, Reichman University, 4610101, Herzliya, Israel.
- Faculty of Computer Science, Technion, 3200003, Haifa, Israel.
| | - Michael Rosenberg
- Institute of Nanotechnology and Advanced Materials, The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002, Ramat Gan, Israel
| | - Zohar Yakhini
- School of Computer Science, Reichman University, 4610101, Herzliya, Israel
- Faculty of Computer Science, Technion, 3200003, Haifa, Israel
| | - Leon Anavy
- School of Computer Science, Reichman University, 4610101, Herzliya, Israel
- Faculty of Computer Science, Technion, 3200003, Haifa, Israel
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7
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Li S, Tan W, Jia X, Miao Q, Liu Y, Yang D. Recent advances in the synthesis of single-stranded DNA in vitro. Biotechnol J 2024; 19:e2400026. [PMID: 38622795 DOI: 10.1002/biot.202400026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/19/2024] [Accepted: 03/25/2024] [Indexed: 04/17/2024]
Abstract
Single-stranded DNA (ssDNA) is the foundation of modern biology, with wide applications in gene editing, sequencing, DNA information storage, and materials science. However, synthesizing ssDNA with high efficiency, high throughput, and low error rate in vitro remains a major challenge. Various methods have been developed for ssDNA synthesis, and some significant results have been achieved. In this review, six main methods were introduced, including solid-phase oligonucleotide synthesis, terminal deoxynucleotidyl transferase-based ssDNA synthesis, reverse transcription, primer exchange reaction, asymmetric polymerase chain reaction, and rolling circle amplification. The advantages and limitations of each method were compared, as well as illustrate their representative achievements and applications. Especially, rolling circle amplification has received significant attention, including ssDNA synthesis, assembly, and application based on recent work. Finally, the future challenges and opportunities of ssDNA synthesis were summarized and discussed. Envisioning the development of new methods and significant progress will be made in the near future with the efforts of scientists around the world.
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Affiliation(s)
- Shuai Li
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, P.R. China
| | - Wei Tan
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, P.R. China
| | - Xuemei Jia
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, P.R. China
| | - Qing Miao
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, P.R. China
| | - Ying Liu
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, P.R. China
| | - Dayong Yang
- Frontiers Science Center for Synthetic Biology, Key Laboratory of Systems Bioengineering (MOE), School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Zhejiang Institute of Tianjin University, Ningbo, Zhejiang, P.R. China
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8
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Ma Y, Zhang Z, Jia B, Yuan Y. Automated high-throughput DNA synthesis and assembly. Heliyon 2024; 10:e26967. [PMID: 38500977 PMCID: PMC10945133 DOI: 10.1016/j.heliyon.2024.e26967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 02/20/2024] [Accepted: 02/22/2024] [Indexed: 03/20/2024] Open
Abstract
DNA synthesis and assembly primarily revolve around the innovation and refinement of tools that facilitate the creation of specific genes and the manipulation of entire genomes. This multifaceted process encompasses two fundamental steps: the synthesis of lengthy oligonucleotides and the seamless assembly of numerous DNA fragments. With the advent of automated pipetting workstations and integrated experimental equipment, a substantial portion of repetitive tasks in the field of synthetic biology can now be efficiently accomplished through integrated liquid handling workstations. This not only reduces the need for manual labor but also enhances overall efficiency. This review explores the ongoing advancements in the oligonucleotide synthesis platform, automated DNA assembly techniques, and biofoundries. The development of accurate and high-throughput DNA synthesis and assembly technologies presents both challenges and opportunities.
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Affiliation(s)
- Yuxin Ma
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Zhaoyang Zhang
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Bin Jia
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yingjin Yuan
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
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9
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Seliger H, Sanghvi YS. An Update on Protection of 5'-Hydroxyl Functions of Nucleosides and Oligonucleotides. Curr Protoc 2024; 4:e999. [PMID: 38439607 DOI: 10.1002/cpz1.999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024]
Abstract
The synthesis of natural and chemically modified nucleosides and oligonucleotides is in great demand due to its increasing number of applications in diverse areas of research. These include tools for diagnostics and proteomics, research reagents for molecular biology, probes for functional genomics, and the design, discovery, development, and manufacture of new therapeutics. The likelihood of success in synthesizing these molecules is often dependent on the correct choice of a protection strategy to block the 5'-hydroxyl group of a carbohydrate moiety, nucleoside, or oligonucleotide. This topic was reviewed extensively in the year 2000. The purpose of this article is to complement and update the original review with recently published methodologies recommended for the protection and deprotection of the 5'-hydroxyl group. © 2024 Wiley Periodicals LLC.
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10
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Schaudy E, Ibañez-Redín G, Parlar E, Somoza MM, Lietard J. Nonaqueous Oxidation in DNA Microarray Synthesis Improves the Oligonucleotide Quality and Preserves Surface Integrity on Gold and Indium Tin Oxide Substrates. Anal Chem 2024; 96:2378-2386. [PMID: 38285499 PMCID: PMC10867803 DOI: 10.1021/acs.analchem.3c04166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/29/2023] [Accepted: 12/29/2023] [Indexed: 01/30/2024]
Abstract
Nucleic acids attached to electrically conductive surfaces are very frequently used platforms for sensing and analyte detection as well as for imaging. Synthesizing DNA on these uncommon substrates and preserving the conductive layer is challenging as this coating tends to be damaged by the repeated use of iodine and water, which is the standard oxidizing medium following phosphoramidite coupling. Here, we thoroughly investigate the use of camphorsulfonyl oxaziridine (CSO), a nonaqueous alternative to I2/H2O, for the synthesis of DNA microarrays in situ. We find that CSO performs equally well in producing high hybridization signals on glass microscope slides, and CSO also protects the conductive layer on gold and indium tin oxide (ITO)-coated slides. DNA synthesis on conductive substrates with CSO oxidation yields microarrays of quality approaching that of conventional glass with intact physicochemical properties.
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Affiliation(s)
- Erika Schaudy
- Institute
of Inorganic Chemistry, University of Vienna, Josef-Holaubek-Platz 2, Vienna 1090, Austria
| | - Gisela Ibañez-Redín
- Institute
of Inorganic Chemistry, University of Vienna, Josef-Holaubek-Platz 2, Vienna 1090, Austria
| | - Etkin Parlar
- Institute
of Inorganic Chemistry, University of Vienna, Josef-Holaubek-Platz 2, Vienna 1090, Austria
| | - Mark M. Somoza
- Institute
of Inorganic Chemistry, University of Vienna, Josef-Holaubek-Platz 2, Vienna 1090, Austria
- Leibniz-Institute
for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Straße 30, Freising 85354, Germany
- Chair
of Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Straße 34, Freising 85354, Germany
| | - Jory Lietard
- Institute
of Inorganic Chemistry, University of Vienna, Josef-Holaubek-Platz 2, Vienna 1090, Austria
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11
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Sabary O, Yucovich A, Shapira G, Yaakobi E. Reconstruction algorithms for DNA-storage systems. Sci Rep 2024; 14:1951. [PMID: 38263421 PMCID: PMC10806084 DOI: 10.1038/s41598-024-51730-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Accepted: 01/09/2024] [Indexed: 01/25/2024] Open
Abstract
Motivated by DNA storage systems, this work presents the DNA reconstruction problem, in which a length-n string, is passing through the DNA-storage channel, which introduces deletion, insertion and substitution errors. This channel generates multiple noisy copies of the transmitted string which are called traces. A DNA reconstruction algorithm is a mapping which receives t traces as an input and produces an estimation of the original string. The goal in the DNA reconstruction problem is to minimize the edit distance between the original string and the algorithm's estimation. In this work, we present several new algorithms for this problem. Our algorithms look globally on the entire sequence of the traces and use dynamic programming algorithms, which are used for the shortest common supersequence and the longest common subsequence problems, in order to decode the original string. Our algorithms do not require any limitations on the input and the number of traces, and more than that, they perform well even for error probabilities as high as 0.27. The algorithms have been tested on simulated data, on data from previous DNA storage experiments, and on a new synthesized dataset, and are shown to outperform previous algorithms in reconstruction accuracy.
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Affiliation(s)
- Omer Sabary
- The Henry and Marilyn Taub Faculty of Computer Science, Technion, 3200003, Haifa, Israel.
| | - Alexander Yucovich
- The Henry and Marilyn Taub Faculty of Computer Science, Technion, 3200003, Haifa, Israel
| | - Guy Shapira
- The Henry and Marilyn Taub Faculty of Computer Science, Technion, 3200003, Haifa, Israel
| | - Eitan Yaakobi
- The Henry and Marilyn Taub Faculty of Computer Science, Technion, 3200003, Haifa, Israel
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12
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Zeng J, Song K, Wang J, Wen H, Zhou J, Ni T, Lu H, Yu Y. Characterization and optimization of 5´ untranslated region containing poly-adenine tracts in Kluyveromyces marxianus using machine-learning model. Microb Cell Fact 2024; 23:7. [PMID: 38172836 PMCID: PMC10763412 DOI: 10.1186/s12934-023-02271-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2023] [Accepted: 12/12/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND The 5´ untranslated region (5´ UTR) plays a key role in regulating translation efficiency and mRNA stability, making it a favored target in genetic engineering and synthetic biology. A common feature found in the 5´ UTR is the poly-adenine (poly(A)) tract. However, the effect of 5´ UTR poly(A) on protein production remains controversial. Machine-learning models are powerful tools for explaining the complex contributions of features, but models incorporating features of 5´ UTR poly(A) are currently lacking. Thus, our goal is to construct such a model, using natural 5´ UTRs from Kluyveromyces marxianus, a promising cell factory for producing heterologous proteins. RESULTS We constructed a mini-library consisting of 207 5´ UTRs harboring poly(A) and 34 5´ UTRs without poly(A) from K. marxianus. The effects of each 5´ UTR on the production of a GFP reporter were evaluated individually in vivo, and the resulting protein abundance spanned an approximately 450-fold range throughout. The data were used to train a multi-layer perceptron neural network (MLP-NN) model that incorporated the length and position of poly(A) as features. The model exhibited good performance in predicting protein abundance (average R2 = 0.7290). The model suggests that the length of poly(A) is negatively correlated with protein production, whereas poly(A) located between 10 and 30 nt upstream of the start codon (AUG) exhibits a weak positive effect on protein abundance. Using the model as guidance, the deletion or reduction of poly(A) upstream of 30 nt preceding AUG tended to improve the production of GFP and a feruloyl esterase. Deletions of poly(A) showed inconsistent effects on mRNA levels, suggesting that poly(A) represses protein production either with or without reducing mRNA levels. CONCLUSION The effects of poly(A) on protein production depend on its length and position. Integrating poly(A) features into machine-learning models improves simulation accuracy. Deleting or reducing poly(A) upstream of 30 nt preceding AUG tends to enhance protein production. This optimization strategy can be applied to enhance the yield of K. marxianus and other microbial cell factories.
