biostudies-literatureKostelansky FCharles UniversityEuropean Regional Development Fund10212-10229https://www.ebi.ac.uk/biostudies/studies/S-EPMC9561273biostudies-literatureUnknown50(18)The short oligodeoxynucleotide (ODN) probes are suitable for good discrimination of point mutations. However, the probes suffer from low melting temperatures. In this work, the strategy of using acridine-4-carboxamide intercalators to improve thermal stabilisation is investigated. The study of large series of acridines revealed that optimal stabilisation is achieved upon decoration of acridine by secondary carboxamide carrying sterically not demanding basic function bound through a two-carbon linker. Two highly active intercalators were attached to short probes (13 or 18 bases; designed as a part of HFE gene) by click chemistry into positions 7 and/or 13 and proved to increase the melting temperate (Tm) of the duplex by almost 8°C for the best combination. The acridines interact with both Nucleic acids researchThermal stabilisation of the short DNA duplexes by acridine-4-carboxamide derivatives.PMC9561273SVV 260 547PRIMUS/20/SCI/013CZ.02.1.01/0.0/0.0/16_019/0000841GAUK 994218Libra AHavlinova ZSzotakova BKucera RKostelansky FZimcik PNovakova VMiletin MfalseThermal stabilisation of the short DNA duplexes by acridine-4-carboxamide derivatives.The short oligodeoxynucleotide (ODN) probes are suitable for good discrimination of point mutations. However, the probes suffer from low melting temperatures. In this work, the strategy of using acridine-4-carboxamide intercalators to improve thermal stabilisation is investigated. The study of large series of acridines revealed that optimal stabilisation is achieved upon decoration of acridine by secondary carboxamide carrying sterically not demanding basic function bound through a two-carbon linker. Two highly active intercalators were attached to short probes (13 or 18 bases; designed as a part of HFE gene) by click chemistry into positions 7 and/or 13 and proved to increase the melting temperate (Tm) of the duplex by almost 8°C for the best combination. The acridines interact with both 2022-01-01T00:00:00Z2022 Oct2025-04-19T03:36:30.627Z2025-04-07T13:43:48.987ZS-EPMC95612733615615210.1093/nar/gkac777