Steroid diamine-nucleic acid interactions: partial insertion of dipyrandium between unstacked base pairs of the poly(dA-dT) duplex in solution.

Abstract

We report on an NMR investigation of steroid diamine-nucleic acid complexes as a function of phosphateto-drug ratios in aqueous solution in order to evaluate the structural and kinetic aspects of the binding of a nonintercalative drug to a synthetic DNA in solution. The nonexchangeable proton chemical shift parameters for the dipyrandium' poly(dA-dT) complex demonstrate unstacking of base pairs and partial insertion of the steroid diamine at the complexation site. The chemical shifts and linewidths of the exchangeable protons as a function of pH demonstrate that the base pairs are intact but partially exposed to solvent at the steroid diamine binding site. The phosphorus chemical shifts suggest that the base pairs unstack upon complex formation without changes in the ww' polynucleotide backbone torsion angles. The NMR line shape parameters require rapid exchange of the steroid diamine among potential binding sites and are consistent with greater segmental flexibility in the complex compared to the synthetic DNA in solution. The NMR experiments are discusse in rela- USA 73,[3068][3069][3070][3071][3072] for the steroid diamine*DNA complex. Recent investigations into the structure and dynamics of nucleic acids suggest that the DNA helix undergoes conformational transitions as a function of salt (1) and solvent (2-4) and that this flexibility may be of fundamental importance in the specificity of interactions of small molecules and macromolecules with nucleic acids (5-7). This flexibility is further manifested in the folding of DNA around histones in chromatin and the packaging of nucleic acids into phage heads. It has been proposed that DNA either folds smoothly (8, 9) or its chain direction changes abruptly by the generation of kinks every few base pairs (10, 11).Sobell and coworkers (11) recently proposed the kink as a key intermediate in the process of drug intercalation into DNA. They suggested further that steroid diamines bind to and stabilize kinked sites in DNA. The kink is generated in this model by partial unstacking and unwinding (-120) of adjacent base pairs, a change in the glycosidic torsion angles and in the sugar pucker to a C3'endo(3'-5')C2'endo configuration, and only minor adjustments in the backbone rotation angles. It is proposed that the steroid diamine binds to DNA through the minor groove at the kink site and that the complex is stabilized by electrostatic interactions with phosphates on partner strands (11).Experimentally, the strong binding of steroid diamines to nucleic acids is saturated at one drug molecule per five nucleotides, corresponding to a neighbor-exclusion model for complex formation (12)(13)(14). Sedimentation studies demonstrate that the steroid diamine unwinds covalently circular superhelical DNA to half the extent on a molar basis as the ethidium bromide intercalative complex (15).NMR spectroscopy can be used to probe the structural aspects of nonintercalative drug-nucleic acid complexes and hence studies were undertaken on the complex of a synthetic DNA [poly(dA...

The Dynamic Character of the BCL2 Promoter i-Motif Provides a Mechanism for Modulation of Gene Expression by Compounds That Bind Selectively to the Alternative DNA Hairpin Structure

“…A comparison of NMR traces 2 and 7 in Figure A, determined at 3 °C, showed that binding of IMC-76 to the DNA produced very little disruption of the existing hairpin but further populated the flexible hairpin species at the expense of the i-motif, as does increasing the pH from 6.0 to 6.6. IMC-76 has a structural resemblance to a steroidal diamine, which has been shown to bind to unstacked base pairs and stabilize the poly­(dA·dT) duplex . We propose that IMC-76 binds in the non-Watson–Crick base-paired regions of the flexible hairpin adjacent to the GC bases because they have greater flexibility than the GC base-paired regions.…”

“…IMC-76 has a structural resemblance to a steroidal diamine, which has been shown to bind to unstacked base pairs and stabilize the poly(dA·dT) duplex. 46 We propose that IMC-76 binds in the non-Watson–Crick base-paired regions of the flexible hairpin adjacent to the GC bases because they have greater flexibility than the GC base-paired regions. IMC-76 is a lipophilic molecule with limited functionality for H-bonding.…”

The Transcriptional Complex Between the BCL2 i-Motif and hnRNP LL Is a Molecular Switch for Control of Gene Expression That Can Be Modulated by Small Molecules

“…Incremental IMC-76 addition sequesters the flexible hairpin form, which contains five GC base pairs. By analogy with the binding of a steroidal diamine to a poly(dA·dT) duplex, 27 IMC-76 most likely binds in the non-Watson–Crick base pair regions where unstacked base pairs exist capped at either side by GC base pairs (Figure 8 B). IMC-76 sequestration of the flexible hairpin species will deplete the i-motif.…”

Human telomere, oncogenic promoter and 5'-UTR G-quadruplexes: diverse higher order DNA and RNA targets for cancer therapeutics

“…The non-planar and non-aromatic steroid diamines have long been of interest as potential nucleic acid-binding ligands since they have been postulated to bind to and stabilize kink sites in DNA ( 242 ). Experimental support for this hypothesis emerged following NMR demonstration of partial insertion of the steroid diamine, dipyrandium, between unstacked base pairs of poly (dA–dT) ( 243 ). Most importantly, a temperature melting fluorescence-based screen of natural and synthetic molecules identified two steroid diamines, malouetine and funtumine that induce G-quadruplex stabilization ( 244 ).…”