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For: Suter SR, Sheu-Gruttadauria J, Schirle NT, Valenzuela R, Ball-Jones AA, Onizuka K, MacRae IJ, Beal PA. Structure-Guided Control of siRNA Off-Target Effects. J Am Chem Soc 2016;138:8667-9. [PMID: 27387838 DOI: 10.1021/jacs.6b06137] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Number Cited by Other Article(s)
1
Pal C, Richter M, Harasgama J, Rozners E. Amide Internucleoside Linkages Suppress the MicroRNA-like Off-Target Activity of Short Interfering RNA. ACS Chem Biol 2025;20:522-528. [PMID: 39813044 DOI: 10.1021/acschembio.4c00824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2025]
2
Nomura K, An S, Kobayashi Y, Kondo J, Shi T, Murase H, Nakamoto K, Kimura Y, Abe N, Ui-Tei K, Abe H. Synthesis of 2'-formamidonucleoside phosphoramidites for suppressing the seed-based off-target effects of siRNAs. Nucleic Acids Res 2024;52:10754-10774. [PMID: 39231537 PMCID: PMC11472056 DOI: 10.1093/nar/gkae741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Revised: 07/31/2024] [Accepted: 08/18/2024] [Indexed: 09/06/2024]  Open
3
Gafur SH, Ghosh S, Richter M, Rozners E. Synthesis and Properties of RNA Modified with Thioamide Internucleoside Linkage. Chembiochem 2024;25:e202400364. [PMID: 38819607 PMCID: PMC11472774 DOI: 10.1002/cbic.202400364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2024] [Revised: 05/23/2024] [Accepted: 05/31/2024] [Indexed: 06/01/2024]
4
Jin SE, Sung JH. Delivery Strategies of siRNA Therapeutics for Hair Loss Therapy. Int J Mol Sci 2024;25:7612. [PMID: 39062852 PMCID: PMC11277092 DOI: 10.3390/ijms25147612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 06/25/2024] [Accepted: 07/01/2024] [Indexed: 07/28/2024]  Open
5
Pal C, Richter M, Rozners E. Synthesis and Properties of RNA Modified with Cationic Amine Internucleoside Linkage. ACS Chem Biol 2024;19:249-253. [PMID: 38314716 PMCID: PMC11058646 DOI: 10.1021/acschembio.3c00784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2024]
6
Rinaldi S, Moroni E, Rozza R, Magistrato A. Frontiers and Challenges of Computing ncRNAs Biogenesis, Function and Modulation. J Chem Theory Comput 2024;20:993-1018. [PMID: 38287883 DOI: 10.1021/acs.jctc.3c01239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2024]
7
Chan A, Tsourkas A. Intracellular Protein Delivery: Approaches, Challenges, and Clinical Applications. BME FRONTIERS 2024;5:0035. [PMID: 38282957 PMCID: PMC10809898 DOI: 10.34133/bmef.0035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 12/14/2023] [Indexed: 01/30/2024]  Open
8
Sato H, Chandela A, Ueno Y. Synthesis and characterization of novel (S)-5'-C-aminopropyl-2'-fluorouridine modified oligonucleotides as therapeutic siRNAs. Bioorg Med Chem 2023;87:117317. [PMID: 37196425 DOI: 10.1016/j.bmc.2023.117317] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 05/04/2023] [Accepted: 05/04/2023] [Indexed: 05/19/2023]
9
Richter M, Viel JA, Kotikam V, Gajula PK, Coyle L, Pal C, Rozners E. Amide Modifications in the Seed Region of the Guide Strand Improve the On-Target Specificity of Short Interfering RNA. ACS Chem Biol 2023;18:7-11. [PMID: 36580486 PMCID: PMC9894624 DOI: 10.1021/acschembio.2c00769] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
10
Luo M, Lee LKC, Peng B, Choi CHJ, Tong WY, Voelcker NH. Delivering the Promise of Gene Therapy with Nanomedicines in Treating Central Nervous System Diseases. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2022;9:e2201740. [PMID: 35851766 PMCID: PMC9475540 DOI: 10.1002/advs.202201740] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 05/19/2022] [Indexed: 06/01/2023]
11
