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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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2
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Kang B, Park SV, Oh SS. Ionic liquid-caged nucleic acids enable active folding-based molecular recognition with hydrolysis resistance. Nucleic Acids Res 2024; 52:73-86. [PMID: 37994697 PMCID: PMC10783497 DOI: 10.1093/nar/gkad1093] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Accepted: 11/07/2023] [Indexed: 11/24/2023] Open
Abstract
Beyond storage and transmission of genetic information in cellular life, nucleic acids can perform diverse interesting functions, including specific target recognition and biochemical reaction acceleration; the versatile biopolymers, however, are acutely vulnerable to hydrolysis-driven degradation. Here, we demonstrate that the cage effect of choline dihydrogen phosphate permits active folding of nucleic acids like water, but prevents their phosphodiester hydrolysis unlike water. The choline-based ionic liquid not only serves as a universal inhibitor of nucleases, exceptionally extending half-lives of nucleic acids up to 6 500 000 times, but highly useful tasks of nucleic acids (e.g. mRNA detection of molecular beacons, ligand recognition of aptamers, and transesterification reaction of ribozymes) can be also conducted with well-conserved affinities and specificities. As liberated from the function loss and degradation risk, the presence of undesired and unknown nucleases does not undermine desired molecular functions of nucleic acids without hydrolysis artifacts even in nuclease cocktails and human saliva.
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Affiliation(s)
- Byunghwa Kang
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk 37673, South Korea
| | - Soyeon V Park
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk 37673, South Korea
| | - Seung Soo Oh
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, Gyeongbuk 37673, South Korea
- Institute for Convergence Research and Education in Advanced Technology (I-CREATE), Yonsei University, Incheon 21983, South Korea
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3
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Liu Q, Wei Y, Wang Z, Song DP, Cui J, Qi H. Sustainable DNA Data Storage on Cellulose Paper. SMALL METHODS 2023; 7:e2201610. [PMID: 37263984 DOI: 10.1002/smtd.202201610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Revised: 04/04/2023] [Indexed: 06/03/2023]
Abstract
DNA is a promising material for high density and long-term archival data storage. In addition to algorithms for encoding digital information into DNA sequences, the DNA writing (chemical synthesis) and reading (DNA sequencing), the preservation of DNA mixtures with high sequence diversity is another critical issue for sustainable, long-term, and large-scale DNA data storage. Here, this work demonstrates a method for low-cost, convenient and sustainable DNA data storage on cellulose paper. A DNA pool comprising thousands of sequences, in which archival data are encoded, is conveniently stored on a cellulose paper with a calculated density as high as 15 TB per mm3 through electrostatic adsorption. This work demonstrates that these digitally encoded DNA pools can be stable for years on the cellulose paper after drying even when directly exposed to air. Furthermore, the reversible electrostatic adsorption enables repeated loading/retrieval of DNA on/off cellulose paper. Therefore, this sustainable DNA preservation on cellulose paper through the convenient electrostatic adsorption exhibits a great advantage in terms of storage capacity and cost that is crucial for practical systems to achieve large-scale and long-time data storage.
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Affiliation(s)
- Qian Liu
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300350, China
| | - Yanan Wei
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300350, China
| | - Zhaoguan Wang
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300350, China
| | - Dong-Po Song
- Tianjin Key Laboratory of Composite and Functional Materials, School of Materials Science and Engineering, Tianjin University, Tianjin, 300350, China
| | - Jingsong Cui
- School of Cyber Science and Engineering, Wuhan University, Wuhan, 430072, China
| | - Hao Qi
- School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300350, China
- Key Laboratory of Systems Bioengineering (Ministry of Education), Tianjin University, Tianjin, 300350, China
- Zhejiang Shaoxing Research Institute of Tianjin University, Zhejiang, 312369, China
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4
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Buko T, Tuczko N, Ishikawa T. DNA Data Storage. BIOTECH 2023; 12:44. [PMID: 37366792 DOI: 10.3390/biotech12020044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/22/2023] [Accepted: 05/23/2023] [Indexed: 06/28/2023] Open
Abstract
The demand for data storage is growing at an unprecedented rate, and current methods are not sufficient to accommodate such rapid growth due to their cost, space requirements, and energy consumption. Therefore, there is a need for a new, long-lasting data storage medium with high capacity, high data density, and high durability against extreme conditions. DNA is one of the most promising next-generation data carriers, with a storage density of 10¹⁹ bits of data per cubic centimeter, and its three-dimensional structure makes it about eight orders of magnitude denser than other storage media. DNA amplification during PCR or replication during cell proliferation enables the quick and inexpensive copying of vast amounts of data. In addition, DNA can possibly endure millions of years if stored in optimal conditions and dehydrated, making it useful for data storage. Numerous space experiments on microorganisms have also proven their extraordinary durability in extreme conditions, which suggests that DNA could be a durable storage medium for data. Despite some remaining challenges, such as the need to refine methods for the fast and error-free synthesis of oligonucleotides, DNA is a promising candidate for future data storage.
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Affiliation(s)
- Tomasz Buko
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Miecznikowa 1, PL-02-096 Warsaw, Poland
| | - Nella Tuczko
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Miecznikowa 1, PL-02-096 Warsaw, Poland
| | - Takao Ishikawa
- Department of Molecular Biology, Institute of Biochemistry, Faculty of Biology, University of Warsaw, Miecznikowa 1, PL-02-096 Warsaw, Poland
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5
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Jung YJ, Kim H, Cheong HK, Lim YB. Magnetic control of self-assembly and disassembly in organic materials. Nat Commun 2023; 14:3081. [PMID: 37248227 DOI: 10.1038/s41467-023-38846-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Accepted: 05/18/2023] [Indexed: 05/31/2023] Open
Abstract
Because organic molecules and materials are generally insensitive or weakly sensitive to magnetic fields, a certain means to enhance their magnetic responsiveness needs to be exploited. Here we show a strategy to amplify the magnetic responsiveness of self-assembled peptide nanostructures by synergistically combining the concepts of perfect α-helix and rod-coil supramolecular building blocks. Firstly, we develop a monomeric, nonpolar, and perfect α-helix (MNP-helix). Then, we employ the MNP-helix as the rod block of rod-coil amphiphiles (rod-coils) because rod-coils are well-suited for fabricating responsive assemblies. We show that the self-assembly processes of the designed rod-coils and disassembly of rod-coil/DNA complexes can be controlled in a magnetically responsive manner using the relatively weak magnetic field provided by the ordinary neodymium magnet [0.07 ~ 0.25 Tesla (T)]. These results demonstrate that magnetically responsive organic assemblies usable under practical conditions can be realized by using rod-coil supramolecular building blocks containing constructively organized diamagnetic moieties.
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Affiliation(s)
- You-Jin Jung
- Department of Materials Science & Engineering, Yonsei University, 50 Yonsei-ro, Seoul, 03722, Republic of Korea
| | - Hyoseok Kim
- Department of Materials Science & Engineering, Yonsei University, 50 Yonsei-ro, Seoul, 03722, Republic of Korea
| | - Hae-Kap Cheong
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang, 28119, Republic of Korea
| | - Yong-Beom Lim
- Department of Materials Science & Engineering, Yonsei University, 50 Yonsei-ro, Seoul, 03722, Republic of Korea.
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6
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Ezekannagha C, Welzel M, Heider D, Hattab G. DNAsmart: Multiple attribute ranking tool for DNA data storage systems. Comput Struct Biotechnol J 2023; 21:1448-1460. [PMID: 36851917 PMCID: PMC9957737 DOI: 10.1016/j.csbj.2023.02.016] [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: 11/25/2022] [Revised: 02/07/2023] [Accepted: 02/07/2023] [Indexed: 02/12/2023] Open
Abstract
In an ever-growing need for data storage capacity, the Deoxyribonucleic Acid (DNA) molecule gains traction as a new storage medium with a larger capacity, higher density, and a longer lifespan over conventional storage media. To effectively use DNA for data storage, it is important to understand the different methods of encoding information in DNA and compare their effectiveness. This requires evaluating which decoded DNA sequences carry the most encoded information based on various attributes. However, navigating the field of coding theory requires years of experience and domain expertise. For instance, domain experts rely on various mathematical functions and attributes to score and evaluate their encodings. To enable such analytical tasks, we provide an interactive and visual analytical framework for multi-attribute ranking in DNA storage systems. Our framework follows a three-step view with user-settable parameters. It enables users to find the optimal en-/de-coding approaches by setting different weights and combining multiple attributes. We assess the validity of our work through a task-specific user study on domain experts by relying on three tasks. Results indicate that all participants completed their tasks successfully under two minutes, then rated the framework for design choices, perceived usefulness, and intuitiveness. In addition, two real-world use cases are shared and analyzed as direct applications of the proposed tool. DNAsmart enables the ranking of decoded sequences based on multiple attributes. In sum, this work unveils the evaluation of en-/de-coding approaches accessible and tractable through visualization and interactivity to solve comparison and ranking tasks.
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Affiliation(s)
- Chisom Ezekannagha
- Department of Mathematics and Computer Science, Philipps-Universität, Hans-Meerwein-Str. 6, Marburg D-35043, Germany.,Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, Marburg D-35043, Germany
| | - Marius Welzel
- Department of Mathematics and Computer Science, Philipps-Universität, Hans-Meerwein-Str. 6, Marburg D-35043, Germany.,Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, Marburg D-35043, Germany
| | - Dominik Heider
- Department of Mathematics and Computer Science, Philipps-Universität, Hans-Meerwein-Str. 6, Marburg D-35043, Germany.,Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, Marburg D-35043, Germany
| | - Georges Hattab
- Department of Mathematics and Computer Science, Philipps-Universität, Hans-Meerwein-Str. 6, Marburg D-35043, Germany.,Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, Marburg D-35043, Germany
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7
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Lynton‐Jenkins JG, Chaine AS, Russell AF, Bonneaud C. Parasite detection and quantification in avian blood is dependent on storage medium and duration. Ecol Evol 2023; 13:e9819. [PMID: 36789332 PMCID: PMC9911630 DOI: 10.1002/ece3.9819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 01/18/2023] [Accepted: 01/23/2023] [Indexed: 02/12/2023] Open
Abstract
Studies of parasites in wild animal populations often rely on molecular methods to both detect and quantify infections. However, method accuracy is likely to be influenced by the sampling approach taken prior to nucleic acid extraction. Avian Haemosporidia are studied primarily through the screening of host blood, and a range of storage mediums are available for the short- to long-term preservation of samples. Previous research has suggested that storage medium choice may impact the accuracy of PCR-based parasite detection, however, this relationship has never been explicitly tested and may be exacerbated by the duration of sample storage. These considerations could also be especially critical for sensitive molecular methods used to quantify infection (qPCR). To test the effect of storage medium and duration on Plasmodium detection and quantification, we split blood samples collected from wild birds across three medium types (filter paper, Queen's lysis buffer, and 96% ethanol) and carried out DNA extractions at five time points (1, 6, 12, 24, and 36 months post-sampling). First, we found variation in DNA yield obtained from blood samples dependent on their storage medium which had subsequent negative impacts on both detection and estimates of Plasmodium copy number. Second, we found that detection accuracy (incidence of true positives) was highest for filter-paper-stored samples (97%), while accuracy for ethanol and Queen's lysis buffer-stored samples was influenced by either storage duration or extraction yield, respectively. Lastly, longer storage durations were associated with decreased copy number estimates across all storage mediums; equating to a 58% reduction between the first- and third-year post-sampling for lysis-stored samples. These results raise questions regarding the utility of standardizing samples by dilution, while also illustrating the critical importance of considering storage approaches in studies of Haemosporidia comparing samples subjected to different storage regimes and/or stored for varying lengths of time.
