CARB 8 |
| Oligonucleotide probes do not have to be comprised of arrays of 5'-to-3' linked nucleotides. Changing nucleotide synthesis orientation in mid-array results in oligonucleotides with inversion linkages (3'-3' or 5'-5') and two 5' or two 3' termini. Using two inversion linkages leads to oligomers with nucleotides oriented 5'-to-3'-3'-to-5'-5'-to-3' or 3'-to-5'-5'-to-3'-3'-to-5'. Self-reporting hairpin constructs comprised of inversion linkages, complementary terminal stem sequences and terminal fluorophore-quencher pairs were compared with molecular beacons and linear probes of related sequences by thermal denaturation, target titration analysis and real-time isothermal sequence amplification. When inversion probe loop sequences hybridize to complementary targets, the inversion probe stem sequences are oriented parallel to the targets and, hence, cannot appreciably interact with flanking target sequences. Hybridization affinity and sequence specificity are thereby reduced to that of linear probes, effectively reducing design complexity and moving towards universal stem sequence rules. |
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Nucleosides, Nucleotides and Oligonucleotides
9:00 AM-11:40 AM, Sunday, 10 September 2006 Hilton San Francisco -- Yosemite C, Oral
Division of Carbohydrate Chemistry |