title: Ternary DNA chip based on a novel thymine spacer group chemistry.
abstract: A novel thymine-based surface chemistry suitable for label-free electrochemical DNA detection is described. It involves a simple two-step sequential process: immobilization of 9-mer thymine-terminated probe DNAs followed by backfilling with 9-mer thymine-based spacers (T9). As compared to commonly used organic spacer groups like 2-mercaptoethanol, 3-mercapto-1-propanol and 6-mercapto-1-hexanol, the 9-mer thymine-based spacers offer a 10-fold improvement in discriminating between complementary and non-complementary target hybridization, which is due mainly to facilitated transport of the redox probes through the probe-DNA/T9 layers. Electrochemical measurements, complemented with Surface Plasmon Resonance (SPR) and Quartz Crystal Microbalance (QCM-D) binding analyses, reveal that optimum selectivity between complementary and non-complementary hybridization is obtained for a sensing surface prepared using probe-DNA and backfiller T9 at equimolar concentration (1:1). At this particular ratio, the probe-DNAs are preferentially oriented and easily accessible to yield a sensing surface with favorable hybridization and electron transfer characteristics. Our findings suggest that oligonucleotide-based spacer groups offer an attractive alternative to short organic thiol spacers in the design of future DNA biochips.
authors.affiliation: Center for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Drive, Singapore 637553, Singapore.
authors.forename: Yanli
authors.initials: Y
authors.lastname: Yang
authors.affiliation: Center for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Drive, Singapore 637553, Singapore.
authors.forename: Umit Hakan
authors.initials: UH
authors.lastname: Yildiz
authors.affiliation: Center for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Drive, Singapore 637553, Singapore.
authors.forename: Jaime
authors.initials: J
authors.lastname: Peh
authors.affiliation: Center for Biomimetic Sensor Science, School of Materials Science and Engineering, Nanyang Technological University, 50 Nanyang Drive, Singapore 637553, Singapore. Electronic address: bliedberg@ntu.edu.sg.
authors.forename: Bo
authors.initials: B
authors.lastname: Liedberg
mesh_terms: D004247:DNA / Q000032:analysis*; D015342:DNA Probes / Q000138:chemical synthesis / Q000737:chemistry*; D055664:Electrochemical Techniques; D000441:Hexanols / Q000737:chemistry; D008623:Mercaptoethanol / Q000737:chemistry; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D020005:Propanols / Q000737:chemistry; D058525:Quartz Crystal Microbalance Techniques; D013438:Sulfhydryl Compounds / Q000737:chemistry; D020349:Surface Plasmon Resonance; D013499:Surface Properties; D013941:Thymine / Q000737:chemistry*
chemical_list: C518434:3-mercaptopropanol; D015342:DNA Probes; D000441:Hexanols; D020005:Propanols; D013438:Sulfhydryl Compounds; D008623:Mercaptoethanol; D004247:DNA; D013941:Thymine; C477019:3-mercaptohexanol
keywords: Electrochemistry; Hybridization; Spacer groups; Surface chemistry; Ternary DNA chip; Thymine