Shiohama Y, Fujita R, Sonokawa M, Hisano M, Kotake Y, Krstic-Demonacos M, Demonacos C, Kashiwazaki G, Kitayama T, Fujii M. Elimination of Off-Target Effect by Chemical Modification of 5′-End of Small Interfering RNA. Nucleic Acid Ther 2022;32:438-447. [DOI: 10.1089/nat.2021.0068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]  Open
12
Wang Q, Fan X, Jing N, Zhao H, Yu L, Tang X. Photoregulation of Gene Expression with Ligand-Modified Caged siRNAs through Host/Guest Interaction. Chembiochem 2021;22:1901-1907. [PMID: 33432703 DOI: 10.1002/cbic.202000763] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 12/22/2020] [Indexed: 02/05/2023]
13
Shinohara F, Oashi T, Harumoto T, Nishikawa T, Takayama Y, Miyagi H, Takahashi Y, Nakajima T, Sawada T, Koda Y, Makino A, Sato A, Hamaguchi K, Suzuki M, Yamamoto J, Tomari Y, Saito JI. siRNA potency enhancement via chemical modifications of nucleotide bases at the 5'-end of the siRNA guide strand. RNA (NEW YORK, N.Y.) 2021;27:163-173. [PMID: 33177188 PMCID: PMC7812868 DOI: 10.1261/rna.073783.119] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 11/05/2020] [Indexed: 05/03/2023]
14
Rydzik AM, Gottschling D, Simon E, Skronska-Wasek W, Rippmann JF, Riether D. Epigenetic Modification 6-Methyladenosine Can Impact the Potency and Specificity of siRNA. Chembiochem 2020;22:491-495. [PMID: 32936508 DOI: 10.1002/cbic.202000551] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Revised: 09/12/2020] [Indexed: 11/12/2022]
15
Kotikam V, Rozners E. Amide-Modified RNA: Using Protein Backbone to Modulate Function of Short Interfering RNAs. Acc Chem Res 2020;53:1782-1790. [PMID: 32658452 DOI: 10.1021/acs.accounts.0c00249] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
16
Kamiya Y, Takeyama Y, Mizuno T, Satoh F, Asanuma H. Investigation of Strand-Selective Interaction of SNA-Modified siRNA with AGO2-MID. Int J Mol Sci 2020;21:ijms21155218. [PMID: 32717920 PMCID: PMC7432901 DOI: 10.3390/ijms21155218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/17/2020] [Accepted: 07/20/2020] [Indexed: 12/22/2022]  Open
17
Nanomedicine in osteosarcoma therapy: Micelleplexes for delivery of nucleic acids and drugs toward osteosarcoma-targeted therapies. Eur J Pharm Biopharm 2020;148:88-106. [PMID: 31958514 DOI: 10.1016/j.ejpb.2019.10.013] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 09/09/2019] [Accepted: 10/31/2019] [Indexed: 02/06/2023]
18
Zimmer AM, Pan YK, Chandrapalan T, Kwong RWM, Perry SF. Loss-of-function approaches in comparative physiology: is there a future for knockdown experiments in the era of genome editing? ACTA ACUST UNITED AC 2019;222:222/7/jeb175737. [PMID: 30948498 DOI: 10.1242/jeb.175737] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
19
Monteleone LR, Matthews MM, Palumbo CM, Thomas JM, Zheng Y, Chiang Y, Fisher AJ, Beal PA. A Bump-Hole Approach for Directed RNA Editing. Cell Chem Biol 2019;26:269-277.e5. [PMID: 30581135 PMCID: PMC6386613 DOI: 10.1016/j.chembiol.2018.10.025] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 09/28/2018] [Accepted: 10/26/2018] [Indexed: 12/17/2022]
20
Chandela A, Ueno Y. Systemic Delivery of Small Interfering RNA Therapeutics: Obstacles and Advances. ACTA ACUST UNITED AC 2019. [DOI: 10.7831/ras.7.10] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
21
Chandela A, Ueno Y. Design, synthesis and evaluation of novel, branched trident small interfering RNA nanostructures for sequence-specific RNAi activity. RSC Adv 2019;9:34166-34171. [PMID: 35529995 PMCID: PMC9073863 DOI: 10.1039/c9ra08071f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 10/15/2019] [Indexed: 12/21/2022]  Open
22
siRNA delivery for treatment of degenerative diseases, new hopes and challenges. J Drug Deliv Sci Technol 2018. [DOI: 10.1016/j.jddst.2018.04.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
