The ATT Strand of AAT·ATT Trinucleotide Repeats Adopts Stable Hairpin Structures Induced by Minor Groove Binding Ligands

Abstract

AAT.ATT is the most abundant and also the most frequently polymorphic class of trinucleotide repeats in the human genome. To characterize its structural properties and conformational changes induced by minor groove ligands, (AAT)(6) and (ATT)(6) oligomers as well as their complexes with DAPI were investigated by electrophoretic mobility and UV thermal stability as well as fluorescence and NMR spectroscopy. The results show that individual (AAT)(6) and (ATT)(6) strands exist principally as monomeric non-hydrogen-bonded structures. Their individual interaction with DAPI induces the formation of base-paired structures with different thermal stabilities by quite spectroscopically distinct binding mechanisms. In the presence of DAPI, (ATT)(6) forms a monomeric hairpin structure stabilized by two ligands located in the minor groove with a strong apparent binding constant of 3.4 x 10(6) M(-)(1). The DAPI-induced (ATT)(6) hairpin is characterized by well-stacked A.T Watson-Crick and T.T wobble base pairs, a high electrophoretic mobility, and a melting temperature of 41 degrees C. Interaction of DAPI with the complementary (AAT)(6) strand favors less stable base-paired structures, and the results are consistent with electrostatic and hydrogen-bond interactions of the ligand with the phosphodiester backbone of (AAT)(6) by minor involvement of DNA bases.

Distribution of Microsatellites in the Genome ofMedicago truncatula: A Resource of Genetic Markers That Integrate Genetic and Physical Maps

“…Similar results were reported for rice (Temnykh et al 2001). It is possible that the secondary structure of repeats (e.g., hairpins; Trotta et al 2000) or specific sequences around microsatellites may affect annealing of primers or polymerase processivity. A total of 617 (77.0%) of the 801 amplified SSR loci were polymorphic between M. truncatula genotypes A17 and A20.…”

In Vitro DNA-Binding, Cleavage Activity with pBR322, Molecular Docking and Antiproliferative Studies of Newly Synthesized Steroidal Imidazolidine Hybrids

“…DNA recognition elements (groove binding) DAPI (minor groove binding) [45] and methyl green (major groove binding) [46] were used to probe the potential interacting site of compound 8 with supercoiled pBR322 DNA. (Figure 7), upon the addition of DAPI (Lane 2), there is apparent inhibition of the cleavage activity of 8 suggesting that the compound is a minor groove binder which is in conformity with many literature reports revealing that imidazolidine derivatives play important roles in several DNA minor groove binding agents such as Hoechst 33258 and Hoechst 33342 [47,48].…”

Chiral nano heterobimetallic DNA receptors: In vitro binding studies, cleavage activity and DNA condensation studies (TEM and AFM imaging)

“…Minor groove binding agent (DAPI) [56] and major groove binding agent (Methyl Green) [57] were used to probe the potential interacting sites of CoeSn complex with pBR322 DNA. Fig.…”