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Affiliation(s)
- Junyuan Zeng
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China
| | - Kunfeng Song
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China
| | - Jingqi Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China
| | - Haimei Wen
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China
| | - Jungang Zhou
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China
| | - Ting Ni
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China
| | - Hong Lu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China
| | - Yao Yu
- State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China.
- Shanghai Engineering Research Center of Industrial Microorganisms, Shanghai, 200438, China.
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13
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Li Q, Yan H. "Difficult" deoxyribonucleotide sequences in the solid-phase synthesis by the phosphoramidite chemistry. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2023; 43:655-663. [PMID: 38116988 DOI: 10.1080/15257770.2023.2295478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 12/11/2023] [Indexed: 12/21/2023]
Abstract
This work catalogued oligonucleotide sequences and sequence compositions based on the overall yield of full-length product obtained by the phosphoramidite chemistry-based solid phase synthesis. In total, 76 sequences with different dinucleotide and trinucleotide repeats were synthesized, and the fully-deprotected products were analyzed by denaturing anion exchange HPLC. Overall, sequences containing more 2'-deoxyadenosine residues were obtained in relatively lower yields, likely due to the relative ease of 2'-deoxyadenosine to undergo depurination during the detritylation reaction. Furthermore, dinucleotide steps, such as d(CG)/d(GC) and d(AG)/d(GA), likely contribute the overall lower yields of full-length products as well.
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Affiliation(s)
- Quanjian Li
- Department of Chemistry, Brock University, St. Catharines, ON, Canada
| | - Hongbin Yan
- Department of Chemistry, Brock University, St. Catharines, ON, Canada
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14
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Yeom H, Kim N, Lee AC, Kim J, Kim H, Choi H, Song SW, Kwon S, Choi Y. Highly Accurate Sequence- and Position-Independent Error Profiling of DNA Synthesis and Sequencing. ACS Synth Biol 2023; 12:3567-3577. [PMID: 37961855 PMCID: PMC10729760 DOI: 10.1021/acssynbio.3c00308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Revised: 11/01/2023] [Accepted: 11/01/2023] [Indexed: 11/15/2023]
Abstract
A comprehensive error analysis of DNA-stored data during processing, such as DNA synthesis and sequencing, is crucial for reliable DNA data storage. Both synthesis and sequencing errors depend on the sequence and the transition of bases of nucleotides; ignoring either one of the error sources leads to technical challenges in minimizing the error rate. Here, we present a methodology and toolkit that utilizes an oligonucleotide library generated from a 10-base-shifted sequence array, which is individually labeled with unique molecular identifiers, to delineate and profile DNA synthesis and sequencing errors simultaneously. This methodology enables position- and sequence-independent error profiling of both DNA synthesis and sequencing. Using this toolkit, we report base transitional errors in both synthesis and sequencing in general DNA data storage as well as degenerate-base-augmented DNA data storage. The methodology and data presented will contribute to the development of DNA sequence designs with minimal error.
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Affiliation(s)
- Huiran Yeom
- Division
of Data Science, College of Information and Communication Technology, The University of Suwon, Hwaseong 18323, Republic of Korea
| | - Namphil Kim
- Department
of Electrical and Computer Engineering, Seoul National University, Seoul 08826, South Korea
| | | | - Jinhyun Kim
- Department
of Electrical and Computer Engineering, Seoul National University, Seoul 08826, South Korea
| | - Hamin Kim
- Department
of Interdisciplinary Program for Bioengineering, Seoul National University, Seoul 08826, South Korea
| | - Hansol Choi
- Bio-MAX
Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Seo Woo Song
- Basic Science
and Engineering Initiative, Children’s Heart Center, Stanford University, Stanford, California 94304, United States
| | - Sunghoon Kwon
- Department
of Electrical and Computer Engineering, Seoul National University, Seoul 08826, South Korea
- Department
of Interdisciplinary Program for Bioengineering, Seoul National University, Seoul 08826, South Korea
- Bio-MAX
Institute, Seoul National University, Seoul 08826, Republic of Korea
| | - Yeongjae Choi
- School
of Materials Science and Engineering, Gwangju
Institute of Science and Technology (GIST), Gwangju 61105, Republic of Korea
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15
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Bi M, Wang Z, Cheng K, Cui Y, He Y, Ma J, Qi M. Construction of transcription factor mutagenesis population in tomato using a pooled CRISPR/Cas9 plasmid library. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 205:108094. [PMID: 37995578 DOI: 10.1016/j.plaphy.2023.108094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 09/25/2023] [Accepted: 10/12/2023] [Indexed: 11/25/2023]
Abstract
Adequate mutant materials are the prerequisite for conducting gene function research or screening novel functional genes in plants. The strategy of constructing a large-scale mutant population using the pooled CRISPR/Cas9-sgRNA library has been implemented in several crops. However, the effective application of this CRISPR/Cas9 large-scale screening strategy to tomato remains to be attempted. Here, we identified 990 transcription factors in the tomato genome, designed and synthesized a CRISPR/Cas9 plasmid library containing 4379 sgRNAs. Using this pooled library, 487 T0 positive plants were obtained, among which 92 plants harbored a single sgRNA sequence, targeting 65 different transcription factors, with a mutation rate of 23%. In the T0 mutant population, the occurrence of homozygous and biallelic mutations was observed at higher frequencies. Additionally, the utilization of a small-scale CRISPR/Cas9 library targeting 30 transcription factors could enhance the efficacy of single sgRNA recognition in positive plants, increasing it from 19% to 42%. Phenotypic characterization of several mutants identified from the mutant population demonstrated the utility of our CRISPR/Cas9 mutant library. Taken together, our study offers insights into the implementation and optimization of CRISPR/Cas9-mediated large-scale knockout library in tomato.
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Affiliation(s)
- Mengxi Bi
- College of Horticulture, Shenyang Agricultural University, Shenyang, China; National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, China; Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang, China; Key Laboratory of Horticultural Equipment, Ministry of Agriculture and Rural Affairs, Shenyang, China
| | - Zhijun Wang
- College of Horticulture, Shenyang Agricultural University, Shenyang, China; National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, China; Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang, China; Key Laboratory of Horticultural Equipment, Ministry of Agriculture and Rural Affairs, Shenyang, China
| | - Keyan Cheng
- College of Horticulture, Shenyang Agricultural University, Shenyang, China; National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, China; Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang, China; Key Laboratory of Horticultural Equipment, Ministry of Agriculture and Rural Affairs, Shenyang, China
| | - Yiqing Cui
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, China; Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang, China
| | - Yi He
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, China; Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang, China
| | - Jian Ma
- College of Horticulture, Shenyang Agricultural University, Shenyang, China; National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, China; Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang, China; Key Laboratory of Horticultural Equipment, Ministry of Agriculture and Rural Affairs, Shenyang, China
| | - Mingfang Qi
- College of Horticulture, Shenyang Agricultural University, Shenyang, China; National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design & Application Technology (Liaoning), Shenyang, China; Key Laboratory of Protected Horticulture (Shenyang Agricultural University), Ministry of Education, Shenyang, China; Key Laboratory of Horticultural Equipment, Ministry of Agriculture and Rural Affairs, Shenyang, China.
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16
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Capponi S, Daniels KG. Harnessing the power of artificial intelligence to advance cell therapy. Immunol Rev 2023; 320:147-165. [PMID: 37415280 DOI: 10.1111/imr.13236] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 06/17/2023] [Indexed: 07/08/2023]
Abstract
Cell therapies are powerful technologies in which human cells are reprogrammed for therapeutic applications such as killing cancer cells or replacing defective cells. The technologies underlying cell therapies are increasing in effectiveness and complexity, making rational engineering of cell therapies more difficult. Creating the next generation of cell therapies will require improved experimental approaches and predictive models. Artificial intelligence (AI) and machine learning (ML) methods have revolutionized several fields in biology including genome annotation, protein structure prediction, and enzyme design. In this review, we discuss the potential of combining experimental library screens and AI to build predictive models for the development of modular cell therapy technologies. Advances in DNA synthesis and high-throughput screening techniques enable the construction and screening of libraries of modular cell therapy constructs. AI and ML models trained on this screening data can accelerate the development of cell therapies by generating predictive models, design rules, and improved designs.
