Article
Biochemical Research Methods
Peng Shen, Xiaojun Qu, Qinyu Ge, Ting Huang, Qingjiang Sun, Zuhong Lu
Summary: DNA is an appealing medium for long-term data storage due to its high density, ease of copying, sustainability, and longevity. This study presents the construction of a magnetic bead spherical nucleic acid (MB-SNA) composite microstructure, which serves as a cost-effective platform for reliable DNA preservation and repeated reading. The findings demonstrate that the MB-SNA microstructure achieves high-capacity storage, reliable preservation, and repeated reading with high accuracy.
ACS SYNTHETIC BIOLOGY
(2023)
Review
Chemistry, Analytical
Siyu Chen, Bo Gong, Cong Zhu, Chunyang Lei, Zhou Nie
Summary: Nucleic acid molecules possess attractive properties for biosensing and bioimaging due to their high designability and structural predictability. CRISPR-Cas systems, with high programmability and flexibility, recognize and cleave nucleic acid targets and have been engineered as multifunctional tools. Integration of nucleic acids with CRISPR-Cas systems has advanced biosensing and bioimaging methodologies, holding great promise in biochemical research and clinical diagnosis.
TRAC-TRENDS IN ANALYTICAL CHEMISTRY
(2023)
Review
Chemistry, Multidisciplinary
Huating Kong, Bo Sun, Feng Yu, Qisheng Wang, Kai Xia, Dawei Jiang
Summary: DNA is a robust material with unique properties, making it suitable for building various nanoscale structures and devices. Structural DNA nanotechnology has found applications in computing, photonics, synthetic biology, biosensing, bioimaging, and therapeutic delivery. The goal of structural DNA nanotechnology is to use DNA molecules to construct three-dimensional crystals as molecular scaffolds for precise alignment and collection of desired molecules. This review showcases different 3D DNA crystals, discussing their design, optimization, applications, and crystallization conditions, as well as the history of nucleic acid crystallography and potential future directions in the era of nanotechnology.
Article
Biochemistry & Molecular Biology
Peter M. Abuja, Daniela Pabst, Benjamin Bourgeois, Martina Loibner, Christine Ulz, Iris Kufferath, Ulrike Fackelmann, Cornelia Stumptner, Rainer Kraemer, Tobias Madl, Kurt Zatloukal
Summary: Molecular diagnostics in healthcare is increasingly dependent on high-quality nucleic acids obtained from appropriately preserved tissue specimens. This study establishes a method for measuring residual water in fixed paraffin-embedded tissue and demonstrates its correlation with the performance of nucleic acids in qRT-PCR analysis. Improving the shelf life of fixed tissue requires meticulous dehydration and dry storage to minimize the degradative influence of residual water on nucleic acids.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Chemistry, Multidisciplinary
Fei Ding, Shuangye Zhang, Qian Chen, Hao Feng, Zhilei Ge, Xiaolei Zuo, Chunhai Fan, Qian Li, Qiang Xia
Summary: Programmable nucleic acid nanotechnology allows the customization of synthetic nucleic acid nanodevices with unprecedented precision, showing potential for precise immunoengineering.
Article
Chemistry, Analytical
Rachelle Turiello, Leah M. Dignan, Brayton Thompson, Melinda Poulter, Jeff Hickey, Jeff Chapman, James P. Landers
Summary: This article describes an automatable rotationally driven microfluidic platform for efficient extraction of SARS-CoV-2 RNA from multiple sample types. The method enables rapid enrichment and extraction of RNA, allowing reliable detection of SARS-CoV-2 using real-time RT-PCR.
ANALYTICAL CHEMISTRY
(2022)
Article
Biology
Hajime Shinoda, Tatsuya Iida, Asami Makino, Mami Yoshimura, Junichiro Ishikawa, Jun Ando, Kazue Murai, Katsumi Sugiyama, Yukiko Muramoto, Masahiro Nakano, Kotaro Kiga, Longzhu Cui, Osamu Nureki, Hiroaki Takeuchi, Takeshi Noda, Hiroshi Nishimasu, Rikiya Watanabe
Summary: opn-SATORI is an automated amplification-free digital RNA detection platform that utilizes CRISPR-Cas13a and microchamber device to complete the detection process from sample mixing to RNA quantification in a short period of time. It is capable of detecting SARS-CoV-2 genomic RNA with a low limit of detection and discriminating between variants with high accuracy.
COMMUNICATIONS BIOLOGY
(2022)
Review
Biochemistry & Molecular Biology
Ousama Al Shanaa, Andrey Rumyantsev, Elena Sambuk, Marina Padkina
Summary: This review discusses the early stages, main developments, and latest technologies of RNA aptamer research, emphasizing the advantages of RNA aptamers compared to antibodies and their potential applications in the near future.
Article
Biotechnology & Applied Microbiology
Myrsini Sakarika, Frederiek-Maarten Kerckhof, Lotte Van Peteghem, Alexandra Pereira, Tim van den Bossche, Robbin Bouwmeester, Ralf Gabriels, Delphi Van Haver, Barbara Ulcar, Lennart Martens, Francis Impens, Nico Boon, Ramon Ganigue, Korneel Rabaey
Summary: In this study, the impact of cultivation conditions on microbial biomass was investigated. It was found that low growth rates resulted in biomass with decreased nucleic acid and increased protein content, while high growth rates led to larger cells that could facilitate more efficient biomass harvesting. The proteome allocation varied with different growth rates, with more ribosomal proteins at higher rates. Variations in amino acid abundance across different cellular components affected the product quality, with higher cysteine and phenylalanine content at low growth rates. The study suggests that targeted growth rates could potentially eliminate the need for costly external amino acid supplements.
