264D

THREE-DIMENSIONAL CRYSTAL STRUCTURE OF THE A-TRACT DNA DODECAMER D(CGCAAATTTGCG) COMPLEXED WITH THE MINOR-GROOVE-BINDING DRUG HOECHST 33258

Summary for 264D

• Entry DOI: 10.2210/pdb264d/pdb
• Descriptor: DNA (5'-D(*CP*GP*CP*AP*AP*AP*TP*TP*TP*GP*CP*G)-3'), 2'-(4-HYDROXYPHENYL)-5-(4-METHYL-1-PIPERAZINYL)-2,5'-BI-BENZIMIDAZOLE (3 entities in total)
• Functional Keywords: b-dna, double helix, complexed with drug, dna
• Total number of polymer chains: 2
• Total formula weight: 7749.31

Authors

Vega, M.C.,Garcia-Saez, I.,Aymami, J.,Eritja, R.,Van Der Marel, G.A.,Van Boom, J.H.,Rich, A.,Coll, M. (deposition date: 1994-09-22, release date: 1995-03-31, Last modification date: 2024-02-14)

Primary citation

Vega, M.C.,Garcia Saez, I.,Aymami, J.,Eritja, R.,Van der Marel, G.A.,Van Boom, J.H.,Rich, A.,Coll, M.
Three-dimensional crystal structure of the A-tract DNA dodecamer d(CGCAAATTTGCG) complexed with the minor-groove-binding drug Hoechst 33258.
Eur.J.Biochem., 222:721-726, 1994

PubMed Abstract: The molecular structure of the DNA A-tract dodecamer d(CGCAAATTTGCG) complexed with the drug Hoechst 33258 has been determined by X-ray diffraction analysis. The Hoechst molecule binds in the DNA minor groove covering the sequence AATTT of the central A-tract, with the piperazine group close to one of the GC regions. The drug molecule makes two three-centered hydrogen bonds from the nitrogen atoms of the benzimidazole rings to the N3 and O2 atoms of the DNA bases. Although a high propeller twist is observed in the A-tract, only one unsymmetrical three-centered hydrogen bond is present in the DNA major groove. The structure is compared with other minor-groove-binding drug complexes and the influence of these drugs on DNA A-tracts is discussed.

PubMed: 7517864
DOI: 10.1111/j.1432-1033.1994.tb18917.x

Experimental method

X-RAY DIFFRACTION (2.44 Å)