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5uza
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==Adenine riboswitch aptamer domain labelled with iodo-uridine by position-selective labelling of RNA (PLOR)== | ==Adenine riboswitch aptamer domain labelled with iodo-uridine by position-selective labelling of RNA (PLOR)== | ||
| - | <StructureSection load='5uza' size='340' side='right' caption='[[5uza]], [[Resolution|resolution]] 2.22Å' scene=''> | + | <StructureSection load='5uza' size='340' side='right'caption='[[5uza]], [[Resolution|resolution]] 2.22Å' scene=''> |
== Structural highlights == | == Structural highlights == | ||
| - | <table><tr><td colspan='2'>[[5uza]] is a 1 chain structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UZA OCA]. For a <b>guided tour on the structure components</b> use [ | + | <table><tr><td colspan='2'>[[5uza]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Vibrio_vulnificus Vibrio vulnificus]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=5UZA OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=5UZA FirstGlance]. <br> |
| - | </td></tr><tr id=' | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">X-ray diffraction, [[Resolution|Resolution]] 2.22Å</td></tr> |
| - | <tr id=' | + | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=ADE:ADENINE'>ADE</scene>, <scene name='pdbligand=IU:5-IODOURIDINE-5-MONOPHOSPHATE'>IU</scene>, <scene name='pdbligand=MG:MAGNESIUM+ION'>MG</scene></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[ | + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=5uza FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5uza OCA], [https://pdbe.org/5uza PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=5uza RCSB], [https://www.ebi.ac.uk/pdbsum/5uza PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=5uza ProSAT]</span></td></tr> |
</table> | </table> | ||
| - | <div style="background-color:#fffaf0;"> | ||
| - | == Publication Abstract from PubMed == | ||
| - | Site-specific incorporation of labeled nucleotides is an extremely useful synthetic tool for many structural studies (e.g., NMR, electron paramagnetic resonance (EPR), fluorescence resonance energy transfer (FRET), and X-ray crystallography) of RNA. However, specific-position-labeled RNAs >60 nt are not commercially available on a milligram scale. Position-selective labeling of RNA (PLOR) has been applied to prepare large RNAs labeled at desired positions, and all the required reagents are commercially available. Here, we present a step-by-step protocol for the solid-liquid hybrid phase method PLOR to synthesize 71-nt RNA samples with three different modification applications, containing (i) a (13)C(15)N-labeled segment; (ii) discrete residues modified with Cy3, Cy5, or biotin; or (iii) two iodo-U residues. The flexible procedure enables a wide range of downstream biophysical analyses using precisely localized functionalized nucleotides. All three RNAs were obtained in <2 d, excluding time for preparing reagents and optimizing experimental conditions. With optimization, the protocol can be applied to other RNAs with various labeling schemes, such as ligation of segmentally labeled fragments. | ||
| - | + | ==See Also== | |
| - | + | *[[Riboswitch 3D structures|Riboswitch 3D structures]] | |
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__TOC__ | __TOC__ | ||
</StructureSection> | </StructureSection> | ||
| - | [[Category: | + | [[Category: Large Structures]] |
| - | [[Category: | + | [[Category: Vibrio vulnificus]] |
| - | [[Category: | + | [[Category: Liu Y]] |
| - | [[Category: | + | [[Category: Stagno JR]] |
| - | [[Category: | + | [[Category: Wang Y-X]] |
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Current revision
Adenine riboswitch aptamer domain labelled with iodo-uridine by position-selective labelling of RNA (PLOR)
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