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Affiliation(s)
| | - Alexis S. Chaine
- Station for Theoretical and Experimental EcologyCNRSMoulisFrance
- Institute for Advanced Studies in ToulouseToulouseFrance
| | - Andrew F. Russell
- Centre for Ecology and ConservationUniversity of ExeterPenrynUK
- Station for Theoretical and Experimental EcologyCNRSMoulisFrance
| | - Camille Bonneaud
- Centre for Ecology and ConservationUniversity of ExeterPenrynUK
- Station for Theoretical and Experimental EcologyCNRSMoulisFrance
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8
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DeSanctis ML, Soranno EA, Messner E, Wang Z, Turner EM, Falco R, Appiah-Madson HJ, Distel DL. Greater than pH 8: The pH dependence of EDTA as a preservative of high molecular weight DNA in biological samples. PLoS One 2023; 18:e0280807. [PMID: 36689492 PMCID: PMC9870144 DOI: 10.1371/journal.pone.0280807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Accepted: 01/08/2023] [Indexed: 01/24/2023] Open
Abstract
Ethylenediaminetetraacetic acid (EDTA) is a divalent cation chelator and chemical preservative that has been shown to be the active ingredient of the popular DNA preservative DESS. EDTA may act to reduce DNA degradation during tissue storage by sequestering divalent cations that are required by nucleases naturally occurring in animal tissues. Although EDTA is typically used between pH 7.5 and 8 in preservative preparations, the capacity of EDTA to chelate divalent cations is known to increase with increasing pH. Therefore, increasing the pH of EDTA-containing preservative solutions may improve their effectiveness as DNA preservatives. To test this hypothesis, we stored tissues from five aquatic species in 0.25 M EDTA adjusted to pH 8, 9, and 10 for 12 months at room temperature before DNA isolation. For comparison, tissues from the same specimens were also stored in 95% ethanol. DNA extractions performed on tissues preserved in EDTA pH 9 or 10 resulted in as great or greater percent recovery of high molecular weight DNA than did extractions from tissues stored at pH 8. In all cases examined, percent recovery of high molecular weight DNA from tissues preserved in EDTA pH 10 was significantly better than that observed from tissues preserved in 95% ethanol. Our results support the conclusion that EDTA contributes to DNA preservation in tissues by chelating divalent cations and suggest that preservative performance can be improved by increasing the pH of EDTA-containing DNA preservative solutions.
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Affiliation(s)
- Mia L. DeSanctis
- Ocean Genome Legacy Center, Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, United States of America
| | - Elizabeth A. Soranno
- Ocean Genome Legacy Center, Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, United States of America
| | - Ella Messner
- Ocean Genome Legacy Center, Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, United States of America
| | - Ziyu Wang
- Ocean Genome Legacy Center, Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, United States of America
| | - Elena M. Turner
- Ocean Genome Legacy Center, Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, United States of America
| | - Rosalia Falco
- Ocean Genome Legacy Center, Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, United States of America
| | - Hannah J. Appiah-Madson
- Ocean Genome Legacy Center, Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, United States of America
| | - Daniel L. Distel
- Ocean Genome Legacy Center, Marine and Environmental Sciences, Northeastern University, Nahant, Massachusetts, United States of America
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9
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Cordsmeier L, Hahn MB. DNA Stability in Biodosimetry, Pharmacy and DNA Based Data-Storage: Optimal Storage and Handling Conditions. Chembiochem 2022; 23:e202200391. [PMID: 35972228 PMCID: PMC9826032 DOI: 10.1002/cbic.202200391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/12/2022] [Indexed: 01/11/2023]
Abstract
DNA long-term stability and integrity is of importance for applications in DNA based bio-dosimetry, data-storage, pharmaceutical quality-control, donor insemination and DNA based functional nanomaterials. Standard protocols for these applications involve repeated freeze-thaw cycles of the DNA, which can cause detrimental damage to the nucleobases, as well as the sugar-phosphate backbone and therefore the whole molecule. Throughout the literature three hypotheses can be found about the underlying mechanisms occurring during freeze-thaw cycles. It is hypothesized that DNA single-strand breaks during freezing can be induced by mechanical stress leading to shearing of the DNA molecule, by acidic pH causing damage through depurination and beta elimination or by the presence of metal ions catalyzing oxidative damage via reactive oxygen species (ROS). Here we test these hypotheses under well defined conditions with plasmid DNA pUC19 in high-purity buffer (1xPBS) at physiological salt and pH 7.4 conditions, under pH 6 and in the presence of metal ions in combination with the radical scavengers DMSO and Ectoine. The results show for the 2686 bp long plasmid DNA, that neither mechanical stress, nor pH 6 lead to degradation during repeated freeze-thaw cycles. In contrast, the presence of metal ions (Fe2+ ) leads to degradation of DNA via the production of radical species.
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Affiliation(s)
- Leo Cordsmeier
- Bundesanstalt für Materialforschung und Prüfung12205BerlinGermany
- Freie Universität BerlinInstitut für Chemie14195BerlinGermany
| | - Marc Benjamin Hahn
- Bundesanstalt für Materialforschung und Prüfung12205BerlinGermany
- Freie Universität BerlinInstitut für Chemie14195BerlinGermany
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10
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Osman OA, Andersson J, Martin-Sanchez PM, Eiler A. National eDNA-based monitoring of Batrachochytrium dendrobatidis and amphibian species in Norway. METABARCODING AND METAGENOMICS 2022. [DOI: 10.3897/mbmg.6.85199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Freshwaters represent the most threatened environments with regard to biodiversity loss and, therefore, there is a need for national monitoring programs to effectively document species distribution and evaluate potential risks for vulnerable species. The monitoring of species for effective management practices is, however, challenged by insufficient data acquisition when using traditional methods. Here we present the application of environmental DNA (eDNA) metabarcoding of amphibians in combination with quantitative PCR (qPCR) assays for an invasive pathogenic chytrid species (Batrachochytrium dendrobatidis -Bd), a potential threat to endemic and endangered amphibian species. Statistical comparison of amphibian species detection using either traditional or eDNA-based approaches showed weak correspondence. By tracking the distribution of Bd over three years, we concluded that the risk for amphibian extinction is low since Bd was only detected at five sites where multiple amphibians were present over the sampled years. Our results show that eDNA-based detection can be used for simultaneous monitoring of amphibian diversity and the presence of amphibian pathogens at the national level in order to assess potential species extinction risks and establish effective management practices. As such our study represents suggestions for a national monitoring program based on eDNA.
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11
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Dahn HA, Mountcastle J, Balacco J, Winkler S, Bista I, Schmitt AD, Pettersson OV, Formenti G, Oliver K, Smith M, Tan W, Kraus A, Mac S, Komoroske LM, Lama T, Crawford AJ, Murphy RW, Brown S, Scott AF, Morin PA, Jarvis ED, Fedrigo O. Benchmarking ultra-high molecular weight DNA preservation methods for long-read and long-range sequencing. Gigascience 2022; 11:6659719. [PMID: 35946988 PMCID: PMC9364683 DOI: 10.1093/gigascience/giac068] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 01/26/2022] [Accepted: 06/16/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Studies in vertebrate genomics require sampling from a broad range of tissue types, taxa, and localities. Recent advancements in long-read and long-range genome sequencing have made it possible to produce high-quality chromosome-level genome assemblies for almost any organism. However, adequate tissue preservation for the requisite ultra-high molecular weight DNA (uHMW DNA) remains a major challenge. Here we present a comparative study of preservation methods for field and laboratory tissue sampling, across vertebrate classes and different tissue types. RESULTS We find that storage temperature was the strongest predictor of uHMW fragment lengths. While immediate flash-freezing remains the sample preservation gold standard, samples preserved in 95% EtOH or 20-25% DMSO-EDTA showed little fragment length degradation when stored at 4°C for 6 hours. Samples in 95% EtOH or 20-25% DMSO-EDTA kept at 4°C for 1 week after dissection still yielded adequate amounts of uHMW DNA for most applications. Tissue type was a significant predictor of total DNA yield but not fragment length. Preservation solution had a smaller but significant influence on both fragment length and DNA yield. CONCLUSION We provide sample preservation guidelines that ensure sufficient DNA integrity and amount required for use with long-read and long-range sequencing technologies across vertebrates. Our best practices generated the uHMW DNA needed for the high-quality reference genomes for phase 1 of the Vertebrate Genomes Project, whose ultimate mission is to generate chromosome-level reference genome assemblies of all ∼70,000 extant vertebrate species.
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Affiliation(s)
| | | | | | - Sylke Winkler
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Saxony 01307, Germany
| | - Iliana Bista
- Tree of Life Program, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
- Department of Genetics, University of Cambridge, Cambridge, Cambridgeshire CB2 3EH, UK
| | | | | | | | - Karen Oliver
- Tree of Life Program, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Michelle Smith
- Tree of Life Program, Wellcome Sanger Institute, Hinxton, Cambridgeshire CB10 1SA, UK
| | - Wenhua Tan
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Saxony 01307, Germany
| | - Anne Kraus
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Saxony 01307, Germany
| | - Stephen Mac
- Arima Genomics, Inc., San Diego, CA 92121, USA
| | - Lisa M Komoroske
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, MA 01003-9285, USA
| | - Tanya Lama
- Department of Environmental Conservation, University of Massachusetts Amherst, Amherst, MA 01003-9285, USA
| | - Andrew J Crawford
- Department of Biological Sciences, Universidad de los Andes, Bogotá 111711, Colombia
| | - Robert W Murphy
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario M5S 3B2, Canada
| | - Samara Brown
- The Rockefeller University, New York, NY 10065, USA
| | - Alan F Scott
- Department of Medicine, Johns Hopkins University, Baltimore, MD 21287, USA
| | - Phillip A Morin
- Southwest Fisheries Science Center, National Marine Fisheries Service, NOAA, La Jolla, CA 92037, USA
| | - Erich D Jarvis
- The Rockefeller University, New York, NY 10065, USA
- Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - Olivier Fedrigo
- Correspondence address. Olivier Fedrigo, Vertebrate Genome Laboratory, The Rockefeller University, 1230 York Avenue, Box 366, New York, NY 10065, USA. E-mail:
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12
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Ezekannagha C, Becker A, Heider D, Hattab G. Design considerations for advancing data storage with synthetic DNA for long-term archiving. Mater Today Bio 2022; 15:100306. [PMID: 35677811 PMCID: PMC9167972 DOI: 10.1016/j.mtbio.2022.100306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 05/05/2022] [Accepted: 05/22/2022] [Indexed: 11/22/2022]
Abstract
Deoxyribonucleic acid (DNA) is increasingly emerging as a serious medium for long-term archival data storage because of its remarkable high-capacity, high-storage-density characteristics and its lasting ability to store data for thousands of years. Various encoding algorithms are generally required to store digital information in DNA and to maintain data integrity. Indeed, since DNA is the information carrier, its performance under different processing and storage conditions significantly impacts the capabilities of the data storage system. Therefore, the design of a DNA storage system must meet specific design considerations to be less error-prone, robust and reliable. In this work, we summarize the general processes and technologies employed when using synthetic DNA as a storage medium. We also share the design considerations for sustainable engineering to include viability. We expect this work to provide insight into how sustainable design can be used to develop an efficient and robust synthetic DNA-based storage system for long-term archiving.
