2kh1

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{{Seed}}
 
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[[Image:2kh1.jpg|left|200px]]
 
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==2-Hydroxy-7-nitrofluorene covalently linked into a 13mer DNA duplex - solution structure of the face-up orientation==
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The line below this paragraph, containing "STRUCTURE_2kh1", creates the "Structure Box" on the page.
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<StructureSection load='2kh1' size='340' side='right'caption='[[2kh1]]' scene=''>
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You may change the PDB parameter (which sets the PDB file loaded into the applet)
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== Structural highlights ==
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or the SCENE parameter (which sets the initial scene displayed when the page is loaded),
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<table><tr><td colspan='2'>[[2kh1]] is a 2 chain structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KH1 OCA]. For a <b>guided tour on the structure components</b> use [https://proteopedia.org/fgij/fg.htm?mol=2KH1 FirstGlance]. <br>
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or leave the SCENE parameter empty for the default display.
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</td></tr><tr id='method'><td class="sblockLbl"><b>[[Empirical_models|Method:]]</b></td><td class="sblockDat" id="methodDat">Solution NMR</td></tr>
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<tr id='ligand'><td class="sblockLbl"><b>[[Ligand|Ligands:]]</b></td><td class="sblockDat" id="ligandDat"><scene name='pdbligand=3DR:1,2-DIDEOXYRIBOFURANOSE-5-PHOSPHATE'>3DR</scene>, <scene name='pdbligand=HNF:7-NITRO-9H-FLUOREN-2-OL'>HNF</scene></td></tr>
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{{STRUCTURE_2kh1| PDB=2kh1 | SCENE= }}
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<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[https://proteopedia.org/fgij/fg.htm?mol=2kh1 FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=2kh1 OCA], [https://pdbe.org/2kh1 PDBe], [https://www.rcsb.org/pdb/explore.do?structureId=2kh1 RCSB], [https://www.ebi.ac.uk/pdbsum/2kh1 PDBsum], [https://prosat.h-its.org/prosat/prosatexe?pdbcode=2kh1 ProSAT]</span></td></tr>
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</table>
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<div style="background-color:#fffaf0;">
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== Publication Abstract from PubMed ==
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We demonstrate that THz vibrational activity of a biopolymer can be measured locally, on the effective length scale for polar solvation, with an embedded molecular probe. For this purpose, the polarity probe 2-hydroxy-7-nitrofluorene was linked into a 13mer DNA duplex opposite an abasic site. The NMR solution structure shows that the fluorene moiety occupies a well-defined position in place of a base pair but can flip around the long axis on a millisecond time scale. Femtosecond optical pump-probe experiments are used to measure the time-resolved Stokes shift of emission from the probe. The dynamic shifts for solution in H(2)O and D(2)O are quantified. Their difference is much larger than that expected for free water, implying that only bound water is observed. A weak 26 cm(-1) spectral oscillation of the emission band is observed, which is not present when the probe is free in solution and is therefore caused by the supramolecular structure (DNA and hydration water).
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===2-Hydroxy-7-nitrofluorene covalently linked into a 13mer DNA duplex - solution structure of the face-up orientation===
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Local THz time domain spectroscopy of duplex DNA via fluorescence of an embedded probe.,Dallmann A, Pfaffe M, Mugge C, Mahrwald R, Kovalenko SA, Ernsting NP J Phys Chem B. 2009 Nov 26;113(47):15619-28. PMID:19764701<ref>PMID:19764701</ref>
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From MEDLINE&reg;/PubMed&reg;, a database of the U.S. National Library of Medicine.<br>
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</div>
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The line below this paragraph, {{ABSTRACT_PUBMED_19764701}}, adds the Publication Abstract to the page
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<div class="pdbe-citations 2kh1" style="background-color:#fffaf0;"></div>
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(as it appears on PubMed at http://www.pubmed.gov), where 19764701 is the PubMed ID number.
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== References ==
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<references/>
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{{ABSTRACT_PUBMED_19764701}}
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__TOC__
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</StructureSection>
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==About this Structure==
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[[Category: Large Structures]]
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2KH1 is a 2 chains structure. Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=2KH1 OCA].
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[[Category: Dallmann A]]
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[[Category: Ernsting NP]]
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==Reference==
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[[Category: Kovalenko SA]]
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<ref group="xtra">PMID:19764701</ref><references group="xtra"/>
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[[Category: Mahrwald R]]
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[[Category: Dallmann, A.]]
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[[Category: Muegge C]]
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[[Category: Ernsting, N P.]]
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[[Category: Pfaffe M]]
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[[Category: Kovalenko, S A.]]
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[[Category: Mahrwald, R.]]
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[[Category: Muegge, C.]]
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[[Category: Pfaffe, M.]]
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[[Category: Base pair mimic]]
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[[Category: Conformational flexibility]]
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[[Category: Dna]]
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[[Category: Solution structure]]
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''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Wed Dec 2 10:03:31 2009''
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Current revision

2-Hydroxy-7-nitrofluorene covalently linked into a 13mer DNA duplex - solution structure of the face-up orientation

PDB ID 2kh1

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