1d30: Difference between revisions
New page: left|200px<br /><applet load="1d30" size="450" color="white" frame="true" align="right" spinBox="true" caption="1d30, resolution 2.400Å" /> '''THE STRUCTURE OF DA... |
No edit summary |
||
| Line 1: | Line 1: | ||
[[Image:1d30.jpg|left|200px]]<br /><applet load="1d30" size=" | [[Image:1d30.jpg|left|200px]]<br /><applet load="1d30" size="350" color="white" frame="true" align="right" spinBox="true" | ||
caption="1d30, resolution 2.400Å" /> | caption="1d30, resolution 2.400Å" /> | ||
'''THE STRUCTURE OF DAPI BOUND TO DNA'''<br /> | '''THE STRUCTURE OF DAPI BOUND TO DNA'''<br /> | ||
==Overview== | ==Overview== | ||
The structure of the DNA fluorochrome 4'-6-diamidine-2-phenyl indole | The structure of the DNA fluorochrome 4'-6-diamidine-2-phenyl indole (DAPI) bound to the synthetic B-DNA oligonucleotide C-G-C-G-A-A-T-T-C-G-C-G has been solved by single crystal x-ray diffraction methods, at a resolution of 2.4 A. The structure is nearly isomorphous with that of the native DNA molecule alone. With one DAPI and 25 waters per DNA double helix, the residual error is 21.5% for the 2428 reflections above the 2-sigma level. DAPI inserts itself edgewise into the narrow minor groove, displacing the ordered spine of hydration. DAPI and a single water molecule together span the four AT base pairs at the center of the duplex. The indole nitrogen forms a bifurcated hydrogen bond with the thymine O2 atoms of the two central base pairs, as with netropsin and Hoechst 33258. The preference of all three of these drugs for AT regions of B-DNA is a consequence of three factors: (1) The intrinsically narrower minor groove in AT regions than in GC regions of B-DNA, leading to a snug fit of the flat aromatic drug rings between the walls of the groove. (2) The more negative electrostatic potential within the minor groove in AT regions, attributable in part to the absence of electropositive-NH2 groups along the floor of the groove, and (3) The steric advantage of the absence of those same guanine-NH2 groups, thus permitting the drug molecule to sink deeper into the groove. Groove width and electrostatic factors are regional, and define the relative receptiveness of a section of DNA since they operate over several contiguous base pairs. The steric factor is local, varying from one base pair to the next, and hence is the means of fine-tuning sequence specificity. | ||
==About this Structure== | ==About this Structure== | ||
1D30 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with DAP as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http:// | 1D30 is a [http://en.wikipedia.org/wiki/Protein_complex Protein complex] structure of sequences from [http://en.wikipedia.org/wiki/ ] with <scene name='pdbligand=DAP:'>DAP</scene> as [http://en.wikipedia.org/wiki/ligand ligand]. Full crystallographic information is available from [http://oca.weizmann.ac.il/oca-bin/ocashort?id=1D30 OCA]. | ||
==Reference== | ==Reference== | ||
| Line 13: | Line 13: | ||
[[Category: Protein complex]] | [[Category: Protein complex]] | ||
[[Category: Cascio, D.]] | [[Category: Cascio, D.]] | ||
[[Category: Dickerson, R | [[Category: Dickerson, R E.]] | ||
[[Category: Goodsell, D | [[Category: Goodsell, D S.]] | ||
[[Category: Grzeskowiak, K.]] | [[Category: Grzeskowiak, K.]] | ||
[[Category: Larsen, T.]] | [[Category: Larsen, T.]] | ||
| Line 22: | Line 22: | ||
[[Category: double helix]] | [[Category: double helix]] | ||
''Page seeded by [http:// | ''Page seeded by [http://oca.weizmann.ac.il/oca OCA ] on Thu Feb 21 12:12:29 2008'' | ||
Revision as of 13:12, 21 February 2008
|
THE STRUCTURE OF DAPI BOUND TO DNA
OverviewOverview
The structure of the DNA fluorochrome 4'-6-diamidine-2-phenyl indole (DAPI) bound to the synthetic B-DNA oligonucleotide C-G-C-G-A-A-T-T-C-G-C-G has been solved by single crystal x-ray diffraction methods, at a resolution of 2.4 A. The structure is nearly isomorphous with that of the native DNA molecule alone. With one DAPI and 25 waters per DNA double helix, the residual error is 21.5% for the 2428 reflections above the 2-sigma level. DAPI inserts itself edgewise into the narrow minor groove, displacing the ordered spine of hydration. DAPI and a single water molecule together span the four AT base pairs at the center of the duplex. The indole nitrogen forms a bifurcated hydrogen bond with the thymine O2 atoms of the two central base pairs, as with netropsin and Hoechst 33258. The preference of all three of these drugs for AT regions of B-DNA is a consequence of three factors: (1) The intrinsically narrower minor groove in AT regions than in GC regions of B-DNA, leading to a snug fit of the flat aromatic drug rings between the walls of the groove. (2) The more negative electrostatic potential within the minor groove in AT regions, attributable in part to the absence of electropositive-NH2 groups along the floor of the groove, and (3) The steric advantage of the absence of those same guanine-NH2 groups, thus permitting the drug molecule to sink deeper into the groove. Groove width and electrostatic factors are regional, and define the relative receptiveness of a section of DNA since they operate over several contiguous base pairs. The steric factor is local, varying from one base pair to the next, and hence is the means of fine-tuning sequence specificity.
About this StructureAbout this Structure
1D30 is a Protein complex structure of sequences from [1] with as ligand. Full crystallographic information is available from OCA.
ReferenceReference
The structure of DAPI bound to DNA., Larsen TA, Goodsell DS, Cascio D, Grzeskowiak K, Dickerson RE, J Biomol Struct Dyn. 1989 Dec;7(3):477-91. PMID:2627296
Page seeded by OCA on Thu Feb 21 12:12:29 2008