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Affiliation(s)
- Chisom Ezekannagha
- Department of Mathematics and Computer Science, Philipps-Universität Marburg, Hans-Meerwein-Str. 6, D-35043, Marburg, Germany
- Corresponding author.
| | - Anke Becker
- Center for Synthetic Microbiology (SYNMIKRO), Philipps-Universität Marburg, Karl-von-Frisch-Str. 14, D-35043, Marburg, Germany
| | - Dominik Heider
- Department of Mathematics and Computer Science, Philipps-Universität Marburg, Hans-Meerwein-Str. 6, D-35043, Marburg, Germany
| | - Georges Hattab
- Department of Mathematics and Computer Science, Philipps-Universität Marburg, Hans-Meerwein-Str. 6, D-35043, Marburg, Germany
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13
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Bennet D, Vo‐Dinh T, Zenhausern F. Current and emerging opportunities in biological medium‐based computing and digital data storage. NANO SELECT 2021. [DOI: 10.1002/nano.202100275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Affiliation(s)
- Devasier Bennet
- Center for Applied NanoBioscience and Medicine College of Medicine Phoenix The University of Arizona Phoenix USA
| | - Tuan Vo‐Dinh
- Department of Biomedical Engineering Department of Chemistry Fitzpatrick Institute for Photonics Duke University Durham North Carolina USA
| | - Frederic Zenhausern
- Center for Applied NanoBioscience and Medicine College of Medicine Phoenix The University of Arizona Phoenix USA
- Department of Basic Medical Sciences College of Medicine Phoenix The University of Arizona Phoenix Arizona USA
- Department of Biomedical Engineering; and BIO5 Institute College of Engineering The University of Arizona Tucson Arizona USA
- School of Pharmaceutical Sciences University of Geneva Geneva Switzerland
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14
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Brogna R, Fan J, Sieme H, Wolkers WF, Oldenhof H. Drying and temperature induced conformational changes of nucleic acids and stallion sperm chromatin in trehalose preservation formulations. Sci Rep 2021; 11:14076. [PMID: 34234244 PMCID: PMC8263733 DOI: 10.1038/s41598-021-93569-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/23/2021] [Indexed: 12/27/2022] Open
Abstract
Even though dried sperm is not viable, it can be used for fertilization as long as its chromatin remains intact. In this study, we investigated drying- and temperature-induced conformational changes of nucleic acids and stallion sperm chromatin. Sperm was diluted in preservation formulations with and without sugar/albumin and subjected to convective drying at elevated temperatures on glass substrates. Accumulation of reactive oxygen species was studied during storage at different temperatures, and the sperm chromatin structure assay was used to assess DNA damage. Fourier transform infrared spectroscopy was used to identify dehydration and storage induced conformational changes in isolated DNA and sperm chromatin. Furthermore, hydrogen bonding in the preservation solutions associated with storage stability were investigated. Reactive oxygen species and DNA damage in dried sperm samples were found to accumulate with increasing storage temperature and storage duration. Non-reducing disaccharides (i.e., trehalose, sucrose) and albumin counteracted oxidative stress and preserved sperm chromatin during dried storage, whereas glucose increased DNA damage during storage. When sperm was dried in the presence of trehalose and albumin, no spectral changes were detected during storage at refrigeration temperatures, whereas under accelerated aging conditions, i.e., storage at 37 °C, spectral changes were detected indicating alterations in sperm chromatin structure.
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Affiliation(s)
- Raffaele Brogna
- Biostabilization Laboratory, Lower Saxony Centre for Biomedical Engineering, Implant Research and Development, University of Veterinary Medicine Hannover, Hannover, Germany
- Unit for Reproductive Medicine, Clinic for Horses, University of Veterinary Medicine Hannover, Bünteweg 15, 30559, Hannover, Germany
| | - Juezhu Fan
- Biostabilization Laboratory, Lower Saxony Centre for Biomedical Engineering, Implant Research and Development, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Harald Sieme
- Unit for Reproductive Medicine, Clinic for Horses, University of Veterinary Medicine Hannover, Bünteweg 15, 30559, Hannover, Germany
| | - Willem F Wolkers
- Biostabilization Laboratory, Lower Saxony Centre for Biomedical Engineering, Implant Research and Development, University of Veterinary Medicine Hannover, Hannover, Germany
- Unit for Reproductive Medicine, Clinic for Horses, University of Veterinary Medicine Hannover, Bünteweg 15, 30559, Hannover, Germany
| | - Harriëtte Oldenhof
- Unit for Reproductive Medicine, Clinic for Horses, University of Veterinary Medicine Hannover, Bünteweg 15, 30559, Hannover, Germany.
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15
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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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16
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Blom MPK. Opportunities and challenges for high-quality biodiversity tissue archives in the age of long-read sequencing. Mol Ecol 2021; 30:5935-5948. [PMID: 33786900 DOI: 10.1111/mec.15909] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 03/06/2021] [Accepted: 03/22/2021] [Indexed: 12/11/2022]
Abstract
The technological ability to characterize genetic variation at a genome-wide scale provides an unprecedented opportunity to study the genetic underpinnings and evolutionary mechanisms that promote and sustain biodiversity. The transition from short- to long-read sequencing is particularly promising and allows a more holistic view on any changes in genetic diversity across time and space. Long-read sequencing has tremendous potential but sequencing success strongly depends on the long-range integrity of DNA molecules and therefore on the availability of high-quality tissue samples. With the scope of genomic experiments expanding and wild populations simultaneously disappearing at an unprecedented rate, access to high-quality samples may soon be a major concern for many projects. The need for high-quality biodiversity tissue archives is therefore urgent but sampling and preserving high-quality samples is not a trivial exercise. In this review, I will briefly outline how long-read sequencing can benefit the study of molecular ecology, how this will substantially increase the demand for high-quality tissues and why it is challenging to preserve DNA integrity. I will then provide an overview of preservation approaches and end with a call for support to acknowledge the efforts needed to assemble high-quality tissue archives. In doing so, I hope to simultaneously motivate field biologists to expand sampling practices and molecular biologists to develop (cost) efficient guidelines for the sampling and long-term storage of tissues. A concerted, interdisciplinary, effort is needed to catalogue the genetic variation underlying contemporary biodiversity and will eventually provide a critical resource for future studies.
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Affiliation(s)
- Mozes P K Blom
- Leibniz Institut für Evolutions- und Biodiversitätsforschung, Museum für Naturkunde, Berlin, Germany
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17
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Narvaez Villarrubia CW, Tumas KC, Chauhan R, MacDonald T, Dattelbaum AM, Omberg K, Gupta G. Long-term stabilization of DNA at room temperature using a one-step microwave assisted process. EMERGENT MATERIALS 2021; 5:307-314. [PMID: 33778372 PMCID: PMC7986179 DOI: 10.1007/s42247-021-00208-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/10/2021] [Indexed: 06/12/2023]
Abstract
UNLABELLED Long-term stabilization of DNA is needed for forensic, clinical, in-field operations and numerous other applications. Although freezing (<-20 °C) and dry storage are currently the preferential methods for long-term storage, a noticeable pre-analytical degradation of DNA over time, upfront capital investment and recurring costs have demonstrated a need for an alternative long-term room-temperature preservation method. Herein, we report a novel, fast (~5 min) silica sol-gel preparation method using a standard microwave-initiated polymerization reaction amenable to stabilization of DNA. The method involves use of one chemical, tetramethoxy silane (TMOS) and eliminates the use of alcohol as co-solvent and catalysts such as acids. In addition, the process involves minimal technical expertise, thus making it an ideal choice for resource-challenged countries and in-field applications. The sol-gel is capable to store and stabilize Escherichia coli DNA in ambient conditions for 210 days. DNA recovered from the sol-gel showed no significant nucleolytic and/or oxidative degradation, outperforming conventional storage conditions at -20 °C, and reported state-of-the-art technology. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s42247-021-00208-3.
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Affiliation(s)
| | - Keyla C. Tumas
- Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM USA
| | - Rajat Chauhan
- Department of Bioengineering, University of Louisville, Louisville, KY 40292 USA
| | - Thomas MacDonald
- Materials Physics and Applications Divison, Los Alamos National Laboratory, Los Alamos, NM USA
| | - Andrew M. Dattelbaum
- Materials Physics and Applications Divison, Los Alamos National Laboratory, Los Alamos, NM USA
| | - Kristin Omberg
- Materials Physics and Applications Divison, Los Alamos National Laboratory, Los Alamos, NM USA
| | - Gautam Gupta
- Department of Chemical Engineering, University of Louisville, Louisville, KY 40292 USA
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18
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Matange K, Tuck JM, Keung AJ. DNA stability: a central design consideration for DNA data storage systems. Nat Commun 2021; 12:1358. [PMID: 33649304 PMCID: PMC7921107 DOI: 10.1038/s41467-021-21587-5] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 02/02/2021] [Indexed: 11/09/2022] Open
Abstract
Data storage in DNA is a rapidly evolving technology that could be a transformative solution for the rising energy, materials, and space needs of modern information storage. Given that the information medium is DNA itself, its stability under different storage and processing conditions will fundamentally impact and constrain design considerations and data system capabilities. Here we analyze the storage conditions, molecular mechanisms, and stabilization strategies influencing DNA stability and pose specific design configurations and scenarios for future systems that best leverage the considerable advantages of DNA storage.
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Affiliation(s)
- Karishma Matange
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA
| | - James M Tuck
- Department of Electrical and Computer Engineering, North Carolina State University, Raleigh, NC, USA.
| | - Albert J Keung
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC, USA.
