Crystal Structures of Nucleosome Core Particles in Complex with Minor Groove DNA Binding Ligand
R. K. Suto, R.S. Edayathumangalam, C.L. White, C. Melander, J.M. Gottesfeld, P.B. Dervan, and K. Luger, Journal of Molecular Biology, 326:371-380, 2003.
The crystal structures of three nucleosome core particles in complex with site-specific DNA binding ligands, the pyrrole-imidazole polyamides, were determined by x-ray crystallography. While the structure of the histone octamer and its interaction with the DNA remain unaffected by ligand binding, nucleosomal DNA undergoes significant structural changes at the ligand binding sites and in adjacent regions to accommodate the ligands.
Sequence-Specific Recognition of DNA in the Nucleosome by Pyrrole-Imidazole Polyamides
J. M. Gottesfeld, C. Melander, R. K. Suto, H. Raviol, K. Luger, and P.
B. Dervan. Journal of Molecular Biology, 309:615-629,
2001.
Probing the accessibility of the minor groove of nucleosomal DNA with pyrrole-imidazole polyamides. Only one half of the DNA (73 base pairs) and associated histones are shown for clarity, in a view down the superhelical axis.
Sequence-specific
pyrrole-imidazole polyamides can access their target sites in the context
of a positioned nucleosome, depending upon the location of the cognate
site with respect to the histone octamer surface (see figure above). In
some instances, polyamides bind to the nucleosome core particle with equal
affinity compared to free DNA (polyamides 1, 2, and 3; turquois regions
in the figure). In other instances, binding is still observed but with
reduced affinity (4; purple regions). In the most extreme cases, 25- to
50-fold reduced affinity for the nucleosome relative to the free DNA is
observed (5 and 6; magenta regions). These results are based on the DNase
I footprinting data shown below. Polyamide models are shown adjacent to
their binding sites (closed circles = imidazole rings; open circles =
pyrrole rings).
DNase
I footprinting data (cited as data not shown in Gottesfeld et al.)
DNase I Footprint Analysis For Binding Polyamides 1 - 6 To -Satellite
DNA and Nucleosome Core Particles: Polyamides are indicated by number
and correspond to the molecules listed below. Binding reactions were for
2 h prior to nuclease digestion and contained the following concentrations
of polyamide: no polyamide (lanes marked 0) and increasing concentrations
of polyamide (ranging from 3 to 300 nM) for both protein-free DNA and
nucleosomes. Lanes marked "-" were not digested with DNase I.
G + A sequencing reactions are shown. The gel autoradiographs are shown
and the locations of polyamide binding sites are indicated along side
the autoradiograms.
| Polyamides | Binding Site Location |
|---|---|
1 ImPyImPy- |
±38-43** |
2 ImPyPyPy- -PyPyPyPy-ß-Dp
|
±36-41 |
| 3 ImImPyPy--PyPyPyPy-ß-Dp
|
±30-35 and ±62-67 |
| 4 ImIm-ß-ImPy--ImPy-ß-PyPy-ß-Dp
|
±22-28 and ±46-52 |
| 5 ImImPyPy--PyImPyPy-ß-Dp
|
±11-16 |
| 6 ImPyPyPy--ImPyPyPy-ß-Dp
|
±6-11 |
* Im = imidazole; Py = pyrrole; =
-aminobutyric acid; ß=
ß-alanine; Dp = dimethylaminopropylamide
** Relative to the dyad of the 146 bp palindromic 
-satellite DNA sequence
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