Comprehensive thermodynamic analysis of 3′ double-nucleotide overhangs neighboring Watson–Crick terminal base pairs

@article{OToole2006ComprehensiveTA,
  title={Comprehensive thermodynamic analysis of 3′ double-nucleotide overhangs neighboring Watson–Crick terminal base pairs},
  author={Amanda S. O'Toole and Stacy A Miller and Nathan Haines and Mathias Zink and Martin J. Serra},
  journal={Nucleic Acids Research},
  year={2006},
  volume={34},
  pages={3338 - 3344}
}
Thermodynamic parameters are reported for duplex formation of 48 self-complementary RNA duplexes containing Watson-Crick terminal base pairs (GC, AU and UA) with all 16 possible 3' double-nucleotide overhangs; mimicking the structures of short interfering RNAs (siRNA) and microRNAs (miRNA). Based on nearest-neighbor analysis, the addition of a second dangling nucleotide to a single 3' dangling nucleotide increases stability of duplex formation up to 0.8 kcal/mol in a sequence dependent manner… CONTINUE READING