title: Molecular recognition of AT-DNA sequences by the induced CD pattern of dibenzotetraaza[14]annulene (DBTAA)-adenine derivatives.
abstract: An investigation of the interactions of two novel and several known DBTAA-adenine conjugates with double-stranded DNA and RNA has revealed the DNA/RNA groove as the dominant binding site, which is in contrast to the majority of previously studied DBTAA analogues (DNA/RNA intercalators). Only DBTAA-propyladenine conjugates revealed the molecular recognition of AT-DNA by an ICD band pattern > 300 nm, whereas significant ICD bands did not appear for other ds-DNA/RNA. A structure-activity relation for the studied series of compounds showed that the essential structural features for the ICD recognition are a) the presence of DNA-binding appendages (adenine side chain and positively charged side chain) on both DBTAA side chains, and b) the presence of a short propyl linker, which does not support intramolecular aromatic stacking between DBTAA and adenine. The observed AT-DNA-ICD pattern differs from previously reported ss-DNA (poly dT) ICD recognition by a strong negative ICD band at 350 nm, which allows for the dynamic differentiation between ss-DNA (poly dT) and coupled ds-AT-DNA.
authors.affiliation: Laboratory for Study of Interactions of Biomacromolecules, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, PO Box 180, HR-10002 Zagreb, Croatia.
authors.forename: Marijana Radić
authors.initials: MR
authors.lastname: Stojković
authors.affiliation: Laboratory for Study of Interactions of Biomacromolecules, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, PO Box 180, HR-10002 Zagreb, Croatia.
authors.forename: Marko
authors.initials: M
authors.lastname: Skugor
authors.affiliation: Department of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Kraków, Poland.
authors.forename: Lukasz
authors.initials: L
authors.lastname: Dudek
authors.affiliation: Department of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Kraków, Poland.
authors.forename: Jarosław
authors.initials: J
authors.lastname: Grolik
authors.affiliation: Department of Chemistry, Jagiellonian University, Ingardena 3, 30-060 Kraków, Poland.
authors.forename: Julita
authors.initials: J
authors.lastname: Eilmes
authors.affiliation: Laboratory for Study of Interactions of Biomacromolecules, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, PO Box 180, HR-10002 Zagreb, Croatia.
authors.forename: Ivo
authors.initials: I
authors.lastname: Piantanida
keywords: AT-DNA recognition; DBTAA-adenine conjugate; circular dichroism; ds-DNA/RNA; minor groove binding; nucleic acids