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We describe the synthesis of a series of DNA-threading bis(9-aminoacridine-4-carboxamides) comprising ethylpiperidino and N-methylpiperidin-4-yl sidechains, joined via neutral flexible alkyl chains, charged flexible polyamine chains and a semi-rigid charged piperazine linker. Their cytotoxicity towards human leukaemic cells gives IC(50) values ranging from 99 to 1100 nM, with the ethylpiperidino series generally being more cytotoxic than the N-methylpiperidin-4-yl series. Measurements with supercoiled DNA indicate that they bisintercalate.
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http://dx.doi.org/10.1016/j.bmc.2008.02.063 | DOI Listing |
BMC Bioinformatics
September 2025
Genome Informatics, Faculty of Technology and Center for Biotechnology, Bielefeld University, 33615, Bielefeld, Germany.
Background: The increasing amount of available genome sequence data enables large-scale comparative studies. A common task is the inference of phylogenies- a challenging task if close reference sequences are not available, genome sequences are incompletely assembled, or the high number of genomes precludes multiple sequence alignment in reasonable time. SANS is an alignment-free, whole-genome based approach for phylogeny estimation.
View Article and Find Full Text PDFChemistryOpen
August 2025
CPCV, Department of Chemistry, Ecole Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005, Paris, France.
Pseudo-rotaxanes are reversibly interlocked molecules with at least one linear molecule threaded into a macrocycle and, contrary to rotaxanes, an advantageous ability to be dissociated. Cyclodextrins constitute attracting macrocyclic host entities to build such dynamic structures for their oligosaccharide nature, conic shape, amphiphilic character and biocompatibility. Here we show that using an azobenzene DNA intercalator as a guest allows to build a pseudo-rotaxane combining several remarkable properties, including light-controlled assembly/disassembly, photoreversible chirality and fluorescence, as well as the capability to affect the melting temperature of double-stranded DNA through intercalator host-guest complexation.
View Article and Find Full Text PDFNat Commun
August 2025
Laboratory of Molecular Biophysics, The Rockefeller University, New York, NY, USA.
Bacterial σ factors bind RNA polymerase (E) to form holoenzyme (Eσ), conferring promoter specificity to E and playing a key role in transcription bubble formation. σ is unique among σ factors in its structure and functional mechanism, requiring activation by specialized AAA+ ATPases. Eσ forms an inactive promoter complex where the N-terminal σ region I (σ-RI) threads through a small DNA bubble.
View Article and Find Full Text PDFPhys Med Biol
August 2025
Medical Physics Unit, McGill University, Montreal, QC, Canada.
To build and validate a simulation framework to perform single-cell and bulk-cell whole genome sequencing simulation of radiation-exposed Monte Carlo (MC) cell models to assist radiation genomics studies.Sequencing the genomes of radiation-damaged cells can provide useful insight into radiation action for radiobiology research. However, carrying out post-irradiation sequencing experiments can often be challenging, expensive, and time-consuming.
View Article and Find Full Text PDFAlgorithms Mol Biol
July 2025
Algorithmic Bioinformatics, Department of Computer Science, Saarland University, Campus E2.1, Saarbrücken, 66123, Saarland, Germany.
Motivation: Short DNA sequences of length k that appear in a single location (e.g., at a single genomic position, in a single species from a larger set of species, etc.
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