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Sequence-Defined DNA Polymers: New Tools for DNA Nanotechnology and Nucleic Acid Therapy.
Acc Chem Res
January 2025
Department of Chemistry, McGill University, 801 Sherbrooke Street West, Montreal, Quebec H3A 0B8, Canada.
ConspectusStructural DNA nanotechnology offers a unique self-assembly toolbox to construct soft materials of arbitrary complexity, through bottom-up approaches including DNA origami, brick, wireframe, and tile-based assemblies. This toolbox can be expanded by incorporating interactions orthogonal to DNA base-pairing such as metal coordination, small molecule hydrogen bonding, π-stacking, fluorophilic interactions, or the hydrophobic effect. These interactions allow for hierarchical and long-range organization in DNA supramolecular assemblies through a DNA-minimal approach: the use of fewer unique DNA sequences to make complex structures.
View Article and Find Full Text PDFSynergistic Activation of TLR7 and 8 Mediated by Reduction of Electrostatic Repulsion.
Chem Pharm Bull (Tokyo)
November 2024
Graduate School of Pharmaceutical Sciences, The University of Tokyo.
Toll-like receptors (TLRs) play central roles in innate immune defense against infection by binding to microbial molecules. TLR7 and TLR8 are highly homologous sensors with an RNA ligand preference for single-stranded RNA (ssRNA). Recent works reveal that these TLR sense degradation products of RNA at two distinct binding sites, designated 1st site and 2nd site, rather than long ssRNA.
View Article and Find Full Text PDFDMS-MapSeq Analysis of Antisense Oligonucleotide Binding to lncRNA PANDA.
Curr Protoc
November 2024
Harvard Medical School, Microbiology Department, Boston, Massachusetts.
While various methods exist for examining and visualizing the structures of RNA molecules, dimethyl sulfate-mutational profiling and sequencing (DMS-MaPseq) stands out for its simplicity and versatility. This technique has been proven effective for studying RNA structures both in vitro and in complex biological settings. We present an updated protocol of DMS-MaPseq, as well as methodology that enables it to be used for detection of antisense oligonucleotides (ASOs) binding to RNA.
View Article and Find Full Text PDFAromatic residues in the oligonucleotide binding domain are essential to the function of the single-stranded DNA binding protein of Helicobacter pylori.
J Biosci Bioeng
January 2025
Institute of Biotechnology, National Tsing Hua University, Hsinchu, Taiwan. Electronic address:
Single-stranded DNA-binding protein (SSB) is essential to DNA replication, DNA repair, and homologous genetic recombination. Our previous study on the crystal structure of a C-terminally truncated SSB from Helicobacter pylori, HpSSBc, in complex with single-stranded DNA (ssDNA) suggests that several aromatic residues, including Phe37, Phe50, Phe56, and Trp84, were involved in ssDNA binding. To investigate the importance of these aromatic residues, the binding activity of four site-directed HpSSB mutants, including F37A HpSSB, F50A HpSSB, F56A HpSSB, and W84A HpSSB, was compared to that of wild-type HpSSB and HpSSBc by means of electrophoresis mobility shift assay (EMSA), tryptophan quenching fluorescence titration, and surface plasmon resonance (SPR).
View Article and Find Full Text PDFMechanistic Basis for a Single Amino Acid Residue Mutation Causing Human DNA Ligase 1 Deficiency, A Rare Pediatric Disease.
J Mol Biol
November 2024
Department of Biomedical Sciences, Florida State University College of Medicine, Tallahassee, FL 32306, USA. Electronic address:
In mammalian cells, DNA ligase 1 (LIG1) functions as the primary DNA ligase in both genomic replication and single-strand break repair. Several reported mutations in human LIG1, including R305Q, R641L, and R771W, cause LIG1 syndrome, a primary immunodeficiency. While the R641L and R771W mutations, respectively located in the nucleotidyl transferase and oligonucleotide binding domains, have been biochemically characterized and shown to reduce catalytic efficiency, the recently reported R305Q mutation within the DNA binding domain (DBD) remains mechanistically unexplored.
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