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19
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Pushparajah D, Jimenez S, Wong S, Alattas H, Nafissi N, Slavcev RA. Advances in gene-based vaccine platforms to address the COVID-19 pandemic. Adv Drug Deliv Rev 2021; 170:113-141. [PMID: 33422546 PMCID: PMC7789827 DOI: 10.1016/j.addr.2021.01.003] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 12/23/2020] [Accepted: 01/01/2021] [Indexed: 01/07/2023]
Abstract
The novel betacoronavirus, SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), has spread across the globe at an unprecedented rate since its first emergence in Wuhan City, China in December 2019. Scientific communities around the world have been rigorously working to develop a potent vaccine to combat COVID-19 (coronavirus disease 2019), employing conventional and novel vaccine strategies. Gene-based vaccine platforms based on viral vectors, DNA, and RNA, have shown promising results encompassing both humoral and cell-mediated immune responses in previous studies, supporting their implementation for COVID-19 vaccine development. In fact, the U.S. Food and Drug Administration (FDA) recently authorized the emergency use of two RNA-based COVID-19 vaccines. We review current gene-based vaccine candidates proceeding through clinical trials, including their antigenic targets, delivery vehicles, and route of administration. Important features of previous gene-based vaccine developments against other infectious diseases are discussed in guiding the design and development of effective vaccines against COVID-19 and future derivatives.
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Affiliation(s)
- Deborah Pushparajah
- School of Pharmacy, University of Waterloo, 10A Victoria St S, Kitchener N2G 1C5, Canada
| | - Salma Jimenez
- School of Pharmacy, University of Waterloo, 10A Victoria St S, Kitchener N2G 1C5, Canada; Theraphage, 151 Charles St W Suite # 199, Kitchener, ON, N2G 1H6, Canada
| | - Shirley Wong
- School of Pharmacy, University of Waterloo, 10A Victoria St S, Kitchener N2G 1C5, Canada
| | - Hibah Alattas
- School of Pharmacy, University of Waterloo, 10A Victoria St S, Kitchener N2G 1C5, Canada
| | - Nafiseh Nafissi
- Mediphage Bioceuticals, 661 University Avenue, Suite 1300, Toronto, ON, M5G 0B7, Canada
| | - Roderick A Slavcev
- School of Pharmacy, University of Waterloo, 10A Victoria St S, Kitchener N2G 1C5, Canada; Mediphage Bioceuticals, 661 University Avenue, Suite 1300, Toronto, ON, M5G 0B7, Canada; Theraphage, 151 Charles St W Suite # 199, Kitchener, ON, N2G 1H6, Canada.
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20
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Tan X, Ge L, Zhang T, Lu Z. Preservation of DNA for data storage. RUSSIAN CHEMICAL REVIEWS 2021. [DOI: 10.1070/rcr4994] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The preservation of DNA has attracted significant interest of scientists in diverse research fields from ancient biological remains to the information field. In light of the different DNA safekeeping requirements (e.g., storage time, storage conditions) in these disparate fields, scientists have proposed distinct methods to maintain the DNA integrity. Specifically, DNA data storage is an emerging research, which means that the binary digital information is converted to the sequences of nucleotides leading to dense and durable data storage in the form of synthesized DNA. The intact preservation of DNA plays a significant role because it is closely related to data integrity. This review discusses DNA preservation methods, aiming to confirm an appropriate one for synthetic oligonucleotides in DNA data storage. First, we analyze the impact factors of the DNA long-term storage, including the intrinsic stability of DNA, environmental factors, and storage methods. Then, the benefits and disadvantages of diverse conservation approaches (e.g., encapsulation-free, chemical encapsulation) are discussed. Finally, we provide advice for storing non-genetic information in DNA in vitro. We expect these preservation suggestions to promote further research that may extend the DNA storage time.
The bibliography includes 99 references.
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21
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Spectral fingerprinting to evaluate effects of storage conditions on biomolecular structure of filter-dried saliva samples and recovered DNA. Sci Rep 2020; 10:21442. [PMID: 33293589 PMCID: PMC7722934 DOI: 10.1038/s41598-020-78306-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 11/06/2020] [Indexed: 12/13/2022] Open
Abstract
Saliva has been widely recognized as a non-invasive, painless and easy-to-collect bodily fluid, which contains biomarkers that can be used for diagnosis of both oral and systemic diseases. Under ambient conditions, salivary biomarkers are subject to degradation. Therefore, in order to minimize degradation during transport and storage, saliva specimens need to be stabilized. The aim of this study was to investigate the feasibility of preserving saliva samples by drying to provide a shelf-stable source of DNA. Human saliva was dried on filters under ambient conditions using sucrose as lyoprotective agent. Samples were stored under different conditions, i.e. varying relative humidity (RH) and temperature. In addition to assessment of different cell types in saliva and their DNA contents, Fourier transform infrared spectroscopy (FTIR) was used to evaluate the effects of storage on biomolecular structure characteristics of saliva. FTIR analysis showed that saliva dried without a lyoprotectant exhibits a higher content of extended β-sheet protein secondary structures compared to samples that were dried with sucrose. In order to evaluate differences in characteristic bands arising from the DNA backbone among differently stored samples, principal component analysis (PCA) was performed, allowing a clear discrimination between groups with/without sucrose as well as storage durations and conditions. Our results indicated that saliva dried on filters in the presence of sucrose exhibits higher biomolecular stability during storage.
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22
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Oosting T, Hilario E, Wellenreuther M, Ritchie PA. DNA degradation in fish: Practical solutions and guidelines to improve DNA preservation for genomic research. Ecol Evol 2020; 10:8643-8651. [PMID: 32884647 PMCID: PMC7452763 DOI: 10.1002/ece3.6558] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/26/2020] [Accepted: 06/10/2020] [Indexed: 12/02/2022] Open
Abstract
The more demanding requirements of DNA preservation for genomic research can be difficult to meet when field conditions limit the methodological approaches that can be used or cause samples to be stored in suboptimal conditions. Such limitations may increase rates of DNA degradation, potentially rendering samples unusable for applications such as genome-wide sequencing. Nonetheless, little is known about the impact of suboptimal sampling conditions. We evaluated the performance of two widely used preservation solutions (1. DESS: 20% DMSO, 0.25 M EDTA, NaCl saturated solution, and 2. Ethanol >99.5%) under a range of storage conditions over a three-month period (sampling at 1 day, 1 week, 2 weeks, 1 month, and 3 months) to provide practical guidelines for DNA preservation. DNA degradation was quantified as the reduction in average DNA fragment size over time (DNA fragmentation) because the size distribution of DNA segments plays a key role in generating genomic datasets. Tissues were collected from a marine teleost species, the Australasian snapper, Chrysophrys auratus. We found that the storage solution has a strong effect on DNA preservation. In DESS, DNA was only moderately degraded after three months of storage while DNA stored in ethanol showed high levels of DNA degradation already within 24 hr, making samples unsuitable for next-generation sequencing. Here, we conclude that DESS was the most promising solution when storing samples for genomic applications. We recognize that the best preservation protocol is highly dependent on the organism, tissue type, and study design. We highly recommend performing similar experiments before beginning a study. This study highlights the importance of testing sample preservation protocols and provides both practical and economical advice to improve DNA preservation when sampling for genome-wide applications.
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Affiliation(s)
- Tom Oosting
- School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
| | - Elena Hilario
- The New Zealand Institute for Plant & Food Research LtdAucklandNew Zealand
| | - Maren Wellenreuther
- Nelson Seafood Research UnitThe New Zealand Institute for Plant & Food Research LtdNelsonNew Zealand
- School of Biological SciencesThe University of AucklandAucklandNew Zealand
| | - Peter A. Ritchie
- School of Biological SciencesVictoria University of WellingtonWellingtonNew Zealand
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23
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Lin KN, Volkel K, Tuck JM, Keung AJ. Dynamic and scalable DNA-based information storage. Nat Commun 2020; 11:2981. [PMID: 32532979 PMCID: PMC7293219 DOI: 10.1038/s41467-020-16797-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2019] [Accepted: 05/20/2020] [Indexed: 11/11/2022] Open
Abstract
The physical architectures of information storage systems often dictate how information is encoded, databases are organized, and files are accessed. Here we show that a simple architecture comprised of a T7 promoter and a single-stranded overhang domain (ss-dsDNA), can unlock dynamic DNA-based information storage with powerful capabilities and advantages. The overhang provides a physical address for accessing specific DNA strands as well as implementing a range of in-storage file operations. It increases theoretical storage densities and capacities by expanding the encodable sequence space and simplifies the computational burden in designing sets of orthogonal file addresses. Meanwhile, the T7 promoter enables repeatable information access by transcribing information from DNA without destroying it. Furthermore, saturation mutagenesis around the T7 promoter and systematic analyses of environmental conditions reveal design criteria that can be used to optimize information access. This simple but powerful ss-dsDNA architecture lays the foundation for information storage with versatile capabilities. The physical architectures of information storage dictate how data is encoded, organised and accessed. Here the authors use DNA with a single-strand overhang as a physical address to access specific data and do in-storage file operations in a scalable and reusuable manner.
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Affiliation(s)
- Kevin N Lin
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Campus Box 7905, Raleigh, NC, 27695-7905, USA
| | - Kevin Volkel
- Department of Electrical and Computer Engineering, North Carolina State University, Campus Box 7911, Raleigh, NC, 27695-7911, USA
| | - James M Tuck
- Department of Electrical and Computer Engineering, North Carolina State University, Campus Box 7911, Raleigh, NC, 27695-7911, USA.
| | - Albert J Keung
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Campus Box 7905, Raleigh, NC, 27695-7905, USA.
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24
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Grass RN, Heckel R, Dessimoz C, Stark WJ. Genomic Encryption of Digital Data Stored in Synthetic DNA. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202001162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Robert N. Grass
- Department of Chemistry and Applied Biosciences ETH Zurich Vladimir-Prelog-Weg 1 8093 Zurich Switzerland
| | - Reinhard Heckel
- Department of Electrical and Computer Engineering Rice University 6100 Main Street Houston TX 77005 USA
- Department of Electrical and Computer Engineering Technical University of Munich Munich Germany
| | - Christophe Dessimoz
- Department of Computational Biology and Center for Integrative Genomics University of Lausanne Lausanne Switzerland
- Swiss Institute of Bioinformatics Lausanne Switzerland
- Department of Genetics, Evolution & Environment and Department of Computer Science University College London UK
| | - Wendelin J. Stark
- Department of Chemistry and Applied Biosciences ETH Zurich Vladimir-Prelog-Weg 1 8093 Zurich Switzerland
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25
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Grass RN, Heckel R, Dessimoz C, Stark WJ. Genomic Encryption of Digital Data Stored in Synthetic DNA. Angew Chem Int Ed Engl 2020; 59:8476-8480. [PMID: 32083389 DOI: 10.1002/anie.202001162] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Indexed: 01/17/2023]
Abstract
Today, we can read human genomes and store digital data robustly in synthetic DNA. Herein, we report a strategy to intertwine these two technologies to enable the secure storage of valuable information in synthetic DNA, protected with personalized keys. We show that genetic short tandem repeats (STRs) contain sufficient entropy to generate strong encryption keys, and that only one technology, DNA sequencing, is required to simultaneously read the key and the data. Using this approach, we experimentally generated 80 bit strong keys from human DNA, and used such a key to encrypt 17 kB of digital information stored in synthetic DNA. Finally, the decrypted information was recovered perfectly from a single massively parallel sequencing run.
