106d: Difference between revisions

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-[[Image:106d.gif|left|200px]]<br /><applet load="106d" size="450" color="white" frame="true" align="right" spinBox="true"
-caption="106d" />
-'''SOLUTION STRUCTURES OF THE I-MOTIF TETRAMERS OF D(TCC), D(5MCCT) AND D(T5MCC). NOVEL NOE CONNECTIONS BETWEEN AMINO PROTONS AND SUGAR PROTONS'''<br />
-==Overview==
+==Solution structures of the i-motif tetramers of D(TCC), D(5MCCT) and D(T5MCC). Novel NOE connections between amino protons and sugar protons==
-BACKGROUND: At slightly acid or even neutral pH, oligodeoxynucleotides, that include a stretch of cytidines form a tetramer structure in which two, parallel-stranded duplexes have their hemi-protonated C.C+ base pairs, face-to-face and fully intercalated, in a so-called i-motif, first, observed serendipitously in [d(TC5)]4. RESULTS: A high-definition, structure of [d(TCC)]4 was computed on the basis of inter-residue, distances corresponding to 21 NOESY cross-peaks measured at short mixing, times. A similarly defined structure of [d(5mCCT)]4 was also obtained. A, small number of very characteristic (amino proton)-(sugar proton), cross-peaks entails the intercalation topology. The structure is generally, similar to that of [d(TC5)]4. The sequence d(T5mCC) forms two tetramers in, comparable proportions. The intercalation topologies are read off the two, patterns of (amino proton)-(sugar proton) cross-peaks: one is the same as, in the d(TCC) tetramer, the other has the intercalated strands shifted by, one base, which avoids the steric hindrance between the methyl groups of, the 5mC pairs of the two duplexes. CONCLUSIONS: The structures obtained in, this work and the procedures introduced to characterize them and to solve, the problems linked to the symmetry of the structure provide tools for, further exploring the conditions required for formation of the i-motif.
+<StructureSection load='106d' size='340' side='right'caption='[[106d]]' scene=''>
+== Structural highlights ==
+<table><tr><td colspan='2'>[[106d]] is a 4 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=106D OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=106D 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=MCY:5-METHYL-2-DEOXYCYTIDINE'>MCY</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=106d FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=106d OCA], [https://pdbe.org/106d PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=106d RCSB], [https://www.ebi.ac.uk/pdbsum/106d PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=106d ProSAT]</span></td></tr>
+</table>
+<div style="background-color:#fffaf0;">
+== Publication Abstract from PubMed ==
+BACKGROUND: At slightly acid or even neutral pH, oligodeoxynucleotides that include a stretch of cytidines form a tetramer structure in which two parallel-stranded duplexes have their hemi-protonated C.C+ base pairs face-to-face and fully intercalated, in a so-called i-motif, first observed serendipitously in [d(TC5)]4. RESULTS: A high-definition structure of [d(TCC)]4 was computed on the basis of inter-residue distances corresponding to 21 NOESY cross-peaks measured at short mixing times. A similarly defined structure of [d(5mCCT)]4 was also obtained. A small number of very characteristic (amino proton)-(sugar proton) cross-peaks entails the intercalation topology. The structure is generally similar to that of [d(TC5)]4. The sequence d(T5mCC) forms two tetramers in comparable proportions. The intercalation topologies are read off the two patterns of (amino proton)-(sugar proton) cross-peaks: one is the same as in the d(TCC) tetramer, the other has the intercalated strands shifted by one base, which avoids the steric hindrance between the methyl groups of the 5mC pairs of the two duplexes. CONCLUSIONS: The structures obtained in this work and the procedures introduced to characterize them and to solve the problems linked to the symmetry of the structure provide tools for further exploring the conditions required for formation of the i-motif.
-==About this Structure==
+Solution structures of the i-motif tetramers of d(TCC), d(5methylCCT) and d(T5methylCC): novel NOE connections between amino protons and sugar protons.,Leroy JL, Gueron M Structure. 1995 Jan 15;3(1):101-20. PMID:7743125<ref>PMID:7743125</ref>
-D 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://ispc.weizmann.ac.il/oca-bin/ocashort?id=106D OCA].
-==Reference==
+From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
-Solution structures of the i-motif tetramers of d(TCC), d(5methylCCT) and d(T5methylCC): novel NOE connections between amino protons and sugar protons., Leroy JL, Gueron M, Structure. 1995 Jan 15;3(1):101-20. PMID:[http://ispc.weizmann.ac.il//pmbin/getpm?pmid=7743125 7743125]
+</div>
-[[Category: Protein complex]]
+<div class="pdbe-citations 106d" style="background-color:#fffaf0;"></div>
-[[Category: Gueron, M.]]
+== References ==
-[[Category: Leroy, J.L.]]
+<references/>
-[[Category: dna]]
+__TOC__
+</StructureSection>
-''Page seeded by [http://ispc.weizmann.ac.il/oca OCA ] on Sat Nov 24 21:44:12 2007''
+[[Category: Large Structures]]
+[[Category: Gueron M]]
+[[Category: Leroy J-L]]