title: Improved design of PPRHs for gene silencing.
abstract: Nowadays, the modulation of gene expression by nucleic acids has become a routine tool in biomedical research for target validation and it is also used to develop new therapeutic approaches. Recently, we developed the so-called polypurine reverse Hoogsteen hairpins (PPRHs) that show high stability and a low immunogenic profile and we demonstrated their efficacy both in vitro and in vivo. In this work, we explored different characteristics of PPRHs to improve their usage as a tool for gene silencing. We studied the role of PPRH length in the range from 20 to 30 nucleotides. We also proved their higher affinity of binding and efficacy on cell viability compared to nonmodified TFOs. To overcome possible off-target effects, we tested wild-type PPRHs, which proved to be capable of binding to their target sequence with more affinity, displaying a higher stability of binding and a higher effect in terms of cell viability. Moreover, we developed a brand new molecule called Wedge-PPRH with the ability to lock the ds-DNA into the displaced structure and proved its efficacy in prostate and breast cancer cell lines.
authors.affiliation: Department of Biochemistry and Molecular Biology, School of Pharmacy, University of Barcelona , 08028 Barcelona, Spain.
authors.forename: Laura
authors.initials: L
authors.lastname: Rodríguez
authors.forename: Xenia
authors.initials: X
authors.lastname: Villalobos
authors.forename: Anna
authors.initials: A
authors.lastname: Solé
authors.forename: Carolina
authors.initials: C
authors.lastname: Lliberós
authors.forename: Carlos J
authors.initials: CJ
authors.lastname: Ciudad
authors.forename: Véronique
authors.initials: V
authors.lastname: Noé
mesh_terms: D001702:Biopharmaceutics; D001943:Breast Neoplasms / Q000235:genetics / Q000378:metabolism / Q000628:therapy; D045744:Cell Line, Tumor; D002470:Cell Survival; D004247:DNA / Q000737:chemistry / Q000235:genetics; D015195:Drug Design; D005260:Female; D020868:Gene Silencing; D005818:Genetic Engineering; D006801:Humans; D051034:Inhibitor of Apoptosis Proteins / Q000235:genetics; D055029:Inverted Repeat Sequences / Q000235:genetics*; D008297:Male; D009690:Nucleic Acid Conformation; D011471:Prostatic Neoplasms / Q000235:genetics / Q000378:metabolism / Q000628:therapy; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D012334:RNA, Neoplasm / Q000235:genetics / Q000378:metabolism; D000077022:Survivin; D019098:Telomerase / Q000235:genetics
chemical_list: C107489:BIRC5 protein, human; D051034:Inhibitor of Apoptosis Proteins; D012333:RNA, Messenger; D012334:RNA, Neoplasm; D000077022:Survivin; D004247:DNA; C509186:TERT protein, human; D019098:Telomerase
keywords: PPRH; Wedge-PPRH; gene silencing; nucleic acid; wild-type