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26
Hu J, Rigo F, Prakash TP, Corey DR. Recognition of c9orf72 Mutant RNA by Single-Stranded Silencing RNAs. Nucleic Acid Ther 2017;27:87-94. [PMID: 28005462 PMCID: PMC5372765 DOI: 10.1089/nat.2016.0655] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 11/15/2016] [Indexed: 01/09/2023]  Open
27
Pallan PS, Prakash TP, de Leon AR, Egli M. Limits of RNA 2′-OH Mimicry by Fluorine: Crystal Structure of Bacillus halodurans RNase H Bound to a 2′-FRNA:DNA Hybrid. Biochemistry 2016;55:5321-5. [DOI: 10.1021/acs.biochem.6b00849] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
28
Yu RZ, Gunawan R, Post N, Zanardi T, Hall S, Burkey J, Kim TW, Graham MJ, Prakash TP, Seth PP, Swayze EE, Geary RS, Henry SP, Wang Y. Disposition and Pharmacokinetics of a GalNAc3-Conjugated Antisense Oligonucleotide Targeting Human Lipoprotein (a) in Monkeys. Nucleic Acid Ther 2016;26:372-380. [PMID: 27500733 DOI: 10.1089/nat.2016.0623] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]  Open
29
Schirle NT, Kinberger GA, Murray HF, Lima WF, Prakash TP, MacRae IJ. Structural Analysis of Human Argonaute-2 Bound to a Modified siRNA Guide. J Am Chem Soc 2016;138:8694-7. [PMID: 27380263 PMCID: PMC4993527 DOI: 10.1021/jacs.6b04454] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
30
Kinberger GA, Prakash TP, Yu J, Vasquez G, Low A, Chappell A, Schmidt K, Murray HM, Gaus H, Swayze EE, Seth PP. Conjugation of mono and di-GalNAc sugars enhances the potency of antisense oligonucleotides via ASGR mediated delivery to hepatocytes. Bioorg Med Chem Lett 2016;26:3690-3. [PMID: 27268307 DOI: 10.1016/j.bmcl.2016.05.084] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 05/24/2016] [Accepted: 05/27/2016] [Indexed: 11/29/2022]
31
Prakash TP, Kinberger GA, Murray HM, Chappell A, Riney S, Graham MJ, Lima WF, Swayze EE, Seth PP. Synergistic effect of phosphorothioate, 5'-vinylphosphonate and GalNAc modifications for enhancing activity of synthetic siRNA. Bioorg Med Chem Lett 2016;26:2817-2820. [PMID: 27161280 DOI: 10.1016/j.bmcl.2016.04.063] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 04/20/2016] [Accepted: 04/21/2016] [Indexed: 12/30/2022]
32
Migawa MT, Prakash TP, Vasquez G, Wan WB, Yu J, Kinberger GA, Østergaard ME, Swayze EE, Seth PP. A convenient synthesis of 5'-triantennary N-acetyl-galactosamine clusters based on nitromethanetrispropionic acid. Bioorg Med Chem Lett 2016;26:2194-7. [PMID: 27025342 DOI: 10.1016/j.bmcl.2016.03.070] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 03/15/2016] [Accepted: 03/16/2016] [Indexed: 10/22/2022]
33
Prakash TP, Yu J, Migawa MT, Kinberger GA, Wan WB, Østergaard ME, Carty RL, Vasquez G, Low A, Chappell A, Schmidt K, Aghajan M, Crosby J, Murray HM, Booten SL, Hsiao J, Soriano A, Machemer T, Cauntay P, Burel SA, Murray SF, Gaus H, Graham MJ, Swayze EE, Seth PP. Comprehensive Structure-Activity Relationship of Triantennary N-Acetylgalactosamine Conjugated Antisense Oligonucleotides for Targeted Delivery to Hepatocytes. J Med Chem 2016;59:2718-33. [PMID: 26914862 DOI: 10.1021/acs.jmedchem.5b01948] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
34