23
Hardcastle T, Novosjolova I, Kotikam V, Cheruiyot SK, Mutisya D, Kennedy SD, Egli M, Kelley ML, van Brabant Smith A, Rozners E. A Single Amide Linkage in the Passenger Strand Suppresses Its Activity and Enhances Guide Strand Targeting of siRNAs. ACS Chem Biol 2018;13:533-536. [PMID: 29298376 PMCID: PMC7755457 DOI: 10.1021/acschembio.7b01012] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
24
Suter SR, Ball-Jones A, Mumbleau MM, Valenzuela R, Ibarra-Soza J, Owens H, Fisher AJ, Beal PA. Controlling miRNA-like off-target effects of an siRNA with nucleobase modifications. Org Biomol Chem 2018;15:10029-10036. [PMID: 29164215 DOI: 10.1039/c7ob02654d] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
25
Seok H, Lee H, Jang ES, Chi SW. Evaluation and control of miRNA-like off-target repression for RNA interference. Cell Mol Life Sci 2018;75:797-814. [PMID: 28905147 PMCID: PMC11105550 DOI: 10.1007/s00018-017-2656-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Revised: 09/06/2017] [Accepted: 09/07/2017] [Indexed: 01/08/2023]
26
Alagia A, Jorge AF, Aviñó A, Cova TFGG, Crehuet R, Grijalvo S, Pais AACC, Eritja R. Exploring PAZ/3'-overhang interaction to improve siRNA specificity. A combined experimental and modeling study. Chem Sci 2018;9:2074-2086. [PMID: 29719684 PMCID: PMC5896489 DOI: 10.1039/c8sc00010g] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 01/15/2018] [Indexed: 12/29/2022]  Open
27
Ahmadzada T, Reid G, McKenzie DR. Fundamentals of siRNA and miRNA therapeutics and a review of targeted nanoparticle delivery systems in breast cancer. Biophys Rev 2018;10:69-86. [PMID: 29327101 PMCID: PMC5803180 DOI: 10.1007/s12551-017-0392-1] [Citation(s) in RCA: 139] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Accepted: 12/15/2017] [Indexed: 12/11/2022]  Open
28
He Y, Yuan C, Chen L, Liu Y, Zhou H, Xu N, Liao DJ. While it is not deliberate, much of today's biomedical research contains logical and technical flaws, showing a need for corrective action. Int J Med Sci 2018;15:309-322. [PMID: 29511367 PMCID: PMC5835702 DOI: 10.7150/ijms.23215] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/08/2017] [Accepted: 12/21/2017] [Indexed: 12/20/2022]  Open
29
Nucleic Acid-Binding Assay of Argonaute Protein Using Fluorescence Polarization. Methods Mol Biol 2017. [PMID: 29030845 DOI: 10.1007/978-1-4939-7339-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
30
Sheng SR, Wu JS, Tang YL, Liang XH. Long noncoding RNAs: emerging regulators of tumor angiogenesis. Future Oncol 2017;13:1551-1562. [PMID: 28513194 DOI: 10.2217/fon-2017-0149] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]  Open
31
Nucleobase azide-ethynylribose click chemistry contributes to stabilizing oligonucleotide duplexes and stem-loop structures. Bioorg Med Chem Lett 2017;27:2655-2658. [PMID: 28457755 DOI: 10.1016/j.bmcl.2017.04.023] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Revised: 03/25/2017] [Accepted: 04/06/2017] [Indexed: 01/17/2023]
32
Harikrishna S, Pradeepkumar PI. Probing the Binding Interactions between Chemically Modified siRNAs and Human Argonaute 2 Using Microsecond Molecular Dynamics Simulations. J Chem Inf Model 2017;57:883-896. [DOI: 10.1021/acs.jcim.6b00773] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
33
Valenzuela RAP, Onizuka K, Ball-Jones AA, Hu T, Suter SR, Beal PA. Guide Strand 3'-End Modifications Regulate siRNA Specificity. Chembiochem 2016;17:2340-2345. [PMID: 27731539 DOI: 10.1002/cbic.201600453] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Indexed: 02/05/2023]
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