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Publications

  1. Nikan M, Osborn MF, Coles AH, Biscans A, Godinho BMDC, Haraszti RA, Sapp E, Echeverria D, DiFiglia M, Aronin N, Khvorova A. Synthesis and Evaluation of Parenchymal Retention and Efficacy of a Metabolically Stable O-Phosphocholine-N-docosahexaenoyl-l-serine siRNA Conjugate in Mouse Brain. Bioconjug Chem. 28(6): 1758-1766 (2017).
  2. Haraszti RA, Roux L, Coles AH, Turanov AA, Alterman JF, Echeverria D, Godinho BMDC, Aronin N, Khvorova A. 5’-Vinylphosphonate improves tissue accumulation and efficacy of conjugated siRNAs in vivo. Nucleic Acids Res. doi: 10.1093/nar/gkx507 (2017).
  3. Khvorova A, Watts, JK. The chemical evolution of oligonucleotide therapies of clinical utility. Nat Biotechnol. 35(3):238-248 (2017).
  4. Ly S, Navaroli DM, Didiot MC, Cardia J, Pandarinathan L, Alterman JF, Fogarty K, Standley C, Lifshitz LM, Bellve KD, Prot M, Echeverria D, Corvera S, Khvorova A. Visualization of self-delivering hydrophobically modified siRNA cellular internalization. Nucleic Acids Res. 45(1): 15-25 (2017).
  5. Haraszti RA, Didiot MC, Sapp E, Leszyk J, Shaffer SA, Rockwell HE, Gao F, Narain NR, DiFiglia M, Kiebish MA, Aronin N, Khvorova A. High-resolution proteomic and lipidomic analysis of exosomes and microvesicles from different cell sources. J Extracell Vesicles. 5:32570 (2016).
  6. Didiot MC, Hall LM, Coles AH, Haraszti RA, Godinho BM, Chase K, Sapp E, Ly S, Alterman JF, Hassler MR, Echeverria D, Raj L, Morrissey DV, DiFiglia M, Aronin N, Khvorova A. Exosome-mediated Delivery of Hydrophobically Modified siRNA for Huntingtin mRNA Silencing. Mol Ther. (10):1836-1847 (2016).
  7. Nikan M, Osborn MF, Coles AH, Godinho BM, Hall LM, Haraszti RA, Hassler MR, Echeverria D, Aronin N,
    Khvorova A. Docosahexaenoic Acid Conjugation Enhances Distribution and Safety of siRNA upon Local Administration in Mouse Brain. Mol Ther Nucleic Acids. 5(8): e344 (2016).
  8. Coles AC, Osborn MF, Alterman JF, Turanov AA, Godinho BM, Kennington L, Chase K, Aronin N, Khvorova A. A High-Throughput Method for Direct Detection of Therapeutic Oligonucleotide-Induced Gene Silencing In Vivo. Nucleic Acid Ther. Nov 23 [Epub ahead of print] (2015).
  9. Alterman JF, Hall LM, Coles AH, Hassler MR, Didiot MC, Chase K, Abraham J, Sottosanti E, Johnson E,
    Sapp E, Osborn MF, Difiglia M, Aronin N, Khvorova A. Hydrophobically Modified siRNAs Silence Huntingtin mRNA in Primary Neurons and Mouse Brain. Mol Ther Nucleic Acids. 1;4: e266 (2015).
  10. Osborn MF, Alterman JF, Nikan M, Cao H, Didiot MC, Hassler MR, Coles AH, Khvorova A. Guanabenz (Wytensin™) selectively enhances uptake and efficacy of hydrophobically modified siRNAs. Nucleic Acids Res. 43(18): 8664-72  (2015).
  11. Khvorova A, Osborn, MF, Hassler MR. Taking charge of siRNA delivery. Nat Biotechnol. 32(12): 1197-98 (2014).
  12. Byrne M, Tzekov R, Wang Y, Rodgers A, Cardia J, Ford G, Holton K, Pandarinathan L, Lapierre J, Stanney W, Bulock K, Shaw S, Libertine L, Fettes K, Khvorova A, Kaushal S, Pavco P. Novel hydrophobically modified asymmetric RNAi compounds (sd-rxRNA) demonstrate robust efficacy in the eye. J Ocul Pharmacol Ther. 29(10): 855-64 (2013).
