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Proflavine, a known intercalator of DNA and RNA, promotes duplex formation by nucleic acids with natural and non-natural backbones that otherwise form duplexes with low thermal stability, and even some that show no sign of duplex formation in the absence of proflavine. These findings demonstrate the potential for intercalators to be used as cofactors for the assembly of rationally designed nucleic acid structures, and could provide fundamental insights regarding intercalation of natural nucleic acid duplexes.
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http://dx.doi.org/10.1039/c6cc00779a | DOI Listing |
Anal Biochem
September 2025
Department of Chemistry and Biotechnology, Graduate School of Engineering, Tottori University, 4-101 Koyama-Cho Minami, Tottori, 680-8552, Japan.
The duplex-forming behavior of an inchworm-type PNA-PEG conjugate (i-PPc), engineered for the selective recognition of point mutations in DNA, was assessed through thermodynamic analysis employing UV melting curves and circular dichroism spectroscopy. The i-PPc demonstrated the ability to form stable duplexes exclusively with fully complementary DNA sequences, while no hybridization with single-base mismatched sequences. This binary on/off hybridization behavior was maintained even under physiologically relevant conditions (37 °C), thereby illustrating the exceptional point mutation discrimination capability of i-PPc.
View Article and Find Full Text PDFMol Cell
September 2025
Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter (VBC), Dr. Bohr-Gasse 3, 1030 Vienna, Austria. Electronic address:
PIWI-clade Argonaute proteins and their associated PIWI-interacting RNAs (piRNAs) are essential guardians of genome integrity, silencing transposable elements through distinct nuclear and cytoplasmic pathways. Nuclear PIWI proteins direct heterochromatin formation at transposon loci, while cytoplasmic PIWIs cleave transposon transcripts to initiate piRNA amplification. Both processes rely on target RNA recognition by PIWI-piRNA complexes, yet how this leads to effector recruitment is unclear.
View Article and Find Full Text PDFRSC Chem Biol
August 2025
Department of Chemistry, Graduate School of Science, Nagoya University, Furo-cho Chikusa-ku Nagoya 464-8602 Japan +81-52-789-3557 +81-52-789-2953.
Peptide nucleic acid (PNA) is a unique class of synthetic nucleic acids with a pseudo-peptide backbone, known for its high nucleic acid recognition capability and its ability to directly recognize double-stranded DNA (dsDNA) the formation of a unique invasion complex. While most natural and artificial nucleic acids form duplexes in an antiparallel configuration due to the general instability of parallel configurations, PNA distinctively forms both antiparallel and parallel duplexes. In this study, we focused on this previously underexplored property of PNA to adopt a parallel duplex configuration and developed a novel double-duplex invasion strategy by leveraging the differences in thermal stability between the antiparallel and parallel orientations of PNA duplexes.
View Article and Find Full Text PDFBiochemistry (Mosc)
August 2025
Institute of Chemical Biology and Fundamental Medicine, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia.
DNA damage results in distortion of the B-form structure of the DNA double helix. Recognition of such distortion by DNA repair proteins is an important stage in the process initiation. Nucleosome structure imposes restrictions on mobility and plasticity of DNA geometry.
View Article and Find Full Text PDFInt J Biol Macromol
September 2025
Hubei Shizhen Laboratory, Wuhan 430061, People's Republic of China; School of Basic Medical Sciences, Hubei University of Chinese Medicine, Wuhan 430065, People's Republic of China. Electronic address:
Infectious herpesviruses are implicated in a broad spectrum of human disorders, from mild cold sores to severe encephalitis and cancers. To combat herpesvirus infections, natural products should be a rich source of potential drug leads. However, natural products have long been bothered by discovering the protein target.
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