A new hydrophobic linker effective for the in situ synthesis of DNA–CPG conjugates as tools for SNP analysis

DNA chips consisting of DNA oligonucleotide probes immobilized on the surface of solid supports are very powerful tools for rapid analysis of multiple samples. In this Letter we describe a new method for the efficient synthesis of DNA probes without their serious elimination by use of a new hydrophobic 16-hyroxydecanoic linker and a new non-aqueous reagent of MeNH2/THF for the deprotection of the base and phosphate protecting groups on CPG resins. The elimination of DNA probes in this new method could be suppressed more than 20-fold compared with the previous method using a hexaethylene glycol linker and concd NH4OH. Moreover, we carried out SNPs detection by use of our DNA–CPG conjugate to show the utility of our new linker and deprotection conditions.