Recognition of Hairpin-Containing Single-Stranded DNA by Oligonucleotides Containing Internal Acridine Derivatives

Abstract

Oligodeoxynucleotides with an internal intercalating agent have been targeted to single-stranded sequences containing hairpin structures. The oligonucleotide binds to nonadjacent single-stranded sequences on both sides of the hairpin structure in such a way as to form a three-way junction. The acridine derivative is inserted at a position that allows it to interact with the three-way junction. The melting temperature (Tm) of complexes formed between the hairpin-containing target and oligonucleotides containing one internal acridine derivative was higher than that obtained with the same target and an unmodified oligonucleotide (DeltaTm = +13 degrees C). The internal acridine provided the oligonucleotide with a higher affinity than covalent attachment to the 5' end. Oligonucleotides could also be designed to recognize a hairpin-containing single-stranded nucleic acid by formation of Watson-Crick hydrogen bonds with a single-stranded part and Hoogsteen hydrogen bonds with the stem of the hairpin. An internal acridine derivative was introduced at the junction between the two domains, the double helix domain with Watson-Crick base pairs and the triple helix domain involving Hoogsteen base triplets in the major groove of the hairpin stem. Oligonucleotides with an internal acridine or an acridine at their 5' end have similar binding affinities for the stem-loop-containing target. The bis-modified oligonucleotide containing two acridines, one at the 5' end and one at an internal site, did not exhibit a higher affinity than the oligonucleotides with only one intercalating agent. The design of oligonucleotides with an internal intercalating agent might be of interest to control gene expression through recognition of secondary structures in single-stranded targets.

Design of Phosphoramidite Monomer for Optimal Incorporation of Functional Intercalator to Main Chain of Oligonucleotide

“…In many cases, functional molecules were tethered to either appropriate position in the nucleotide or the terminus of the main chain of the oligonucleotide. The introduction of functional molecules to the middle of main chain is also attractive, since these molecules can be placed at predetermined positions in helically structured duplexes and thus show various specific functions ( − ). One of the most important factors in this main chain modification is the design of a monomer unit that bears the functional molecules.…”

Synthesis and monitored selection of nucleotide surrogates for binding T:A base pairs in homopurine-homopyrimidine DNA triple helices

“…In particular, the residues linking PNA and DNA portions have proven difficult to design and less prone to obey Watson-Crick base pairing rules as stringently as their neighbors (32,33). Earlier work on modified oligonucleotides for triplex formation had shown, however, that appending an intercalator internally can be more beneficial for target affinity than appending it to the terminus, in agreement with the high target affinity found for 12l (34). Though anthraquinone-bearing 12l does bind to the duplex target with greater affinity than the best among the unmodified oligonucleotides tested (G-containing 14), it does show only moderate selectivity in its interactions with duplexes.…”

Photoswitching of Site-Selective RNA Scission by Sequential Incorporation of Azobenzene and Acridine Residues in a DNA Oligomer

“…The acridine ring in X 1 is 9-amino-6-chloro-2-methoxyacridine. This residue is the most popular acridine residue, which is often used as a duplex stabilizer or a fluorescent label [14, 15]. The linker moiety in X 1 is a flexible alkyl chain, and the stereochemistry of the branching point is not controlled.…”