View source for 1tuq


==NMR Structure Analysis of the B-DNA Dodecamer CTCtCACGTGGAG with a tricyclic cytosin base analogue==
<StructureSection load='1tuq' size='340' side='right'caption='[[1tuq]]' scene=''>
== Structural highlights ==
<table><tr><td colspan='2'>[[1tuq]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1TUQ OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=1TUQ FirstGlance]. <br>
</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=TC1:3-(5-PHOSPHO-2-DEOXY-BETA-D-RIBOFURANOSYL)-2-OXO-1,3-DIAZA-PHENOTHIAZINE'>TC1</scene></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=1tuq FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=1tuq OCA], [https://pdbe.org/1tuq PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=1tuq RCSB], [https://www.ebi.ac.uk/pdbsum/1tuq PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=1tuq ProSAT]</span></td></tr>
</table>
<div style="background-color:#fffaf0;">
== Publication Abstract from PubMed ==
The influence of the highly fluorescent tricyclic cytosine base analogue (tC) on duplex DNA conformation is investigated. The duplex properties are characterized by absorbance and circular dichroism (CD) for all combinations of neighbouring bases to tC, and an NMR structure is determined for one tC-containing sequence. For the oligonucleotides with one tC incorporated instead of cytosine, the melting temperature is increased on average by 2.7 degrees C above that for the unmodified ones. CD spectra are practically identical for modified and unmodified sequences, indicating an unperturbed B-DNA conformation. The NMR structure determination of the self-complementary sequence 5'-CTC(tC)ACGTGGAG shows a DNA conformation consistent with B-form for the whole duplex. The root-mean-square distance for the nucleotides of the eight central base pairs between the 10 structures with lowest CYANA target functions and a mean structure is 0.45 +/- 0.17 A. The NMR data confirm correct base pairing for tC by the observation of both intrastrand and interstrand imino proton NOEs. Altogether, this suggests that tC works well as a cytosine analogue, i.e. it is situated in the base stack, forming hydrogen bonds with G in the complementary strand, without distorting the DNA backbone conformation. This first example of an artificial, highly fluorescent DNA base that does not perturb the DNA conformation could have valuable applications for the study of the structure and dynamics of nucleic acid systems.

DNA adopts normal B-form upon incorporation of highly fluorescent DNA base analogue tC: NMR structure and UV-Vis spectroscopy characterization.,Engman KC, Sandin P, Osborne S, Brown T, Billeter M, Lincoln P, Norden B, Albinsson B, Wilhelmsson LM Nucleic Acids Res. 2004 Sep 27;32(17):5087-95. Print 2004. PMID:15452275<ref>PMID:15452275</ref>

From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
</div>
<div class="pdbe-citations 1tuq" style="background-color:#fffaf0;"></div>
== References ==
<references/>
__TOC__
</StructureSection>
[[Category: Large Structures]]
[[Category: Albinsson B]]
[[Category: Billeter M]]
[[Category: Brown T]]
[[Category: Engman KC]]
[[Category: Lincoln P]]
[[Category: Norden B]]
[[Category: Osborne S]]
[[Category: Sandin P]]
[[Category: Wilhelmsson LM]]