Scanning of guanine-guanine mismatches in DNA by synthetic ligands using surface plasmon resonance.
Here we have designed and synthesized ligands that specifically bind with high affinity (K(d) = 53 nM) to the guanine (G)-guanine mismatch, one of four types of single-nucleotide polymorphism (SNP). Detection of the G-G mismatch was performed by a surface plasmon resonance (SPR) assay using a sensor chip carrying the G-G specific ligand on its surface. The accuracy of the G-G mismatch detection by the SPR sensor was demonstrated by a marked SPR response obtained only for the DNA containing the G-G mismatch. DNAs containing G-A and G-T mismatches, as well as a fully matched duplex, produced only a weak response. Furthermore, this assay was found applicable for the detection of SNP existing in PCR amplification products of a 652-nucleotide sequence of the HSP70-2 gene.
Nakatani
K
K
Department of Synthetic Chemistry and Biological Chemistry, Faculty of Engineering, Kyoto University, Kyoto 606-8501, Japan. nakatani@sbchem.kyoto-u.ac.jp
Sando
S
S
Saito
I
I
D020137:Base Pair Mismatch; D020029:Base Pairing; D001483:Base Sequence; D004247:DNA / Q000737:chemistry* / Q000235:genetics*; D003850:Deoxyribonuclease I; D005821:Genetic Techniques; D007700:Kinetics; D008024:Ligands; D008969:Molecular Sequence Data; D009693:Nucleic Acid Hybridization; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D020641:Polymorphism, Single Nucleotide; D020349:Surface Plasmon Resonance / Q000379:methods*
D008024:Ligands; D009838:Oligodeoxyribonucleotides; D004247:DNA; D003850:Deoxyribonuclease I