We describe a DNA base pair (bp) stacking driven 3D crystallization of 70-80 nm gold nanospheres (Au NSs) into a large-area, face-centered-cubic (FCC) lattice. Although great advances have been achieved over the past decade, DNA nanoparticle (NP) crystallization has relied solely on the base complementary binding. This limits the accessible crystal size particularly for the larger and heavier Au NPs (>50 nm). In this work, we argue that the use of DNA bp-stacking (so-called blunt-end stacking) instead of complementary binding can widen the scope of controlled interparticle interactions used to assemble larger Au colloids into a larger-area crystal. Through the optimization of the melting transition, relatively large Au NSs (e.g., 75 nm) with nearly ideal roundness can be crystallized into FCC crystals with the area of up to approximately 1400 μm. A strong metallodielectric stopband is experimentally observed in the visible range, confirming the high quality of our self-assembled Au colloidal crystals.
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http://dx.doi.org/10.1021/acs.langmuir.0c00239 | DOI Listing |
Nat Chem
January 2025
State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China.
The synthesis of large RNA with precise modifications at specific positions is in high demand for both basic research and therapeutic applications, but efficient methods are limited. Engineered DNA polymerases have recently emerged as attractive tools for RNA labelling, offering distinct advantages over conventional RNA polymerases. Here, through semi-rational designs, we engineered a DNA polymerase variant and used it to precisely incorporate a diverse range of modifications, including base modifications, 2'-ribose modifications and backbone modifications, into desired positions within RNA.
View Article and Find Full Text PDFStructural variations (SVs) play important roles in genetic diversity, evolution, and carcinogenesis and are, as such, important for human health. However, it remains unclear how spatial proximity of double-strand breaks (DSBs) affects the formation of SVs. To investigate if spatial proximity between two DSBs affects DNA repair, we used data from 3C experiments (Hi-C, ChIA-PET, and ChIP-seq) to identify highly interacting loci on six different chromosomes.
View Article and Find Full Text PDFInt J Syst Evol Microbiol
January 2025
Division of Neurogenetics, Center for Neurological Diseases and Cancer, Nagoya University Graduate School of Medicine, Nagoya, Japan.
Small, obligately anaerobic strains 13CB8C, 13CB11C, 13CB18C and 13GAM1G were isolated from a faecal sample in a patient with Parkinson's disease with a history of duodenal resection. After conducting a comprehensive polyphasic taxonomic analysis including genomic analysis, we propose the establishment of one new genus and four new species. The novel bacteria are sp.
View Article and Find Full Text PDFJ Phys Chem B
January 2025
Institute of Quantitative Biology, College of Life Sciences, and School of Physics, Zhejiang University, Hangzhou, Zhejiang 310058, China.
The emergence of nanopores in two-dimensional (2D) nanomaterials offers an attractive solid-state platform for high-throughput and low-cost DNA sequencing. However, several challenges remain to be addressed before their wide application, including the too-fast DNA translocation speed (compared to state-of-the-art single nucleoside detection techniques) and too large noise/signal ratios due to DNA fluctuations inside the nanopores. Here, we use molecular dynamics (MD) simulations to demonstrate the feasibility of utilizing RNA-DNA interactions in modulating DNA translocations in 2D MoS nanopores.
View Article and Find Full Text PDFChromatin remodeling enzymes play a crucial role in the organization of chromatin, enabling both stability and plasticity of genome regulation. These enzymes use a Snf2-type ATPase motor to move nucleosomes, but how they translocate DNA around the histone octamer is unclear. Here we use cryo-EM to visualize the continuous motion of nucleosomal DNA induced by human chromatin remodeler SNF2H, an ISWI family member.
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