title: Amides are excellent mimics of phosphate internucleoside linkages and are well tolerated in short interfering RNAs.
abstract: RNA interference (RNAi) has become an important tool in functional genomics and has an intriguing therapeutic potential. However, the current design of short interfering RNAs (siRNAs) is not optimal for in vivo applications. Non-ionic phosphate backbone modifications may have the potential to improve the properties of siRNAs, but are little explored in RNAi technologies. Using X-ray crystallography and RNAi activity assays, the present study demonstrates that 3'-CH2-CO-NH-5' amides are excellent replacements for phosphodiester internucleoside linkages in RNA. The crystal structure shows that amide-modified RNA forms a typical A-form duplex. The amide carbonyl group points into the major groove and assumes an orientation that is similar to the P-OP2 bond in the phosphate linkage. Amide linkages are well hydrated by tandem waters linking the carbonyl group and adjacent phosphate oxygens. Amides are tolerated at internal positions of both the guide and passenger strand of siRNAs and may increase the silencing activity when placed near the 5'-end of the passenger strand. As a result, an siRNA containing eight amide linkages is more active than the unmodified control. The results suggest that RNAi may tolerate even more extensive amide modification, which may be useful for optimization of siRNAs for in vivo applications.
authors.affiliation: Department of Chemistry, Binghamton University, The State University of New York, Binghamton, NY 13902, USA.
authors.forename: Daniel
authors.initials: D
authors.lastname: Mutisya
authors.affiliation: Department of Chemistry, Binghamton University, The State University of New York, Binghamton, NY 13902, USA.
authors.forename: Chelliah
authors.initials: C
authors.lastname: Selvam
authors.affiliation: Global Research and Development in Molecular Biology, Thermo Fisher Scientific Bioscience Division, Lafayette, CO 80026, USA.
authors.forename: Benjamin D
authors.initials: BD
authors.lastname: Lunstad
authors.affiliation: Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA.
authors.forename: Pradeep S
authors.initials: PS
authors.lastname: Pallan
authors.affiliation: Global Research and Development in Molecular Biology, Thermo Fisher Scientific Bioscience Division, Lafayette, CO 80026, USA.
authors.forename: Amanda
authors.initials: A
authors.lastname: Haas
authors.affiliation: Global Research and Development in Molecular Biology, Thermo Fisher Scientific Bioscience Division, Lafayette, CO 80026, USA.
authors.forename: Devin
authors.initials: D
authors.lastname: Leake
authors.affiliation: Department of Biochemistry, School of Medicine, Vanderbilt University, Nashville, TN 37232, USA erozners@binghamton.edu.
authors.forename: Martin
authors.initials: M
authors.lastname: Egli
authors.affiliation: Department of Chemistry, Binghamton University, The State University of New York, Binghamton, NY 13902, USA erozners@binghamton.edu.
authors.forename: Eriks
authors.initials: E
authors.lastname: Rozners
mesh_terms: D000577:Amides / Q000737:chemistry*; D006367:HeLa Cells; D006801:Humans; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D010710:Phosphates / Q000737:chemistry; D034622:RNA Interference; D034741:RNA, Small Interfering / Q000138:chemical synthesis / Q000737:chemistry*
chemical_list: D000577:Amides; D010710:Phosphates; D034741:RNA, Small Interfering