Sensitive analysis of single nucleotide variation by Cas13d orthologs, EsCas13d and RspCas13d

Precipitation of Magnetic Iron Oxide Induced by Sporosarcina pasteurii Cells

Sporosarcina pasteurii (S. pasteurii) is bacterium notable for its highly efficient urea degradation ability. Due to its high urease activity, S. pasteurii has been successfully utilized in applications including solidifying soil or sand, termed “bio-concrete”. In addition to calcium carbonate precipitation, urease isolated from the jack bean plant was recently demonstrated to induce the formation of magnetic iron oxide particles from soluble ferrous ion in a designed reaction. However, it remained unknown if a similar magnetic material could be formed using whole cells with high urease activity under biocompatible conditions. Here, we demonstrated that magnetic iron oxide with a highly ordered structure could be formed on the surface of S. pasteurii cells with a theoretical product of 1.17 mg in a 2-mL reaction. Moreover, the cells surrounded by the precipitated magnetic iron oxide maintained their viability. Due to the simple cultivation of S. pasteurii, the process developed in this study could be useful for the green synthesis of magnetic iron oxide, basic research on the mechanism of magnetic microbial-induced precipitation (MIP), and related engineering applications.

Accurate genotyping of fragmented DNA using a toehold assisted padlock probe

Using Artificial Neural Networks to Model Errorsin Biochemical Manipulation of DNA Molecules

Construction of a system for single-stranded DNA isolation

A mixed culture of bacterial cells enables an economic DNA storage on a large scale

Low-Bias Manipulation of DNA Oligo Pool for Robust Data Storage

Emerging Methods for Efficient and Extensive Incorporation of Non-canonical Amino Acids Using Cell-Free Systems

Current and Emerging Methods for the Synthesis of Single-Stranded DNA

Methods for synthesizing arbitrary single-strand DNA (ssDNA) fragments are rapidly becoming fundamental tools for gene editing, DNA origami, DNA storage, and other applications. To meet the rising application requirements, numerous methods have been developed to produce ssDNA. Some approaches allow the synthesis of freely chosen user-defined ssDNA sequences to overcome the restrictions and limitations of different length, purity, and yield. In this perspective, we provide an overview of the representative ssDNA production strategies and their most significant challenges to enable the readers to make informed choices of synthesis methods and enhance the availability of increasingly inexpensive synthetic ssDNA. We also aim to stimulate a broader interest in the continued development of efficient ssDNA synthesis techniques and improve their applications in future research.

Dynamic Genome Editing Using In Vivo Synthesized Donor ssDNA in Escherichia coli

As a key element of genome editing, donor DNA introduces the desired exogenous sequence while working with other crucial machinery such as CRISPR-Cas or recombinases. However, current methods for the delivery of donor DNA into cells are both inefficient and complicated. Here, we developed a new methodology that utilizes rolling circle replication and Cas9 mediated (RC-Cas-mediated) in vivo single strand DNA (ssDNA) synthesis. A single-gene rolling circle DNA replication system from Gram-negative bacteria was engineered to produce circular ssDNA from a Gram-positive parent plasmid at a designed sequence in Escherichia coli. Furthermore, it was demonstrated that the desired linear ssDNA fragment could be cut out using CRISPR-associated protein 9 (CRISPR-Cas9) nuclease and combined with lambda Red recombinase as donor for precise genome engineering. Various donor ssDNA fragments from hundreds to thousands of nucleotides in length were synthesized in E. coli cells, allowing successive genome editing in growing cells. We hope that this RC-Cas-mediated in vivo ssDNA on-site synthesis system will be widely adopted as a useful new tool for dynamic genome editing.

DNA-Based Bulk Hydrogel Materials and Biomedical Application

Being a natural polymer, DNA attracts extensive attention and possesses great potential to open a new way for researches of biomedical or material science. In the past few decades, approaches have been developed to bring DNA into the realm of bulk materials. In this review, we discussed the progresses achieved for fabrication of novel materials with a large physical dimension from the DNA polymer.