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Affiliation(s)
- Sara Capponi
- Department of Functional Genomics and Cellular Engineering, IBM Almaden Research Center, San Jose, California, USA
- Center for Cellular Construction, San Francisco, California, USA
| | - Kyle G Daniels
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, California, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
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17
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Abram KZ, Udaondo Z. Leveraging nature to advance data storage: DNA as a storage medium. Microb Biotechnol 2023; 16:1709-1712. [PMID: 37300423 PMCID: PMC10443336 DOI: 10.1111/1751-7915.14291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 05/22/2023] [Indexed: 06/12/2023] Open
Affiliation(s)
- Kaleb Z. Abram
- Department of Biomedical InformaticsUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
| | - Zulema Udaondo
- Department of Biomedical InformaticsUniversity of Arkansas for Medical SciencesLittle RockArkansasUSA
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18
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Romero EO, Saucedo AT, Hernández-Meléndez JR, Yang D, Chakrabarty S, Narayan ARH. Enabling Broader Adoption of Biocatalysis in Organic Chemistry. JACS AU 2023; 3:2073-2085. [PMID: 37654599 PMCID: PMC10466347 DOI: 10.1021/jacsau.3c00263] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 09/02/2023]
Abstract
Biocatalysis is becoming an increasingly impactful method in contemporary synthetic chemistry for target molecule synthesis. The selectivity imparted by enzymes has been leveraged to complete previously intractable chemical transformations and improve synthetic routes toward complex molecules. However, the implementation of biocatalysis in mainstream organic chemistry has been gradual to this point. This is partly due to a set of historical and technological barriers that have prevented chemists from using biocatalysis as a synthetic tool with utility that parallels alternative modes of catalysis. In this Perspective, we discuss these barriers and how they have hindered the adoption of enzyme catalysts into synthetic strategies. We also summarize tools and resources that already enable organic chemists to use biocatalysts. Furthermore, we discuss ways to further lower the barriers for the adoption of biocatalysis by the broader synthetic organic chemistry community through the dissemination of resources, demystifying biocatalytic reactions, and increasing collaboration across the field.
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Affiliation(s)
- Evan O. Romero
- Life Sciences Institute & Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Anthony T. Saucedo
- Life Sciences Institute & Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - José R. Hernández-Meléndez
- Life Sciences Institute & Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Di Yang
- Life Sciences Institute & Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Suman Chakrabarty
- Life Sciences Institute & Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Alison R. H. Narayan
- Life Sciences Institute & Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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19
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Verardo D, Adelizzi B, Rodriguez-Pinzon DA, Moghaddam N, Thomée E, Loman T, Godron X, Horgan A. Multiplex enzymatic synthesis of DNA with single-base resolution. SCIENCE ADVANCES 2023; 9:eadi0263. [PMID: 37418522 PMCID: PMC10328407 DOI: 10.1126/sciadv.adi0263] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/05/2023] [Indexed: 07/09/2023]
Abstract
Enzymatic DNA synthesis (EDS) is a promising benchtop and user-friendly method of nucleic acid synthesis that, instead of solvents and phosphoramidites, uses mild aqueous conditions and enzymes. For applications such as protein engineering and spatial transcriptomics that require either oligo pools or arrays with high sequence diversity, the EDS method needs to be adapted and certain steps in the synthesis process spatially decoupled. Here, we have used a synthesis cycle comprising a first step of site-specific silicon microelectromechanical system inkjet dispensing of terminal deoxynucleotidyl transferase enzyme and 3' blocked nucleotide, and a second step of bulk slide washing to remove the 3' blocking group. By repeating the cycle on a substrate with an immobilized DNA primer, we show that microscale spatial control of nucleic acid sequence and length is possible, which, here, are assayed by hybridization and gel electrophoresis. This work is distinctive for enzymatically synthesizing DNA in a highly parallel manner with single base control.
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Affiliation(s)
| | | | | | | | | | - Tessa Loman
- DNA Script, 67 Avenue de Fontainebleau, 94270 Le Kremlin-Bicêtre, France
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20
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Smith JA, Nguyen BH, Carlson R, Bertram JG, Palluk S, Arlow DH, Strauss K. Spatially Selective Electrochemical Cleavage of a Polymerase-Nucleotide Conjugate. ACS Synth Biol 2023; 12:1716-1726. [PMID: 37192389 PMCID: PMC10278165 DOI: 10.1021/acssynbio.3c00044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Indexed: 05/18/2023]
Abstract
Novel enzymatic methods are poised to become the dominant processes for de novo synthesis of DNA, promising functional, economic, and environmental advantages over the longstanding approach of phosphoramidite synthesis. Before this can occur, however, enzymatic synthesis methods must be parallelized to enable production of multiple DNA sequences simultaneously. As a means to this parallelization, we report a polymerase-nucleotide conjugate that is cleaved using electrochemical oxidation on a microelectrode array. The developed conjugate maintains polymerase activity toward surface-bound substrates with single-base control and detaches from the surface at mild oxidative voltages, leaving an extendable oligonucleotide behind. Our approach readies the way for enzymatic DNA synthesis on the scale necessary for DNA-intensive applications such as DNA data storage or gene synthesis.
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Affiliation(s)
- Jake A. Smith
- Microsoft
Research, Redmond, Washington 98052, United States
- Paul
G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Bichlien H. Nguyen
- Microsoft
Research, Redmond, Washington 98052, United States
- Paul
G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Rob Carlson
- Microsoft
Research, Redmond, Washington 98052, United States
| | | | - Sebastian Palluk
- Ansa
Biotechnologies, Emeryville, California 94608, United States
| | - Daniel H. Arlow
- Ansa
Biotechnologies, Emeryville, California 94608, United States
| | - Karin Strauss
- Microsoft
Research, Redmond, Washington 98052, United States
- Paul
G. Allen School of Computer Science and Engineering, University of Washington, Seattle, Washington 98195, United States
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21
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Lau B, Chandak S, Roy S, Tatwawadi K, Wootters M, Weissman T, Ji HP. Magnetic DNA random access memory with nanopore readouts and exponentially-scaled combinatorial addressing. Sci Rep 2023; 13:8514. [PMID: 37231057 PMCID: PMC10213054 DOI: 10.1038/s41598-023-29575-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 02/07/2023] [Indexed: 05/27/2023] Open
Abstract
The storage of data in DNA typically involves encoding and synthesizing data into short oligonucleotides, followed by reading with a sequencing instrument. Major challenges include the molecular consumption of synthesized DNA, basecalling errors, and limitations with scaling up read operations for individual data elements. Addressing these challenges, we describe a DNA storage system called MDRAM (Magnetic DNA-based Random Access Memory) that enables repetitive and efficient readouts of targeted files with nanopore-based sequencing. By conjugating synthesized DNA to magnetic agarose beads, we enabled repeated data readouts while preserving the original DNA analyte and maintaining data readout quality. MDRAM utilizes an efficient convolutional coding scheme that leverages soft information in raw nanopore sequencing signals to achieve information reading costs comparable to Illumina sequencing despite higher error rates. Finally, we demonstrate a proof-of-concept DNA-based proto-filesystem that enables an exponentially-scalable data address space using only small numbers of targeting primers for assembly and readout.
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Affiliation(s)
- Billy Lau
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, 94304, USA
| | - Shubham Chandak
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Sharmili Roy
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Kedar Tatwawadi
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Mary Wootters
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Tsachy Weissman
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA.
| | - Hanlee P Ji
- Division of Oncology, Department of Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.
- Stanford Genome Technology Center, Stanford University, Palo Alto, CA, 94304, USA.
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22
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Xu C, Ma B, Dong X, Lei L, Hao Q, Zhao C, Liu H. Assembly of Reusable DNA Blocks for Data Storage Using the Principle of Movable Type Printing. ACS APPLIED MATERIALS & INTERFACES 2023; 15:24097-24108. [PMID: 37184884 DOI: 10.1021/acsami.3c01860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Due to its high coding density and longevity, DNA is a compelling data storage alternative. However, current DNA data storage systems rely on the de novo synthesis of enormous DNA molecules, resulting in low data editability, high synthesis costs, and restrictions on further applications. Here, we demonstrate the programmable assembly of reusable DNA blocks for versatile data storage using the ancient movable type printing principle. Digital data are first encoded into nucleotide sequences in DNA hairpins, which are then synthesized and immobilized on solid beads as modular DNA blocks. Using DNA polymerase-catalyzed primer exchange reaction, data can be continuously replicated from hairpins on DNA blocks and attached to a primer in tandem to produce new information. The assembly of DNA blocks is highly programmable, producing various data by reusing a finite number of DNA blocks and reducing synthesis costs (∼1718 versus 3000 to 30,000 US$ per megabyte using conventional methods). We demonstrate the flexible assembly of texts, images, and random numbers using DNA blocks and the integration with DNA logic circuits to manipulate data synthesis. This work suggests a flexible paradigm by recombining already synthesized DNA to build cost-effective and intelligent DNA data storage systems.
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Affiliation(s)
- Chengtao Xu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University Institution, 2# Sipailou, Nanjing, Jiangsu 210096, China
| | - Biao Ma
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University Institution, 2# Sipailou, Nanjing, Jiangsu 210096, China
| | - Xing Dong
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University Institution, 2# Sipailou, Nanjing, Jiangsu 210096, China
| | - Lanjie Lei
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University Institution, 2# Sipailou, Nanjing, Jiangsu 210096, China
| | - Qing Hao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University Institution, 2# Sipailou, Nanjing, Jiangsu 210096, China
| | - Chao Zhao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University Institution, 2# Sipailou, Nanjing, Jiangsu 210096, China
| | - Hong Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University Institution, 2# Sipailou, Nanjing, Jiangsu 210096, China
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23
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Zhang Q, Xia K, Jiang M, Li Q, Chen W, Han M, Li W, Ke R, Wang F, Zhao Y, Liu Y, Fan C, Gu H. Catalytic DNA-Assisted Mass Production of Arbitrary Single-Stranded DNA. Angew Chem Int Ed Engl 2023; 62:e202212011. [PMID: 36347780 DOI: 10.1002/anie.202212011] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 10/25/2022] [Accepted: 11/08/2022] [Indexed: 11/11/2022]
Abstract
Synthetic single-stranded (ss) DNA is a cornerstone for life and materials science, yet the purity, quantity, length, and customizability of synthetic DNA are still limiting in various applications. Here, we present PECAN, paired-end cutting assisted by DNAzymes (DNA enzymes or deoxyribozymes), which enables mass production of ssDNA of arbitrary sequence (up to 7000 nucleotides, or nt) with single-base precision. At the core of PECAN technique are two newly identified classes of DNAzymes, each robustly self-hydrolyzing with minimal sequence requirement up- or down-stream of its cleavage site. Flanking the target ssDNA with a pair of such DNAzymes generates a precursor ssDNA amplifiable by pseudogene-recombinant bacteriophage, which subsequently releases the target ssDNA in large quantities after efficient auto-processing. PECAN produces ssDNA of virtually any terminal bases and compositions with >98.5 % purity at the milligram-to-gram scale. We demonstrate the feasibility of using PECAN ssDNA for RNA in situ detection, homology-directed genome editing, and DNA-based data storage.
