Remarkable stabilization of antiparallel DNA triplexes by strong stacking effects of consecutively modified nucleobases containing thiocarbonyl groups

The consecutive arrangement of 2′-deoxy-6-thioguanosines (s⁶Gs) and 4-thiothymidines (s⁴Ts) in antiparallel triplex-forming oligonucleotides (TFOs) considerably stabilized the resulting antiparallel triplexes with high base recognition ability by the strong stacking effects of thiocarbonyl groups. This result was remarkable because chemical modifications of the sugar moieties and nucleobases of antiparallel TFOs generally destabilize triplex structures. Moreover, in comparison with unmodified TFOs, it was found that TFOs containing s⁶Gs and s⁴Ts could selectively bind to the complementary DNA duplex but not to mismatched DNA duplexes or single-stranded RNA.     

Synthesis of and triplex formation in oligonucleotides containing 2′-deoxy-6-thioxanthosine

This study aimed to synthesize triplex-forming oligonucleotides (TFOs) containing 2′-deoxy-6-thioxanthosine (s⁶X) and 2′-deoxy-6-thioguanosine (s⁶Gs) residues and examined their triplex-forming ability. Consecutive arrangement of s⁶X and s⁶Gs residues increased the triplex-forming ability of the oligonucleotides more than 50 times, compared with the unmodified TFOs. Moreover, the stability of triplex containing a mismatched pair was much lower than that of the full-matched triplex, though s⁶X could form a s⁶X-GC mismatched pair via tautomerization of s⁶X. The present results reveal excellent properties of modified TFOs containing s⁶Xs and s⁶Gs residues, which may be harnessed in gene therapy and DNA nanotechnology.     

Synthesis of 2′-O-(N-methylcarbamoylethyl) 5-methyl-2-thiouridine and its application to splice-switching oligonucleotides

The effect of 2′-O-(N-methylcarbamoyl)ethyl (MCE) modification on splice-switching oligonucleotides (SSO) was systematically evaluated. The incorporation of five MCE nucleotides at the 5′-termini of SSOs effectively improved the splice switching effect. In addition, the incorporation of 2′-O-(N-methylcarbamoylethyl)-5-methyl-2-thiouridine (s²T_MCE), a duplex-stabilizing nucleotide with an MCE modification, into SSOs further improved splice switching. These SSOs may be useful for the treatment of genetic diseases associated with splicing errors.     

The impact of non-genetic heterogeneity on cancer cell death

The goal of cancer chemotherapy is to induce homogeneous cell death within the population of targeted cancer cells. However, no two cells are exactly alike at the molecular level, and sensitivity to drug-induced cell death, therefore, varies within a population. Genetic alterations can contribute to this variability and lead to selection for drug resistant clones. However, there is a growing appreciation for the role of non-genetic variation in producing drug-tolerant cellular states that exhibit reduced sensitivity to cell death for extended periods of time, from hours to weeks. These cellular states may result from individual variation in epigenetics, gene expression, metabolism, and other processes that impact drug mechanism of action or the execution of cell death. Such population-level non-genetic heterogeneity may contribute to treatment failure and provide a cellular “substrate” for the emergence of genetic alterations that confer frank drug resistance.