Synthetic Alu RNA Production Protocol

D-PDB and DB were synthesized via reversible addition-fragmentation chain transfer polymerization as described previously (22 (link)). Alu DNA sequences were obtained from the GrCh37 (hg19) assembly. Synthetic Alu DNA with a SP6 promoter incorporated at the 5′ end was obtained from Integrated DNA Technologies (IDT DNA). Alu RNA was reverse transcribed using synthetic Alu DNA templates (IDT DNA) and MEGAscript SP6 (Invitrogen) in overnight reactions at 37°C. Reaction products were treated with Turbo DNase, precipitated with lithium chloride, and purified using the RNeasy MiniElute Cleanup Kit (Qiagen). Alu RNAs were not treated with phosphatases to remove 5′ phosphate groups. To quantitate yields, absorbance was determined at 260 nm. To ensure that the Alu RNAs were of the predicted size, gel electrophoresis was employed.