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Affiliation(s)
- Qiao Zhang
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai, 200433, China
| | - Kai Xia
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai, 200433, China.,Department of Chemical Biology, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 201108, China.,Shanghai Frontier Innovation Research Institute, Shanghai, 201108, China
| | - Meng Jiang
- School of Medicine and School of Biomedical Science, Huaqiao University, Fujian, 362021, China
| | - Qingting Li
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai, 200433, China.,Department of Chemical Biology, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 201108, China
| | - Weigang Chen
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Mingzhe Han
- Frontier Science Center for Synthetic Biology (Ministry of Education), Tianjin University, Tianjin, 300072, China
| | - Wei Li
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai, 200433, China
| | - Rongqin Ke
- School of Medicine and School of Biomedical Science, Huaqiao University, Fujian, 362021, China
| | - Fei Wang
- Department of Chemical Biology, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 201108, China
| | - Yongxing Zhao
- Department of Pharmaceutics, School of Pharmaceutical Sciences, Key Laboratory of Targeting Therapy and Diagnosis for Critical Diseases, and Key Laboratory of Advanced Drug Preparation Technologies, Zhengzhou University, Henan, 450001, China
| | - Yuehua Liu
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai, 200433, China
| | - Chunhai Fan
- Department of Chemical Biology, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 201108, China
| | - Hongzhou Gu
- Fudan University Shanghai Cancer Center, and the Shanghai Key Laboratory of Medical Epigenetics, Institutes of Biomedical Sciences, Shanghai Stomatological Hospital, Fudan University, Shanghai, 200433, China.,Department of Chemical Biology, School of Chemistry and Chemical Engineering, Frontiers Science Center for Transformative Molecules, National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 201108, China
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24
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Hoose A, Vellacott R, Storch M, Freemont PS, Ryadnov MG. DNA synthesis technologies to close the gene writing gap. Nat Rev Chem 2023; 7:144-161. [PMID: 36714378 PMCID: PMC9869848 DOI: 10.1038/s41570-022-00456-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 57.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/29/2022] [Indexed: 01/24/2023]
Abstract
Synthetic DNA is of increasing demand across many sectors of research and commercial activities. Engineering biology, therapy, data storage and nanotechnology are set for rapid developments if DNA can be provided at scale and low cost. Stimulated by successes in next generation sequencing and gene editing technologies, DNA synthesis is already a burgeoning industry. However, the synthesis of >200 bp sequences remains unaffordable. To overcome these limitations and start writing DNA as effectively as it is read, alternative technologies have been developed including molecular assembly and cloning methods, template-independent enzymatic synthesis, microarray and rolling circle amplification techniques. Here, we review the progress in developing and commercializing these technologies, which are exemplified by innovations from leading companies. We discuss pros and cons of each technology, the need for oversight and regulatory policies for DNA synthesis as a whole and give an overview of DNA synthesis business models.
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Affiliation(s)
- Alex Hoose
- National Physical Laboratory, Teddington, Middlesex UK
| | | | - Marko Storch
- London Biofoundry, Translation and Innovation Hub, Imperial College White City Campus, London, UK
- Section of Structural and Synthetic Biology, Faculty of Medicine, Imperial College London, London, UK
| | - Paul S. Freemont
- London Biofoundry, Translation and Innovation Hub, Imperial College White City Campus, London, UK
- Section of Structural and Synthetic Biology, Faculty of Medicine, Imperial College London, London, UK
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25
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Doricchi A, Platnich CM, Gimpel A, Horn F, Earle M, Lanzavecchia G, Cortajarena AL, Liz-Marzán LM, Liu N, Heckel R, Grass RN, Krahne R, Keyser UF, Garoli D. Emerging Approaches to DNA Data Storage: Challenges and Prospects. ACS NANO 2022; 16:17552-17571. [PMID: 36256971 PMCID: PMC9706676 DOI: 10.1021/acsnano.2c06748] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
With the total amount of worldwide data skyrocketing, the global data storage demand is predicted to grow to 1.75 × 1014 GB by 2025. Traditional storage methods have difficulties keeping pace given that current storage media have a maximum density of 103 GB/mm3. As such, data production will far exceed the capacity of currently available storage methods. The costs of maintaining and transferring data, as well as the limited lifespans and significant data losses associated with current technologies also demand advanced solutions for information storage. Nature offers a powerful alternative through the storage of information that defines living organisms in unique orders of four bases (A, T, C, G) located in molecules called deoxyribonucleic acid (DNA). DNA molecules as information carriers have many advantages over traditional storage media. Their high storage density, potentially low maintenance cost, ease of synthesis, and chemical modification make them an ideal alternative for information storage. To this end, rapid progress has been made over the past decade by exploiting user-defined DNA materials to encode information. In this review, we discuss the most recent advances of DNA-based data storage with a major focus on the challenges that remain in this promising field, including the current intrinsic low speed in data writing and reading and the high cost per byte stored. Alternatively, data storage relying on DNA nanostructures (as opposed to DNA sequence) as well as on other combinations of nanomaterials and biomolecules are proposed with promising technological and economic advantages. In summarizing the advances that have been made and underlining the challenges that remain, we provide a roadmap for the ongoing research in this rapidly growing field, which will enable the development of technological solutions to the global demand for superior storage methodologies.
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Affiliation(s)
- Andrea Doricchi
- Istituto
Italiano di Tecnologia, via Morego 30, I-16163 Genova, Italy
- Dipartimento
di Chimica e Chimica Industriale, Università
di Genova, via Dodecaneso
31, 16146 Genova, Italy
| | - Casey M. Platnich
- Cavendish
Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K.
| | - Andreas Gimpel
- Institute
for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zurich, Switzerland
| | - Friederikee Horn
- Technical
University of Munich, Department of Electrical
and Computer Engineering Munchen, Bayern, DE 80333, Germany
| | - Max Earle
- Cavendish
Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K.
| | - German Lanzavecchia
- Istituto
Italiano di Tecnologia, via Morego 30, I-16163 Genova, Italy
- Dipartimento
di Fisica, Università di Genova, via Dodecaneso 33, 16146 Genova, Italy
| | - Aitziber L. Cortajarena
- Center
for Cooperative Research in Biomaterials (CICbiomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, 20014 Donostia-San Sebastián, Spain
- Ikerbasque, Basque
Foundation for Science, 48009 Bilbao, Spain
| | - Luis M. Liz-Marzán
- Center
for Cooperative Research in Biomaterials (CICbiomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo de Miramón 194, 20014 Donostia-San Sebastián, Spain
- Ikerbasque, Basque
Foundation for Science, 48009 Bilbao, Spain
- Biomedical
Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Av. Monforte de Lemos, 3-5. Pabellón 11.
Planta 0, 28029 Madrid, Spain
| | - Na Liu
- Second
Physics Institute, University of Stuttgart, 70569 Stuttgart, Germany
- Max Planck Institute for Solid State Research, 70569 Stuttgart, Germany
| | - Reinhard Heckel
- Technical
University of Munich, Department of Electrical
and Computer Engineering Munchen, Bayern, DE 80333, Germany
| | - Robert N. Grass
- Institute
for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1, 8093 Zurich, Switzerland
| | - Roman Krahne
- Istituto
Italiano di Tecnologia, via Morego 30, I-16163 Genova, Italy
| | - Ulrich F. Keyser
- Cavendish
Laboratory, University of Cambridge, JJ Thomson Avenue, Cambridge CB3 0HE, U.K.
| | - Denis Garoli
- Istituto
Italiano di Tecnologia, via Morego 30, I-16163 Genova, Italy
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26
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Oliveira SMD, Densmore D. Hardware, Software, and Wetware Codesign Environment for Synthetic Biology. BIODESIGN RESEARCH 2022; 2022:9794510. [PMID: 37850136 PMCID: PMC10521664 DOI: 10.34133/2022/9794510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 08/10/2022] [Indexed: 10/19/2023] Open
Abstract
Synthetic biology is the process of forward engineering living systems. These systems can be used to produce biobased materials, agriculture, medicine, and energy. One approach to designing these systems is to employ techniques from the design of embedded electronics. These techniques include abstraction, standards, modularity, automated design, and formal semantic models of computation. Together, these elements form the foundation of "biodesign automation," where software, robotics, and microfluidic devices combine to create exciting biological systems of the future. This paper describes a "hardware, software, wetware" codesign vision where software tools can be made to act as "genetic compilers" that transform high-level specifications into engineered "genetic circuits" (wetware). This is followed by a process where automation equipment, well-defined experimental workflows, and microfluidic devices are explicitly designed to house, execute, and test these circuits (hardware). These systems can be used as either massively parallel experimental platforms or distributed bioremediation and biosensing devices. Next, scheduling and control algorithms (software) manage these systems' actual execution and data analysis tasks. A distinguishing feature of this approach is how all three of these aspects (hardware, software, and wetware) may be derived from the same basic specification in parallel and generated to fulfill specific cost, performance, and structural requirements.
