Minor groove RNA triplex in the crystal structure of a ribosomal frameshifting viral pseudoknot

The structure of 4′,6-diamidine-2-phenylindole (DAPI) bound to the synthetic B-DNA oligonucleotide d(CGTGAATTCACG) has been solved in space groupP212121by 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.

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Targeting the DNA minor groove with fused ring dicationic compounds: Comparison of in silico screening and a high-resolution crystal structure

Bioorganic & Medicinal Chemistry Letters ◽

10.1016/j.bmcl.2005.10.036 ◽

2006 ◽

Vol 16 (1) ◽

pp. 15-19 ◽

Cited By ~ 10

Author(s):

Nancy H. Campbell ◽

David A. Evans ◽

Michael P.H. Lee ◽

Gary N. Parkinson ◽

Stephen Neidle

Keyword(s):

Crystal Structure ◽

High Resolution ◽

In Silico ◽

Minor Groove ◽

In Silico Screening ◽

Dna Minor Groove ◽

Fused Ring

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Preferred orientation in an angled intercalation site of a chloro-substituted Λ -[Ru(TAP) 2 (dppz)] 2+ complex bound to d(TCGGCGCCGA) 2

Philosophical Transactions of The Royal Society A Mathematical Physical and Engineering Sciences ◽

10.1098/rsta.2012.0525 ◽

2013 ◽

Vol 371 (1995) ◽

pp. 20120525 ◽

Cited By ~ 9

Author(s):

James P. Hall ◽

Hanna Beer ◽

Katrin Buchner ◽

David J. Cardin ◽

Christine J. Cardin

Keyword(s):

Crystal Structure ◽

Ruthenium Complex ◽

Double Helix ◽

Minor Groove ◽

Preferred Orientation ◽

Atomic Resolution ◽

Oligonucleotide Duplex ◽

First Time

The crystal structure of the ruthenium DNA ‘light-switch’ complex Λ -[Ru(TAP) 2 (11-Cl-dppz)] 2+ (TAP=tetraazaphenanthrene, dppz=dipyrido[3,2- a ′:2′,3′- c ]phenazine) bound to the oligonucleotide duplex d(TCGGCGCCGA) 2 is reported. The synthesis of the racemic ruthenium complex is described for the first time, and the racemate was used in this study. The crystal structure, at atomic resolution (1.0 Å), shows one ligand as a wedge in the minor groove, resulting in the 51 ° kinking of the double helix, as with the parent Λ -[Ru(TAP) 2 (dppz)] 2+ . Each complex binds to one duplex by intercalation of the dppz ligand and also by semi-intercalation of one of the orthogonal TAP ligands into a second symmetrically equivalent duplex. The 11-chloro substituent binds with the major component (66%) oriented with the 11-chloro substituent on the purine side of the terminal step of the duplex.

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