454D

INTERCALATION AND MAJOR GROOVE RECOGNITION IN THE 1.2 A RESOLUTION CRYSTAL STRUCTURE OF RH[ME2TRIEN]PHI BOUND TO 5'-G(5IU)TGCAAC-3'

Summary for 454D

• Entry DOI: 10.2210/pdb454d/pdb
• Descriptor: 5'-D(*GP*(5IU)P*TP*GP*CP*AP*AP*C)-3', DELTA-ALPHA-RH[2R,9R-DIAMINO-4,7-DIAZADECANE]9,10-PHENANTHRENEQUINONE DIIMINE (3 entities in total)
• Functional Keywords: metallointercalator, intercalation, major groove recognition, photoexcitable, dna
• Total number of polymer chains: 10
• Total formula weight: 27776.85

Authors

Kielkopf, C.L.,Erkkila, K.E.,Hudson, B.P.,Barton, J.K.,Rees, D.C. (deposition date: 1999-03-03, release date: 2000-02-21, Last modification date: 2024-04-03)

Primary citation

Kielkopf, C.L.,Erkkila, K.E.,Hudson, B.P.,Barton, J.K.,Rees, D.C.
Structure of a photoactive rhodium complex intercalated into DNA.
Nat.Struct.Biol., 7:117-121, 2000

PubMed Abstract: Intercalating complexes of rhodium(III) are strong photo-oxidants that promote DNA strand cleavage or electron transfer through the double helix. The 1.2 A resolution crystal structure of a sequence-specific rhodium intercalator bound to a DNA helix provides a rationale for the sequence specificity of rhodium intercalators. It also explains how intercalation in the center of an oligonucleotide modifies DNA conformation. The rhodium complex intercalates via the major groove where specific contacts are formed with the edges of the bases at the target site. The phi ligand is deeply inserted into the DNA base pair stack. The primary conformational change of the DNA is a doubling of the rise per residue, with no change in sugar pucker from B-form DNA. Based upon the five crystallographically independent views of an intercalated DNA helix observed in this structure, the intercalator may be considered as an additional base pair with specific functional groups positioned in the major groove.

PubMed: 10655613
DOI: 10.1038/72385

Experimental method

X-RAY DIFFRACTION (1.2 Å)