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Affiliation(s)
- Robert N Grass
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1, 8093, Zurich, Switzerland
| | - Reinhard Heckel
- Department of Electrical and Computer Engineering, Rice University, 6100 Main Street, Houston, TX, 77005, USA.,Department of Electrical and Computer Engineering, Technical University of Munich, Munich, Germany
| | - Christophe Dessimoz
- Department of Computational Biology and Center for Integrative Genomics, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Department of Genetics, Evolution & Environment and Department of Computer Science, University College, London, UK
| | - Wendelin J Stark
- Department of Chemistry and Applied Biosciences, ETH Zurich, Vladimir-Prelog-Weg 1, 8093, Zurich, Switzerland
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26
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Kumar G, Eble JE, Gaither MR. A practical guide to sample preservation and pre-PCR processing of aquatic environmental DNA. Mol Ecol Resour 2019; 20:29-39. [PMID: 31633859 DOI: 10.1111/1755-0998.13107] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 10/04/2019] [Accepted: 10/11/2019] [Indexed: 11/30/2022]
Abstract
Environmental DNA (eDNA) is rapidly growing in popularity as a tool for community assessments and species detection. While eDNA approaches are now widely applied, there is not yet agreement on best practices for sample collection and processing. Investigators looking to integrate eDNA approaches into their research programme are required to examine a growing collection of disparate studies to make an often uncertain decision about which protocols best fit their needs. To promote the application of eDNA approaches and to encourage the generation of high-quality data, here we review the most common techniques for the collection, preservation and extraction of metazoan eDNA from water samples. Specifically, we focus on experimental studies that compare various methods and outline the numerous challenges associated with eDNA. While the diverse applications of eDNA do not lend themselves to a one-size-fits-all recommendation, in most cases, capture/concentration of eDNA on cellulose nitrate filters (with pore size determined by water turbidity), followed by storage of filters in Longmire's buffer and extraction with a DNeasy Blood & Tissue Kit (or similar) has been shown to provide sufficient, high-quality DNA. However, we also emphasize the importance of testing and optimizing protocols for the system of interest.
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Affiliation(s)
- Girish Kumar
- Department of Biology, University of Central Florida, Genomics and Bioinformatics Cluster, Orlando, FL, USA
| | - Jeff E Eble
- Department of Ocean Engineering and Marine Sciences, Florida Institute of Technology, Melbourne, FL, USA
| | - Michelle R Gaither
- Department of Biology, University of Central Florida, Genomics and Bioinformatics Cluster, Orlando, FL, USA
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Zupanič Pajnič I, Marrubini G, Pogorelc BG, Zupanc T, Previderè C, Fattorini P. On the long term storage of forensic DNA in water. Forensic Sci Int 2019; 305:110031. [PMID: 31707238 DOI: 10.1016/j.forsciint.2019.110031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 10/21/2019] [Accepted: 10/28/2019] [Indexed: 11/19/2022]
Abstract
A rectrospective study was conducted on the effect of the long term storage of 122 DNA samples resuspended in water, one of the elution media still suggested by well established protocols. These DNA samples come from four different kinds of forensically relevant samples (saliva swabs, FTA card bloodstains, nails and II° World War bones) extracted in 2008-2018 and stored at - 20°C (n=113 of groups #1-#5) and at +4°C (n=9 of the group #6), respectively. At the time of the present study (2019), quantitative PCR (qPCR) was employed as tool for assessing the degradation of the samples. The employment of the Human Quantifiler Kit showed that the median loss of DNA ranged from 17.8% to 66.6% in groups #1-#5 while it was 85.0% in group #6. However, it is likely that these values represent an underestimation due to the shortness of the qPCR probe (62 bp). Noteworthy, the DNA loss was statistically significant in each of the six groups (p values ≤ 0.0167). Thus, in agreement with the data on spontaneous DNA decay, no forensic DNA sample should be stored in water for long term periods. In conclusion, the results of this technical note warn against the use of water for this purpose.
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Affiliation(s)
- Irena Zupanič Pajnič
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Slovenia.
| | | | | | - Tomaž Zupanc
- Institute of Forensic Medicine, Faculty of Medicine, University of Ljubljana, Slovenia.
| | - Carlo Previderè
- Department of Public Health, Experimental and Forensic Medicine, Section of Legal Medicine and Forensic Sciences, University of Pavia, Italy.
| | - Paolo Fattorini
- Department of Medicine, Surgery and Health, University of Trieste, Italy.
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Ferro P, Ortega-Pinazo J, Martínez B, Jiménez Á, Gómez-Zumaquero JM, Hortas ML, Díaz T. On the Use of Buffy or Whole Blood for Obtaining DNA of High Quality and Functionality: What Is the Best Option? Biopreserv Biobank 2019; 17:577-582. [PMID: 31429592 DOI: 10.1089/bio.2019.0024] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Human biobanks are collections of biological samples and health information that allow the organization of biomedical research for upgrading the knowledge of human disorders from different diseases (cancer, allergies, rare diseases, etc.), and reach real answers for diagnosis and treatment. A wide range of samples can be stored in these biorepositories such as hair, nails, urine, tissue, whole blood, red blood cells, buffy coat, plasma, serum, DNA, and RNA. Among these, buffy coat and whole blood are widely used by researchers because they can obtain DNA and RNA from these matrices. Some preliminary studies have been performed on animals to evaluate the quality and functionality of the nucleic acids obtained from some of these matrices, although more in-depth studies are needed in this area. In this study, blood samples extracted by venipuncture from 30 healthy volunteers were used to obtain DNA from buffy coat and whole blood. The purity and integrity of the nucleic acids obtained were assessed by spectrophotometry, fluorimetry, and agarose electrophoresis, and functionality was assessed by PCR and real-time PCR. Another aspect tested in this study was based on the comparison between short-term and long-term storage at -80°C and fresh samples from both matrices to evaluate the storage conditions at the biobank. Results showed differences in the yield obtained from both matrices as a function of the storage time, although the functionality of all the obtained DNA remained intact.
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Affiliation(s)
- Pedro Ferro
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga (IBIMA), Malaga, Spain
| | - Jesús Ortega-Pinazo
- Neuroimmunology and Neuroinflammation Group, Instituto de Investigación Biomédica de Málaga (IBIMA), UGC Neurociencias, Hospital Regional Universitario de Málaga, Malaga, Spain
| | - Beatriz Martínez
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga (IBIMA), Malaga, Spain
| | - Álvaro Jiménez
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga (IBIMA), Malaga, Spain
| | | | | | - Tatiana Díaz
- Andalusian Public Health System Biobank, Instituto de Investigación Biomédica de Málaga (IBIMA), Malaga, Spain
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Abstract
DNA outperforms most conventional storage media in terms of information retention time, physical density, and volumetric coding capacity. Advances in synthesis and sequencing technologies have enabled implementations of large synthetic DNA databases with impressive storage capacity and reliable data recovery. Several robust DNA storage architectures featuring random access, error correction, and content rewritability have been constructed with the potential for scalability and cost reduction. We survey these recent achievements and discuss alternative routes for overcoming the hurdles of engineering practical DNA storage systems. We also review recent exciting work on in vivo DNA memory including intracellular recorders constructed by programmable genome editing tools. Besides information storage, DNA could serve as a versatile molecular computing substrate. We highlight several state-of-the-art DNA computing techniques such as strand displacement, localized hybridization chain reactions, and enzymatic reaction networks. We summarize how these simple primitives have facilitated rational designs and implementations of in vitro DNA reaction networks that emulate digital/analog circuits, artificial neural networks, or nonlinear dynamic systems. We envision these modular primitives could be strategically adapted for sophisticated database operations and massively parallel computations on DNA databases. We also highlight in vivo DNA computing modules such as CRISPR logic gates for building scalable genetic circuits in living cells. To conclude, we discuss various implications and challenges of DNA-based storage and computing, and we particularly encourage innovative work on bridging these two areas of research to further explore molecular parallelism and near-data processing. Such integrated molecular systems could lead to far-reaching applications in biocomputing, security, and medicine.
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Samsuwan J, Somboonchokepisal T, Akaraputtiporn T, Srimuang T, Phuengsukdaeng P, Suwannarat A, Mutirangura A, Kitkumthorn N. A method for extracting DNA from hard tissues for use in forensic identification. Biomed Rep 2018; 9:433-438. [PMID: 30402227 DOI: 10.3892/br.2018.1148] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 09/10/2018] [Indexed: 11/05/2022] Open
Abstract
With deceased and decayed bodies, personal identification is performed using hard tissue DNA, commonly extracted from bone. The quantity and quality of DNA used in the polymerase chain reaction (PCR) amplification step is critical for a successful outcome. Since enamel is the strongest tissue in the human body, it was hypothesized that teeth may preserve DNA better than bones. In the present study, porcine teeth and bone samples were exposed to a variety of environments that imitated personal identification conditions, and DNA extracted from the teeth and bone samples was compared, using a PCR amplification method. The porcine teeth and bones were exposed to 11 different conditions for 5 different time periods to imitate a series of common crime scenes. DNA was extracted by a standard phenol-chloroform method. To test DNA quality, PCR was performed with primers designed to amplify porcine β-actin (ACTB) and mitochondrial DNA (mtDNA) sequences. The results demonstrated that the quality of DNA extracted from teeth was greater than that extracted from bone in the following environments: Buried in sand, soaked in caustic soda and burnt with rubber. By contrast, the quality of DNA extracted from bone was greater than that extracted from teeth when samples were buried in soil or submerged in water. There was no discernable difference in the quality of DNA extracted from bones and teeth in several environments, including being submerged in seawater, soaked in sulfuric acid, left in open air, and stored at 4, -20 and -80°C. Additionally, the results suggested that PCR using mtDNA primers performed better than that using ACTB primers. Finally, it was indicated that components of seawater may inhibit PCR amplification. The preliminary data reported here may provide basic guidelines for selecting the optimum source of DNA in each case.
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Affiliation(s)
- Jarunya Samsuwan
- Sub Division of Forensic Biochemistry, Institute of Forensic Medicine, Police General Hospital, Royal Thai Police, Bangkok 10330, Thailand
| | | | | | | | | | | | - Apiwat Mutirangura
- Center of Excellence in Molecular Genetics of Cancer and Human Diseases, Department of Anatomy, Faculty of Medicine, Chulalongkorn University, Bangkok 10330, Thailand
| | - Nakarin Kitkumthorn
- Department of Oral Biology, Faculty of Dentistry, Mahidol University, Bangkok 10400, Thailand
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Dean GH, Asmarayani R, Ardiyani M, Santika Y, Triono T, Mathews S, Webb CO. Generating DNA sequence data with limited resources for molecular biology: Lessons from a barcoding project in Indonesia. APPLICATIONS IN PLANT SCIENCES 2018; 6:e01167. [PMID: 30131909 PMCID: PMC6055555 DOI: 10.1002/aps3.1167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2017] [Accepted: 05/15/2018] [Indexed: 05/29/2023]
Abstract
The advent of the DNA sequencing age has led to a revolution in biology. The rapid and cost-effective generation of high-quality sequence data has transformed many fields, including those focused on discovering species and surveying biodiversity, monitoring movement of biological materials, forensic biology, and disease diagnostics. There is a need to build capacity to generate useful sequence data in countries with limited historical access to laboratory resources, so that researchers can benefit from the advantages offered by these data. Commonly used molecular techniques such as DNA extraction, PCR, and DNA sequencing are within the reach of small laboratories in many countries, with the main obstacles to successful implementation being lack of funding and limited practical experience. Here we describe a successful approach that we developed to obtain DNA sequence data during a small DNA barcoding project in Indonesia.
