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| | {{STRUCTURE_108d| PDB=108d | SCENE= }} | | {{STRUCTURE_108d| PDB=108d | SCENE= }} |
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| - | '''THE SOLUTION STRUCTURE OF A DNA COMPLEX WITH THE FLUORESCENT BIS INTERCALATOR TOTO DETERMINED BY NMR SPECTROSCOPY'''
| + | ===THE SOLUTION STRUCTURE OF A DNA COMPLEX WITH THE FLUORESCENT BIS INTERCALATOR TOTO DETERMINED BY NMR SPECTROSCOPY=== |
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| - | ==Overview==
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| - | We have used two-dimensional 1H NMR spectroscopy to determine the solution structure of the DNA oligonucleotide d(5'-CGCTAGCG-3')2 complexed with the bis-intercalating dye 1,1'-(4,4,8,8-tetramethyl-4,8-diazaundecamethylene)bis[4-(3-methyl -2,3- dihydrobenzo-1,3-thiazolyl-2-methylidene)qui nolinium] tetraiodide (TOTO). The determination of the structure was based on total relaxation matrix analysis of the NOESY cross-peak intensities using the program MARDIGRAS. Improved procedures to consider the experimental "noise" in NOESY spectra during these calculations have been employed. The NOE-derived distance restraints were applied in restrained molecular dynamics calculations. Twenty final structures each were generated for the TOTO complex from both A-form and B-form dsDNA starting structures. The root-mean-square (rms) deviation of the coordinates for the 40 structures of the complex was 1.45 A. The local DNA structure is distorted in the complex. The helix is unwound by 60 degrees and has an overall helical repeat of 12 base pairs, caused by bis-intercalation of TOTO. The poly(propylenamine) linker chain is located in the minor groove of dsDNA. Calculations indicate that the benzothiazole ring system is twisted relative to the quinoline in the uncomplexed TOTO molecule. The site selectivity of TOTO for the CTAG-CTAG site is explained by its ability to adapt to the base pair propeller twist of dsDNA to optimize stacking and the hydrophobic interaction between the thymidine methyl group and the benzothiazole ring. There is a 3000-fold fluorescence enhancement upon binding of TOTO to dsDNA. Rotation about the cyanine methine bonds is possible in free TOTO, allowing relaxation nonradiatively. When bound to dsDNA, the benzothiazole ring and the quinolinium ring are clamped by the nucleobases preventing this rotation, and the chromophore loses excitation energy by fluorescence instead.
| + | The line below this paragraph, {{ABSTRACT_PUBMED_7612596}}, adds the Publication Abstract to the page |
| | + | (as it appears on PubMed at http://www.pubmed.gov), where 7612596 is the PubMed ID number. |
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| | + | {{ABSTRACT_PUBMED_7612596}} |
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| | ==About this Structure== | | ==About this Structure== |
| - | Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=108D OCA]. | + | Full experimental information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=108D OCA]. |
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| | ==Reference== | | ==Reference== |
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| | [[Category: Nmr]] | | [[Category: Nmr]] |
| | [[Category: Toto,bis-thiazole orange]] | | [[Category: Toto,bis-thiazole orange]] |
| - | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Fri May 2 09:25:16 2008'' | + | |
| | + | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Mon Jun 30 15:21:15 2008'' |
Revision as of 12:21, 30 June 2008
Template:STRUCTURE 108d
THE SOLUTION STRUCTURE OF A DNA COMPLEX WITH THE FLUORESCENT BIS INTERCALATOR TOTO DETERMINED BY NMR SPECTROSCOPY
Template:ABSTRACT PUBMED 7612596
About this Structure
Full experimental information is available from OCA.
Reference
Solution structure of a DNA complex with the fluorescent bis-intercalator TOTO determined by NMR spectroscopy., Spielmann HP, Wemmer DE, Jacobsen JP, Biochemistry. 1995 Jul 11;34(27):8542-53. PMID:7612596
Page seeded by OCA on Mon Jun 30 15:21:15 2008
