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PDBsum entry 108d

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dna_rna ligands links
DNA PDB id
108d
Jmol PyMol
Contents
DNA/RNA
Ligands
TOT
PDB id:
108d
Name: DNA
Title: The solution structure of a DNA complex with the fluorescent bis intercalator toto determined by nmr spectroscopy
Structure: DNA (5'-d( Cp Gp Cp Tp Ap Gp Cp G)-3'). Chain: a, b. Engineered: yes
Source: Synthetic: yes. Other_details: chemically synthesized
NMR struc: 40 models
Authors: H.P.Spielmann,D.E.Wemmer,J.P.Jacobsen
Key ref:
H.P.Spielmann et al. (1995). Solution structure of a DNA complex with the fluorescent bis-intercalator TOTO determined by NMR spectroscopy. Biochemistry, 34, 8542-8553. PubMed id: 7612596 DOI: 10.1021/bi00027a004
Date:
31-Jan-95     Release date:   03-Jun-95    
 Headers
 References

 

 
DOI no: 10.1021/bi00027a004 Biochemistry 34:8542-8553 (1995)
PubMed id: 7612596  
 
 
Solution structure of a DNA complex with the fluorescent bis-intercalator TOTO determined by NMR spectroscopy.
H.P.Spielmann, D.E.Wemmer, J.P.Jacobsen.
 
  ABSTRACT  
 
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.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20179820 F.Persson, and J.O.Tegenfeldt (2010).
DNA in nanochannels--directly visualizing genomic information.
  Chem Soc Rev, 39, 985-999.  
19072931 F.Persson, F.Westerlund, J.O.Tegenfeldt, and A.Kristensen (2009).
Local conformation of confined DNA studied using emission polarization anisotropy.
  Small, 5, 190-193.  
18554066 C.Zhang, F.Zhang, J.A.van Kan, and J.R.van der Maarel (2008).
Effects of electrostatic screening on the conformation of single DNA molecules confined in a nanochannel.
  J Chem Phys, 128, 225109.  
18350383 J.Ghasemi, S.h.Ahmadi, A.I.Ahmad, and S.Ghobadi (2008).
Spectroscopic characterization of thiazole orange-3 DNA interaction.
  Appl Biochem Biotechnol, 149, 9.  
17411048 G.L.Silva, V.Ediz, D.Yaron, and B.A.Armitage (2007).
Experimental and computational investigation of unsymmetrical cyanine dyes: understanding torsionally responsive fluorogenic dyes.
  J Am Chem Soc, 129, 5710-5718.  
15351985 J.L.Uy, C.L.Asbury, T.W.Petersen, and G.van den Engh (2004).
The polarization of fluorescence of DNA stains depends on the incorporation density of the dye molecules.
  Cytometry A, 61, 18-25.  
12770889 T.E.Malliavin, J.Gau, K.Snoussi, and J.L.Leroy (2003).
Stability of the I-motif structure is related to the interactions between phosphodiester backbones.
  Biophys J, 84, 3838-3847.  
11950085 E.Privat, T.Melvin, F.Mérola, G.Schweizer, S.Prodhomme, U.Asseline, and P.Vigny (2002).
Fluorescent properties of oligonucleotide-conjugated thiazole orange probes.
  Photochem Photobiol, 75, 201-210.  
11683032 E.Privat, T.Melvin, U.Asseline, and P.Vigny (2001).
Oligonucleotide-conjugated thiazole orange probes as "light-up" probes for messenger ribonucleic acid molecules in living cells.
  Photochem Photobiol, 74, 532-541.  
11421063 G.Cosa, K.S.Focsaneanu, J.R.McLean, J.P.McNamee, and J.C.Scaiano (2001).
Photophysical properties of fluorescent DNA-dyes bound to single- and double-stranded DNA in aqueous buffered solution.
  Photochem Photobiol, 73, 585-599.  
10742604 M.Ogris, E.Wagner, and P.Steinlein (2000).
A versatile assay to study cellular uptake of gene transfer complexes by flow cytometry.
  Biochim Biophys Acta, 1474, 237-243.  
10757981 M.Thompson, and N.W.Woodbury (2000).
Fluorescent and photochemical properties of a single zinc finger conjugated to a fluorescent DNA-binding probe.
  Biochemistry, 39, 4327-4338.  
10212573 F.J.Alba, and J.R.Daban (1999).
Inhibition of peroxyoxalate chemiluminescence by intercalation of fluorescent acceptors between DNA bases.
  Photochem Photobiol, 69, 405-409.  
10404969 M.L.Bennink, O.D.Schärer, R.Kanaar, K.Sakata-Sogawa, J.M.Schins, J.S.Kanger, B.G.de Grooth, and J.Greve (1999).
Single-molecule manipulation of double-stranded DNA using optical tweezers: interaction studies of DNA with RecA and YOYO-1.
  Cytometry, 36, 200-208.  
9836579 H.P.Spielmann (1998).
Dynamics of a bis-intercalator DNA complex by 1H-detected natural abundance 13C NMR spectroscopy.
  Biochemistry, 37, 16863-16876.  
9653137 J.Jing, J.Reed, J.Huang, X.Hu, V.Clarke, J.Edington, D.Housman, T.S.Anantharaman, E.J.Huff, B.Mishra, B.Porter, A.Shenker, E.Wolfson, C.Hiort, R.Kantor, C.Aston, and D.C.Schwartz (1998).
Automated high resolution optical mapping using arrayed, fluid-fixed DNA molecules.
  Proc Natl Acad Sci U S A, 95, 8046-8051.  
9612138 J.Nygren, N.Svanvik, and M.Kubista (1998).
The interactions between the fluorescent dye thiazole orange and DNA.
  Biopolymers, 46, 39-51.  
9013654 A.N.Glazer, and R.A.Mathies (1997).
Energy-transfer fluorescent reagents for DNA analyses.
  Curr Opin Biotechnol, 8, 94.  
8604342 B.Akerman, and E.Tuite (1996).
Single- and double-strand photocleavage of DNA by YO, YOYO and TOTO.
  Nucleic Acids Res, 24, 1080-1090.  
8738321 C.Carlsson, A.Larsson, and M.Jonsson (1996).
Influence of optical probing with YOYO on the electrophoretic behavior of the DNA molecule.
  Electrophoresis, 17, 642-651.  
8600453 L.F.Hansen, L.K.Jensen, and J.P.Jacobsen (1996).
Bis-intercalation of a homodimeric thiazole orange dye in DNA in symmetrical pyrimidine-pyrimidine-purine-purine oligonucleotides.
  Nucleic Acids Res, 24, 859-867.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time.

 

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