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Affiliation(s)
- Samuel M. D. Oliveira
- Department of Electrical and Computer Engineering, Boston University, MA 02215, USA
- Biological Design Center, Boston University, MA 02215, USA
| | - Douglas Densmore
- Department of Electrical and Computer Engineering, Boston University, MA 02215, USA
- Biological Design Center, Boston University, MA 02215, USA
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27
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Simple synthesis of massively parallel RNA microarrays via enzymatic conversion from DNA microarrays. Nat Commun 2022; 13:3772. [PMID: 35773271 PMCID: PMC9246885 DOI: 10.1038/s41467-022-31370-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 06/14/2022] [Indexed: 11/20/2022] Open
Abstract
RNA catalytic and binding interactions with proteins and small molecules are fundamental elements of cellular life processes as well as the basis for RNA therapeutics and molecular engineering. In the absence of quantitative predictive capacity for such bioaffinity interactions, high throughput experimental approaches are needed to sufficiently sample RNA sequence space. Here we report on a simple and highly accessible approach to convert commercially available customized DNA microarrays of any complexity and density to RNA microarrays via a T7 RNA polymerase-mediated extension of photocrosslinked methyl RNA primers and subsequent degradation of the DNA templates. RNA microarrays have many potential applications, but are difficult to produce. Here, the AUs present a method for converting commercial, customizable DNA microarrays into RNA microarrays using an accessible three-step process involving primer photocrosslinking, extension, and template degradation.
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28
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Robson JM, Green AA. Closing the loop on crowdsourced science. Proc Natl Acad Sci U S A 2022; 119:e2205897119. [PMID: 35687665 PMCID: PMC9231617 DOI: 10.1073/pnas.2205897119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Affiliation(s)
- James M. Robson
- Department of Biomedical Engineering, Boston University, Boston, MA 02215
- Biological Design Center, Boston University, Boston, MA 02215
| | - Alexander A. Green
- Department of Biomedical Engineering, Boston University, Boston, MA 02215
- Biological Design Center, Boston University, Boston, MA 02215
- Molecular Biology, Cell Biology & Biochemistry Program, Graduate School of Arts and Sciences, Boston University, Boston, MA 02215
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29
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Vaknin I, Amit R. Molecular and experimental tools to design synthetic enhancers. Curr Opin Biotechnol 2022; 76:102728. [PMID: 35525178 DOI: 10.1016/j.copbio.2022.102728] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 03/16/2022] [Accepted: 04/03/2022] [Indexed: 11/03/2022]
Abstract
Understanding the grammar of enhancers and how they regulate gene expression is key for both basic research and for the pharma and biotech industries. The design and characterization of synthetic enhancers can expand the known regulatory space. This is achieved by the utilization of DNA Oligo Libraries (OLs), which facilitates screening of as many as millions of synthetic enhancer variants simultaneously. This review includes the latest commercial DNA OL synthesis technology and its capabilities, and a general 'know-how' guide for the design, construction, and analysis of OL-based synthetic enhancer characterization experiments. Specifically, we focus on synthetic-enhancer-based massively parallel reporter assay, Sort-seq methodologies (e.g. flow cytometry, deep sequencing), and a brief description of machine learning-based attempts for OL-analysis and follow-up validation experiments.
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Affiliation(s)
- Inbal Vaknin
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 3200000, Israel
| | - Roee Amit
- Department of Biotechnology and Food Engineering, Technion - Israel Institute of Technology, Haifa 3200000, Israel; The Russell Berrie Nanotechnology Institute, Technion - Israel Institute of Technology, Haifa 3200000, Israel.
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30
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Zhang Z, Weng Z, Yao J, Liu D, Zhang L, Zhang L, Xie G. Toehold-mediated nonenzymatic DNA strand displacement coupling UDG mediated PCR and multi-code magnetic beads for DNA genotyping. Microchem J 2022. [DOI: 10.1016/j.microc.2022.107340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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31
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Lu X, Li J, Li C, Lou Q, Peng K, Cai B, Liu Y, Yao Y, Lu L, Tian Z, Ma H, Wang W, Cheng J, Guo X, Jiang H, Ma Y. Enzymatic DNA Synthesis by Engineering Terminal Deoxynucleotidyl Transferase. ACS Catal 2022. [DOI: 10.1021/acscatal.1c04879] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Xiaoyun Lu
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, Shanxi 710072, China
- Zhonghe Gene Technology Co., Ltd., Tianjin 300308, China
| | - Jinlong Li
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Congyu Li
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Tianjin University of Science&Technology, Tianjin 300457, China
| | - Qianqian Lou
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Kai Peng
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Bijun Cai
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Ying Liu
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yonghong Yao
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Lina Lu
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Zhenyang Tian
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Hongwu Ma
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Wen Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi’an, Shanxi 710072, China
| | - Jian Cheng
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Xiaoxian Guo
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Huifeng Jiang
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
| | - Yanhe Ma
- National Center of Technology Innovation for Synthetic Biology, Tianjin 300308, China
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin 300308, China
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32
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Qi Z, Jung C, Bandilla P, Ludwig C, Heron M, Sophie Kiesel A, Museridze M, Philippou‐Massier J, Nikolov M, Renna Max Schnepf A, Unnerstall U, Ceolin S, Mühlig B, Gompel N, Soeding J, Gaul U. Large-scale analysis of Drosophila core promoter function using synthetic promoters. Mol Syst Biol 2022; 18:e9816. [PMID: 35156763 PMCID: PMC8842121 DOI: 10.15252/msb.20209816] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Revised: 01/11/2022] [Accepted: 01/13/2022] [Indexed: 02/02/2023] Open
Abstract
The core promoter plays a central role in setting metazoan gene expression levels, but how exactly it "computes" expression remains poorly understood. To dissect its function, we carried out a comprehensive structure-function analysis in Drosophila. First, we performed a genome-wide bioinformatic analysis, providing an improved picture of the sequence motifs architecture. We then measured synthetic promoters' activities of ~3,000 mutational variants with and without an external stimulus (hormonal activation), at large scale and with high accuracy using robotics and a dual luciferase reporter assay. We observed a strong impact on activity of the different types of mutations, including knockout of individual sequence motifs and motif combinations, variations of motif strength, nucleosome positioning, and flanking sequences. A linear combination of the individual motif features largely accounts for the combinatorial effects on core promoter activity. These findings shed new light on the quantitative assessment of gene expression in metazoans.
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Affiliation(s)
- Zhan Qi
- Department of Biochemistry, Gene CenterLudwig‐Maximillians‐Universität MünchenFeodor‐Lynen‐str 25MunichGermany
| | - Christophe Jung
- Department of Biochemistry, Gene CenterLudwig‐Maximillians‐Universität MünchenFeodor‐Lynen‐str 25MunichGermany
| | - Peter Bandilla
- Department of Biochemistry, Gene CenterLudwig‐Maximillians‐Universität MünchenFeodor‐Lynen‐str 25MunichGermany
| | - Claudia Ludwig
- Department of Biochemistry, Gene CenterLudwig‐Maximillians‐Universität MünchenFeodor‐Lynen‐str 25MunichGermany
| | - Mark Heron
- Department of Biochemistry, Gene CenterLudwig‐Maximillians‐Universität MünchenFeodor‐Lynen‐str 25MunichGermany
| | - Anja Sophie Kiesel
- Department of Biochemistry, Gene CenterLudwig‐Maximillians‐Universität MünchenFeodor‐Lynen‐str 25MunichGermany
| | - Mariam Museridze
- Department of Biology II, Evolutionary BiologyLudwig‐Maximilians‐Universität MünchenPlanegg‐MartinsriedGermany
| | - Julia Philippou‐Massier
- Department of Biochemistry, Gene CenterLudwig‐Maximillians‐Universität MünchenFeodor‐Lynen‐str 25MunichGermany
| | - Miroslav Nikolov
- Department of Biochemistry, Gene CenterLudwig‐Maximillians‐Universität MünchenFeodor‐Lynen‐str 25MunichGermany
| | - Alessio Renna Max Schnepf
- Department of Biochemistry, Gene CenterLudwig‐Maximillians‐Universität MünchenFeodor‐Lynen‐str 25MunichGermany
| | - Ulrich Unnerstall
- Department of Biochemistry, Gene CenterLudwig‐Maximillians‐Universität MünchenFeodor‐Lynen‐str 25MunichGermany
| | - Stefano Ceolin
- Department of Biology II, Evolutionary BiologyLudwig‐Maximilians‐Universität MünchenPlanegg‐MartinsriedGermany
| | - Bettina Mühlig
- Department of Biology II, Evolutionary BiologyLudwig‐Maximilians‐Universität MünchenPlanegg‐MartinsriedGermany
| | - Nicolas Gompel
- Department of Biology II, Evolutionary BiologyLudwig‐Maximilians‐Universität MünchenPlanegg‐MartinsriedGermany
| | - Johannes Soeding
- Department of Biochemistry, Gene CenterLudwig‐Maximillians‐Universität MünchenFeodor‐Lynen‐str 25MunichGermany
- Max Planck Institute for Biophysical ChemistryGöttingenGermany
| | - Ulrike Gaul
- Department of Biochemistry, Gene CenterLudwig‐Maximillians‐Universität MünchenFeodor‐Lynen‐str 25MunichGermany
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33
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Zhao Q, Chapman A, Huang Y, Ferguson M, McBride S, Kelly M, Weiner M, Li X. Ligand-Directed GPCR Antibody Discovery. Methods Mol Biol 2022; 2394:319-342. [PMID: 35094336 DOI: 10.1007/978-1-0716-1811-0_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Developing affinity reagents recognizing and modulating G-protein coupled receptors (GPCR) function by traditional animal immunization or in vitro screening methods is challenging. Some anti-GPCR antibodies exist on the market, but the success rate of development is still poor compared with antibodies targeting soluble or peripherally anchored proteins. More importantly, most of these antibodies do not modulate GPCR function. The current pipeline for antibody development primarily screens for overall affinity rather than functional epitope recognition. We developed a new strategy utilizing natural ligand affinity to generate a library of antibody variants with an inherent bias toward the active site of the GPCR. Instead of using phage libraries displaying antibodies with random CDR sequences at polymorphism sites observed in natural immune repertoire sequences, we generated focused antibody libraries with a natural ligand encoded within or conjugated to one of the CDRs or the N-terminus. To tailor antibody binding to the active site, we limited the sequence randomization of the antibody in regions holstering the ligand while leaving the ligand-carrying part unaltered in the first round of randomization. With hits from the successful first round, the second round of randomization of the ligand-carrying part was then performed to eliminate the bias of the ligand. Based on our results on three different GPCR targets, the proposed pipeline will enable the rapid generation of functional antibodies (both agonists and antagonists) against high-value targets with poor function epitope exposures including GPCR, channels, transporters as well as cell surface targets whose binding site is heavily masked by glycosylation.
