Published online 9 January 2004
Nucleic Acids Research, 2004, Vol. 32, No. 1 278-286
© 2004 Oxford University Press
Detection of guanine–adenine mismatches by surface plasmon resonance sensor carrying naphthyridine–azaquinolone hybrid on the surface
1 Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University, Kyoto, Japan and 2 PRESTO, Japan Science and Technology Agency (JST), Kyoto 615-8510, Japan
*To whom correspondence should be addressed. Tel: +81 75 383 2756; Fax: +81 75 383 2759; Email: nakatani{at}sbchem.kyoto-u.ac.jp
We have discovered a new molecule naphthyridine–azaquinolone hybrid (Npt–Azq) that strongly stabilized the guanine-adenine (G-A) mismatch in duplex DNA. In the presence of Npt–Azq, the melting temperature (Tm) of 5'-d(CTA ACG GAA TG)-3'/3'-d(GAT TGA CTT AC)-5' containing a single G-A mismatch increased by 15.4°C, whereas fully matched duplex increased its Tm only by 2.2°C. Npt–Azq was immobilized on the sensor surface for the surface plasmon resonance (SPR) assay to examine SPR detection of duplexes containing a G-A mismatch. Distinct SPR signals were observed when 27mer DNA containing a G-A mismatch was analyzed by the Npt–Azq immobilized sensor surfaces, whereas the signal of the fully matched duplex was 
6-fold weaker in intensity. The SPR signals for the G-A mismatch were proportional to the concentration of DNA in a range up to 1 µM, confirming that the SPR signal is in fact due to the binding of the G-A mismatch to Npt–Azq immobilized on the surface. Examination of all 16 G-A mismatches regarding the flanking sequence revealed that the sensor surface reported here is applicable to eight flanking sequences, covering 50% of all possible G-A mismatches.
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