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

Abstract

Chirally pure phosphoramidite monomers bearing 9-amino-6-chloro-2-methoxyacridine were synthesized from D- or L-threoninol and omega-aminocarboxylic acid, and incorporated into oligonucleotides. These acridine-DNA conjugates formed stable duplexes with complementary RNA because of intercalation of the acridine to DNA/RNA heteroduplexes. The stability of duplexes was not very dependent on either the chirality of the central carbon bearing the acridine or the length of the side chain. However, the ability for site-selective activation of the phosphodiester linkage in front of the acridine, which induced Lu(III)-promoted RNA scission, was strongly dependent on these two factors. The largest activation was achieved when the monomer unit was prepared from L-threoninol and 4-aminobutyric acid and the acridine was bound to the amino group. By attaching the more acidic 9-amino-2-methoxy-6-nitroacridine to this optimized scaffold, a quite effective acridine-DNA conjugate for site-selective RNA scission was obtained.

Synthesis of Photo-Responsive Acridine-Modified DNA and Its Application to Site-Selective RNA Scission

“…Although the results in Table 2 indicate that the interactions between the acridine and adjacent base pairs seem to be roughly the same before and after the UV irradiation, a slight difference of the orientation of the acridine in the DNA/RNA duplex probably causes notable change in the efficiency of site-selective RNA scission. As shown in a previous work, [15] the scission activities of DNAs bearing modified acridines were quite different even It was accordingly suggested that subtle difference in the orientations of the acridine residues notably alters the scission activity.…”

“…[5][6][7][8][9][10][11][12] Recently, we incorporated an acridine to oligonucleotides and used these conjugates for site-selective scission of RNA. [13][14][15] There, the phosphodiester linkages of the RNA in front of the acridine were activated by noncovalent interactions such as local perturbation of RNA-backbone conformations and promptly hydrolyzed by metal ions. One attractive functionalization of such biochemical tool is to add photo-responsibility, because light can then trigger RNA scission at 1176 K. Tanaka et al…”

Site-Selective Artificial Ribonucleases and their Applications

“…2.5 times as effective as 16-R [44]. As the consequence of these systematic studies, the most active artificial ribonuclease was obtained when highly acidic 9-amino-2-methoxy-6-nitroacridine was introduced to oligonucleotide with the use of optically pure L-threoninol-derived linker (17) [45].…”

DNA functionalization by dynamic chemistry

“…Within a post-synthetic strategy, a nucleotide analog is modified with a reactive functional group, incorporated into oligonucleotides by standard solid–phase synthesis and reacted with the desired molecules on the oligonucleotide level. As amines and thiols are among the widely used groups introduced for the post-synthetic modifications, the acyclic threoninol linker (2-amino-1,3-butanediol) [14–21] constitutes an attractive choice for oligonucleotide functionalization. Threoninol can be introduced in oligonucleotides via the corresponding phosphoramidite generating a ribose-free abasic site on the backbone that provides the amine group for later functionalization [22–28].…”