Suzanne de Bruijn

165 The development of a genetic therapy for DFNA21 SUPPLEMENTARY TABLE Table S1. Chemical and thermodynamic properties of AON molecules AON AON sequence 2 nd structure free energy (kcal/mol) Self-dimerization (kcal/mol) Free energy of bimolecular structure (kcal/mol) As DNA As RNA As DNA As RNA Mutant allele Wildtype allele Delta AON 1 G*A*G*C*C* T*C *T*T*T*G*T*G*A*T*G*T*T*T*C 1.5 -1.6 -4.4 -6.8 -33.9 -26.9 7.0 AON 2 T*G*T*G*A*G*C*C* T*C *T*T*T*G*T*G*A*T*G*T 1.6 0.1 -4.4 -6.8 -35.2 -28.2 7.0 AON 3 A*G*A*T*G*T*G*A*G*C*C* T*C *T*T*T*G*T*G*A 1.6 1.6 -4.4 -6.8 -35.3 -28.3 7.0 AON 6 (G*A*G*)C*C* T*C *T*T*T*G*T*G*(A*U*G*U*U*U*C) 1.5 -1.6 -4.4 -6.8 -33.9 -26.9 7.0 AON 7 (A*U*G*U*G*)A*G*C*C* T*C *T*T*T*G*(U*G*A*U*G) 1.6 1.6 -4.4 -6.8 -34.5 -27.5 7.0 Phosphorothioate links in the antisense oligonucleotide (AON) sequences are indicated by the asterisks between bases. The 2’-O-methyl RNA bases are placed between brackets. Allele-discriminating bases for the c.1696_1707del RIPOR2 allele are indicated by bold underlined fonts. The RNAstructure webserver (http://rna.urmc.rochester.edu/RNAstructureWeb/) was used to predict the secondary structure free and self-dimerization energies of each molecule. Gapmer molecules were analyzed as both DNA and RNA molecules, since the RNA-structure webserver cannot take the chemical modification or gapmer composition into account. Candidate AON molecules were selected according to the criteria presented by Slijkerman et al. 19 A Nucleotide BLAST analysis (NCBI) was performed to confirm specificity of the designed molecules.