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Affiliation(s)
- Gillian H. Dean
- Department of BotanyUniversity of British ColumbiaVancouverV6T1Z4British ColumbiaCanada
| | - Rani Asmarayani
- Herbarium BogorienseBotany DivisionResearch Center for BiologyIndonesian Institute of Sciences (LIPI)Cibinong16911BogorWest JavaIndonesia
- Present address:
Department of BiologyUniversity of Missouri–St. LouisSt. LouisMissouri63121USA
| | - Marlina Ardiyani
- Herbarium BogorienseBotany DivisionResearch Center for BiologyIndonesian Institute of Sciences (LIPI)Cibinong16911BogorWest JavaIndonesia
| | - Yessi Santika
- Herbarium BogorienseBotany DivisionResearch Center for BiologyIndonesian Institute of Sciences (LIPI)Cibinong16911BogorWest JavaIndonesia
| | - Teguh Triono
- Herbarium BogorienseBotany DivisionResearch Center for BiologyIndonesian Institute of Sciences (LIPI)Cibinong16911BogorWest JavaIndonesia
- Present address:
Zoological Society of London (ZSL) Indonesia ProgramBogor16128Indonesia
| | - Sarah Mathews
- Arnold Arboretum of Harvard UniversityBostonMassachusetts02131USA
- Present address:
CSIROAustralian National HerbariumCanberraAustralian Capital Territory2601Australia
| | - Campbell O. Webb
- Arnold Arboretum of Harvard UniversityBostonMassachusetts02131USA
- Present address:
University of Alaska Museum of the NorthFairbanksAlaska99775USA
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Liu Y, Zheng Z, Gong H, Liu M, Guo S, Li G, Wang X, Kaplan DL. DNA preservation in silk. Biomater Sci 2018; 5:1279-1292. [PMID: 28561097 DOI: 10.1039/c6bm00741d] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
The structure of DNA is susceptible to alterations at high temperature and on changing pH, irradiation and exposure to DNase. Options to protect and preserve DNA during storage are important for applications in genetic diagnosis, identity authentication, drug development and bioresearch. In the present study, the stability of total DNA purified from human dermal fibroblast cells, as well as that of plasmid DNA, was studied in silk protein materials. The DNA/silk mixtures were stabilized on filter paper (silk/DNA + filter) or filter paper pre-coated with silk and treated with methanol (silk/DNA + PT-filter) as a route to practical utility. After air-drying and water extraction, 50-70% of the DNA and silk could be retrieved and showed a single band on electrophoretic gels. 6% silk/DNA + PT-filter samples provided improved stability in comparison with 3% silk/DNA + filter samples and DNA + filter samples for DNA preservation, with ∼40% of the band intensity remaining at 37 °C after 40 days and ∼10% after exposure to UV light for 10 hours. Quantitative analysis using the PicoGreen assay confirmed the results. The use of Tris/borate/EDTA (TBE) buffer enhanced the preservation and/or extraction of the DNA. The DNA extracted after storage maintained integrity and function based on serving as a functional template for PCR amplification of the gene for zinc finger protein 750 (ZNF750) and for transgene expression of red fluorescence protein (dsRed) in HEK293 cells. The high molecular weight and high content of a crystalline beta-sheet structure formed on the coated surfaces likely accounted for the preservation effects observed for the silk/DNA + PT-filter samples. Although similar preservation effects were also obtained for lyophilized silk/DNA samples, the rapid and simple processing available with the silk-DNA-filter membrane system makes it appealing for future applications.
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Affiliation(s)
- Yawen Liu
- National Engineering Laboratory for Modern Silk, College of Textile and Clothing Engineering, Soochow University, Suzhou 215123, People's Republic of China.
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Miernyk KM, DeByle CK, Rudolph KM. Evaluation of Two Matrices for Long-Term, Ambient Storage of Bacterial DNA. Biopreserv Biobank 2017; 15:529-534. [PMID: 29130748 DOI: 10.1089/bio.2017.0040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Culture-independent molecular analyses allow researchers to identify diverse microorganisms. This approach requires microbiological DNA repositories. The standard for DNA storage is liquid nitrogen or ultralow freezers. These use large amounts of space, are costly to operate, and could fail. Room temperature DNA storage is a viable alternative. In this study, we investigated storage of bacterial DNA using two ambient storage matrices, Biomatrica DNAstable® Plus and GenTegra® DNA. METHODS We created crude and clean DNA extracts from five Streptococcus pneumoniae isolates. Extracts were stored at -30°C (our usual DNA storage temperature), 25°C (within the range of temperatures recommended for the products), and 50°C (to simulate longer storage time). Samples were stored at -30°C with no product and dried at 25°C and 50°C with no product, in Biomatrica DNAstable Plus or GenTegra DNA. We analyzed the samples after 0, 1, 2, 4, 8, 16, 32, and 64 weeks using the Nanodrop 1000 to determine the amount of DNA in each aliquot and by real-time PCR for the S. pneumoniae genes lytA and psaA. Using a 50°C storage temperature, we simulated 362 weeks of 25°C storage. RESULTS The average amount of DNA in aliquots stored with a stabilizing matrix was 103%-116% of the original amount added to the tubes. This is similar to samples stored at -30°C (average 102%-121%). With one exception, samples stored with a stabilizing matrix had no change in lytA or psaA cycle threshold (Ct) value over time (Ct range ≤2.9), similar to samples stored at -30°C (Ct range ≤3.0). Samples stored at 25°C with no stabilizing matrix had Ct ranges of 2.2-5.1. CONCLUSION DNAstable Plus and GenTegra DNA can protect dried bacterial DNA samples stored at room temperature with similar effectiveness as at -30°C. It is not effective to store bacterial DNA at room temperature without a stabilizing matrix.
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Affiliation(s)
- Karen M Miernyk
- Arctic Investigations Program, Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention (CDC) , Anchorage, Alaska
| | - Carolynn K DeByle
- Arctic Investigations Program, Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention (CDC) , Anchorage, Alaska
| | - Karen M Rudolph
- Arctic Investigations Program, Division of Preparedness and Emerging Infections, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention (CDC) , Anchorage, Alaska
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35
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Oldenhof H, Zhang M, Narten K, Bigalk J, Sydykov B, Wolkers WF, Sieme H. Freezing-induced uptake of disaccharides for preservation of chromatin in freeze-dried stallion sperm during accelerated aging†. Biol Reprod 2017; 97:892-901. [DOI: 10.1093/biolre/iox142] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 11/06/2017] [Indexed: 11/13/2022] Open
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36
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Zhang M, Oldenhof H, Sydykov B, Bigalk J, Sieme H, Wolkers WF. Freeze-drying of mammalian cells using trehalose: preservation of DNA integrity. Sci Rep 2017; 7:6198. [PMID: 28740099 PMCID: PMC5524761 DOI: 10.1038/s41598-017-06542-z] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 06/14/2017] [Indexed: 11/09/2022] Open
Abstract
The aim of this study was to investigate preservation of biomolecular structures, particularly DNA, in freeze-dried fibroblasts, after loading with trehalose via freezing-induced uptake. Cells were freeze-dried with trehalose alone or in a mixture of albumin and trehalose. Albumin was added to increase the glass transition temperature and storage stability. No viable cells were recovered after freeze-drying and rehydration. FTIR studies showed that membrane phase behavior of freeze-dried cells resembles that of fresh cells. However, one day after rehydration membrane phase separation was observed, irrespective of the presence or absence of trehalose during freeze-drying. Freeze-drying did not affect the overall protein secondary structure. Analysis of DNA damage via single cell gel electrophoresis (‘comet assay’) showed that DNA damage progressively increased with storage duration and temperature. DNA damage was prevented during storage at 4 °C. It is shown that trehalose reduces DNA damage during storage, whereas addition of albumin did not seem to have an additional protective effect on storage stability (i.e. DNA integrity) despite the fact that albumin increased the glass transition temperature. Taken together, DNA in freeze-dried somatic cells can be preserved using trehalose as protectant and storage at or below 4 °C.
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Affiliation(s)
- Miao Zhang
- Institute of Multiphase Processes, Leibniz Universität Hannover, Hannover, Germany
| | - Harriëtte Oldenhof
- Unit for Reproductive Medicine, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Bulat Sydykov
- Institute of Multiphase Processes, Leibniz Universität Hannover, Hannover, Germany
| | - Judith Bigalk
- Unit for Reproductive Medicine, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Harald Sieme
- Unit for Reproductive Medicine, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Willem F Wolkers
- Institute of Multiphase Processes, Leibniz Universität Hannover, Hannover, Germany.
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Zhu B, Zhao Y, Dai J, Wang J, Xing S, Guo L, Chen N, Qu X, Li L, Shen J, Shi J, Li J, Wang L. Preservation of DNA Nanostructure Carriers: Effects of Freeze-Thawing and Ionic Strength during Lyophilization and Storage. ACS APPLIED MATERIALS & INTERFACES 2017; 9:18434-18439. [PMID: 28547989 DOI: 10.1021/acsami.7b04784] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
DNA nanostructures have attracted wide interest in biomedical applications, especially as nanocarriers for drug delivery. Therefore, it is important to ensure the structural integrity of DNA nanostructures under ambient temperature storage. In this study, we examined lyophilization-based preservation of DNA nanostructures by investigating the structural integrity of different DNA nanostructures reconstituted from lyophilization. We demonstrated that lyophilization under appropriate ionic strength is amenable to the storage of DNA nanostructures. Compared with that stored in liquid solution, DNA nanostructure carriers reconstituted from lyophilization showed significantly better structural integrity after an accelerated aging test equivalent to 100-day room-temperature storage.
