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An alternative photo-cross-linker having a d-threoninol skeleton instead of the 2'-deoxyribose backbone in 3-cyanovinylcarbazole (K) was investigated to improve the photoreactivity of photo-cross-linkers; the photo-cross-linking rate of 3-cyanovinylcarbazole with d-threoninol (D) was found to be greater than that of K. Therefore, in this study, a novel photo-cross-linker having pyranocarbazole (X) and d-threoninol instead of the 2'-deoxyribose backbone in X (D) was developed. The D in double-stranded DNA photo-cross-linked to a pyrimidine base at the -1 position of a complementary strand similar to X. Furthermore, the photoreactivity of D was significantly higher than that of X. The introduction of d-threoninol improved the reactivity of pyranocarbazole to cytosine, the use of D may extend the applicability of the photo-cross-linking reaction for DNA manipulation. In particular, this novel photo-cross-linker can contribute to the photochemical regulation of gene expression or biological events in a living cell.
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http://dx.doi.org/10.1039/c9ra06145b | DOI Listing |
Int J Mol Sci
July 2025
Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, 8 Akad. Lavrentyeva Ave., 630090 Novosibirsk, Russia.
Modified oligonucleotides (oligos) are widely used as convenient tools in many scientific fields, including biomedical applications and therapies. In particular, oligos with lipophilic groups attached to the backbone ensure penetration of the cell membrane without the need for transfection. This study examines the interaction between amphiphilic DNA duplexes, in which one of the chains contains a lipophilic substituent, and several DNA repair proteins, particularly DNA-damage-dependent PARPs, using various biochemical approaches.
View Article and Find Full Text PDFCurr Issues Mol Biol
July 2025
Research and Higher Education Center of UNEPROP, Hermosillo 83105, Mexico.
The dynamic phosphorylation of the human RNA Pol II CTD establishes a code applicable to all eukaryotic transcription processes. However, the ability of these specific post-translational modifications to convey molecular signals through structural changes remains unclear. We previously explained that each gene can be modeled as a combination of n circuits connected in parallel.
View Article and Find Full Text PDFJ Phys Chem B
August 2025
Department of Materials Chemistry, Nagoya University, Nagoya 464-8603, Japan.
Nucleic acid therapies have emerged as promising treatments for various diseases associated with aberrant gene expression. Cationic lipid-nucleic acid complexes (lipoplexes) remain at the forefront of such therapeutic approaches as drug delivery carriers. To facilitate the study of these carriers through coarse-grained molecular dynamics (CG-MD) simulations, we extend our surface property fitting coarse-grained (SPICA) force field to develop a reliable DNA model with enhanced compatibility with lipids.
View Article and Find Full Text PDFSpectrochim Acta A Mol Biomol Spectrosc
December 2025
IMMM - UMR 6283 CNRS, Le Mans Université, Avenue Olivier Messiaen, 72085 Le Mans, Cedex 9, France; Nanobiophotonics and Laser Microspectroscopy Center, Interdisciplinary Research Institute in Bio-Nano-Sciences, Babes-Bolyai University, 42 T. Laurian Str., 400271 Cluj-Napoca, Romania; Department of
Aptamers are single-stranded DNA or RNA oligonucleotides with a unique secondary structure. Target binding induces conformational changes in the secondary structure. Conformation-induced changes in some characteristic Raman bands of DNA aptamer, upon binding to aflatoxin B1 (AFB1), were probed using surface enhanced Raman spectroscopy (SERS).
View Article and Find Full Text PDFJ Phys Chem B
May 2025
Department of Chemical and Biological Sciences, National Institute of Technology Meghalaya, Saitsophen, Sohra (Cherrapunjee), 793108, India.
Oxidative damage to DNA has significant consequences for human health and is identified as one of the key contributors to the onset and advancement of several diseases. Therefore, it is crucial to prevent oxidatively driven DNA lesions in both humans and other organisms. This study investigated the potential of daphnetin to protect DNA from oxidative damage and its binding interaction with calf thymus DNA (ct-DNA) employing multispectroscopic techniques, viscosity measurements, gel electrophoresis, docking studies, and molecular dynamics (MD) simulation.
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