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| | ==Chimeric hairpin with 2',5'-linked RNA loop and DNA stem== | | ==Chimeric hairpin with 2',5'-linked RNA loop and DNA stem== |
| - | <StructureSection load='1me0' size='340' side='right' caption='[[1me0]], [[NMR_Ensembles_of_Models | 10 NMR models]]' scene=''> | + | <StructureSection load='1me0' size='340' side='right'caption='[[1me0]]' scene=''> |
| | == Structural highlights == | | == Structural highlights == |
| - | <table><tr><td colspan='2'>[[1me0]] is a 1 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ME0 OCA]. For a <b>guided tour on the structure components</b> use [http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1ME0 FirstGlance]. <br> | + | <table><tr><td colspan='2'>[[1me0]] is a 1 chain structure with sequence from [https://en.wikipedia.org/wiki/Synthetic_construct Synthetic construct]. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ME0 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1ME0 FirstGlance]. <br> |
| - | </td></tr><tr id='NonStdRes'><td class="sblockLbl"><b>[[Non-Standard_Residue|NonStd Res:]]</b></td><td class="sblockDat"><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> | + | </td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR, 10 models</td></tr> |
| - | <tr id='related'><td class="sblockLbl"><b>[[Related_structure|Related:]]</b></td><td class="sblockDat">[[1me1|1me1]]</td></tr>
| + | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1me0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1me0 OCA], [https://pdbe.org/1me0 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1me0 RCSB], [https://www.ebi.ac.uk/pdbsum/1me0 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1me0 ProSAT]</span></td></tr> |
| - | <tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=1me0 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1me0 OCA], [http://www.rcsb.org/pdb/explore.do?structureId=1me0 RCSB], [http://www.ebi.ac.uk/pdbsum/1me0 PDBsum]</span></td></tr> | + | |
| | </table> | | </table> |
| | <div style="background-color:#fffaf0;"> | | <div style="background-color:#fffaf0;"> |
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| | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> | | From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br> |
| | </div> | | </div> |
| | + | <div class="pdbe-citations 1me0" style="background-color:#fffaf0;"></div> |
| | == References == | | == References == |
| | <references/> | | <references/> |
| | __TOC__ | | __TOC__ |
| | </StructureSection> | | </StructureSection> |
| - | [[Category: Damha, M J]] | + | [[Category: Large Structures]] |
| - | [[Category: Denisov, A Y]] | + | [[Category: Synthetic construct]] |
| - | [[Category: Gehring, K]] | + | [[Category: Damha MJ]] |
| - | [[Category: Hannoush, R N]] | + | [[Category: Denisov AY]] |
| - | [[Category: Dna]] | + | [[Category: Gehring K]] |
| - | [[Category: Hairpin]] | + | [[Category: Hannoush RN]] |
| - | [[Category: Rna]]
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| Structural highlights
Publication Abstract from PubMed
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.
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:13129354[1]
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
References
- ↑ Denisov AY, Hannoush RN, Gehring K, Damha MJ. A novel RNA motif based on the structure of unusually stable 2',5'-linked r(UUCG) loops. J Am Chem Soc. 2003 Sep 24;125(38):11525-31. PMID:13129354 doi:10.1021/ja036207k
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