title: The Use of Minimal RNA Toeholds to Trigger the Activation of Multiple Functionalities.
abstract: Current work reports the use of single-stranded RNA toeholds of different lengths to promote the reassociation of various RNA-DNA hybrids, which results in activation of multiple split functionalities inside human cells. The process of reassociation is analyzed and followed with a novel computational multistrand secondary structure prediction algorithm and various experiments. All of our previously designed RNA/DNA nanoparticles employed single-stranded DNA toeholds to initiate reassociation. The use of RNA toeholds is advantageous because of the simpler design rules, the shorter toeholds, and the smaller size of the resulting nanoparticles (by up to 120 nucleotides per particle) compared to the same hybrid nanoparticles with single-stranded DNA toeholds. Moreover, the cotranscriptional assemblies result in higher yields for hybrid nanoparticles with ssRNA toeholds.
authors.affiliation: Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute , Frederick, Maryland 21702, United States.|Department of Chemistry, University of North Carolina at Charlotte , 9201 University City Boulevard, Charlotte, North Carolina 28223, United States.
authors.forename: Kirill A
authors.initials: KA
authors.lastname: Afonin
authors.affiliation: Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute , Frederick, Maryland 21702, United States.|Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research , Frederick, Maryland 21702, United States.
authors.forename: Mathias
authors.initials: M
authors.lastname: Viard
authors.affiliation: HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute , Frederick, Maryland 21702, United States.
authors.forename: Philip
authors.initials: P
authors.lastname: Tedbury
authors.affiliation: Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research , Frederick, Maryland 21702, United States.
authors.forename: Eckart
authors.initials: E
authors.lastname: Bindewald
authors.affiliation: Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute , Frederick, Maryland 21702, United States.
authors.forename: Lorena
authors.initials: L
authors.lastname: Parlea
authors.affiliation: Department of Chemistry, University of North Carolina at Charlotte , 9201 University City Boulevard, Charlotte, North Carolina 28223, United States.
authors.forename: Marshall
authors.initials: M
authors.lastname: Howington
authors.affiliation: Department of Chemistry, University of North Carolina at Charlotte , 9201 University City Boulevard, Charlotte, North Carolina 28223, United States.
authors.forename: Melissa
authors.initials: M
authors.lastname: Valdman
authors.affiliation: Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute , Frederick, Maryland 21702, United States.
authors.forename: Alizah
authors.initials: A
authors.lastname: Johns-Boehme
authors.affiliation: Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute , Frederick, Maryland 21702, United States.
authors.forename: Cara
authors.initials: C
authors.lastname: Brainerd
authors.affiliation: HIV Dynamics and Replication Program, Center for Cancer Research, National Cancer Institute , Frederick, Maryland 21702, United States.
authors.forename: Eric O
authors.initials: EO
authors.lastname: Freed
authors.affiliation: Gene Regulation and Chromosome Biology Laboratory, Center for Cancer Research, National Cancer Institute , Frederick, Maryland 21702, United States.
authors.forename: Bruce A
authors.initials: BA
authors.lastname: Shapiro
mesh_terms: D045744:Cell Line, Tumor; D004277:DNA, Single-Stranded / Q000737:chemistry* / Q000235:genetics; D006367:HeLa Cells; D006801:Humans; D008958:Models, Molecular; D053758:Nanoparticles / Q000737:chemistry*; D036103:Nanotechnology; D009693:Nucleic Acid Hybridization; D034622:RNA Interference; D034741:RNA, Small Interfering / Q000737:chemistry* / Q000235:genetics; D014162:Transfection
chemical_list: D004277:DNA, Single-Stranded; D034741:RNA, Small Interfering
keywords: RNA interference; RNA nanoparticles; RNA nanotechnology; RNA−DNA hybrid reassociation