|
|
| (10 intermediate revisions not shown.) |
| Line 1: |
Line 1: |
| - | [[Image:2q1r.gif|left|200px]] | |
| | | | |
| - | <!--
| + | ==Crystal Structure Analysis of the RNA Dodecamer CGCGAAUUAGCG, with a G-A mismatch.== |
| - | The line below this paragraph, containing "STRUCTURE_2q1r", creates the "Structure Box" on the page.
| + | <StructureSection load='2q1r' size='340' side='right'caption='[[2q1r]], [[Resolution|resolution]] 1.12Å' scene=''> |
| - | You may change the PDB parameter (which sets the PDB file loaded into the applet)
| + | == Structural highlights == |
| - | or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
| + | <table><tr><td colspan='2'>[[2q1r]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q1R OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2Q1R FirstGlance]. <br> |
| - | or leave the SCENE parameter empty for the default display.
| + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 1.12Å</td></tr> |
| - | -->
| + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | {{STRUCTURE_2q1r| PDB=2q1r | SCENE= }}
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2q1r FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2q1r OCA], [https://pdbe.org/2q1r PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2q1r RCSB], [https://www.ebi.ac.uk/pdbsum/2q1r PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2q1r ProSAT]</span></td></tr> |
| - | | + | </table> |
| - | '''Crystal Structure Analysis of the RNA Dodecamer CGCGAAUUAGCG, with a G-A mismatch.'''
| + | __TOC__ |
| - | | + | </StructureSection> |
| - | | + | [[Category: Large Structures]] |
| - | ==Overview== | + | [[Category: Li F]] |
| - | Short interfering RNA (siRNA) duplexes are currently being evaluated as antisense agents for gene silencing. Chemical modification of siRNAs is widely expected to be required for therapeutic applications in order to improve delivery, biostability and pharmacokinetic properties. Beyond potential improvements in the efficacy of oligoribonucleotides, chemical modification may also provide insight into the mechanism of mRNA downregulation mediated by the RNA-protein effector complexes (RNA-induced silencing complex or RISC). We have studied the in vitro activity in HeLa cells of siRNA duplexes against firefly luciferase with substitutions in the guide strand of U for the apolar ribo-2,4-difluorotoluyl nucleotide (rF) [Xia, J. et al. (2006) ACS Chem. Biol., 1, 176-183] as well as of C for rF. Whereas an internal rF:A pair adjacent to the Ago2 ('slicer' enzyme) cleavage site did not affect silencing relative to the native siRNA duplex, the rF:G pair and other mismatches such as A:G or A:A were not tolerated. The crystal structure at atomic resolution determined for an RNA dodecamer duplex with rF opposite G manifests only minor deviations between the geometries of rF:G and the native U:G wobble pair. This is in contrast to the previously found, significant deviations between the geometries of rF:A and U:A pairs. Comparison between the structures of the RNA duplex containing rF:G and a new structure of an RNA with A:G mismatches with the structures of standard Watson-Crick pairs in canonical duplex RNA leads to the conclusion that local widening of the duplex formed by the siRNA guide strand and the targeted region of mRNA is the most likely reason for the intolerance of human Ago2 (hAgo2), the RISC endonuclease, toward internal mismatch pairs involving native or chemically modified RNA. Contrary to the influence of shape, the thermodynamic stabilities of siRNA duplexes with single rF:A, A:A, G:A or C:A (instead of U:A) or rF:G pairs (instead of C:G) show no obvious correlation with their activities. However, incorporation of three rF:A pairs into an siRNA duplex leads to loss of activity. Our structural and stability data also shed light on the role of organic fluorine as a hydrogen bond acceptor. Accordingly, UV melting (T(M)) data, osmotic stress measurements, X-ray crystallography at atomic resolution and the results of semi-empirical calculations are all consistent with the existence of weak hydrogen bonds between fluorine and the H-N1(G) amino group in rF:G pairs of the investigated RNA dodecamers.
| + | [[Category: Pallan PS]] |
| - | | + | |
| - | ==About this Structure== | + | |
| - | 2Q1R is a [[Single protein]] structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2Q1R OCA].
| + | |
| - | | + | |
| - | ==Reference== | + | |
| - | Crystal structure, stability and in vitro RNAi activity of oligoribonucleotides containing the ribo-difluorotoluyl nucleotide: insights into substrate requirements by the human RISC Ago2 enzyme., Li F, Pallan PS, Maier MA, Rajeev KG, Mathieu SL, Kreutz C, Fan Y, Sanghvi J, Micura R, Rozners E, Manoharan M, Egli M, Nucleic Acids Res. 2007;35(19):6424-38. Epub 2007 Sep 18. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/17881374 17881374]
| + | |
| - | [[Category: Single protein]]
| + | |
| - | [[Category: Li, F.]] | + | |
| - | [[Category: Pallan, P S.]] | + | |
| - | [[Category: G-a mismatch]] | + | |
| - | [[Category: Rna]] | + | |
| - | [[Category: Rnai]] | + | |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sun May 4 14:10:57 2008''
| + | |
