Tolerance of N-heteroaryl modifications on guanine bases in a DNA G-quadruplex.

To systematically determine the effect of N2-heteroaryl modification on the stability of G-quadruplex structures, six types of N2-heteroarylated deoxyguanosines were incorporated into oligonucleotides with intramolecular quadruplex-forming sequences obtained from the human telomere sequence. A UV melting experiment, electrophoretic mobility shift assay, and circular dichroism were performed to evaluate the influence of N2-heteroaryl modification. Among the N2-heteroaryl modifications used in this study, N2-(pyrimidin-2-yl) modification markedly destabilized the G-quadruplex structure.

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 (sT), a duplex-stabilizing nucleotide with an MCE modification, into SSOs further improved splice switching.

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 (sX) and 2'-deoxy-6-thioguanosine (sGs) residues and examined their triplex-forming ability. Consecutive arrangement of sX and sGs 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 sX could form a sX-GC mismatched pair via tautomerization of sX.

Synthesis of oligonucleotides containing 2-N-heteroarylguanine residues and their effect on duplex/triplex stability.

To systematically understand the effect of 2-N-heteroarylguanine (G) modification on the stability of higher-order DNA structures, nucleoside derivatives and oligodeoxyribonucleotides containing guanine residues modified with four kinds of hereroaryl groups on the 2-amino group were synthesized. The stabilities of the DNA duplex and the parallel-oriented DNA triplex containing these Gs were studied by measuring their melting temperatures (T). T experiments and DFT calculations of the modified guanine nucleobases suggested that the base pair formation energy and stability of the two conformations, i.

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 (s(6)Gs) and 4-thiothymidines (s(4)Ts) 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 s(6)Gs and s(4)Ts could selectively bind to the complementary DNA duplex but not to mismatched DNA duplexes or single-stranded RNA.