Liang XH, Shen W, Sun H, Kinberger GA, Prakash TP, Nichols JG, Crooke ST. Hsp90 protein interacts with phosphorothioate oligonucleotides containing hydrophobic 2'-modifications and enhances antisense activity. Nucleic Acids Res 2016;44:3892-907. [PMID: 26945041 PMCID: PMC4856991 DOI: 10.1093/nar/gkw144] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 02/25/2016] [Indexed: 02/05/2023]  Open
35
Rahdar M, McMahon MA, Prakash TP, Swayze EE, Bennett CF, Cleveland DW. Synthetic CRISPR RNA-Cas9-guided genome editing in human cells. Proc Natl Acad Sci U S A 2015;112:E7110-7. [PMID: 26589814 PMCID: PMC4697396 DOI: 10.1073/pnas.1520883112] [Citation(s) in RCA: 130] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]  Open
36
Burel SA, Hart CE, Cauntay P, Hsiao J, Machemer T, Katz M, Watt A, Bui HH, Younis H, Sabripour M, Freier SM, Hung G, Dan A, Prakash TP, Seth PP, Swayze EE, Bennett CF, Crooke ST, Henry SP. Hepatotoxicity of high affinity gapmer antisense oligonucleotides is mediated by RNase H1 dependent promiscuous reduction of very long pre-mRNA transcripts. Nucleic Acids Res 2015;44:2093-109. [PMID: 26553810 PMCID: PMC4797265 DOI: 10.1093/nar/gkv1210] [Citation(s) in RCA: 126] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2015] [Accepted: 10/27/2015] [Indexed: 12/24/2022]  Open
37
Prakash TP, Brad Wan W, Low A, Yu J, Chappell AE, Gaus H, Kinberger GA, Østergaard ME, Migawa MT, Swayze EE, Seth PP. Solid-phase synthesis of 5'-triantennary N-acetylgalactosamine conjugated antisense oligonucleotides using phosphoramidite chemistry. Bioorg Med Chem Lett 2015;25:4127-30. [PMID: 26299345 DOI: 10.1016/j.bmcl.2015.08.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 07/30/2015] [Accepted: 08/06/2015] [Indexed: 11/20/2022]
38
Østergaard ME, Yu J, Kinberger GA, Wan WB, Migawa MT, Vasquez G, Schmidt K, Gaus HJ, Murray HM, Low A, Swayze EE, Prakash TP, Seth PP. Efficient Synthesis and Biological Evaluation of 5'-GalNAc Conjugated Antisense Oligonucleotides. Bioconjug Chem 2015;26:1451-5. [PMID: 26011654 DOI: 10.1021/acs.bioconjchem.5b00265] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
39
Prakash TP, Lima WF, Murray HM, Li W, Kinberger GA, Chappell AE, Gaus H, Seth PP, Bhat B, Crooke ST, Swayze EE. Identification of metabolically stable 5'-phosphate analogs that support single-stranded siRNA activity. Nucleic Acids Res 2015;43:2993-3011. [PMID: 25753666 PMCID: PMC4381071 DOI: 10.1093/nar/gkv162] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 02/16/2015] [Accepted: 02/19/2015] [Indexed: 12/23/2022]  Open
40
Liu J, Hu J, Hicks JA, Prakash TP, Corey DR. Modulation of Splicing by Single-Stranded Silencing RNAs. Nucleic Acid Ther 2015;25:113-20. [PMID: 25757055 DOI: 10.1089/nat.2014.0527] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
41
Pandey SK, Nowak A, Perkins J, Ferng A, Prakash TP. Effect of 2'-O-[2-[2-(N,N-dimethylamino)ethoxy]ethyl] modification on activity of gapmer antisense oligonucleotides containing 2',4'-constrained 2'-O-ethyl nucleic acid. Bioorg Med Chem Lett 2015;25:1688-1691. [PMID: 25804718 DOI: 10.1016/j.bmcl.2015.03.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Revised: 02/26/2015] [Accepted: 03/02/2015] [Indexed: 01/30/2023]
42
Hu J, Liu J, Narayanannair KJ, Lackey JG, Kuchimanchi S, Rajeev KG, Manoharan M, Swayze EE, Lima WF, Prakash TP, Xiang Q, Martinez C, Corey DR. Allele-selective inhibition of mutant atrophin-1 expression by duplex and single-stranded RNAs. Biochemistry 2014;53:4510-8. [PMID: 24981774 PMCID: PMC4108179 DOI: 10.1021/bi500610r] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
