5NBE

[Ru(TAP)2(dppz-11-CN)]2+ bound to d(TCGGCGCCGA)2

Summary for 5NBE

• Entry DOI: 10.2210/pdb5nbe/pdb
• Descriptor: DNA (5'-D(*TP*CP*GP*GP*CP*GP*CP*CP*GP*A)-3'), lambda-[Ru(tap2-dppz-CN)]2+, BARIUM ION, ... (4 entities in total)
• Functional Keywords: ruthenium, intercalation, dna, asymmetric
• Biological source: synthetic construct
• Total number of polymer chains: 1
• Total formula weight: 3956.06

Authors

McQuaid, K.T.,Hall, J.P.,Cardin, C.J. (deposition date: 2017-03-01, release date: 2018-03-21, Last modification date: 2024-01-10)

Primary citation

McQuaid, K.,Hall, J.P.,Brazier, J.A.,Cardin, D.J.,Cardin, C.J.
X-ray Crystal Structures Show DNA Stacking Advantage of Terminal Nitrile Substitution in Ru-dppz Complexes.
Chemistry, 24:15859-15867, 2018

PubMed Abstract: The new complexes [Ru(TAP) (11-CN-dppz)] , [Ru(TAP) (11-Br-dppz)] and [Ru(TAP) (11,12-diCN-dppz)] are reported. The addition of nitrile substituents to the dppz ligand of the DNA photo-oxidising complex [Ru(TAP) (dppz)] promote π-stacking interactions and ordered binding to DNA, as shown by X-ray crystallography. The structure of Λ-[Ru(TAP) (11-CN-dppz)] with the DNA duplex d(TCGGCGCCGA) shows, for the first time with this class of complex, a closed intercalation cavity with an AT base pair at the terminus. The structure obtained is compared to that formed with the 11-Br and 11,12-dinitrile derivatives, highlighting the stabilization of syn guanine by this enantiomer when the terminal base pair is GC. In contrast the AT base pair has the normal Watson-Crick orientation, highlighting the difference in charge distribution between the two purine bases and the complementarity of the dppz-purine interaction. The asymmetry of the cavity highlights the importance of the purine-dppz-purine stacking interaction.

PubMed: 30063271
DOI: 10.1002/chem.201803021

Experimental method

X-RAY DIFFRACTION (1.51 Å)