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Affiliation(s)
- Qi Zhao
- Abcam plc, Branford, CT, USA.
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34
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Xu C, Ma B, Gao Z, Dong X, Zhao C, Liu H. Electrochemical DNA synthesis and sequencing on a single electrode with scalability for integrated data storage. SCIENCE ADVANCES 2021; 7:eabk0100. [PMID: 34767438 PMCID: PMC8589306 DOI: 10.1126/sciadv.abk0100] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
DNA has been considered as a compelling candidate for digital data storage due to advantages such as high coding density, long retention time, and low energy consumption. Despite many works reported, the development of a DNA-based database of full integration, high efficiency, and practical applicability is still challenging. In this work, we report the synthesis and sequencing of DNA on a single electrode with scalability for an integrated DNA-based data storage system. The synthesis of DNA is based on phosphoramidite chemistry and electrochemical deprotection. The sequencing relies on charge redistribution originated from polymerase-catalyzed primer extension, leading to a measurable current spike. By regeneration of the electrode after sequencing, repeated sequencing can be achieved to improve the accuracy. A SlipChip device is developed to simplify the liquid introduction involved in DNA synthesis and sequencing. As the proof-of-concept experiment, text information is stored in the system and then accurately retrieved.
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35
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Exploring liver cancer biology through functional genetic screens. Nat Rev Gastroenterol Hepatol 2021; 18:690-704. [PMID: 34163045 DOI: 10.1038/s41575-021-00465-x] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/06/2021] [Indexed: 02/06/2023]
Abstract
As the fourth leading cause of cancer-related death in the world, liver cancer poses a major threat to human health. Although a growing number of therapies have been approved for the treatment of hepatocellular carcinoma in the past few years, most of them only provide a limited survival benefit. Therefore, an urgent need exists to identify novel targetable vulnerabilities and powerful drug combinations for the treatment of liver cancer. The advent of functional genetic screening has contributed to the advancement of liver cancer biology, uncovering many novel genes involved in tumorigenesis and cancer progression in a high-throughput manner. In addition, this unbiased screening platform also provides an efficient tool for the exploration of the mechanisms involved in therapy resistance as well as identifying potential targets for therapy. In this Review, we describe how functional screens can help to deepen our understanding of liver cancer and guide the development of new therapeutic strategies.
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36
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A broad analysis of splicing regulation in yeast using a large library of synthetic introns. PLoS Genet 2021; 17:e1009805. [PMID: 34570750 PMCID: PMC8496845 DOI: 10.1371/journal.pgen.1009805] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 10/07/2021] [Accepted: 09/03/2021] [Indexed: 11/19/2022] Open
Abstract
RNA splicing is a key process in eukaryotic gene expression, in which an intron is spliced out of a pre-mRNA molecule to eventually produce a mature mRNA. Most intron-containing genes are constitutively spliced, hence efficient splicing of an intron is crucial for efficient regulation of gene expression. Here we use a large synthetic oligo library of ~20,000 variants to explore how different intronic sequence features affect splicing efficiency and mRNA expression levels in S. cerevisiae. Introns are defined by three functional sites, the 5’ donor site, the branch site, and the 3’ acceptor site. Using a combinatorial design of synthetic introns, we demonstrate how non-consensus splice site sequences in each of these sites affect splicing efficiency. We then show that S. cerevisiae splicing machinery tends to select alternative 3’ splice sites downstream of the original site, and we suggest that this tendency created a selective pressure, leading to the avoidance of cryptic splice site motifs near introns’ 3’ ends. We further use natural intronic sequences from other yeast species, whose splicing machineries have diverged to various extents, to show how intron architectures in the various species have been adapted to the organism’s splicing machinery. We suggest that the observed tendency for cryptic splicing is a result of a loss of a specific splicing factor, U2AF1. Lastly, we show that synthetic sequences containing two introns give rise to alternative RNA isoforms in S. cerevisiae, demonstrating that merely a synthetic fusion of two introns might be suffice to facilitate alternative splicing in yeast. Our study reveals novel mechanisms by which introns are shaped in evolution to allow cells to regulate their transcriptome. In addition, it provides a valuable resource to study the regulation of constitutive and alternative splicing in a model organism. RNA splicing is a process in which parts of a new pre-mRNA are spliced out of the mRNA molecule to produce eventually a mature mRNA. Those RNA segments that are spliced out are termed introns, and they are found in most genes in eukaryotic organisms. Hence regulation of this process has a major role in the control of gene expression. The budding yeast S. cerevisiae is a popular model organism for eukaryotic cell biology, but in terms of splicing it differs, as it has only few intron-containing genes. Nevertheless, this species has been used to study basic principles of splicing regulation based on its ~300 introns. Here we used the technology of a large synthetic genetic library to introduce many new intron-containing genes to the yeast genome, to explore splicing regulation at a wider scope than was possible so far. Reassuringly, our results confirm known regulatory mechanisms, and further expand our understanding of splicing regulation, specifically how the yeast splicing machinery interacts with the end of introns, and how through evolution introns have evolved to avoid unwanted misidentifications of this end. We further demonstrate the potential of the yeast splicing machinery to alternatively splice a two-intron gene, which is common in other eukaryotes but rare in yeast. Our work presents a first-of-its-kind resource for the systematic study of splicing in live cells.
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37
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Barber KW, Shrock E, Elledge SJ. CRISPR-based peptide library display and programmable microarray self-assembly for rapid quantitative protein binding assays. Mol Cell 2021; 81:3650-3658.e5. [PMID: 34390675 DOI: 10.1016/j.molcel.2021.07.027] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/25/2021] [Accepted: 07/21/2021] [Indexed: 01/08/2023]
Abstract
CRISPR-inspired systems have been extensively developed for applications in genome editing and nucleic acid detection. Here, we introduce a CRISPR-based peptide display technology to facilitate customized, high-throughput in vitro protein interaction studies. We show that bespoke peptide libraries fused to catalytically inactive Cas9 (dCas9) and barcoded with unique single guide RNA (sgRNA) molecules self-assemble from a single mixed pool to programmable positions on a DNA microarray surface for rapid, multiplexed binding assays. We develop dCas9-displayed saturation mutagenesis libraries to characterize antibody-epitope binding for a commercial anti-FLAG monoclonal antibody and human serum antibodies. We also show that our platform can be used for viral epitope mapping and exhibits promise as a multiplexed diagnostics tool. Our CRISPR-based peptide display platform and the principles of complex library self-assembly using dCas9 could be adapted for rapid interrogation of varied customized protein libraries or biological materials assembly using DNA scaffolding.
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Affiliation(s)
- Karl W Barber
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Ellen Shrock
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Stephen J Elledge
- Division of Genetics, Brigham and Women's Hospital, Howard Hughes Medical Institute, Boston, MA 02115, USA; Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
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38
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Currin A, Parker S, Robinson CJ, Takano E, Scrutton NS, Breitling R. The evolving art of creating genetic diversity: From directed evolution to synthetic biology. Biotechnol Adv 2021; 50:107762. [PMID: 34000294 PMCID: PMC8299547 DOI: 10.1016/j.biotechadv.2021.107762] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 04/21/2021] [Accepted: 04/25/2021] [Indexed: 12/31/2022]
Abstract
The ability to engineer biological systems, whether to introduce novel functionality or improved performance, is a cornerstone of biotechnology and synthetic biology. Typically, this requires the generation of genetic diversity to explore variations in phenotype, a process that can be performed at many levels, from single molecule targets (i.e., in directed evolution of enzymes) to whole organisms (e.g., in chassis engineering). Recent advances in DNA synthesis technology and automation have enhanced our ability to create variant libraries with greater control and throughput. This review highlights the latest developments in approaches to create such a hierarchy of diversity from the enzyme level to entire pathways in vitro, with a focus on the creation of combinatorial libraries that are required to navigate a target's vast design space successfully to uncover significant improvements in function.
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Affiliation(s)
- Andrew Currin
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom.
| | - Steven Parker
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Christopher J Robinson
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Eriko Takano
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Nigel S Scrutton
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom
| | - Rainer Breitling
- Manchester Centre for Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM), Manchester Institute of Biotechnology, The University of Manchester, Manchester M1 7DN, United Kingdom.
