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An isoindoline-nitroxide derivative of guanine (Ǵ, "G-spin") was shown to bind specifically and effectively to abasic sites in duplex RNAs. Distance measurements on a Ǵ-labeled duplex RNA with PELDOR (DEER) showed a strong orientation dependence. Thus, Ǵ is a readily synthesized, orientation-selective spin label for "mix and measure" PELDOR experiments.
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http://dx.doi.org/10.1039/c6cc08387k | DOI Listing |
J Mol Biol
March 2025
Department of Chemistry and Biochemistry University of California, Los Angeles Los Angeles, CA 90095-1569.
I am Distinguished Professor in the Chemistry and Biochemistry Department at University of California, Los Angeles, where I was hired in 1985 as the first female assistant professor in the department. I received my PhD from University of California, San Diego, under the guidance of Professor David Kearns, where I used NMR spectroscopy to study drug binding to random sequence DNA and published the first two-dimensional NMR spectra of short synthetic DNA duplexes. From 1982-1985 I was a Damon Runyon-Walter Winchell Postdoctoral fellow in the Professor Alexander Rich laboratory, where I investigated structures of Z-DNA by NMR.
View Article and Find Full Text PDFNat Commun
March 2025
Institute of Biotechnology, National Taiwan University, Taipei, Taiwan.
Helper-component proteinase (HC-Pro), encoded by potyviruses, function as viral suppressors of RNA silencing (VSRs). Despite their conserved role, HC-Pros share approximately 40% similarity, implying potential differences in VSR efficiency, particularly in their ability to inhibit HEN1 methyltransferase activity. This study investigated the inhibitory potential of HC-Pros from different potyviruses in transgenic plants.
View Article and Find Full Text PDFBiochemistry
March 2025
Department of Biology, Tufts University, Medford, Massachusetts 02130, United States.
Gp2.5, an essential single-stranded DNA-binding protein encoded by bacteriophage T7, is integral to various steps of DNA metabolism. Unlike other single-stranded DNA binding proteins, it greatly facilitates the annealing of complementary DNA strands.
View Article and Find Full Text PDFCommun Biol
March 2025
Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, ul. Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland.
Although the existence of overlapping protein-coding genes in eukaryotic genomes is known for decades, their role in regulating expression remains far from fully understood. Here, the mechanism regulating the expression of head-to-head overlapping genes, a pair of INO80E and HIRIP3 genes is presented. Based on a series of experiments, we show that the expression of these genes is strongly dependent on sense/antisense interactions.
View Article and Find Full Text PDFJ Phys Chem B
March 2025
Department of High-Fidelity Model Acceleration Research, Division of National Supercomputing, Korea Institute of Science and Technology Information, Daejeon 34141, Republic of Korea.
This study investigates the thermodynamic parameters of 1300 RNA/DNA hybrid duplexes, including both natural and chemically modified forms, using molecular dynamics (MD) simulations. Modified duplexes consist of phosphorothioate (PS) backbones and 2'--methoxyethyl (MOE) modifications, both commonly used in therapeutic oligonucleotides. Hybridization enthalpy and entropy were calculated from MD trajectories using molecular mechanics Poisson-Boltzmann surface area (MMPBSA) and molecular mechanics generalized Born surface area (MMGBSA) approaches.
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