MICROBIAL CELL FACTORIES
(2023)
Article
Chemistry, Analytical
Tong Luo, Jiacheng Li, Yao He, Hui Liu, Zhiwei Deng, Xi Long, Qingqing Wan, Jiacheng Ding, Zan Gong, Yanjing Yang, Shian Zhong
Summary: In this study, we developed a novel CRISPR-based biosensor by combining CRISPR/Cas12a with Au-nanobeacon, which allows for direct and rapid detection of nucleic acids in complex biological fluids with high sensitivity.
ANALYTICAL CHEMISTRY
(2022)
Article
Biochemistry & Molecular Biology
Nicole L. Welch, Meilin Zhu, Catherine Hua, Juliane Weller, Marzieh Ezzaty Mirhashemi, Tien G. Nguyen, Sreekar Mantena, Matthew R. Bauer, Bennett M. Shaw, Cheri M. Ackerman, Sri Gowtham Thakku, Megan W. Tse, Jared Kehe, Marie-Martine Uwera, Jacqueline S. Eversley, Derek A. Bielwaski, Graham McGrath, Joseph Braidt, Jeremy Johnson, Felecia Cerrato, Gage K. Moreno, Lydia A. Krasilnikova, Brittany A. Petros, Gabrielle L. Gionet, Ewa King, Richard C. Huard, Samantha K. Jalbert, Michael L. Cleary, Nicholas A. Fitzgerald, Stacey B. Gabriel, Glen R. Gallagher, Sandra C. Smole, Lawrence C. Madoff, Catherine M. Brown, Matthew W. Keller, Malania M. Wilson, Marie K. Kirby, John R. Barnes, Daniel J. Park, Katherine J. Siddle, Christian T. Happi, Deborah T. Hung, Michael Springer, Bronwyn L. MacInnis, Jacob E. Lemieux, Eric Rosenberg, John A. Branda, Paul C. Blainey, Pardis C. Sabeti, Cameron Myhrvold
Summary: A microfluidic CRISPR-based platform called mCARMEN enables multiplexed and high-throughput identification of a wide range of respiratory viruses, including specific SARS-CoV-2 variants. The platform combines cost-effectiveness, diagnostic-grade performance, and a streamlined workflow for clinical use.
Article
Biochemistry & Molecular Biology
Bartosz Adamczyk, Michal Zurkowski, Marta Szachniuk, Tomasz Zok
Summary: WebTetrado is a web server for analyzing quadruplex structures, providing a user-friendly interface and many advanced features such as automatic identification, annotation, classification, and visualization of the motifs. It supports various types of quadruplexes and can process 3D models from experimental or in silico sources.
NUCLEIC ACIDS RESEARCH
(2023)
Review
Biotechnology & Applied Microbiology
Jingwen Wang, Han Jiang, Leiming Pan, Xiuying Gu, Chaogeng Xiao, Pengpeng Liu, Yulong Tang, Jiehong Fang, Xiaoqian Li, Chenze Lu
Summary: As nucleic acid testing becomes crucial in various research fields, there is an increasing demand for rapid on-site testing methods. This review discusses recent advances in on-chip methods for sample preparation, amplification, and detection in the nucleic acid testing procedure. It covers integration strategies for sample preparation, various on-chip amplification methods, and evaluation of potential detection methods. The review also highlights the importance of improving the speed and integration of all steps onto a single chip for future developments in nucleic acid testing.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Review
Biochemistry & Molecular Biology
Furong Zhao, Siying Xie, Bingzhi Li, Xing Zhang
Summary: This review discusses the roles of carbohydrates and glycoconjugates in organisms and the applications of FNAs-based biosensors in detecting disease-related substances. By summarizing construction strategies and biosensing applications, challenges and development opportunities in this area are highlighted.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2022)
Article
Biochemistry & Molecular Biology
Tina Y. Liu, Gavin J. Knott, Dylan C. J. Smock, John J. Desmarais, Sungmin Son, Abdul Bhuiya, Shrutee Jakhanwal, Noam Prywes, Shreeya Agrawal, Maria Diaz de Leon Derby, Neil A. Switz, Maxim Armstrong, Andrew R. Harris, Emeric J. Charles, Brittney W. Thornton, Parinaz Fozouni, Jeffrey Shu, Stephanie Stephens, G. Renuka Kumar, Chunyu Zhao, Amanda Mok, Anthony T. Iavarone, Arturo M. Escajeda, Roger McIntosh, Shin E. Kim, Eli J. Dugan, Katherine S. Pollard, Ming X. Tan, Melanie Ott, Daniel A. Fletcher, Liana F. Lareau, Patrick D. Hsu, David F. Savage, Jennifer A. Doudna
Summary: The direct, amplification-free detection of RNA through CRISPR nucleases enables rapid and sensitive RNA detection, particularly suitable for point-of-care infection diagnosis.
NATURE CHEMICAL BIOLOGY
(2021)