Article
Biochemistry & Molecular Biology
Martin Guhmann, Stefanie Reuter, Jan Hartung, Ralf Mrowka
Summary: Preselection digests are a common strategy to reduce background in molecular cloning, but manually selecting appropriate restriction enzymes is not straightforward. The online tool preselector.uni-jena.de uses regular expressions to identify restriction enzyme recognition sites in DNA sequences provided by users, helping researchers design preselection digestion strategies efficiently.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Richard J. Roberts, Tamas Vincze, Janos Posfai, Dana Macelis
Summary: REBASE is a comprehensive database of information about restriction-modification (RM) system components, providing details on recognition and cleavage sites for restriction enzymes and DNA methyltransferases, their commercial availability, sensitivity to methylation, crystal and sequence data. The database is regularly updated and can be accessed through a website and FTP.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Plant Sciences
Lingping Zhu, Teng Zhang, Teemu H. Teeri
Summary: The study identified two reductase genes involved in sporopollenin biosynthesis in gerbera, with functions similar to an Arabidopsis reductase gene. In addition to these two reductase genes, another reductase gene in gerbera plays a crucial role in pollen development.
HORTICULTURE RESEARCH
(2021)
Review
Chemistry, Inorganic & Nuclear
Mateusz D. Tomczyk, Nikodem Kuznik, Krzysztof Walczak
Summary: The first part of the review summarizes more than three decades of research on cyclen complexes that exhibit hydrolytic or transesterification activity against phosphodiesters. The second part focuses on complexes that cleave phosphodiesters oxidatively. The review includes results for nearly 200 examples of metal complexes of cyclen and its derivatives, as well as metal-free catalysts based on the cyclen scaffold.
COORDINATION CHEMISTRY REVIEWS
(2023)
Article
Biochemistry & Molecular Biology
Maliha Tasnim, T. Jacob Selph, Jason Olcott, Jonathon T. Hill
Summary: In this study, it was found that the Type-IIS restriction enzyme MmeI, which recognizes the asymmetric sequence TCCRAC, can cut across a double-strand break (DSB). The efficiency of cutting depends on both overhang length and temperature.
MOLECULAR BIOLOGY REPORTS
(2023)
Article
Biochemistry & Molecular Biology
Rui Cheng, Fengtao Huang, Hui Wu, Xuelin Lu, Yan Yan, Bingbing Yu, Xionglue Wang, Bin Zhu
Summary: The arms race between bacteria and phages has driven the development of bacterial defense systems, with the GajA protein from the Gabija system showcasing a unique sequence-specific DNA nicking endonuclease activity regulated by nucleotide concentration. This mechanism allows for the suppression of endonuclease activity under normal conditions, activating it only when NTP and dNTP are depleted during phage invasion.
NUCLEIC ACIDS RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Branko Rihtman, Richard J. Puxty, Alexia Hapeshi, Yan-Jiun Lee, Yuanchao Zhan, Slawomir Michniewski, Nicholas R. Waterfield, Feng Chen, Peter Weigele, Andrew D. Millard, David J. Scanlan, Yin Chen
Summary: Marine bacterial viruses, particularly those infecting the marine roseobacter clade, play a significant role in microbial diversity, ecosystem function, and host evolution. The discovery of unique phages with dU-containing DNA suggests the establishment of a novel family (Naomiviridae), indicating their global importance and diversity in comparison to other well-known bacteriophages like Podoviridae in the oceans.
Article
Biochemistry & Molecular Biology
Brandi A. Buckner, Ashley M. Lato, Shawn R. Campagna, Diana M. Downs
Summary: The Rid protein family is divided into nine subfamilies, with RutC being the founding member of one subfamily. RutC was found to have 3-aminoacrylate deaminase activity and play a role in facilitating certain reactions. Compared to other Rid proteins, RutC showed similarities and differences in substrate specificity.
