TY - GEN
T1 - Prediction of antisense oligonucleotide binding affinity and activity in cell culture
AU - Walton, S. Patrick
AU - Jayaraman, Arul
AU - Stephanopoulos, Gregory N.
AU - Yarmush, Martin L.
AU - Roth, Charles M.
PY - 1999
Y1 - 1999
N2 - We have developed a method that uses RNA secondary structure prediction and an appropriate thermodynamic cycle to predict the free energy of hybridization between an antisense oligonucleotide and its target mRNA. We applied this method to determine, theoretically, the oligonucleotides which bind most strongly to the rabbit β-globin (RBG) mRNA, for which a large experimental data set is available. The model accurately predicts the trend in binding affinity and, more importantly, identifies the highest binding affinity sequences quite accurately (six out of the highest ten). Recent data indicate that the method also yields sequences that inhibit the production of the gp130 cytokine signaling protein in the H35 rat hepatoma cell line.
AB - We have developed a method that uses RNA secondary structure prediction and an appropriate thermodynamic cycle to predict the free energy of hybridization between an antisense oligonucleotide and its target mRNA. We applied this method to determine, theoretically, the oligonucleotides which bind most strongly to the rabbit β-globin (RBG) mRNA, for which a large experimental data set is available. The model accurately predicts the trend in binding affinity and, more importantly, identifies the highest binding affinity sequences quite accurately (six out of the highest ten). Recent data indicate that the method also yields sequences that inhibit the production of the gp130 cytokine signaling protein in the H35 rat hepatoma cell line.
UR - https://www.scopus.com/pages/publications/0033357146
UR - https://www.scopus.com/pages/publications/0033357146#tab=citedBy
M3 - Conference contribution
AN - SCOPUS:0033357146
SN - 0780356756
T3 - Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings
SP - 96
BT - Annual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings
PB - IEEE
T2 - Proceedings of the 1999 IEEE Engineering in Medicine and Biology 21st Annual Conference and the 1999 Fall Meeting of the Biomedical Engineering Society (1st Joint BMES / EMBS)
Y2 - 13 October 1999 through 16 October 1999
ER -