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Affiliation(s)
- Bing Zhu
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility; CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
- University of Chinese Academy of Sciences , Beijing 10049, China
| | - Yan Zhao
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility; CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
- University of Chinese Academy of Sciences , Beijing 10049, China
| | - Jiangbing Dai
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility; CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
- University of Chinese Academy of Sciences , Beijing 10049, China
| | - Jianbang Wang
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility; CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
- University of Chinese Academy of Sciences , Beijing 10049, China
| | - Shu Xing
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility; CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Linjie Guo
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility; CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Nan Chen
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility; CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Xiangmeng Qu
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University , Shanghai 200241, China
| | - Li Li
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University , Shanghai 200241, China
| | - Juwen Shen
- Shanghai Key Laboratory of Green Chemistry and Chemical Processes, School of Chemistry and Molecular Engineering, East China Normal University , Shanghai 200241, China
| | - Jiye Shi
- UCB Pharma , 208 Bath Road, Slough SL1 3WE, United Kingdom
| | - Jiang Li
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility; CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
| | - Lihua Wang
- Division of Physical Biology and Bioimaging Center, Shanghai Synchrotron Radiation Facility; CAS Key Laboratory of Interfacial Physics and Technology; Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, China
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38
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Muller R, Betsou F, Barnes MG, Harding K, Bonnet J, Kofanova O, Crowe JH. Preservation of Biospecimens at Ambient Temperature: Special Focus on Nucleic Acids and Opportunities for the Biobanking Community. Biopreserv Biobank 2016; 14:89-98. [DOI: 10.1089/bio.2015.0022] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
| | - Fay Betsou
- Integrated Biobank of Luxembourg, Luxembourg, Luxembourg
| | | | - Keith Harding
- Damar Research Scientists, Damar, Cupar Muir, United Kingdom
| | - Jacques Bonnet
- Imagene, Genopole Campus 1, Evry, France
- Université de Bordeaux Segalen, Institut Bergonié, Bordeaux, France
| | - Olga Kofanova
- Integrated Biobank of Luxembourg, Luxembourg, Luxembourg
| | - John H. Crowe
- Department of Molecular and Cellular Biology, University of California, Davis, California
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39
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Clark KD, Sorensen M, Nacham O, Anderson JL. Preservation of DNA in nuclease-rich samples using magnetic ionic liquids. RSC Adv 2016. [DOI: 10.1039/c6ra05932e] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Magnetic ionic liquids (MIL) can serve as DNA preservation media in nuclease-rich environments. Plasmid DNA exhibited structural stability for up to 1 week in MILs.
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40
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Tolios A, Teupser D, Holdt LM. Preanalytical Conditions and DNA Isolation Methods Affect Telomere Length Quantification in Whole Blood. PLoS One 2015; 10:e0143889. [PMID: 26636575 PMCID: PMC4670203 DOI: 10.1371/journal.pone.0143889] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 11/10/2015] [Indexed: 11/30/2022] Open
Abstract
Telomeres are located at chromosome ends and their length (TL) has been associated with aging and human diseases such as cancer. Whole blood DNA is frequently used for TL measurements but the influence of preanalytical conditions and DNA isolation methods on TL quantification has not been thoroughly investigated. To evaluate potential preanalytical as well as methodological bias on TL, anonymized leftover EDTA-whole blood samples were pooled according to leukocyte counts and were incubated with and without actinomycin D to induce apoptosis as a prototype of sample degradation. DNA was isolated from fresh blood pools and after freezing at -80°C. Commercially available kits using beads (Invitrogen), spin columns (Qiagen, Macherey-Nagel and 5prime) or precipitation (Stratec/Invisorb) and a published isopropanol precipitation protocol (IPP) were used for DNA isolation. TL was assessed by qPCR, and normalized to the single copy reference gene 36B4 using two established single-plex and a new multiplex protocol. We show that the method of DNA isolation significantly affected TL (e.g. 1.86-fold longer TL when comparing IPP vs. Invitrogen). Sample degradation led to an average TL decrease of 22% when using all except for one DNA isolation method (5prime). Preanalytical storage conditions did not affect TL with exception of samples that were isolated with the 5prime kit, where a 27% increase in TL was observed after freezing. Finally, performance of the multiplex qPCR protocol was comparable to the single-plex assays, but showed superior time- and cost-effectiveness and required > 80% less DNA. Findings of the current study highlight the need for standardization of whole blood processing and DNA isolation in clinical study settings to avoid preanalytical bias of TL quantification and show that multiplex assays may improve TL/SCG measurements.
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Affiliation(s)
- Alexander Tolios
- Institute of Laboratory Medicine, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Daniel Teupser
- Institute of Laboratory Medicine, Ludwig-Maximilians-University Munich, Munich, Germany
| | - Lesca M Holdt
- Institute of Laboratory Medicine, Ludwig-Maximilians-University Munich, Munich, Germany
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41
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Inderbitzin P, Subbarao KV. Verticillium systematics and evolution: how confusion impedes Verticillium wilt management and how to resolve it. PHYTOPATHOLOGY 2014; 104:564-74. [PMID: 24548214 DOI: 10.1094/phyto-11-13-0315-ia] [Citation(s) in RCA: 100] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Verticillium wilts are important vascular wilt diseases that affect many crops and ornamentals in different regions of the world. Verticillium wilts are caused by members of the ascomycete genus Verticillium, a small group of 10 species that are related to the agents of anthracnose caused by Colletotrichum species. Verticillium has a long and complicated taxonomic history with controversies about species boundaries and long overlooked cryptic species, which confused and limited our knowledge of the biology of individual species. We first review the taxonomic history of Verticillium, provide an update and explanation of the current system of classification and compile host range and geographic distribution data for individual species from internal transcribed spacer (ITS) GenBank records. Using Verticillium as an example, we show that species names are a poor vehicle for archiving and retrieving information, and that species identifications should always be backed up by DNA sequence data and DNA extracts that are made publicly available. If such a system were made a prerequisite for publication, all species identifications could be evaluated retroactively, and our knowledge of the biology of individual species would be immune from taxonomic changes, controversy and misidentification. Adoption of this system would improve quarantine practices and the management of diseases caused by various plant pathogens.
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42
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Duarte C, Salm E, Dorvel B, Reddy B, Bashir R. On-chip parallel detection of foodborne pathogens using loop-mediated isothermal amplification. Biomed Microdevices 2014; 15:821-30. [PMID: 23620454 DOI: 10.1007/s10544-013-9769-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
According to estimates issued by the Center for Disease Control and Prevention, one out of six Americans will get sick during this year due to consumption of contaminated products and there will be 50,000 related hospitalizations. To control and treat the responsible foodborne diseases, rapid and accurate detection of pathogens is extremely important. A portable device capable of performing nucleic acid amplification will enable the effective detection of infectious agents in multiple settings, leading to better enforcement of food safety regulations. This work demonstrates the multiplexed detection of food pathogens through loop-mediated isothermal amplification on a silicon chip. Silane passivation is used to prevent the adsorption of the polymerase on silicon oxide, which can severely inhibit nucleic acid amplification. We demonstrate the multiplexed screening of virulence genes of Listeria monocytogenes, Escherichia coli, and Salmonella by dehydrating the corresponding primers in oxidized silicon wells. Droplets of 30 nL with reagents for nucleic acid amplification and lysate of suspected pathogens are arrayed on micro-machined wells with an automated microinjection system. We show that dehydrated primers re-suspend when other reagents are microinjected, and the resulting mix can be used to specifically amplify the targeted gene. Results of characterization experiments demonstrate sensitivity down to a few templates per reaction, specificity that enables multiplexed screening, and robustness that allows amplification without DNA extraction.
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Affiliation(s)
- Carlos Duarte
- Department of Electrical and Computer Engineering, William L. Everitt Laboratory, University of Illinois at Urbana-Champaign, 1406 W. Green St., Urbana, IL 61801, USA
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Frippiat C, Noel F. Efficiency of a novel forensic room-temperature DNA storage medium. Forensic Sci Int Genet 2014; 9:81-4. [PMID: 24528585 DOI: 10.1016/j.fsigen.2013.11.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 10/09/2013] [Accepted: 11/30/2013] [Indexed: 11/25/2022]
Abstract
The success of forensic genetics has led to considerable numbers of DNA samples that must be stored. Thus, the ability to preserve the integrity of forensic samples is essential. The possibility of retesting these samples after many years should be guaranteed. DNA storage typically requires the use of freezers. Recently, a new method that enables DNA to be stored at room temperature was developed. This technology is based on the principles of anhydrobiosis and thus permits room-temperature storage of DNA. This study evaluates the ability of this technology to preserve DNA samples mimicking true mixture casework samples for long periods of time. Mixed human DNA from 2 or 3 persons and at low concentrations was dried and stored for a period ranging from 6 months to 2 years in the presence of a desiccant. The quality of the stored DNA was evaluated based on quantitative peak height results from Short Tandem Repeat (STR) genotyping and the number of observed alleles. Furthermore, we determined whether this matrix has a potential inhibitory or enhancing effect on the PCR genotyping reactions. In our previous work, we demonstrated the considerable potential of this new technology. The present study complements our previous work. Our results show that after 2 years of aging at room temperature, there is a decrease in the number of observed alleles and in the peak height of these alleles.
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Affiliation(s)
- Christophe Frippiat
- National Institute of Criminalistics and Criminology, Chaussée de Vilvoorde 100, 1120 Brussels, Belgium.
| | - Fabrice Noel
- National Institute of Criminalistics and Criminology, Chaussée de Vilvoorde 100, 1120 Brussels, Belgium
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Leinonen MK, Anttila A, Malila N, Dillner J, Forslund O, Nieminen P. Type- and age-specific distribution of human papillomavirus in women attending cervical cancer screening in Finland. Br J Cancer 2013; 109:2941-50. [PMID: 24136148 PMCID: PMC3844908 DOI: 10.1038/bjc.2013.647] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2013] [Revised: 08/08/2013] [Accepted: 09/25/2013] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND Large-scale data on type-specific HPV prevalences and disease burden are needed to monitor the impact of HPV vaccination and to plan for HPV-based cervical screening. METHODS 33 043 women (aged 25-65) were screened for HPV by a Hybrid Capture 2 (HC2) in a population-based programme. HPV-positive women (n=2574) were triaged by cytology and HPV genotyped using PCR-Luminex. Type-specific prevalence of HPV infection and its correlation to findings in cytology triage and histology as well as Population Attributable Fractions for a referral to colposcopy and findings in histology were calculated. RESULTS Among HC2-positive women, 61.5% had normal, 23.1% had ASC-US and 15.5% had LSIL or more severe (LSIL+) results in cytology. Out of HC2-positive samples, 57% contained the 13 Group 1/2A HPV types, which were targeted by the HC2, 15% contained Group 2B types, 8.5% Group 3 types and 30% were found to be negative in HPV genotyping. The proportion of samples positive for HPV by the HC2, but negative in HPV genotyping increased with age and decreased with increasing cytological abnormality. The most frequent types were HPV 16 (0.9% of screened women and 12.1% of the HC2-positive women), HPV 31 (0.7% and 8.9%, respectively) and HPV 52 (0.5% and 6.3%, respectively). The prevalence of Group 1/2A HPV types increased with increasing CIN grade and attributed 78.3% (95% CI 53.4-89.9) of the CIN 3+ lesions, while HPV 16 attributed 55.8% (40.0-67.5) of them. CONCLUSION The type-specific prevalence of HPV were slightly lower than the average in international meta-analyses. Genotyping for HPV 16 better identified women with CIN 3+ than cytology triage at the threshold of LSIL+. The high proportion of women that were HC2-positive but HPV-negative in genotyping suggests that HPV genotyping may be useful also for validation of results in HPV screening. The large-scale HPV genotyping data were found to be directly useful for planning further preventive efforts for cervical cancer.
