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| | ==Chimeric hairpin with 2',5'-linked RNA loop and RNA stem== |
| The line below this paragraph, containing "STRUCTURE_1me1", creates the "Structure Box" on the page.
| | <StructureSection load='1me1' size='340' side='right'caption='[[1me1]]' 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'>[[1me1]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ME1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ME1 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">Solution NMR</td></tr> |
| --> | | <tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=5GP:GUANOSINE-5-MONOPHOSPHATE'>5GP</scene>, <scene name='pdbligand=C5P:CYTIDINE-5-MONOPHOSPHATE'>C5P</scene>, <scene name='pdbligand=U5P:URIDINE-5-MONOPHOSPHATE'>U5P</scene></td></tr> |
| {{STRUCTURE_1me1| PDB=1me1 | SCENE= }}
| | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1me1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1me1 OCA], [https://pdbe.org/1me1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1me1 RCSB], [https://www.ebi.ac.uk/pdbsum/1me1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1me1 ProSAT]</span></td></tr> |
| | | </table> |
| '''CHIMERIC HAIRPIN WITH 2',5'-LINKED RNA LOOP AND RNA STEM''' | | __TOC__ |
| | | </StructureSection> |
| | | [[Category: Large Structures]] |
| ==Overview== | | [[Category: Damha MJ]] |
| We have recently shown that hairpins containing 2',5'-linked RNA loops exhibit superior thermodynamic stability compared to native hairpins comprised of 3',5'-RNA loops [Hannoush, R. N.; Damha, M. J. J. Am. Chem. Soc. 2001, 123, 12368-12374]. A remarkable feature of the 2',5'-r(UUCG) tetraloop is that, unlike the corresponding 3',5'-linked tetraloop, its stability is virtually independent of the hairpin stem composition. Here, we determine the solution structure of unusually stable hairpins of the sequence 5'-G(1)G(2)A(3)C(4)-(U(5)U(6)C(7)G(8))-G(9)(U/T(10))C(11)C(12)-3' containing a 2',5'-linked RNA (UUCG) loop and either an RNA or a DNA stem. The 2',5'-linked RNA loop adopts a new fold that is completely different from that previously observed for the native 3',5'-linked RNA loop. The 2',5'-RNA loop is stabilized by (a). U5.G8 wobble base pairing, with both nucleotide residues in the anti-conformation, (b). extensive base stacking, and (c). sugar-base and sugar-sugar contacts, all of which contribute to the extra stability of this hairpin structure. The U5:G8 base pair stacks on top of the C4:G9 loop-closing base pair and thus appears as a continuation of the stem. The loop uracil U6 base stacks above U5 base, while the cytosine C7 base protrudes out into the solvent and does not participate in any of the stabilizing interactions. The different sugar pucker and intrinsic bonding interactions within the 2',5'-linked ribonucleotides help explain the unusual stability and conformational properties displayed by 2',5'-RNA tetraloops. These findings are relevant for the design of more effective RNA-based aptamers, ribozymes, and antisense agents and identify the 2',5'-RNA loop as a novel structural motif.
| | [[Category: Denisov AY]] |
| | | [[Category: Gehring K]] |
| ==About this Structure== | | [[Category: Hannoush RN]] |
| Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ME1 OCA].
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| ==Reference==
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| A novel RNA motif based on the structure of unusually stable 2',5'-linked r(UUCG) loops., Denisov AY, Hannoush RN, Gehring K, Damha MJ, J Am Chem Soc. 2003 Sep 24;125(38):11525-31. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/13129354 13129354]
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| [[Category: Damha, M J.]]
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| [[Category: Denisov, A Y.]] | |
| [[Category: Gehring, K.]] | |
| [[Category: Hannoush, R N.]] | |
| [[Category: Hairpin]] | |
| [[Category: Rna]] | |
| ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Sat May 3 00:55:56 2008''
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