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Recognition of Nucleotides and Polynucleotides by Phenanthridinium and Diazapyrenium Derivatives in Aqueous Media

Tumir, Lidija-Marija; Piantanida, Ivo; Žinić, Mladen (2005) Recognition of Nucleotides and Polynucleotides by Phenanthridinium and Diazapyrenium Derivatives in Aqueous Media. Kemija u industriji, 54 (2). pp. 43-55. ISSN 0022-9830

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Abstract

Interactions of 4,9-diazapyrenium cations with nucleotides and polynucleotides were studied in buffered aqueous solution (pH 5 or 7) by UV-Vis, fluorescence, NMR and viscometry. The formation of stacked nucleotide / 4,9-diazapyrenium and nucleotide-phenanthridinium complexes of 1 : 1 stoichiometry with log Ks 1.6 - 2.8 and log Ks<1 to 2.3, respectively, suggests that larger surface of the former cationic heteroaromatics does not considerably enhance nucleotide binding. The stability constants were found independent on nucleotide charge suggesting the dominance of aromatic stacking over coulombic interactions in such complexes. Monomeric 4,9-diazapyrenium cations bind to ss- and ds-polynucleotides by intercalation. Affinities were found to be essentially independent on the number of permanent charges present in the aromatic system but strongly dependent on a type of substituents attached. 2,7-Diamino substituted 4,9-diazapyrenium derivative has shown the highest affinity toward polynucleotides, the highest double helix stabilisation and highly specific fluorescence response on binding to double-stranded G - C (quenching) and A - U(T) (emission increase) polymers. Interactions of 2,7-diamino-4,9-diazapyrenium derivative with ss-polynucleotides, in contrast to other derivatives, depend strikingly on the nucleobase composition and in some cases on pH. The bis(4,9-diazapyrenium) dicationic derivatives, differing in rigidity and length of the linkers connecting diazapyrenium units, were found to bind ds-polynucleotides by monointercalation; some of them exhibited strong additional interactions of the non-intercalated diazapyrenium unit with the outer surface of a polynucleotide. The novel phenanthridinium - nucleobase conjugates were prepared and studied by spectroscopic methods. An analysis of 1H NMR, UV-Vis and fluorescence spectra in aqueous media revealed intramolecular aromatic stacking interaction between phenanthridinium unit and nucleobase, resulting with folded conformation of molecules. Fluorimetric titrations showed that phenanthridinium- nucleobase conjugates 9, 10, 15 and 16 and reference phenanthridinium compounds 9 and 14 form 1 : 1 non-covalent complexes with nucleotides in water with binding constants ranging from 101 to 102 mol-1 dm3, while compounds 11 and 13 form intercalative type of 1 : 1 complexes with nucleotide aromatic unit inserted between phenanthridinium and covalently attached nucleobase, yielding binding constants of 103 -104 mol-1 dm3. Conjugates are binding either complementary or non-complementary nucleotides, showing a lack of any base recognition. Aromatic π...π stacking interactions are found to be dominant in complexes of all studied compounds with nucleotides. Adenine containing N-protonated conjugates 10 and 11 exhibit specific spectroscopic changes and two orders of magnitude higher affinity toward poly-U than uracil conjugates 12 and 13 and the reference compound 9 due to the existence of specific interactions between adenine and uracil, possibly Watson-Crick hydrogen bonding between the bases stacked on the phenanthridinium moiety. Contrary to 10 and 11, the N-methylphenanthridinium- -adenine conjugate 16 exhibited at pH 5 preferred binding to double stranded (ds-) poly-AH+. The binding studies of N-methylated compounds 14-16 with ss-polynucleotides showed no preference of conjugates to polynucleotides containing complementary nucleobases. The results reveal that the presence of protonated or permanently charged intercalator units in the conjugates dramatically changes their binding preferences for polynucleotides.

Item Type: Article
Uncontrolled Keywords: Phenanthridinium; diazapyrenium; DNA; RNA; intercalation
Subjects: NATURAL SCIENCES > Chemistry
Divisions: Division of Organic Chemistry and Biochemistry
Depositing User: Lidija-Marija Tumir
Date Deposited: 21 Nov 2013 13:46
Last Modified: 27 Feb 2014 14:45
URI: http://fulir.irb.hr/id/eprint/1036

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