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Melting transition of oriented Li-DNA fibers submerged in ethanol solutions.
Biopolymers
March 2021
Université de Lyon, Ecole Normale Supérieure de Lyon, Laboratoire de Physique, CNRS, UMR 5672, Lyon, France.
The melting transition of Li-DNA fibers immersed in ethanol-water solutions has been studied using calorimetry and neutron diffraction techniques. The data have been analyzed using the Peyrard-Bishop-Dauxois model to determine the strengths of the intra- and inter-base pair potentials. The data and analysis show that the potentials are weaker than those for DNA in water.
View Article and Find Full Text PDFImprovement of a miRNA inhibitor by intracellular selection.
Biosci Biotechnol Biochem
July 2020
Department of Bioengineering, Graduate School of Engineering, Osaka City University, Osaka, Japan.
Unlabelled: Sequences surrounding the miRNA binding domain of the miRNA inhibitor LidNA were selected intracellularly. The library was transfected into cells, and then, inhibitors that were associated with argonaute 2 were selected. The potent inhibitors were slowly degraded intracellularly, while the lower-activity inhibitors were rapidly degraded.
View Article and Find Full Text PDFStructural improvement of LidNA: delta-type LidNA is a potent miRNA inhibitor constructed with unmodified DNA.
Biosci Biotechnol Biochem
June 2020
Department of Bioengineering, Graduate School of Engineering, Osaka City University, Osaka, Japan.
Many miRNA inhibitors have been developed, including chemically modified oligonucleotides, such as 2'--methylated RNA and locked nucleic acid (LNA). Unmodified DNA has not yet been reported as a miRNA inhibitor due to relatively low DNA/miRNA binding affinity. We designed a structured DNA, LidNA, which was constructed with unmodified DNA, consisting of a complementary sequence to the target miRNA flanked by two structured DNA regions, such as double-stranded DNA.
View Article and Find Full Text PDFBinding affinity of ssDNA is improved by attachment of dsDNA regions.
J Biosci Bioeng
September 2014
Department of Bioengineering, Graduate School of Engineering, Osaka City University, Sugimoto 3-3-138, Sumiyoshi-ku, Osaka 558-8585, Japan.
LidNA, a microRNA inhibitor consisting of a microRNA binding ssDNA region sandwiched between dsDNA regions had higher affinity to target oligonucleotides than that without dsDNA region. This enhancement in affinity was found to be owing to the suppressed mobility of ssDNA region by the presence of dsDNA regions.
View Article and Find Full Text PDFConformational transitions of the phosphodiester backbone in native DNA: two-dimensional magic-angle-spinning 31P-NMR of DNA fibers.
Biophys J
September 1997
Division of Physical Chemistry, Arrhenius Laboratory, University of Stockholm, Sweden.
Solid-state 31P-NMR is used to investigate the orientation of the phosphodiester backbone in NaDNA-, LiDNA-, MgDNA-, and NaDNA-netropsin fibers. The results for A- and B-DNA agree with previous interpretations. We verify that the binding of netropsin to NaDNA stabilizes the B form, and find that in NaDNA, most of the phosphate groups adopt a conformation typical of the A form, although there are minor components with phosphate orientations close to the B form.
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