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Updated: May 2, 2026

Genome-wide Mapping of Drug-DNA Interactions in Cells with COSMIC Crosslinking of Small Molecules to Isolate Chromatin
Published on: January 20, 2016
Small cyclen-imidazolium-containing molecules and their interactions with DNA
Yang Zhang1, Chun-Yan Li, Ji Zhang
1Key Laboratory of Green Chemistry and Technology (Ministry of Education), College of Chemistry, Sichuan University, Chengdu 610064, P. R. China, (fax: +86-28-85415886).
New organic molecules effectively condense DNA for potential gene delivery. Higher molecular weight compounds show promise, with one molecule successfully transferring DNA into cells with low cytotoxicity compared to PEI 25 kDa.
Area of Science:
- Supramolecular Chemistry
- Biomaterials Science
- Gene Therapy
Background:
- Gene delivery vectors are crucial for therapeutic applications.
- Developing non-viral vectors with low cytotoxicity is a key challenge.
- Cyclen and imidazolium-based molecules offer potential as DNA-binding agents.
Purpose of the Study:
- To synthesize and characterize novel organic molecules with varying cyclen and imidazolium units.
- To evaluate their DNA condensation capabilities and potential as gene delivery vectors.
- To assess their cytotoxicity and DNA release properties.
Main Methods:
- Synthesis of three small organic molecules.
- Agarose gel electrophoresis and ethidium bromide exclusion assays for DNA condensation.
- Dynamic light scattering (DLS) and transmission electron microscopy (TEM) for particle analysis.
- Cellular uptake studies using BEL-7402 cells and lipid DOPE.
- Cytotoxicity assays comparing with Polyethylenimine (PEI) 25 kDa.
Main Results:
- Synthesized molecules effectively condensed plasmid DNA.
- Higher molecular weight compounds achieved full DNA condensation at lower weight/weight ratios.
- DNA-protein complexes formed nanosized spherical particles.
- One compound (10) demonstrated partial DNA release at 200 mM NaCl.
- Compound 10 facilitated plasmid DNA transfer into BEL-7402 cells in the presence of DOPE.
- Exhibited significantly lower cytotoxicity than PEI 25 kDa.
Conclusions:
- Novel cyclen-imidazolium organic molecules are effective DNA condensing agents.
- Molecular weight influences DNA condensation efficiency.
- These compounds show potential as non-viral gene delivery vectors with reduced toxicity.
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