Substitution of C-5 propynyl-dC (pdC) for dC and C-5 propynyl-dU (pdU) for dT are effective strategies to enhance base pairing. Using these base substitutions, duplex stability and melting temperatures are raised by the following amounts: C-5 propynyl-C 2.8° per substitution; C-5 propynyl-U 1.7° per substitution. AP-dC (G-clamp) substitutes for dC and is another very important modified nucleoside that enhances hybridization by 7-21° per substitution depending upon the sequence and location of the AP-dC. The ability of these modified bases to enhance binding while maintaining specificity has proven useful in antisense research and in the synthesis of high affinity probes. AP-dC is also a fluorescent nucleoside and should find uses in DNA structural research.
Coupling: No changes needed from standard method recommended by synthesizer manufacturer.
Deprotection: Deprotection in Ammonium Hydroxide requires a minimum of 12 hours at 55 °C.