Studies on the Unique RNA Duplex Destabilization by an Azoniacyclophane − NMR Titrations with Mono- and Oligonucleotides of the RNA and DNA Types

Abstract

The mechanism of the unique destabilization of a folded RNA by the azoniacyclophane CP66 has been investigated by complexation studies with mono-and short singlestranded oligonucleotides as models. For the mononucleotides, NMR titrations revealed only a slight difference of binding free energy ∆G between RNA-type nucleotides compared to DNA analogues, with ∆∆G values of up to 1.3 kJ/ mol. The complexation-induced NMR shifts (CIS values) both in the ligand and in the cyclophane were also similar for deoxyribo-and ribonucleotides, suggesting similar inclusion geometries in both series. Similar observations had been made earlier on the CIS effects of denatured single-strand polymers. Titrations with dinucleotides showed a slight preference for ribose derivatives, with ∆G = −11.2 kJ/mol for ApA and −13.2 kJ/mol for ApG, and −9.9 kJ/mol for dApdA. With the dinucleotides and with selected tri-and tetranucleotides,

Synthesis and Molecular Recognition of Pyrenophanes with Polycationic or Amphiphilic Functionalities: Artificial Plate-Shaped Cavitant Incorporating Arenes and Nucleotides in Water

“…There have already been numerous studies about the development of host molecules for nucleotides . One efficient strategy for the recognition of nucleotides is to use cationic macrocycles which recognize phosphate moieties, for example, azoniacrowns, − azoniacyclophanes, and protonated sapphyrins . Lehn, Hosseini, and co-workers have reported a series of azoniacyclophanes. 5b,− Furthermore, acridine-armed azoniacyclophanes 28d,e associated with nucleotides as multipoint recognition hosts by both electrostatic and π-stacking interactions.…”

“…Cyclophane is representative of a class of versatile macrocyclic compounds on which various functionalities could be conferred by the proper choice of arenes, bridges, and substituents . These compounds have attracted much attention from their moderately rigid cavity, especially as hydrophobic host molecules. − Some of them are constructed by use of polycyclic arenes such as acridine, phenanthridine, quinacridine, ethanoanthracene, or flavin units, and proper arrangement of the polyaromatics produced a plate-shaped cavity on the cyclophanes. During the course of our study about molecular recognition, , we have developed a macrocyclic pyrenophane structure 1a (Figure ), in which two planes of pyrene are facing arranged across a pair of bridging spacers …”