Analytical Sciences

Enhancement of the Binding Ability of a Ligand for Nucleobase Recognition by Introducing a Methyl Group

Qing DAI,* Chun-Yan XU,* Yusuke SATO,* Keitaro YOSHIMOTO,** Seiichi NISHIZAWA,* and Norio TERAMAE*

*Department of Chemistry, Graduate School of Science, Tohoku University, and CREST, Japan Science and Technology Agency (JST), Aoba-ku, Sendai 980-8578, Japan
**Bioengineering Laboratory, RIKEN (The Institute of Physical and Chemical Research), Hirosawa 2-1, Wako, Saitama 351-0198, Japan

The recognition ability of pteridine derivatives for nucleobases opposite an abasic (AP) site in an oligodeoxynucleotide (ODN) duplex is enhanced by using a propylene residue (Spacer-C3) as an AP site. The recognition ability is further enhanced both by attaching methyl groups to a fluorescent ligand and by measuring the fluorescence response at 5°C; 6.2 × 10⁶ M^-1 of the binding constant is attained between 2-amino-6,7-dimethyl-4-hydroxypteridine and guanine opposite the AP site in water.

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