43
Prakash TP, Graham MJ, Yu J, Carty R, Low A, Chappell A, Schmidt K, Zhao C, Aghajan M, Murray HF, Riney S, Booten SL, Murray SF, Gaus H, Crosby J, Lima WF, Guo S, Monia BP, Swayze EE, Seth PP. Targeted delivery of antisense oligonucleotides to hepatocytes using triantennary N-acetyl galactosamine improves potency 10-fold in mice. Nucleic Acids Res 2014;42:8796-807. [PMID: 24992960 PMCID: PMC4117763 DOI: 10.1093/nar/gku531] [Citation(s) in RCA: 418] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]  Open
44
Yu J, Pandey SK, Khatri H, Prakash TP, Swayze EE, Seth PP. Synthesis and antisense properties of 2'-O-(2S-methoxypropyl)-RNA-modified gapmer antisense oligonucleotides. ChemMedChem 2014;9:2040-4. [PMID: 24891270 DOI: 10.1002/cmdc.201402099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Indexed: 11/06/2022]
45
Liang XH, Shen W, Sun H, Prakash TP, Crooke ST. TCP1 complex proteins interact with phosphorothioate oligonucleotides and can co-localize in oligonucleotide-induced nuclear bodies in mammalian cells. Nucleic Acids Res 2014;42:7819-32. [PMID: 24861627 PMCID: PMC4081088 DOI: 10.1093/nar/gku484] [Citation(s) in RCA: 74] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]  Open
46
Hu J, Liu J, Yu D, Aiba Y, Lee S, Pendergraff H, Boubaker J, Artates JW, Lagier-Tourenne C, Lima WF, Swayze EE, Prakash TP, Corey DR. Exploring the effect of sequence length and composition on allele-selective inhibition of human huntingtin expression by single-stranded silencing RNAs. Nucleic Acid Ther 2014;24:199-209. [PMID: 24694346 DOI: 10.1089/nat.2013.0476] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]  Open
47
Migawa MT, Prakash TP, Vasquez G, Seth PP, Swayze EE. Synthesis and biophysical properties of constrained D-altritol nucleic acids (cANA). Org Lett 2013;15:4316-9. [PMID: 23937264 DOI: 10.1021/ol401730d] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
48
Liu J, Yu D, Aiba Y, Pendergraff H, Swayze EE, Lima WF, Hu J, Prakash TP, Corey DR. ss-siRNAs allele selectively inhibit ataxin-3 expression: multiple mechanisms for an alternative gene silencing strategy. Nucleic Acids Res 2013;41:9570-83. [PMID: 23935115 PMCID: PMC3814390 DOI: 10.1093/nar/gkt693] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]  Open
49
Prakash TP, Lima WF, Murray HM, Elbashir S, Cantley W, Foster D, Jayaraman M, Chappell AE, Manoharan M, Swayze EE, Crooke ST. Lipid nanoparticles improve activity of single-stranded siRNA and gapmer antisense oligonucleotides in animals. ACS Chem Biol 2013;8:1402-6. [PMID: 23614580 DOI: 10.1021/cb4001316] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
50
Egli M, Minasov G, Tereshko V, Pallan PS, Teplova M, Inamati GB, Lesnik EA, Owens SR, Ross BS, Prakash TP, Manoharan M. Correction to Probing the Influence of Stereoelectronic Effects on the Biophysical Properties of Oligonucleotides: Comprehensive Analysis of the RNA Affinity, Nuclease Resistance, and Crystal Structure of Ten 2′-O-Ribonucleic Acid Modifications. Biochemistry 2013. [DOI: 10.1021/bi4002166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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