Structural Modification Changes the DNA Binding Mode of Cation-Substituted Anthraquinone Photonucleases:  Association by Intercalation or Minor Groove Binding Determines the DNA Cleavage Efficiency†

Biochemistry ◽  
1997 ◽  
Vol 36 (34) ◽  
pp. 10463-10473 ◽  
Author(s):  
David T. Breslin ◽  
Changjun Yu ◽  
Danith Ly ◽  
Gary B. Schuster
Keyword(s):  
Dna Binding ◽  
Dna Cleavage ◽  
Structural Modification ◽  
Binding Mode ◽  
Minor Groove ◽  
Minor Groove Binding ◽  
Groove Binding ◽  
Cleavage Efficiency

scholarly journals DNA Minor Groove Binding with Bisbenzamidine-Ru(II) Complexes

2019 ◽  
Author(s):  
Mateo I. Sánchez ◽  
Gustavo Rama ◽  
Renata Calo ◽  
Kübra Ucar ◽  
Per Lincoln ◽  
...  
Keyword(s):  
Dna Cleavage ◽  
Coordination Compounds ◽  
Photophysical Properties ◽  
Organic Ligand ◽  
Minor Groove ◽  
The Other ◽  
Minor Groove Binding ◽  
Binding Agent ◽  
Groove Binding ◽  
Dna Minor Groove

We report the first Ru(II) coordination compounds that interact with DNA through a canonical minor groove insertion mode and with selectivity for A/T rich sites. This was made possible by integrating a bis‑benzamidine minor groove DNA-binding agent with a ruthenium(II) complex. Importantly, one of the enantiomers (Δ‑[Ru(bpy)<sub>2</sub><b>b4bpy</b>]<sup>2+</sup>, <b>Δ‑4Ru</b>) shows a considerably higher DNA affinity than the parent organic ligand and than the other enantiomer, particularly for the AATT sequence, while the other enantiomer preferentially targets long AAATTT sites with overall lower affinity. Finally, we demonstrate that the photophysical properties of these new binders can be exploited for DNA cleavage using visible light.

Inhibition of DNA Binding by Human Estrogen-Related Receptor 2 and Estrogen Receptor α with Minor Groove Binding Polyamides†

Biochemistry ◽  
2005 ◽  
Vol 44 (11) ◽  
pp. 4196-4203 ◽  
Author(s):  
Micah D. Gearhart ◽  
Liliane Dickinson ◽  
Jennifer Ehley ◽  
Christian Melander ◽  
Peter B. Dervan ◽  
...  
Keyword(s):  
Estrogen Receptor ◽  
Dna Binding ◽  
Minor Groove ◽  
Estrogen Receptor Α ◽  
Minor Groove Binding ◽  
Groove Binding ◽  
Estrogen Related Receptor

scholarly journals Genetic Analysis of Phage Mu Mor Protein Amino Acids Involved in DNA Minor Groove Binding and Conformational Changes

2011 ◽  
Vol 286 (41) ◽  
pp. 35852-35862 ◽  
Author(s):  
Muthiah Kumaraswami ◽  
Lakshmi Avanigadda ◽  
Rajendra Rai ◽  
Hee-Won Park ◽  
Martha M. Howe
Keyword(s):  
Dna Binding ◽  
Rna Polymerase ◽  
Binding Site ◽  
Conformational Changes ◽  
Minor Groove ◽  
Minor Groove Binding ◽  
Groove Binding ◽  
Specific Chemical ◽  
Mutant Proteins ◽  
Dna Minor Groove

Gene expression during lytic development of bacteriophage Mu occurs in three phases: early, middle, and late. Transcription from the middle promoter, Pm, requires the phage-encoded activator protein Mor and the bacterial RNA polymerase. The middle promoter has a −10 hexamer, but no −35 hexamer. Instead Pm has a hyphenated inverted repeat that serves as the Mor binding site overlapping the position of the missing −35 element. Mor binds to this site as a dimer and activates transcription by recruiting RNA polymerase. The crystal structure of the His-Mor dimer revealed three structural elements: an N-terminal dimerization domain, a C-terminal helix-turn-helix DNA-binding domain, and a β-strand linker between the two domains. We predicted that the highly conserved residues in and flanking the β-strand would be essential for the conformational flexibility and DNA minor groove binding by Mor. To test this hypothesis, we carried out single codon-specific mutagenesis with degenerate oligonucleotides. The amino acid substitutions were identified by DNA sequencing. The mutant proteins were characterized for their overexpression, solubility, DNA binding, and transcription activation. This analysis revealed that the Gly-Gly motif formed by Gly-65 and Gly-66 and the β-strand side chain of Tyr-70 are crucial for DNA binding by His-tagged Mor. Mutant proteins with substitutions at Gly-74 retained partial activity. Treatment with the minor groove- and GC-specific chemical chromomycin A3 demonstrated that chromomycin prevented His-Mor binding but could not disrupt a pre-formed His-Mor·DNA complex, consistent with the prediction that Mor interacts with the minor groove of the GC-rich spacer in the Mor binding site.

scholarly journals DNA Minor Groove Binding with Bisbenzamidine-Ru(II) Complexes

2019 ◽  
Author(s):  
Mateo I. Sánchez ◽  
Gustavo Rama ◽  
Renata Calo ◽  
Kübra Ucar ◽  
Per Lincoln ◽  
...  
Keyword(s):  
Dna Cleavage ◽  
Coordination Compounds ◽  
Photophysical Properties ◽  
Organic Ligand ◽  
Minor Groove ◽  
The Other ◽  
Minor Groove Binding ◽  
Binding Agent ◽  
Groove Binding ◽  
Dna Minor Groove

We report the first Ru(II) coordination compounds that interact with DNA through a canonical minor groove insertion mode and with selectivity for A/T rich sites. This was made possible by integrating a bis‑benzamidine minor groove DNA-binding agent with a ruthenium(II) complex. Importantly, one of the enantiomers (Δ‑[Ru(bpy)<sub>2</sub><b>b4bpy</b>]<sup>2+</sup>, <b>Δ‑4Ru</b>) shows a considerably higher DNA affinity than the parent organic ligand and than the other enantiomer, particularly for the AATT sequence, while the other enantiomer preferentially targets long AAATTT sites with overall lower affinity. Finally, we demonstrate that the photophysical properties of these new binders can be exploited for DNA cleavage using visible light.

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