CAPTURE OF SINGLE-STRANDED-DNA ASSISTED BY OLIGONUCLEOTIDE MODULES

Real-time biospecific interaction analysis was employed to monitor dir ect capture of a hepatitis C virus (HCV) derived polymerase chain reac tion (PCR) product by nucleic acid hybridization. Different formats fo r hybridization were used to study the interaction between a single-st randed HCV PCR product and capture oligonucleotides immobilized on a s ensor chip via streptavidin-biotin chemistry. By employing a prehybrid ization step in solution with nonbiotin oligonucleotides complementary to the single-stranded target and adjacent to the immobilized probe, a significant capture was achieved in comparison to the low capture ef ficiency obtained using single immobilized probes (9-36 mer). High cap ture efficiencies were also observed when shorter immobilized probes w ere used in combination with strings of adjacently positioned prehybri dized probes (i.e., modules). Interestingly, the introduction of singl e nucleotide gaps between prehybridized and/or immobilized probes dram atically reduced the capture efficiency. These results suggest that fl exible systems for capture could be designed from libraries of short o ligonucleotides (9 mers) used in module fashion, taking advantage of s tacking interactions between the oligonucleotides. The potential appli cations of such oligonucleotide-assisted capture systems are discussed . (C) 1998 Academic Press.