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

Kenji Yamada; Yusaku Hattori; Takeshi Inde; Takashi Kanamori; Akihiro Ohkubo; Kohji Seio; Mitsuo Sekine

doi:10.1016/j.bmcl.2012.11.079

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

Bioorg Med Chem Lett. 2013 Feb 1;23(3):776-8. doi: 10.1016/j.bmcl.2012.11.079. Epub 2012 Dec 1.

Authors

Kenji Yamada¹, Yusaku Hattori, Takeshi Inde, Takashi Kanamori, Akihiro Ohkubo, Kohji Seio, Mitsuo Sekine

Affiliation

¹ Department of Life Science, Tokyo Institution of Technology, 4259 Nagatsuta, Yokohama 226-8501, Japan.

PMID: 23287737
DOI: 10.1016/j.bmcl.2012.11.079

Abstract

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.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Base Pairing
Base Sequence
Computer Simulation
DNA / chemistry*
Models, Molecular*
Molecular Sequence Data
Sulfhydryl Compounds / chemistry*

Substances

Sulfhydryl Compounds
triplex DNA
DNA