Sbirkova-Dimitrova Hristina I, Shivachev Boris
Institute of Mineralogy and Crystallography (IMC), Bulgarian Academy of Sciences, Acad. Georgi Bonchev Str., Bl. 107, 1113 Sofia, Bulgaria.
Acta Crystallogr F Struct Biol Commun. 2017 Sep 1;73(Pt 9):500-504. doi: 10.1107/S2053230X17011384. Epub 2017 Aug 14.
The structure of 4',6-diamidine-2-phenylindole (DAPI) bound to the synthetic B-DNA oligonucleotide d(CGTGAATTCACG) has been solved in space group P222 by single-crystal X-ray diffraction at a resolution of 2.2 Å. The structure is nearly isomorphous to that of the previously reported crystal structure of the oligonucleotide d(CGTGAATTCACG) alone. The adjustments in crystal packing between the native DNA molecule and the DNA-DAPI complex are described. DAPI lies in the narrow minor groove near the centre of the B-DNA fragment, positioned over the A-T base pairs. It is bound to the DNA by hydrogen-bonding and van der Waals interactions. Comparison of the two structures (with and without ligand) shows that DAPI inserts into the minor groove, displacing the ordered spine waters. Indeed, as DAPI is hydrophobic it confers this behaviour on the DNA and thus restricts the presence of water molecules.
通过分辨率为2.2 Å的单晶X射线衍射，在空间群P222中解析了与合成的B-DNA寡核苷酸d（CGTGAATTCACG）结合的4',6-二脒基-2-苯基吲哚（DAPI）的结构。该结构与之前报道的仅寡核苷酸d（CGTGAATTCACG）的晶体结构几乎同晶型。描述了天然DNA分子与DNA-DAPI复合物之间晶体堆积的调整。DAPI位于B-DNA片段中心附近狭窄的小沟中，位于A-T碱基对上方。它通过氢键和范德华相互作用与DNA结合。两种结构（有配体和无配体）的比较表明，DAPI插入小沟，取代了有序的脊状水分子。实际上，由于DAPI是疏水的，它赋予DNA这种行为，从而限制了水分子的存在。