JOURNAL OF BIOLOGICAL CHEMISTRY
(2021)
Review
Chemistry, Physical
Reuben B. Leveson-Gower, Gerard Roelfes
Summary: Friedel-Crafts alkylation and acylation reactions are important in synthetic and industrial chemistry. Researchers have expanded the application of these reactions through directed evolution and created bio-hybrid catalysts. This review summarizes these efforts and discusses future routes for more efficient and benign Friedel-Crafts reactions.
Article
Chemistry, Multidisciplinary
Tsuyoshi Mashima, Bas J. H. M. Rosier, Koji Oohora, Tom F. A. de Greef, Takashi Hayashi, Luc Brunsveld
Summary: Hexameric hemoprotein (HTHP) is used as a scaffold protein for the assembly and activation of the apoptotic signalling enzyme caspase-9, employing short DNA elements for modular recruitment domains. This allows for advanced control over protein assembly and activity state.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Multidisciplinary Sciences
Agnieszka M. Murakami, Katsuhiro Nagatomo, Ichro Miyoshi, Shirou Itagaki, Yasutaka Niwa, Manabu Murakami
Summary: A new method was developed to analyze protein-protein interactions using a dual-inducible prokaryotic expression system. This method involved constructing a chimeric fusion toxin gene to evaluate protein-protein binding. The study identified a new binding site in a voltage-dependent calcium channel.
SCIENTIFIC REPORTS
(2023)
Article
Nanoscience & Nanotechnology
Rong Ni, Ruilu Feng, Ying Chau
Summary: Nonviral vectors are a safer alternative to viral vectors for gene therapy, and artificial viruses combining viral and nonviral vector strengths have emerged as safe and efficient gene delivery vectors. In this study, peptide-DNA coassembled nanoparticles were developed as a new efficient vector for gene delivery, achieving high transfection efficiency through the introduction of rationally designed functional short peptide modules. These nanoparticles achieved over 90% transfection efficiency in a serum-containing medium. This work demonstrates the effectiveness of the module-based design approach and lays the groundwork for potential biomedical applications of peptide-based biomaterials.
ACS APPLIED NANO MATERIALS
(2023)
Article
Chemistry, Multidisciplinary
Yunqi Yang, Qinyi Lu, Yu Chen, Marcello DeLuca, Gaurav Arya, Yonggang Ke, Stefan Zauscher
Summary: DNA nanotechnology allows for the creation of precise and tunable nanostructures for biomedical applications. However, the stability of these structures is compromised in biological environments due to degradation by nucleases. This study demonstrates a strategy to enhance the stability of the structures by utilizing enzymatic polymerization to grow polynucleotide brushes on DNA nanostructures. The ability to control the spatial and temporal growth of these brushes offers potential applications in drug delivery and supramolecular assembly.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2023)
Article
Chemistry, Multidisciplinary
Xiaojin Zhang, Yichuan Wang, Yu Dai, Fan Xia
Summary: We fabricated peptide-nanoparticle conjugates (AuNP@CDs-Azo-peptide) by the self-assembly of cyclodextrin-capped gold nanoparticles (AuNP@CDs) and azobenzene-terminated peptide (Azo-peptide) through host-guest interactions. AuNP@CDs-Azo-peptide exhibits hydrolase-like activity, which can be tuned by amino acid sequences.
Article
Biophysics
Jeanne E. van Dongen, Johanna T. W. Berendsen, Jan C. T. Eijkel, Loes Segerink
Summary: Research shows that by using restriction enzymes in combination with Cas12a for in vitro experiments, it is possible to differentiate the methylation levels of single CpG sites in DNA. This method works by digesting non-methylated sequences, influencing R-loop formation, and determining methylation positions through collateral trans-cleavage activity. The modularity of Cas12a and MSRE in the sensing method provides high versatility for studying single CpG methylation sites in disease detection.
BIOSENSORS & BIOELECTRONICS
(2021)