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39
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Lietard J, Leger A, Erlich Y, Sadowski N, Timp W, Somoza MM. Chemical and photochemical error rates in light-directed synthesis of complex DNA libraries. Nucleic Acids Res 2021; 49:6687-6701. [PMID: 34157124 PMCID: PMC8266620 DOI: 10.1093/nar/gkab505] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/24/2021] [Accepted: 06/17/2021] [Indexed: 11/30/2022] Open
Abstract
Nucleic acid microarrays are the only tools that can supply very large oligonucleotide libraries, cornerstones of the nascent fields of de novo gene assembly and DNA data storage. Although the chemical synthesis of oligonucleotides is highly developed and robust, it is not error free, requiring the design of methods that can correct or compensate for errors, or select for high-fidelity oligomers. However, outside the realm of array manufacturers, little is known about the sources of errors and their extent. In this study, we look at the error rate of DNA libraries synthesized by photolithography and dissect the proportion of deletion, insertion and substitution errors. We find that the deletion rate is governed by the photolysis yield. We identify the most important substitution error and correlate it to phosphoramidite coupling. Besides synthetic failures originating from the coupling cycle, we uncover the role of imperfections and limitations related to optics, highlight the importance of absorbing UV light to avoid internal reflections and chart the dependence of error rate on both position on the array and position within individual oligonucleotides. Being able to precisely quantify all types of errors will allow for optimal choice of fabrication parameters and array design.
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Affiliation(s)
- Jory Lietard
- Institute of Inorganic Chemistry, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - Adrien Leger
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Norah Sadowski
- Johns Hopkins University, Department of Molecular Biology and Genetics, Baltimore, MD, USA
| | - Winston Timp
- Johns Hopkins University, Department of Molecular Biology and Genetics, Baltimore, MD, USA.,Johns Hopkins University, Departments of Biomedical Engineering, Molecular Biology and Genetics and Medicine, Division of Infectious Disease, Baltimore, MD, USA
| | - Mark M Somoza
- Institute of Inorganic Chemistry, University of Vienna, Althanstraße 14, 1090 Vienna, Austria.,Chair of Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising, Germany.,Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Straße 34, 85354 Freising, Germany
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40
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Xu C, Zhao C, Ma B, Liu H. Uncertainties in synthetic DNA-based data storage. Nucleic Acids Res 2021; 49:5451-5469. [PMID: 33836076 PMCID: PMC8191772 DOI: 10.1093/nar/gkab230] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 02/16/2021] [Accepted: 03/22/2021] [Indexed: 12/12/2022] Open
Abstract
Deoxyribonucleic acid (DNA) has evolved to be a naturally selected, robust biomacromolecule for gene information storage, and biological evolution and various diseases can find their origin in uncertainties in DNA-related processes (e.g. replication and expression). Recently, synthetic DNA has emerged as a compelling molecular media for digital data storage, and it is superior to the conventional electronic memory devices in theoretical retention time, power consumption, storage density, and so forth. However, uncertainties in the in vitro DNA synthesis and sequencing, along with its conjugation chemistry and preservation conditions can lead to severe errors and data loss, which limit its practical application. To maintain data integrity, complicated error correction algorithms and substantial data redundancy are usually required, which can significantly limit the efficiency and scale-up of the technology. Herein, we summarize the general procedures of the state-of-the-art DNA-based digital data storage methods (e.g. write, read, and preservation), highlighting the uncertainties involved in each step as well as potential approaches to correct them. We also discuss challenges yet to overcome and research trends in the promising field of DNA-based data storage.
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Affiliation(s)
- Chengtao Xu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Chao Zhao
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Biao Ma
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
| | - Hong Liu
- State Key Laboratory of Bioelectronics, School of Biological Science and Medical Engineering, Southeast University, Nanjing, Jiangsu 210096, China
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41
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Abstract
DNA synthesis technology has progressed to the point that it is now practical to synthesize entire genomes. Quite a variety of methods have been developed, first to synthesize single genes but ultimately to massively edit or write from scratch entire genomes. Synthetic genomes can essentially be clones of native sequences, but this approach does not teach us much new biology. The ability to endow genomes with novel properties offers special promise for addressing questions not easily approachable with conventional gene-at-a-time methods. These include questions about evolution and about how genomes are fundamentally wired informationally, metabolically, and genetically. The techniques and technologies relating to how to design, build, and deliver big DNA at the genome scale are reviewed here. A fuller understanding of these principles may someday lead to the ability to truly design genomes from scratch.
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Affiliation(s)
- Weimin Zhang
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University Langone Health, New York, NY 10016, USA; , ,
| | - Leslie A Mitchell
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University Langone Health, New York, NY 10016, USA; , ,
| | - Joel S Bader
- Department of Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland 21218, USA;
| | - Jef D Boeke
- Institute for Systems Genetics and Department of Biochemistry and Molecular Pharmacology, New York University Langone Health, New York, NY 10016, USA; , , .,Department of Biomedical Engineering, New York University Tandon School of Engineering, New York, NY 11201, USA
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42
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Yoo E, Choe D, Shin J, Cho S, Cho BK. Mini review: Enzyme-based DNA synthesis and selective retrieval for data storage. Comput Struct Biotechnol J 2021; 19:2468-2476. [PMID: 34025937 PMCID: PMC8113751 DOI: 10.1016/j.csbj.2021.04.057] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 04/20/2021] [Accepted: 04/22/2021] [Indexed: 11/26/2022] Open
Abstract
The market for using and storing digital data is growing, with DNA synthesis emerging as an efficient way to store massive amounts of data. Storing information in DNA mainly consists of two steps: data writing and reading. The writing step requires encoding data in DNA, building one nucleotide at a time as a form of single-stranded DNA (ssDNA). Once the data needs to be read, the target DNA is selectively retrieved and sequenced, which will also be in the form of an ssDNA. Recently, enzyme-based DNA synthesis is emerging as a new method to be a breakthrough on behalf of decades-old chemical synthesis. A few enzymatic methods have been presented for data memory, including the use of terminal deoxynucleotidyl transferase. Besides, enzyme-based amplification or denaturation of the target strand into ssDNA provides selective access to the desired dataset. In this review, we summarize diverse enzymatic methods for either synthesizing ssDNA or retrieving the data-containing DNA.
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Affiliation(s)
- Eojin Yoo
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Donghui Choe
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Jongoh Shin
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Suhyung Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea.,Innovative Biomaterials Research Center, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
| | - Byung-Kwan Cho
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea.,Innovative Biomaterials Research Center, KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
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43
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Mondal T, Nerantzaki M, Flesch K, Loth C, Maaloum M, Cong Y, Sheiko SS, Lutz JF. Large Sequence-Defined Supramolecules Obtained by the DNA-Guided Assembly of Biohybrid Poly(phosphodiester)s. Macromolecules 2021. [DOI: 10.1021/acs.macromol.0c02581] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Tathagata Mondal
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, 23 rue du Loess, 67034 Strasbourg Cedex 2, France
| | - Maria Nerantzaki
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, 23 rue du Loess, 67034 Strasbourg Cedex 2, France
| | - Kevin Flesch
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, 23 rue du Loess, 67034 Strasbourg Cedex 2, France
| | - Capucine Loth
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, 23 rue du Loess, 67034 Strasbourg Cedex 2, France
| | - Mounir Maaloum
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, 23 rue du Loess, 67034 Strasbourg Cedex 2, France
| | - Yidan Cong
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Sergei S. Sheiko
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599-3290, United States
| | - Jean-François Lutz
- Université de Strasbourg, CNRS, Institut Charles Sadron UPR22, 23 rue du Loess, 67034 Strasbourg Cedex 2, France
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44
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Nedrud D, Coyote-Maestas W, Schmidt D. A large-scale survey of pairwise epistasis reveals a mechanism for evolutionary expansion and specialization of PDZ domains. Proteins 2021; 89:899-914. [PMID: 33620761 DOI: 10.1002/prot.26067] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 02/02/2021] [Accepted: 02/18/2021] [Indexed: 12/21/2022]
Abstract
Deep mutational scanning (DMS) facilitates data-driven models of protein structure and function. Here, we adapted Saturated Programmable Insertion Engineering (SPINE) as a programmable DMS technique. We validate SPINE with a reference single mutant dataset in the PSD95 PDZ3 domain and then characterize most pairwise double mutants to study epistasis. We observe wide-spread proximal negative epistasis, which we attribute to mutations affecting thermodynamic stability, and strong long-range positive epistasis, which is enriched in an evolutionarily conserved and function-defining network of "sector" and clade-specifying residues. Conditional neutrality of mutations in clade-specifying residues compensates for deleterious mutations in sector positions. This suggests that epistatic interactions between these position pairs facilitated the evolutionary expansion and specialization of PDZ domains. We propose that SPINE provides easy experimental access to reveal epistasis signatures in proteins that will improve our understanding of the structural basis for protein function and adaptation.
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Affiliation(s)
- David Nedrud
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Willow Coyote-Maestas
- Department of Biochemistry, Molecular Biology & Biophysics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Daniel Schmidt
- Department of Genetics, Cell Biology & Development, University of Minnesota, Minneapolis, Minnesota, USA
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45
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Lim CK, Nirantar S, Yew WS, Poh CL. Novel Modalities in DNA Data Storage. Trends Biotechnol 2021; 39:990-1003. [PMID: 33455842 DOI: 10.1016/j.tibtech.2020.12.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 12/14/2020] [Accepted: 12/15/2020] [Indexed: 10/22/2022]
Abstract
The field of storing information in DNA has expanded exponentially. Most common modalities involve encoding information from bits into synthesized nucleotides, storage in liquid or dry media, and decoding via sequencing. However, limitations to this paradigm include the cost of DNA synthesis and sequencing, along with low throughput. Further unresolved questions include the appropriate media of storage and the scalability of such approaches for commercial viability. In this review, we examine various storage modalities involving the use of DNA from a systems-level perspective. We compare novel methods that draw inspiration from molecular biology techniques that have been devised to overcome the difficulties posed by standard workflows and conceptualize potential applications that can arise from these advances.
