In this work we use a combination of 3D-TEM tomography, energy filtered TEM, single molecule DNA translocation experiments, and numerical modeling to show a more precise relationship between nanopore shape and ionic conductance and show that changes in geometry while in solution can account for most deviations between predicted and measured conductance. We compare the structural stability of ion beam sculpted (IBS), IBS-annealed, and TEM drilled nanopores. We demonstrate that annealing can significantly improve the stability of IBS made pores. Furthermore, the methods developed in this work can be used to predict pore conductance and current drop amplitudes of DNA translocation events for a wide variety of pore geometries. We discuss that chemical dissolution is one mechanism of the geometry change for SiNx nanopores and show that small modification in fabrication procedure can significantly increase the stability of IBS nanopores.
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http://dx.doi.org/10.1088/0957-4484/26/4/044001 | DOI Listing |
We lack tools to edit DNA sequences at scales necessary to study 99% of the human genome that is noncoding. To address this gap, we applied CRISPR prime editing to insert recombination handles into repetitive sequences, up to 1697 per cell line, which enables generating large-scale deletions, inversions, translocations, and circular DNA. Recombinase induction produced more than 100 stochastic megabase-sized rearrangements in each cell.
View Article and Find Full Text PDFACS Appl Mater Interfaces
January 2025
Division of Micro and Nanosystems, KTH Royal Institute of Technology, Malvinas väg 10, Stockholm 100 44, Sweden.
Solid-state nanopores offer unique possibilities for biomolecule sensing; however, scalable production of sub-5 nm pores with precise diameter control remains a manufacturing challenge. In this work, we developed a scalable method to fabricate sub-5 nm nanopores in silicon (Si) nanomembranes through metal-assisted chemical etching (MACE) using gold nanoparticles. Notably, we present a previously unreported self-limiting effect that enables sub-5 nm nanopore formation from both 10 and 40 nm nanoparticles in the 12 nm thick monocrystalline device layer of a silicon-on-insulator substrate.
View Article and Find Full Text PDFBiochem Genet
January 2025
Department of Physiology, University of Louisville School of Medicine, Louisville, KY, 40202, USA.
Although DNA methyltransferase 1 (DNMT1) and RNA editor ADAR triplications exist in Down syndrome (DS), their specific roles remain unclear. DNMT methylates DNA, yielding S-adenosine homocysteine (SAH), subsequently converted to homocysteine (Hcy) and adenosine by S-adenosine homocysteine (Hcy) hydrolase (SAHH). ADAR converts adenosine to inosine and uric acid.
View Article and Find Full Text PDFGigascience
January 2025
Leibniz Institute for the Analysis of Biodiversity Change, Museum Koenig Bonn, 53113 Bonn, Germany.
Background: In this study, we present an in-depth analysis of the Eurasian minnow (Phoxinus phoxinus) genome, highlighting its genetic diversity, structural variations, and evolutionary adaptations. We generated an annotated haplotype-phased, chromosome-level genome assembly (2n = 50) by integrating high-fidelity (HiFi) long reads and chromosome conformation capture data (Hi-C).
Results: We achieved a haploid size of 940 megabase pairs (Mbp) for haplome 1 and 929 Mbp for haplome 2 with high scaffold N50 values of 36.
Stem Cell Res Ther
January 2025
College & Hospital of Stomatology, Key Laboratory of Oral Diseases Research of Anhui Province, Anhui Medical University, Hefei, 230032, China.
Background: The aging of bone marrow mesenchymal stem cells (BMSCs) impairs bone tissue regeneration, contributing to skeletal disorders. LncRNA NEAT1 is considered as a proliferative inhibitory role during cellular senescence, but the relevant mechanisms remain insufficient. This study aims to elucidate how NEAT1 regulates mitotic proteins during BMSCs aging.
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