José M Ibarra-Soza

University of California, Davis, Davis, California, United States

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Publications (4)33.12 Total impact

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    Kelly J Phelps · José M Ibarra-Soza · Kiet Tran · Andrew J Fisher · Peter A Beal
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    ABSTRACT: Ribonucleoside analogs bearing terminal alkynes, including 7-ethynyl-8-aza-7-deazaadenosine (7-EAA), are useful for RNA modification applications. However, while alkyne- and triazole-bearing ribonucleosides are in wide spread use, very little information is available on the impact of these modifications on RNA structure. By solving crystal structures for RNA duplexes containing these analogs, we show that, like adenosine, 7-EAA and a triazole derived from 7-EAA base pair with uridine and are well accommodated within an A-form helix. We show copper-catalyzed azide/alkyne cycloaddition (CuAAC) reactions with 7-EAA are sensitive to the RNA secondary structure context with single stranded sites reacting faster than duplex sites. 7-EAA and its triazole products are recognized in RNA template strands as adenosine by avian myoblastosis virus reverse transcriptase (AMV-RT). In addition, 7-EAA in RNA is a substrate for an active site mutant of the RNA editing adenosine deaminase ADAR2. These studies extend our understanding of the impact of these novel nucleobase analogs and set the stage for their use in probing RNA structure and metabolism.
    Full-text · Article · Jun 2014 · ACS Chemical Biology
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    ABSTRACT: Short interfering RNAs (siRNAs) are promising drug candidates for a wide range of targets including those previously considered "undruggable". However, properties associated with the native RNA structure limit drug development and chemical modifications are necessary. Here we describe the structure-guided discovery of functional modifications for the guide strand 5' end using computational screening with the high resolution structure of human Ago2, the key nuclease on the RNA interference pathway. Our results indicate the guide strand 5'-end nucleotide need not engage in Watson-Crick (W/C) H-bonding but must fit the general shape of the 5'-end binding site in MID/PIWI domains of hAgo2 for efficient knockdown. 1,2,3-Triazol-4-yl bases formed from the CuAAC reaction of azides and 1-ethynylribose, which is readily incorporated into RNA via the phosphoramidite, perform well at the guide strand 5'-end. In contrast, purine derivatives with modified Hoogsteen faces or N2 substituents are poor choices for 5'-end modifications. Finally, we identified a 1,2,3-triazol-4-yl base incapable of W/C H-bonding that performs well at guide strand position 12, where base pairing to target was expected to be important. This work expands the repertoire of functional nucleotide analogs for siRNAs.
    No preview · Article · Oct 2013 · Journal of the American Chemical Society
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    ABSTRACT: Here we describe the synthesis of new 7-substituted 8-aza-7-deazaadenosine ribonucleoside phosphoramidites and their use in generating major groove-modified duplex RNAs. A 7-ethynyl analog leads to further structural diversification of the RNA via post-automated RNA synthesis azide-alkyne cycloaddition reactions. In addition, we report preliminary studies on the effects of eight different purine 7-position modifications on RNA duplex stability and pairing specificity. Finally, the effect on RNAi activity of this type of modification at eight different positions in an siRNA guide strand has been explored. Analogs were identified with large 7-position substituents that maintain adenosine pairing specificity and are well-tolerated at specific positions in an siRNA guide strand.
    No preview · Article · Jul 2012 · Organic & Biomolecular Chemistry
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    ABSTRACT: Immune stimulation is a significant hurdle in the development of effective and safe RNA interference therapeutics. Here, we address this problem in the context of a mimic of microRNA-122 by employing novel nucleobase and known 2'-ribose modifications. The nucleobase modifications are analogues of adenosine and guanosine that contain cyclopentyl and propyl minor-groove projections. Via a site-by-site chemical modification analysis, we identify several immunostimulatory 'hot spots' within the miRNA guide strand at which single base modifications significantly reduce immune stimulation. A duplex containing one base modification on each strand proved to be most effective in preventing immune stimulation.
    Full-text · Article · Jun 2011 · Journal of the American Chemical Society