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Affiliation(s)
- Cheng Kai Lim
- NUS Graduate School of Integrative Sciences and Engineering, National University of Singapore, Singapore 119077, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Centre for Life Sciences, National University of Singapore, Singapore 117456, Singapore
| | | | - Wen Shan Yew
- Department of Biochemistry, Faculty of Medicine, National University of Singapore, Singapore 117597, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Centre for Life Sciences, National University of Singapore, Singapore 117456, Singapore
| | - Chueh Loo Poh
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore 117583, Singapore; NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), Centre for Life Sciences, National University of Singapore, Singapore 117456, Singapore.
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46
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Molecular and evolutionary processes generating variation in gene expression. Nat Rev Genet 2020; 22:203-215. [PMID: 33268840 DOI: 10.1038/s41576-020-00304-w] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2020] [Indexed: 12/18/2022]
Abstract
Heritable variation in gene expression is common within and between species. This variation arises from mutations that alter the form or function of molecular gene regulatory networks that are then filtered by natural selection. High-throughput methods for introducing mutations and characterizing their cis- and trans-regulatory effects on gene expression (particularly, transcription) are revealing how different molecular mechanisms generate regulatory variation, and studies comparing these mutational effects with variation seen in the wild are teasing apart the role of neutral and non-neutral evolutionary processes. This integration of molecular and evolutionary biology allows us to understand how the variation in gene expression we see today came to be and to predict how it is most likely to evolve in the future.
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47
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Meiser LC, Koch J, Antkowiak PL, Stark WJ, Heckel R, Grass RN. DNA synthesis for true random number generation. Nat Commun 2020; 11:5869. [PMID: 33208744 PMCID: PMC7675991 DOI: 10.1038/s41467-020-19757-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 10/28/2020] [Indexed: 11/09/2022] Open
Abstract
The volume of securely encrypted data transmission required by today's network complexity of people, transactions and interactions increases continuously. To guarantee security of encryption and decryption schemes for exchanging sensitive information, large volumes of true random numbers are required. Here we present a method to exploit the stochastic nature of chemistry by synthesizing DNA strands composed of random nucleotides. We compare three commercial random DNA syntheses giving a measure for robustness and synthesis distribution of nucleotides and show that using DNA for random number generation, we can obtain 7 million GB of randomness from one synthesis run, which can be read out using state-of-the-art sequencing technologies at rates of ca. 300 kB/s. Using the von Neumann algorithm for data compression, we remove bias introduced from human or technological sources and assess randomness using NIST's statistical test suite.
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Affiliation(s)
- Linda C Meiser
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1, CH-8093, Zurich, Switzerland
| | - Julian Koch
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1, CH-8093, Zurich, Switzerland
| | - Philipp L Antkowiak
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1, CH-8093, Zurich, Switzerland
| | - Wendelin J Stark
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1, CH-8093, Zurich, Switzerland
| | - Reinhard Heckel
- Department of Electrical and Computer Engineering, Technical University of Munich, Arcistrasse 21, 80333, Munich, Germany
| | - Robert N Grass
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Vladimir-Prelog-Weg 1, CH-8093, Zurich, Switzerland.
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48
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Schaudy E, Somoza MM, Lietard J. l-DNA Duplex Formation as a Bioorthogonal Information Channel in Nucleic Acid-Based Surface Patterning. Chemistry 2020; 26:14310-14314. [PMID: 32515523 PMCID: PMC7702103 DOI: 10.1002/chem.202001871] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Indexed: 01/02/2023]
Abstract
Photolithographic in situ synthesis of nucleic acids enables extremely high oligonucleotide sequence density as well as complex surface patterning and combined spatial and molecular information encoding. No longer limited to DNA synthesis, the technique allows for total control of both chemical and Cartesian space organization on surfaces, suggesting that hybridization patterns can be used to encode, display or encrypt informative signals on multiple chemically orthogonal levels. Nevertheless, cross-hybridization reduces the available sequence space and limits information density. Here we introduce an additional, fully independent information channel in surface patterning with in situ l-DNA synthesis. The bioorthogonality of mirror-image DNA duplex formation prevents both cross-hybridization on chimeric l-/d-DNA microarrays and also results in enzymatic orthogonality, such as nuclease-proof DNA-based signatures on the surface. We show how chimeric l-/d-DNA hybridization can be used to create informative surface patterns including QR codes, highly counterfeiting resistant authenticity watermarks, and concealed messages within high-density d-DNA microarrays.
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Affiliation(s)
- Erika Schaudy
- Institute of Inorganic ChemistryFaculty of ChemistryUniversity of ViennaAlthanstraße 14, UZA II1090ViennaAustria
| | - Mark M. Somoza
- Institute of Inorganic ChemistryFaculty of ChemistryUniversity of ViennaAlthanstraße 14, UZA II1090ViennaAustria
- Chair of Food Chemistry and Molecular and Sensory ScienceTechnical University of MunichLise-Meitner-Straße 3485354FreisingGermany
- Leibniz-Institute for Food Systems BiologyTechnical University of MunichLise-Meitner-Straße 3485354FreisingGermany
| | - Jory Lietard
- Institute of Inorganic ChemistryFaculty of ChemistryUniversity of ViennaAlthanstraße 14, UZA II1090ViennaAustria
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49
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Shimko TC, Fordyce PM, Orenstein Y. DeCoDe: degenerate codon design for complete protein-coding DNA libraries. Bioinformatics 2020; 36:3357-3364. [PMID: 32176271 DOI: 10.1093/bioinformatics/btaa162] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 02/13/2020] [Accepted: 03/13/2020] [Indexed: 11/12/2022] Open
Abstract
MOTIVATION High-throughput protein screening is a critical technique for dissecting and designing protein function. Libraries for these assays can be created through a number of means, including targeted or random mutagenesis of a template protein sequence or direct DNA synthesis. However, mutagenic library construction methods often yield vastly more nonfunctional than functional variants and, despite advances in large-scale DNA synthesis, individual synthesis of each desired DNA template is often prohibitively expensive. Consequently, many protein-screening libraries rely on the use of degenerate codons (DCs), mixtures of DNA bases incorporated at specific positions during DNA synthesis, to generate highly diverse protein-variant pools from only a few low-cost synthesis reactions. However, selecting DCs for sets of sequences that covary at multiple positions dramatically increases the difficulty of designing a DC library and leads to the creation of many undesired variants that can quickly outstrip screening capacity. RESULTS We introduce a novel algorithm for total DC library optimization, degenerate codon design (DeCoDe), based on integer linear programming. DeCoDe significantly outperforms state-of-the-art DC optimization algorithms and scales well to more than a hundred proteins sharing complex patterns of covariation (e.g. the lab-derived avGFP lineage). Moreover, DeCoDe is, to our knowledge, the first DC design algorithm with the capability to encode mixed-length protein libraries. We anticipate DeCoDe to be broadly useful for a variety of library generation problems, ranging from protein engineering attempts that leverage mutual information to the reconstruction of ancestral protein states. AVAILABILITY AND IMPLEMENTATION github.com/OrensteinLab/DeCoDe. CONTACT yaronore@bgu.ac.il. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Polly M Fordyce
- Department of Genetics
- Department of Bioengineering
- Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Yaron Orenstein
- School of Electrical and Computer Engineering, Ben-Gurion University of the Negev, Beer-Sheva 8410501, Israel
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50
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Antkowiak PL, Lietard J, Darestani MZ, Somoza MM, Stark WJ, Heckel R, Grass RN. Low cost DNA data storage using photolithographic synthesis and advanced information reconstruction and error correction. Nat Commun 2020; 11:5345. [PMID: 33093494 PMCID: PMC7582880 DOI: 10.1038/s41467-020-19148-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 09/29/2020] [Indexed: 12/02/2022] Open
Abstract
Due to its longevity and enormous information density, DNA is an attractive medium for archival storage. The current hamstring of DNA data storage systems-both in cost and speed-is synthesis. The key idea for breaking this bottleneck pursued in this work is to move beyond the low-error and expensive synthesis employed almost exclusively in today's systems, towards cheaper, potentially faster, but high-error synthesis technologies. Here, we demonstrate a DNA storage system that relies on massively parallel light-directed synthesis, which is considerably cheaper than conventional solid-phase synthesis. However, this technology has a high sequence error rate when optimized for speed. We demonstrate that even in this high-error regime, reliable storage of information is possible, by developing a pipeline of algorithms for encoding and reconstruction of the information. In our experiments, we store a file containing sheet music of Mozart, and show perfect data recovery from low synthesis fidelity DNA.
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Affiliation(s)
- Philipp L Antkowiak
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093, Zürich, Switzerland
| | - Jory Lietard
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Althanstraße 14, A-1090, Vienna, Austria
| | - Mohammad Zalbagi Darestani
- Department of Electrical and Computer Engineering, Rice University, 6100 Main St., Houston, TX, 77005, USA
| | - Mark M Somoza
- Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Althanstraße 14, A-1090, Vienna, Austria
- Chair of Food Chemistry and Molecular Sensory Science, Technical University of Munich, Lise-Meitner-Straße 34, 85354, Freising, Germany
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Straße 34, 85354, Freising, Germany
| | - Wendelin J Stark
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093, Zürich, Switzerland
| | - Reinhard Heckel
- Department of Electrical and Computer Engineering, Rice University, 6100 Main St., Houston, TX, 77005, USA.
- Department of Electrical and Computer Engineering, Technical University of Munich, Theresienstr. 90, 80333, Munich, Germany.
| | - Robert N Grass
- Department of Chemistry and Applied Biosciences, ETH Zürich, Vladimir-Prelog-Weg 1-5, 8093, Zürich, Switzerland.
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