  13. Khvorova A, Wolfson A. New competition in RNA regulation. Nat Biotechnol. 30(1): 58-9 (2012).
  14. Lapierre J, Salomon W, Cardia J, Bulock K, Lam JT, Stanney WJ, Ford G, Smith-Anzures B, Woolf T, Kamens J, Khvorova A, Samarsky D. Potent and systematic RNAi mediated silencing with single oligonucleotide compounds. RNA. 17(6): 1032-7 (2011).
  15. Kamens J, Pavco P, Khvorova A. A path to orally active RNAi therapeutics. Drug Delivery Technology. 10(6): 66-70 (2010).
  16. Robertson B, Dalby AB, Karpilow J, Khvorova A, Leake D, Vermeulen A. Specificity and functionality of microRNA inhibitors. Silence. 1(1): 10 (2010).
  17. Anderson E, Boese Q, Khvorova A, Karpilow J. Identifying siRNA-Induced Off-Targets by Microarray Analysis. in Methods in Molecular Biology, vol 442: RNAi: Design and Application (Sailen Barik) 45-63. Humana Press (2008).
  18. Khvorova A, Boese Q, Marshall WS. Rational siRNA design for RNA interference: Optimizations for therapeutic use and current applications. in Modern Biopharmaceuticals: Design, Development and Optimization (Jörg Knäblein) 243-268. Wiley-VCH Verlag GmbH (2008).
  19. Simpson KJ, Selfors LM, Bui J, Reynolds A, Leake D, Khvorova A, et al. Identification of genes that regulate epithelial cell migration using an siRNA screening approach. Nat Cell Biol. 10(9): 1027-38 (2008).
  20. Kisseleva N, Khvorova A, Westhof E, Schiemann O, Wolfson AD. The different role of high-affinity and low-affinity metal ions in cleavage by a tertiary stabilized cis hammerhead ribozyme from tobacco ringspot virus. Oligonucleotides. 18(2): 101-10 (2008).
  21. Anderson EM, Birmingham A, Baskerville S, Reynolds A, Maksimova E, Leake D, Fedorov Y, Karpilow J, Khvorova A. Experimental validation of the importance of seed complement frequency to siRNA specificity. RNA. 14(5): 853-61 (2008).
  22. Li L, Lin X, Khvorova A, Fesik SW, Shen Y. Defining the optimal parameters for hairpin-based knockdown constructs. RNA. 13(10): 1765-74 (2007).
  23. Birmingham A, Anderson E, Sullivan K, Reynolds A, Boese Q, Leake D, Karpilow J, Khvorova A. A protocol for designing siRNAs with high functionality and specificity. Nature Protocols. 2(9): 2068-78 (2007).
  24. Vermeulen A, Robertson B, Dalby AB, Marshall WS, Karpilow J, Leake D, Khvorova A, Baskerville S. Double-stranded regions are essential design components of potent inhibitors of RISC function. RNA. 13(5): 723-30 (2007).
  25. Fedorov Y, Anderson EM, Birmingham A, Reynolds A, Karpilow J, Robinson K, Leake D, Marshall WS, Khvorova A. Off-target effects by siRNA can induce toxic phenotype. RNA. 12(7): 1188-96 (2006).
  26. Jackson AL, Burchard J, Leake D, Reynolds A, Schelter J, Guo J, Johnson JM, Lim L, Karpilow J, Nichols K, Marshall W, Khvorova A, Linsley PS. Position-specific chemical modification of siRNAs reduces "off-target" transcript silencing. RNA. 12(7): 1197-205 (2006).
  27. Reynolds A, Anderson EM, Vermeulen A, Fedorov Y, Robinson K, Leake D, Karpilow J, Marshall WS, Khvorova A. Induction of the interferon response by siRNA is cell type- and duplex length-dependent. RNA. 12(6): 988-93 (2006).
  28. Anderson EM, Miller P, Ilsley D, Marshall W, Khvorova A, Stein CA, et al. Gene profiling study of G3139- and bcl-2-targeting siRNAs identifies a unique G3139 molecular signature. Cancer Gene Ther. 13(4): 406-14 (2006).
