ABSTRACT
A tetracationic supramolecular cylinder, [Fe(2)L(3)](4+) (L=C(25)H(20)N(4)), with a triple-helical architecture, is just the right size to fit into the major groove of DNA but too big to fit into the minor groove. A detailed NMR spectroscopic analysis supported by molecular dynamics (MD) calculations shows unambiguously the close fit between the cylinder and a duplex oligonucleotide, [d(GACGGCCGTC)(2)]. Furthermore, only the left-handed enantiomer of the cylinder seems to fit the groove geometry. With both free and complexed species of [Fe(2)L(3)](4+) and DNA in solution, the NMR spectra are too complicated for a detailed structure determination. Based on differences in chemical shifts and extensive MD calculations, a realistic qualitative picture of the DNA-cylinder adduct is presented. Several sets of chemical shifts assigned to the protons of the three ligand strands in the cylinder indicate that the iron complex situated in the major groove exhibits restricted rotation on the NMR timescale around the cylindrical axis. The NMR NOE data support a model where the cylinder undergoes both a translational and rotational oscillation in the major groove. The results of an NOE restrained MD calculation indicates that the cylinder induces a 40 degrees bend of the double helix, in accordance with linear dichroism measurements. Other distinct features to be noticed are the very low value of the helical twist (16 degrees) induced at the G(4)C(5) step.
Subject(s)
DNA/chemistry , Iron/chemistry , Oligonucleotides/chemistry , Indicators and Reagents , Magnetic Resonance Spectroscopy , Models, Molecular , Nucleic Acid ConformationABSTRACT
We have designed a synthetic tetracationic metallo-supramolecular cylinder that targets the major groove of DNA with a binding constant in excess of 10(7) M(-1) and induces DNA bending and intramolecular coiling. The two enantiomers of the helical molecule bind differently to DNA and have different structural effects. We report the characterization of the interactions by a range of biophysical techniques. The M helical cylinder binds to the major groove and induces dramatic intramolecular coiling. The DNA bending is less dramatic for the P enantiomer.
Subject(s)
DNA/chemistry , Metals/metabolism , Animals , Cattle , Circular Dichroism , Hydrogen-Ion Concentration , Iron/chemistry , Ligands , Microscopy, Atomic Force , Models, Chemical , Models, Molecular , Nucleic Acid Conformation , Protein Binding , Spectrophotometry , TemperatureABSTRACT
In the groove! A tetracationic supramolecular cylinder, [Fe2 L3 ]4+ (L=C25 H20 N4 ), with a triple-helical architecture is just the right size to fit into the major groove of DNA and too big to fit into the minor groove. NMR spectroscopic data confirm that the cylinder binds in the major groove. Linear dichroism shows that very low loadings of [Fe2 L3 ]4+ have a dramatic bending effect on the DNA and atomic force microscopy images show that this is an intramolecular effect resulting in coils of DNA.
