We apologize for Proteopedia being slow to respond. For the past two years, a new implementation of Proteopedia has been being built. Soon, it will replace this 18-year old system. All existing content will be moved to the new system at a date that will be announced here.

1ac3

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (08:05, 10 April 2024) (edit) (undo)
 
(10 intermediate revisions not shown.)
Line 1: Line 1:
-
[[Image:1ac3.gif|left|200px]]
 
-
<!--
+
==SOLUTION STRUCTURE OF AN RNA-DNA HYBRID DUPLEX CONTAINING A 3'-THIOFORMACETAL LINKER AND AN RNA A-TRACT, NMR, 8 STRUCTURES==
-
The line below this paragraph, containing "STRUCTURE_1ac3", creates the "Structure Box" on the page.
+
<StructureSection load='1ac3' size='340' side='right'caption='[[1ac3]]' 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'>[[1ac3]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AC3 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1AC3 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=TCP:5-METHYLTHYMIDINE'>TCP</scene>, <scene name='pdbligand=TSP:3-THIO-THYMIDINE-5-PHOSPHATE'>TSP</scene></td></tr>
-
{{STRUCTURE_1ac3| PDB=1ac3 | SCENE= }}
+
<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=1ac3 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1ac3 OCA], [https://pdbe.org/1ac3 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1ac3 RCSB], [https://www.ebi.ac.uk/pdbsum/1ac3 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1ac3 ProSAT]</span></td></tr>
-
 
+
</table>
-
'''SOLUTION STRUCTURE OF AN RNA-DNA HYBRID DUPLEX CONTAINING A 3'-THIOFORMACETAL LINKER AND AN RNA A-TRACT, NMR, 8 STRUCTURES'''
+
__TOC__
-
 
+
</StructureSection>
-
 
+
[[Category: Large Structures]]
-
==Overview==
+
[[Category: Cross CW]]
-
Neutral and achiral backbone linkers are promising replacements for the phosphodiester linkages of antisense oligonucleotides that target mRNA sequences. Results are presented here for the solution structure elucidation by NMR of an RNA x DNA hybrid duplex, r(GCGCAAAACGCG) x d(CGCGTT-SCH2O-TTGCGC) (designated RIII), containing a 3'-thioformacetal (3'-TFMA) backbone substitution in the DNA strand. The 3'-thioformacetal linker can be accommodated in the hybrid duplex in a conformation that is drastically different from its form in a DNA x DNA duplex but close to that of the canonical A-form helix, reflecting the sequence requirement for hybridization. While the global features of RIII are similar to what are described in the literature, the 3'-TFMA modification drives sugar puckers of the adjacent residues to more C3'-endo-like conformations and causes distortions in related twist angles and helical rises. The helical conformation analyses of each of the two strands and the hybrid duplex enable a clear account of the conformational variability of both the DNA and RNA strands. The A-tract in the RNA strand features an overall straight helix and a more prominent bend at the 3'-end CG step. The structure of RIII provides a structural basis for the improved thermal stability of RIII compared to the corresponding DNA x DNA duplex and insights into the factors that are important concerns for the design of new, effective antisense oligonucleotides.
+
[[Category: Gao X]]
-
 
+
[[Category: Rice JS]]
-
==About this Structure==
+
-
1AC3 is a [[Single protein]] structure. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1AC3 OCA].
+
-
 
+
-
==Reference==
+
-
Solution structure of an RNA x DNA hybrid duplex containing a 3'-thioformacetal linker and an RNA A-tract., Cross CW, Rice JS, Gao X, Biochemistry. 1997 Apr 8;36(14):4096-107. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/9100003 9100003]
+
-
[[Category: Single protein]]
+
-
[[Category: Cross, C W.]]
+
-
[[Category: Gao, X.]]
+
-
[[Category: Rice, J S.]]
+
-
[[Category: Antisense oligonucleotide]]
+
-
[[Category: Dna]]
+
-
[[Category: Hybrid duplex]]
+
-
[[Category: Nmr]]
+
-
[[Category: Rna]]
+
-
[[Category: Structure]]
+
-
[[Category: Thioformacetal backbone modification]]
+
-
''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 10:05:17 2008''
+

Current revision

SOLUTION STRUCTURE OF AN RNA-DNA HYBRID DUPLEX CONTAINING A 3'-THIOFORMACETAL LINKER AND AN RNA A-TRACT, NMR, 8 STRUCTURES

PDB ID 1ac3

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/1ac3"
Personal tools