Large stacking stability of a base pair-mimic nucleotide on the DNA duplex

We synthesized novel adenosine derivatives tethering an aromatic hydrocarbon group by an amido linker. The single adenosine derivatives at 5′ dangling end stabilized the DNA duplex of 5′-ATGCGCAT-3′ more or equally than Watson-Crick base pair. When the number of the dangling residues increased from...

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Bibliographic Details
Published in:Nucleic Acids Symposium Series 2003-09, Vol.3 (1), p.79-80
Main Authors: Uotani, Yuuki, Nakano, Shu-ichi, Nakashima, Shoji, Anno, Yosuke, Fujii, Masayuki, Sugimoto, Naoki
Format: Article
Language:English
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Summary:We synthesized novel adenosine derivatives tethering an aromatic hydrocarbon group by an amido linker. The single adenosine derivatives at 5′ dangling end stabilized the DNA duplex of 5′-ATGCGCAT-3′ more or equally than Watson-Crick base pair. When the number of the dangling residues increased from one to three, the duplex stability became larger by 1.8∼3.6 kcal/mol. When the adenosine derivative was opposite to an abasic site in a DNA duplex, the destabilization by the abasic site was significantly reduced. These observations suggest that the adenosine derivatives developed in this study can stack with a DNA base pair by forming a base pair-mimic geometry.
ISSN:0261-3166
1746-8272
DOI:10.1093/nass/3.1.79