225d: Difference between revisions

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~~{{Seed}}~~

~~[[Image:225d.png|left|200px]]~~

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==A TETRAMERIC DNA STRUCTURE WITH PROTONATED CYTOSINE:CYTOSINE BASE PAIRS==

~~The line below this paragraph, containing~~ "~~STRUCTURE_225d~~", ~~creates the~~ "~~Structure Box~~" on the ~~page.~~

~~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'>[[225d]] is a 4 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=225D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=225D 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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=225d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=225d OCA], [https://pdbe.org/225d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=225d RCSB], [https://www.ebi.ac.uk/pdbsum/225d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=225d ProSAT]</span></td></tr>

~~{{STRUCTURE_225d| PDB=225d | SCENE= }}~~

</table>

== Publication Abstract from PubMed ==

Oligomers containing tracts of cytidine form hemiprotonated base pairs at acid pH and have been considered to be double-stranded. We have solved the structure of the DNA oligomer 5'-d(TCCCCC) at acid pH and find that it is a four-stranded complex in which two base-paired parallel-stranded duplexes are intimately associated, with their base pairs fully intercalated. The relative orientation of the duplexes is antiparallel, so that each base pair is face-to-face with its neighbours. The NMR spectrum displays only six spin systems, showing that the structure is highly symmetrical on the NMR timescale; the four strands are equivalent. A model derived by energy minimization and constrained molecular dynamics shows excellent compatibility with the observed nuclear Overhauser effects (NOEs) particularly for the very unusual inter-residue sugar-sugar NOEs H1'-H1', H1'-H2" and H1'-H4'. These NOEs are probably diagnostic for such tetrameric structures.

~~===~~A ~~TETRAMERIC~~ DNA ~~STRUCTURE WITH PROTONATED CYTOSINE~~:~~CYTOSINE BASE PAIRS===~~

A tetrameric DNA structure with protonated cytosine.cytosine base pairs.,Gehring K, Leroy JL, Gueron M Nature. 1993 Jun 10;363(6429):561-5. PMID:8389423<ref>PMID:8389423</ref>

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.<br>

~~<!--~~

</div>

~~The line below this paragraph, {{ABSTRACT_PUBMED_8389423}}~~, ~~adds the Publication Abstract to~~ the ~~page~~

~~(as it appears on PubMed at http://www~~.~~pubmed~~.~~gov), where 8389423 is the PubMed ID number~~.

== References ==

-->

~~{{ABSTRACT_PUBMED_8389423}}~~

__TOC__

</StructureSection>

==~~About this Structure==~~

[[Category: Large Structures]]

~~Full experimental information is available from [http~~:/~~/oca.weizmann.ac.il/oca-bin/ocashort?id=225D OCA].~~

[[Category: Gehring K]]

[[Category: Gueron M]]

==~~Reference~~==

[[Category: Leroy JL]]

~~A tetrameric DNA structure with protonated cytosine.cytosine base pairs., Gehring K, Leroy JL, Gueron M, Nature. 1993 Jun 10;363(6429):561-5. PMID:[http:~~/~~/www.ncbi.nlm.nih.gov/pubmed/8389423 8389423]~~

~~[[Category: Gehring, K.]]~~

~~[[Category: Gueron, M.]]~~

[[Category: ~~Leroy, J L.~~]]

[[Category: ~~Dna~~]]

[[Category: ~~Intercalated cytosine tetrad~~]]

[[Category: ~~Nmr~~]]

~~''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 13:46:31 2008''~~

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@@ Line 1: / Line 1: @@
-{{Seed}}
-[[Image:225d.png|left|200px]]
-<!--
+==A TETRAMERIC DNA STRUCTURE WITH PROTONATED CYTOSINE:CYTOSINE BASE PAIRS==
-The line below this paragraph, containing "STRUCTURE_225d", creates the "Structure Box" on the page.
+<StructureSection load='225d' size='340' side='right'caption='[[225d]]' 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'>[[225d]] is a 4 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=225D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=225D 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='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=225d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=225d OCA], [https://pdbe.org/225d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=225d RCSB], [https://www.ebi.ac.uk/pdbsum/225d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=225d ProSAT]</span></td></tr>
-{{STRUCTURE_225d|  PDB=225d  |  SCENE=  }}
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+Oligomers containing tracts of cytidine form hemiprotonated base pairs at acid pH and have been considered to be double-stranded. We have solved the structure of the DNA oligomer 5'-d(TCCCCC) at acid pH and find that it is a four-stranded complex in which two base-paired parallel-stranded duplexes are intimately associated, with their base pairs fully intercalated. The relative orientation of the duplexes is antiparallel, so that each base pair is face-to-face with its neighbours. The NMR spectrum displays only six spin systems, showing that the structure is highly symmetrical on the NMR timescale; the four strands are equivalent. A model derived by energy minimization and constrained molecular dynamics shows excellent compatibility with the observed nuclear Overhauser effects (NOEs) particularly for the very unusual inter-residue sugar-sugar NOEs H1'-H1', H1'-H2" and H1'-H4'. These NOEs are probably diagnostic for such tetrameric structures.
-===A TETRAMERIC DNA STRUCTURE WITH PROTONATED CYTOSINE:CYTOSINE BASE PAIRS===
+A tetrameric DNA structure with protonated cytosine.cytosine base pairs.,Gehring K, Leroy JL, Gueron M Nature. 1993 Jun 10;363(6429):561-5. PMID:8389423<ref>PMID:8389423</ref>
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-<!--
+</div>
-The line below this paragraph, {{ABSTRACT_PUBMED_8389423}}, adds the Publication Abstract to the page
+<div class="pdbe-citations 225d" style="background-color:#fffaf0;"></div>
-(as it appears on PubMed at http://www.pubmed.gov), where 8389423 is the PubMed ID number.
+== References ==
--->
+<references/>
-{{ABSTRACT_PUBMED_8389423}}
+__TOC__
+</StructureSection>
-==About this Structure==
+[[Category: Large Structures]]
-Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=225D OCA].
+[[Category: Gehring K]]
+[[Category: Gueron M]]
-==Reference==
+[[Category: Leroy JL]]
-A tetrameric DNA structure with protonated cytosine.cytosine base pairs., Gehring K, Leroy JL, Gueron M, Nature. 1993 Jun 10;363(6429):561-5. PMID:[http://www.ncbi.nlm.nih.gov/pubmed/8389423 8389423]
-[[Category: Gehring, K.]]
-[[Category: Gueron, M.]]
-[[Category: Leroy, J L.]]
-[[Category: Dna]]
-[[Category: Intercalated cytosine tetrad]]
-[[Category: Nmr]]
-''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Tue Jul 29 13:46:31 2008''