  29. Birmingham A, Anderson EM, Reynolds A, Ilsley-Tyree D, Leake D, Fedorov Y, Baskerville S, Maksimova E, Robinson K, Karpilow J, Marshall WS, Khvorova A. 3' UTR seed matches, but not overall identity, are associated with RNAi off-targets. Nature Methods. 3(3): 199-204 (2006).
  30. Birmingham A, Anderson EM, Marshall WS, Khvorova A. Maximum sequence alignment fails to predict off-targeted gene regulation by RNAi. 2005 IEEE computational systems bioinformatics conference, workshops and poster abstract. (2005).
  31. Benimetskaya L, Lai JC, Khvorova A, Wu S, Miller P, Stein CA. Induction of apoptosis by G3139 in melanoma cells. Ann N Y Acad Sci. 1058: 235-45 (2005).
  32. Vermeulen A, Behlen L, Reynolds A, Wolfson A, Marshall WS, Karpilow J, Khvorova A. The contributions of dsRNA structure to dicer specificity and efficiency. RNA. 11(5): 674-82 (2005).
  33. Fedorov Y, King A, Anderson E, Karpilow J, Ilsey D, Marshall W, Khvorova A. Different delivery methods - different expression profiles. Nature Methods. 2(4): 241 (2005).
  34. Lai JC, Benimetskaya L, Khvorova A, Wu S, Hua E, Miller P, et al. Phosphorothioate oligodeoxynucleotides and G3139 induce apoptosis in 518A2 melanoma cells. Molecular Cancer Therapeutics. 4(2): 305-15 (2005).
  35. Boese Q, Leake D, Reynolds A, Read S, Scaringe SA, Marshall WS, Khvorova A. Mechanistic insights aid computational short interfering RNA design. Methods Enzymol. 392: 73-96 (2005).
  36. Kisseleva N, Khvorova A, Westhof E, Schiemann O. Binding of manganese(II) to a tertiary stabilized hammerhead ribozyme as studied by electron paramagnetic resonance spectroscopy. RNA. 11(1): 1-6 (2005).
  37. Benimetskaya L, Lai JC, Khvorova A, Wu S, Hua E, Miller P, et al. Relative bcl-2 independence of drug-induced cytotoxicity and resistance in 518A2 melanoma cells. Clinical Cancer Research. 10(24): 8371-9 (2004).
  38. Saksmerprome V, Roychowdhury-Saha M, Jayasena S, Khvorova A, Burke DH. Artificial tertiary motifs stabilize trans-cleaving hammerhead ribozymes under conditions of submillimolar divalent ions and high temperatures. RNA. 10(12): 1916-24 (2004).
  39. Miller JT, Khvorova A, Scaringe SA, Le Grice SFJ. Synthetic tRNA lys,3 as the replication primer for the HIV-1HXB2 and HIV-1Mal genomes. Nucleic Acids Res. 32(15): 4687-95 (2004).
  40. Canny MD, Jucker FM, Kellogg E, Khvorova A, Jayasena SD, Pardi A. Fast cleavage kinetics of a natural hammerhead ribozyme. J Am Chem Soc. 126(35): 10848-9 (2004).
  41. Hsieh AC, Bo R, Manola J, Vazquez F, Bare O, Khvorova A, et al. A library of siRNA duplexes targeting the phosphoinositide 3-kinase pathway: Determinants of gene silencing for use in cell-based screens. Nucleic Acids Res. 32(3): 893-901 (2004).
  42. Penedo JC, Wilson TJ, Jayasena SD, Khvorova A, Lilley DMJ. Folding of the natural hammerhead ribozyme is enhanced by interaction of auxiliary elements. RNA. 10(5): 880-8 (2004).
  43. Raffo A, Lai JC, Stein CA, Miller P, Scaringe S, Khvorova A, et al. Antisense RNA down-regulation of bcl-2 expression in DU145 prostate cancer cells does not diminish the cytostatic effects of G3139 (oblimersen). Clinical Cancer Research. 10(9): 3195-206 (2004).
