Conformational modulation of DNA by polyamide binding: structural effects of f-Im-Py-Im based derivatives on 5′-ACGCGT-3′

Shuo Wang, Yun Chai, Balaji Babu, Vijay Satam, Moses Lee, W. David Wilson
2013 Journal of Molecular Recognition  
The DNA sequence 5'-ACGCGT-3' is in the core site of the Mlu1 cell-cycle box, a transcriptional element in the promoter region of human Dbf4 gene which is highly correlated with a large number of aggressive solid cancers. The polyamide formamido-Imidazole-Pyrrole-Imidazole-Amine + (f-Im-Py-Im-Am + ) can target the minor groove of 5'-ACGCGT-3' as an antiparallel stacked dimer and has shown good activity in inhibiting transcription factor (TF) binding. Recently, f-Im-Py-Im-Am + derivatives that
more » ... volve different orthogonally positioned substituents were synthesized to target the same binding site, and some of them have displayed improved binding and pharmacological properties. In this study, the gel electrophoresis-ligation ladders assay was used to evaluate the conformational effects of f-Im-Py-Im-Am + and derivatives on the target DNA, an essential factor for establishing the molecular basis of polyamide-DNA complexes and their TF inhibition. The results show that the ACGCGT site in DNA has a relatively wide minor groove and a B-form like overall structure. After binding with f-Im-Py-Im-Am + derivatives, the DNA conformation is changed as indicated by the different mobilities in the gel. These conformational effects on DNA will at least help to point to the mechanism for the observed Mlu 1 inhibition activity of these polyamides. Therefore, modulating DNA transcription by locking the DNA shape or altering the minor groove geometry to affect the binding affinity of certain TFs is an attractive possible therapeutic mechanism for polyamides. Some of the substituents are charged with electrostatic interactions with DNA phosphate groups and their charge effects on DNA gel mobility have been observed.
doi:10.1002/jmr.2273 pmid:23784989 pmcid:PMC3814215 fatcat:75ypieid65afzhbpazr33skz74