2'-O-Methyl oligoribonucleotides with four kinds of 2'-O-modified uridine derivatives were synthesised. Their duplex stability, hydration behavior and exonuclease resistance were studied by spectroscopic analyses and molecular dynamics simulations. Consequently, 2'-O-modification of the uridine residue with 2-carbamoylethyl or 2-(N-methylcarbamoyl)ethyl groups resulted in a significant improvement of the exonuclease resistance without the loss of duplex stability.
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http://dx.doi.org/10.1039/c4ob01260g | DOI Listing |
Redox Biol
January 2025
University of Chicago, Department of Molecular Genetics and Cell Biology, 929 E. 57th Street, Chicago, IL, 60637, USA. Electronic address:
During its catalytic cycle, the homodimeric ATPase topoisomerase II alpha (TOP2A) cleaves double stranded DNA and remains covalently bound to 5' ends via tyrosine phosphodiester bonds. After passing a second, intact duplex through, TOP2A rejoins the break and releases from the DNA. Thereby, TOP2A can relieve strain accumulated during transcription, replication and chromatin remodeling and disentangle sister chromatids for mitosis.
View Article and Find Full Text PDFBiosens Bioelectron
January 2025
Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Sichuan Province Engineering Technology Research Center of Molecular Diagnosis of Clinical Diseases, Molecular Diagnosis of Clinical Diseases Key Laboratory of Luzhou, Sichuan, 646000, China. Electronic address:
Colorectal cancer (CRC) is a leading cause of cancer-related deaths globally, necessitating the development of sensitive and minimally invasive diagnostic approaches. In this study, we present a novel diagnostic strategy by integrating dumbbell probe-mediated CRISPR/Cas13a with nicking-induced DNA cascade reaction (DP-bridged Cas13a/NDCR) for highly sensitive microRNA (miRNA) detection. Target miRNA triggers Cas13a-mediated cleavage of the dumbbell probe, releasing an intermediate strand that hybridizes with a methylene blue-labeled hairpin probe on the electrode surface.
View Article and Find Full Text PDFJ Phys Chem B
January 2025
Department of Physics of Complex Systems, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700106, India.
In DNA double helices, Hoogsteen (HG) base pairing is an alternative mode of Watson-Crick (WC) base pairing. HG bp has a different hydrogen bonding pattern than WC bp. We investigate here the binding energy of homeodomain proteins with a HG-DNA duplex, where DNA adopts a HG bp in its sequence.
View Article and Find Full Text PDFCommun Chem
January 2025
Chemistry of Functional Molecules, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki, Japan.
Psoralen-conjugated triplex-forming oligonucleotides (Ps-TFOs) have been employed for the photodynamic regulation of gene expression by the photo-cross-linking of psoralen with the target DNA. However, stable triplex formation requires a consecutive purine base sequence in one strand of the target DNA duplexes. The pyrimidine-base interruption in the consecutive purine base sequence drastically decreases the thermodynamic stability of the corresponding triplex, which hampers the TFO application.
View Article and Find Full Text PDFACS Macro Lett
January 2025
Department of Physics, Kent State University, Kent, Ohio 44242, United States.
We investigate the impact of poly adenine (poly-A) sequences on the type and stability of liquid crystalline (LC) phases formed by concentrated solutions of gapped DNA (two duplex arms bridged by a flexible single strand) using synchrotron small-angle X-ray scattering and polarizing optical microscopy. While samples with mixed sequence form layered (smectic) phases, poly-A samples demonstrate a columnar phase at lower temperatures (5-35 °C), not previously observed in GDNA samples, and a smectic-B phase of exceptional stability at higher temperatures (35-65 °C). We present a model that connects the formation of these LC phases with the unique characteristics of poly-A sequences, which manifest in various biological contexts, including DNA condensation and nucleosome formation.
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