Bioactivity of 2′-deoxyinosine-incorporated aptamer AS1411

Abstract

Aptamers can be chemically modified to enhance nuclease resistance and increase target affinity. In this study, we performed chemical modification of 2′-deoxyinosine in AS1411, an anti-proliferative G-rich oligodeoxynucleotide aptamer, which binds selectively to the nucleolin protein. Its function was augmented when 2′-deoxyinosine was incorporated at positions 12, 13, 15, and 24 of AS1411, respectively. In addition, double incorporation of 2′-deoxyinosine at positions 12 and 24 (FAN-1224dI), 13 and 24 (FAN-1324dI), and 15 and 24 (FAN-1524dI) promoted G-quartet formation, as well as inhibition of DNA replication and tumor cell growth, and induced S-phase cell cycle arrest. In further animal experiments, FAN-1224dI, FAN-1324dI and FAN-1524dI resulted in enhanced treatment effects than AS1411 alone. These results suggested that the position and number of modification substituents in AS1411 are critical parameters to improve the diagnostic and therapeutic function of the aptamer. Structural investigations of the FAN-1524dI/nucleolin complex structure, using molecular dynamics simulation, revealed the critical interactions involving nucleolin and 2′-dI incorporated AS1411 compared with AS1411 alone. These findings augment understanding of the role of 2′-deoxyinosine moieties in interactive binding processes.

The Bioactivity of D-/L-Isonucleoside- and 2′-Deoxyinosine-Incorporated Aptamer AS1411s Including DNA Replication/MicroRNA Expression

“…For the 2′-dI, the larger aromatic ring at position 24 increased the stacking interactions, and similar results were also obtained when it was incorporated at positions 15 and 24 ( Figure 5 BD). 25 Apparently, modification at positions 6, 12, or 24 did not have direct effects on the binding process, but this is likely to contribute to the stability and changes in the local conformation of the G4 structure to some extent.…”

“…This phenomenon has also been observed in our previous studies when 2′-dI was incorporated at positions 15 and 24. 25 Although the binding mode does not cause drastic structural changes upon substitutions, these changes led to new structure features. These additional interactions provide a good explanation for the improved bioactivity of FCL-II.…”

“…Based on experimental results, D-/L-isoT increased the aptamer activities in a stronger way. We have used D-/L-isoNA to modify more than 5 different aptamers, including TBA, 21 AS1411, 25 GBI-10, 22 , 23 , 24 BC-15, and DT-2 (unpublished data). Some of these are G-quadruplexes, and some are not.…”

“… 18 , 19 , 20 , 21 , 22 , 23 , 24 Furthermore, as a naturally occurring base, 2′-deoxyinosine (2′-dI) ( Figure 1 ) offers a huge advantage in non-immunogenic clinical application. 25 With this strategy, the local spatial conformation, especially around the incorporation site, could be properly optimized, resulting in enhanced bioactivity.

Figure 1 The Structure of D-/L-isoT, 2′-dI, and Quadruplex Structure of AS1411 2′-dI, 2′-deoxyinosine.

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“…In our previous studies, simulated complex models have been successfully built to investigate the critical interactions in the binding process. 25 …”