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Affiliation(s)
- M K Leinonen
- Finnish Cancer Registry, Pieni Roobertinkatu 9, FI-00130 Helsinki, Finland
| | - A Anttila
- Mass Screening Registry, Finnish Cancer Registry, Pieni Roobertinkatu 9, FI-00130 Helsinki, Finland
| | - N Malila
- Finnish Cancer Registry, Pieni Roobertinkatu 9, FI-00130 Helsinki, Finland
- Tampere School of Health Sciences, University of Tampere, Medisiinarinkatu 3, FI-33014 Tampere, Finland
| | - J Dillner
- Department of Medical Microbiology, Lund University, Jan Waldenströms gata 59, 205 02 Malmö, Sweden
- Departments of Laboratory Medicine, Medical Epidemiology and Biostatistics, Karolinska Institute, SE-17177 Stockholm, Sweden
| | - O Forslund
- Department of Medical Microbiology, Lund University, Jan Waldenströms gata 59, 205 02 Malmö, Sweden
| | - P Nieminen
- Department of Obstetrics and Gynecology, Helsinki University Central Hospital, Turuntie 150, FI-02740 Espoo, Finland
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Rajatileka S, Luyt K, El-Bokle M, Williams M, Kemp H, Molnár E, Váradi A. Isolation of human genomic DNA for genetic analysis from premature neonates: a comparison between newborn dried blood spots, whole blood and umbilical cord tissue. BMC Genet 2013; 14:105. [PMID: 24168095 PMCID: PMC3817355 DOI: 10.1186/1471-2156-14-105] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Accepted: 09/17/2013] [Indexed: 12/17/2022] Open
Abstract
Background Genotyping requires biological sample collection that must be reliable, convenient and acceptable for patients and clinicians. Finding the most optimal procedure of sample collection for premature neonates who have a very limited blood volume is a particular challenge. The aim of the current study was to evaluate the use of umbilical cord (UC) tissue and newborn dried blood spot (DBS)-extracted genomic DNA (gDNA) as an alternative to venous blood-derived gDNA from premature neonates for molecular genetic analysis. All samples were obtained from premature newborn infants between 24-32 weeks of gestation. Paired blood and UC samples were collected from 31 study participants. gDNA was extracted from ethylenediaminetetraacetic acid (EDTA) anticoagulant-treated blood samples (~500 μl) and newborn DBSs (n = 723) using QIAamp DNA Micro kit (Qiagen Ltd., Crawley, UK); and from UC using Qiagen DNAeasy Blood and Tissue kit (Qiagen Ltd., Crawley, UK). gDNA was quantified and purity confirmed by measuring the A260:A280 ratio. PCR amplification and pyrosequencing was carried out to determine suitability of the gDNA for molecular genetic analysis. Minor allele frequency of two unrelated single nucleotide polymorphisms (SNPs) was calculated using the entire cohort. Results Both whole blood samples and UC tissue provided good quality and yield of gDNA, which was considerably less from newborn DBS. The gDNA purity was also reduced after 3 years of storage of the newborn DBS. PCR amplification of three unrelated genes resulted in clear products in all whole blood and UC samples and 86%-100% of newborn DBS. Genotyping using pyrosequencing showed 100% concordance in the paired UC and whole blood samples. Minor allele frequencies of the two SNPs indicated that no maternal gDNA contamination occurred in the genotyping of the UC samples. Conclusions gDNAs from all three sources are suitable for standard PCR and pyrosequencing assays. Given that UC provide good quality and quantity gDNA with 100% concordance in the genetic analysis with whole blood, it can replace blood sampling from premature infants. This is likely to reduce the stress and potential side effects associated with invasive sample collection and thus, greatly facilitate participant recruitment for genetic studies.
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Affiliation(s)
| | | | | | | | | | | | - Anikó Váradi
- Centre for Research in Biosciences, Department of Biological, Biomedical and Analytical Sciences, Faculty of Health and Applied Sciences, University of the West of England, Bristol BS16 1QY, UK.
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Assessment of viable bacteria and bacterial DNA in blood and bloodstain specimens stored under various conditions. J Forensic Leg Med 2013; 20:1035-40. [PMID: 24237815 DOI: 10.1016/j.jflm.2013.09.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 09/23/2013] [Accepted: 09/28/2013] [Indexed: 11/24/2022]
Abstract
Microbial forensic specimens that are collected at biocrime and bioterrorism scenes include blood, tissue, cloths containing biological fluids, swabs, water, soil, and aerosols. It is preferable that pathogens in such specimens are alive and kept in a steady state. Specimens may be stored for a prolonged period before analysis; therefore, it is important to understand the effect of the storage conditions on the pathogens contained within the specimens. In this study, we prepared blood and bloodstain specimens containing Gram-negative or -positive bacteria, stored the samples for 482 days under various conditions, and measured viable bacterial counts and total bacterial contents in the samples. Viable bacteria were preserved well in the samples stored at -30 and -80 °C, but were diminished or undetectable in the samples stored at 4 °C and room temperature. The total bacterial content was maintained in the blood samples stored at -30 and -80 °C and in the bloodstain samples stored under all temperature conditions, but decreased in the blood samples stored at 4 °C and room temperature. This study showed that the storage conditions affected viable bacteria and bacterial DNA and that freezing and drying were significant for their long-term storage. We provide important information for the storage of microbial forensic specimens.
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Straube D, Juen A. Storage and shipping of tissue samples for DNA analyses: A case study on earthworms. EUROPEAN JOURNAL OF SOIL BIOLOGY 2013; 57:13-18. [PMID: 26109838 PMCID: PMC4461180 DOI: 10.1016/j.ejsobi.2013.04.001] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/28/2012] [Revised: 04/05/2013] [Accepted: 04/11/2013] [Indexed: 06/04/2023]
Abstract
Nowadays, molecular analyses play an important role in studies of soil dwelling animals, for example in taxonomy, phylogeography or food web analyses. The quality of the DNA, used for later molecular analyses, is an important factor and depends on collection and preservation of samples prior to DNA extraction. Ideally, DNA samples are frozen immediately upon collection, but if samples are collected in the field, suitable preservation methods might be limited due to unavailability of resources or remote field sites. Moreover, shipping samples over long distances can cause loss of DNA quality e.g. by thawing or leaking of preservation liquid. In this study we use earthworms, a key organism in soil research, to compare three different DNA preservation methods - freezing at -20 °C, storing in 75% ethanol, and freeze drying. Samples were shipped from the United States of America to Austria. The DNA of the samples was extracted using two different extraction methods, peqGOLD™ and Chelex® 100. The DNA amplification success was determined by amplifying four DNA fragments of different length. The PCR amplification success is significantly influenced by preservation method and extraction method and differed significantly depending on the length of the DNA fragment. Freeze drying samples was the best preservation method when samples were extracted using the silica based extraction method peqGOLD™. For samples that were extracted with Chelex® 100, storage in ethanol was the best preservation method. However, the overall amplification success was significantly lower for the extraction procedure based on Chelex® 100. The detection of the small DNA fragments was higher and independent from the extraction method, while the amplification success was significantly reduced for the longer DNA fragments. We recommend freeze drying of DNA samples, especially when they have to be shipped for longer distances. No special packaging or declaration is needed for freeze dried samples, and the risk of thawing is excluded. Storage of freeze dried samples also reduces costs because samples can be kept at room temperature in a desiccator. It should be noted, that the extraction methods showed significant differences in DNA amplification success. Thus, the extraction method should be taken into account when choosing the preservation method.
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Affiliation(s)
- Daniela Straube
- Corresponding author. Tel.: +43 (0) 512 507 51678; fax: +43 (0) 512 507 51799.
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Goldman N, Bertone P, Chen S, Dessimoz C, LeProust EM, Sipos B, Birney E. Towards practical, high-capacity, low-maintenance information storage in synthesized DNA. Nature 2013; 494:77-80. [PMID: 23354052 DOI: 10.1038/nature11875] [Citation(s) in RCA: 384] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2012] [Accepted: 12/12/2012] [Indexed: 11/09/2022]
Abstract
Digital production, transmission and storage have revolutionized how we access and use information but have also made archiving an increasingly complex task that requires active, continuing maintenance of digital media. This challenge has focused some interest on DNA as an attractive target for information storage because of its capacity for high-density information encoding, longevity under easily achieved conditions and proven track record as an information bearer. Previous DNA-based information storage approaches have encoded only trivial amounts of information or were not amenable to scaling-up, and used no robust error-correction and lacked examination of their cost-efficiency for large-scale information archival. Here we describe a scalable method that can reliably store more information than has been handled before. We encoded computer files totalling 739 kilobytes of hard-disk storage and with an estimated Shannon information of 5.2 × 10(6) bits into a DNA code, synthesized this DNA, sequenced it and reconstructed the original files with 100% accuracy. Theoretical analysis indicates that our DNA-based storage scheme could be scaled far beyond current global information volumes and offers a realistic technology for large-scale, long-term and infrequently accessed digital archiving. In fact, current trends in technological advances are reducing DNA synthesis costs at a pace that should make our scheme cost-effective for sub-50-year archiving within a decade.
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Affiliation(s)
- Nick Goldman
- European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SD, UK.
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Kalyanasundaram D, Kim JH, Yeo WH, Oh K, Lee KH, Kim MH, Ryew SM, Ahn SG, Gao D, Cangelosi GA, Chung JH. Rapid extraction and preservation of genomic DNA from human samples. Anal Bioanal Chem 2013; 405:1977-83. [PMID: 23307121 DOI: 10.1007/s00216-012-6637-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2012] [Revised: 11/24/2012] [Accepted: 12/06/2012] [Indexed: 11/29/2022]
Abstract
Simple and rapid extraction of human genomic DNA remains a bottleneck for genome analysis and disease diagnosis. Current methods using microfilters require cumbersome, multiple handling steps in part because salt conditions must be controlled for attraction and elution of DNA in porous silica. We report a novel extraction method of human genomic DNA from buccal swab and saliva samples. DNA is attracted onto a gold-coated microchip by an electric field and capillary action while the captured DNA is eluted by thermal heating at 70 °C. A prototype device was designed to handle four microchips, and a compatible protocol was developed. The extracted DNA using microchips was characterized by qPCR for different sample volumes, using different lengths of PCR amplicon, and nuclear and mitochondrial genes. In comparison with a commercial kit, an equivalent yield of DNA extraction was achieved with fewer steps. Room-temperature preservation for 1 month was demonstrated for captured DNA, facilitating straightforward collection, delivery, and handling of genomic DNA in an environment-friendly protocol.
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Affiliation(s)
- D Kalyanasundaram
- Department of Mechanical Engineering, University of Washington, Seattle, WA 98195, USA
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Lee SB, Clabaugh KC, Silva B, Odigie KO, Coble MD, Loreille O, Scheible M, Fourney RM, Stevens J, Carmody GR, Parsons TJ, Pozder A, Eisenberg AJ, Budowle B, Ahmad T, Miller RW, Crouse CA. Assessing a novel room temperature DNA storage medium for forensic biological samples. Forensic Sci Int Genet 2012; 6:31-40. [DOI: 10.1016/j.fsigen.2011.01.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2009] [Revised: 12/21/2010] [Accepted: 01/17/2011] [Indexed: 01/27/2023]
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