This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


1me1

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (06:31, 1 May 2024) (edit) (undo)
 
(13 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1me1.gif|left|200px]]<br /><applet load="1me1" size="350" color="white" frame="true" align="right" spinBox="true"
 
-
caption="1me1" />
 
-
'''CHIMERIC HAIRPIN WITH 2',5'-LINKED RNA LOOP AND RNA STEM'''<br />
 
-
==Overview==
+
==Chimeric hairpin with 2',5'-linked RNA loop and RNA stem==
-
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.
+
<StructureSection load='1me1' size='340' side='right'caption='[[1me1]]' scene=''>
-
 
+
== Structural highlights ==
-
==About this Structure==
+
<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>
-
1ME1 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1ME1 OCA].
+
</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>
-
==Reference==
+
<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>
-
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://ispc.weizmann.ac.il//pmbin/getpm?pmid=13129354 13129354]
+
</table>
-
[[Category: Protein complex]]
+
__TOC__
-
[[Category: Damha, M J.]]
+
</StructureSection>
-
[[Category: Denisov, A Y.]]
+
[[Category: Large Structures]]
-
[[Category: Gehring, K.]]
+
[[Category: Damha MJ]]
-
[[Category: Hannoush, R N.]]
+
[[Category: Denisov AY]]
-
[[Category: (2']]
+
[[Category: Gehring K]]
-
[[Category: 5')-rna]]
+
[[Category: Hannoush RN]]
-
[[Category: hairpin]]
+
-
[[Category: rna]]
+
-
 
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 13:54:17 2008''
+

Current revision

Chimeric hairpin with 2',5'-linked RNA loop and RNA stem

PDB ID 1me1

Drag the structure with the mouse to rotate

Proteopedia Page Contributors and Editors (what is this?)

OCA

Retrieved from "http://52.214.119.220/wiki/index.php/1me1"
Personal tools