Croatica Chemica Acta, Vol. 99 No. 1, 2026.
Original scientific paper
https://doi.org/10.5562/cca4215
Comprehensive Tutorial: Characterization of Small Molecule–DNA Noncovalent Binding Interactions
Gordan Horvat
; Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, HR-10000 Zagreb, Croatia
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Ivo Piantanida
; Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, HR-10000 Zagreb, Croatia
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* Corresponding author.
Supplements: cca4215_supplement.pdf
Abstract
Non-covalent interactions between small molecules and nucleic acids are essential to many biological processes and the function of numerous therapeutic and diagnostic agents. These interactions are complex due to the structural diversity of DNA / RNA forms and the variety of possible binding modes. Factors such as nucleic acid topology, sequence, ionic conditions, and ligand aggregation further complicate analysis. Because no single technique can capture the full picture, a combination of spectroscopic and biochemical methods is required for accurate characterization. By combining working principles of four most common and available experimental methods with interpretative guidance and methodological details, this tutorial aspires to be a comprehensive reference for both novice and experienced researchers working in the field of small molecule–nucleic acid interactions. All discussed concepts apply equally to other types of DNA or RNA, and are generally relevant to most non-covalent ligand–biomolecule (including protein) interactions.
Keywords
non-covalent binding to DNA; UV-Vis; fluorescence; thermal denaturation; circular dichroism; indicator displacement assay
Hrčak ID:
347265
URI
Publication date:
17.1.2026.
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