Interaction of three-way DNA junctions with steroids

Abstract

DNA aptamers that bind to cholic acid were previously isolated by an in vitro selection method. Secondary structural prediction and deletion-mutant experiments suggested that the cholic-acid binding regions of 19 sequenced clones could form three-way-junction structures. In this article, the secondary structures of the sequenced clones and the structural requirements for binding to cholic acid were evaluated. A course of mutational-analysis and chemical-modification experiments provided strong support for the predicted secondary structure and also indicated that the binding site is located at the branching point of the three-way junction. Sequence analysis revealed that the sequences of the three base pairs flanking the junction of the three stems are highly conserved among selected clones. The evaluation of the relative binding of several bile acids and structurally related steroids with the aptamer was also carried out. The results revealed a broad range of selectivity and preference for hydrophobic steroids rather than for cholic acid upon binding, indicating that the binding is driven by a hydrophobic interaction. The experimental results reported here allowed us to propose a structural model of a binding site formed by three Watson-Crick base pairs.

Structure and dynamics of three-way DNA junctions: atomic force microscopy studies

“…Such a DNA structure-dependent electrostatic effect may contribute to structural recognition of the junctions by junction-specific enzymes, e.g. resolvases (41,42), and low molecular weight ligands (43).…”

Sequence-selective Modification of DNA Cytosine by Using Junction-forming DNA Probes and Its Application to the Detection of Single Cytosine Methylation

“…osmium tetroxide, but those in the three stems were fairly protected from such reagents by base-pair stacking. 14 In this report, we demonstrated a single C-modification by bisulfite and aminooxy reagents in the target DNA by placing it at the branching point of the TWJ using two DNA probes (Fig. 2B).…”

Nucleic acid aptamer molecular recognition principles and application in liquid chromatography and capillary electrophoresis

“…However, there is also a significant number of aptamers, which have been selected toward small molecules [21]. Despite the polyanionic nature of aptamers, it is important to indicate that several reports have selected oligonucleotidic sequences displaying a significant affinity toward anionic targets [22][23][24]. Szostak and coworkers [25] have even described a RNA aptamer that is capable of both strong and highly specific interactions with the triphosphate group of ATP in the presence of Mg 2+ .…”