  44. Huang F, Khvorova A, Marshall W, Sorkin A. Analysis of clathrin-mediated endocytosis of epidermal growth factor receptor by RNA interference. J Biol Chem. 279(16): 16657-61 (2004).
  45. Reynolds A, Leake D, Boese Q, Scaringe S, Marshall WS, Khvorova A. Rational siRNA design for RNA interference. Nat Biotechnol. 22(3): 326-30 (2004).
  46. Li T, Chang C-, Jin D-, Lin P-, Khvorova A, Stafford DW. Identification of the gene for vitamin K epoxide reductase. Nature. 427(6974): 541-4 (2004).
  47. Khvorova A, Reynolds A, Jayasena SD. Functional siRNAs and miRNAs exhibit strand bias. Cell. 115(2): 209-16 (2003).
  48. Khvorova A, Lescoute A, Westhof E, Jayasena SD. Sequence elements outside the hammerhead ribozyme catalytic core enable intracellular activity. Nat Struct Biol. 10(9): 708-12 (2003).
  49. Wilson JA, Jayasena S, Khvorova A, Sabatinos S, Rodrigue-Gervais IG, Arya S, et al. RNA interference blocks gene expression and RNA synthesis from hepatitis C replicons propagated in human liver cells. Proc Natl Acad Sci U S A. 100(5): 2783-8 (2003).
  50. Vlassov A, Khvorova A, Yarus M. Binding and disruption of phospholipid bilayers by supramolecular RNA complexes. Proc Natl Acad Sci U S A. 98(14): 7706-11 (2001).
  51. Amaya E, Khvorova A, Piggot PJ. Analysis of promoter recognition in vivo directed by σF of bacillus subtilis by using random-sequence oligonucleotides. J Bacteriol. 183(12): 3623-30 (2001).
  52. Khvorova A, Chary VK, Hilbert DW, Piggot PJ. The chromosomal location of the bacillus subtilis sporulation gene spoIIR is important for its function. J Bacteriol. 182(16): 4425-9 (2000).
  53. Khvorova A, Motorin Y, Wolfson AD. Pyrophosphate mediates the effect of certain tRNA mutations on aminoacylation of yeast tRNA(phe). Nucleic Acids Res. 27(22): 4451-6 (1999).
  54. Wolfson AD, Khvorova AM, Sauter C, Florentz C, Giegé R. Mimics of yeast tRNA(asp) and their recognition by aspartyl-tRNA synthetase. Biochemistry. 38(37): 11926-32 (1999).
  55. Khvorova A, Kwak Y, Tamkun M, Majerfeld I, Yarus M. RNAs that bind and change the permeability of phospholipid membranes. Proc Natl Acad Sci U S A. 96(19): 10649-54 (1999).
  56. Khvorova A, Zhang L, Higgins ML, Piggot PJ. The spoIIE locus is involved in the Spo0A-dependent switch in the location of FtsZ rings in bacillus subtilis. J Bacteriol. 180(5): 1256-60 (1998).
  57. Khvorova AM, Motorin IA, Vol'fson AD. Mechanism of discrimination of tRNA(phe) from E. coli by yeast phenylalanine-tRNA-synthetase. Biokhimiya. 58(4): 613-9 (1993).
  58. Khvorova AM, Motorin YA, Wolfson AD, Gladilin KL. Anticodon-dependent aminoacylation of RNA minisubstrate by lysyl-tRNA synthetase. FEBS Lett. 314(3): 256-8 (1992).
  59. Khvorova AM, Motorin IA, Wolfson AD. Pyrophosphate-dependent inactivation of tyrosyl-tRNA synthetase during aminoacylation of heterologous tRNA. Biokhimiya. 57(12): 1913-6 (1992).
  60. Khvorova AM, Motorin YA, Wolfson AD. Crucial role of pyrophosphate in the aminoacylation of E. coli tRNAPhe by yeast phenylalanyl-tRNA synthetase. FEBS Lett. 311(2): 139-42 (1992).
  61. Khvorova AM, Motorin IA, Wolfson AD, Gladilin KL. Specific aminoacylation of oligo U-CCA lysyl-tRNA-synthetase molecules. Dokl Akad Nauk. 325(1): 179-82 (1992).
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