Induced fit DNA recognition by a minor groove binding analogue of Hoechst 33258: fluctuations in DNA A tract structure investigated by NMR and molecular dynamics simulations.

NMR analysis and molecular dynamics simulations of d(GGTAATTACC)(2) and its complex with a tetrahydropyrimidinium analogue of Hoechst 33258 suggest that DNA minor groove recognition in solution involves a combination of conformational selection and induced fit, rather than binding to a preorganised site. Analysis of structural fluctuations in the bound and unbound states suggests that the degree of induced fit observed is primarily a consequence of optimising van der Waals contacts with the walls of the minor groove resulting in groove narrowing through: (i) changes in base step parameters, including increased helical twist and propeller twist; (ii) changes to the sugar-phosphate backbone conformation to engulf the bound ligand; (iii) suppression of bending modes at the TpA steps. In contrast, the geometrical arrangement of hydrogen bond acceptors on the groove floor appears to be relatively insensitive to DNA conformation (helical twist and propeller twist). We suggest that effective recognition of DNA sequences (in this case an A tract structure) appears to depend to a significant extent on the sequence being flexible enough to be able to adopt the geometrically optimal conformation compatible with the various binding interactions, rather than involving 'lock and key' recognition.

DNA minor groove recognition by bis-benzimidazole analogues of Hoechst 33258: insights into structure-DNA affinity relationships assessed by fluorescence titration measurements.

Fluorescence titration measurements have been used to examine the binding interaction of a number of analogues of the bis -benzimidazole DNA minor groove binding agent Hoechst 33258 with the decamer duplex d(GCAAATTTGC)2. The method of continuous variation in ligand concentration (Job plot analysis) reveals a 1:1 binding stoichiometry for all four analogues; binding constants are independent of drug concentration (in the range [ligand] = 0.1-5 microM). The four analogues studied were chosen in order to gain some insight into the relative importance of a number of key structural features for minor groove recognition, namely (i) steric bulk of the N -methylpiperazine ring, (ii) ligand hydrophobicity, (iii) isohelicity with the DNA minor groove and (iv) net ligand charge. This was achieved, first, by replacing the bulky, non-planar N -methylpiperazine ring with a less bulky planar charged imidazole ring permitting binding to a narrower groove, secondly, by linking the N -methylpiperazine ring to the phenyl end of the molecule to give the molecule a more linear, less isohelical conformation and, finally, by introducing a charged imidazole ring in place of the phenolic OH making it dicationic, enabling the contribution of the additional electrostatic interaction and extended conformation to be assessed. Delta G values were measured at 20 degrees C in the range -47.6 to -37.5 kJ mol-1 and at a number of pH values between 5.0 and 7.2. We find a very poor correlation between Delta G values determined by fluorescence titration and effects of ligand binding on DNA melting temperatures, concluding that isothermal titration methods provide the most reliable method of determining binding affinities. Our results indicate that the bulky N -methylpiperazine ring imparts a large favourable binding interaction, despite its apparent requirement for a wider minor groove, which others have suggested arises in a large part from the hydrophobic effect. The binding constant appears to be insensitive to the isohelical arrangement of the constituent rings which in these analogues gives the same register of hydrogen bonding interactions with the floor of the groove.

DNA minor groove recognition by a tetrahydropyrimidinium analogue of hoechst 33258: NMR and molecular dynamics studies of the complex with d(GGTAATTACC)2.

Hoechst 43254 (H43254), a 2,3,4,5-tetrahydropyrimidin-1-ium analogue of the bis-benzimidazole minor groove binding agent Hoechst 33258 (H33258), has been studied by NMR and restrained molecular dynamics in its complex with d(GGTAATTACC)2. We investigate the origin of the enhanced complex stability afforded by the replacement of the N-methylpiperazine ring of H33258 with the tetrahydropyrimidinium ring of H43254, the latter presenting the opportunity for specific minor groove-directed recognition through a pyrimidinium NH. A set of 25 drug-DNA NOEs define the binding site with some precision and are used as part of the structural analysis using restrained molecular dynamics simulations considering explicit solvation and the treatment of electrostatic interactions using the particle mesh Ewald method within AMBER 4.1. Starting with three different initial structures with the drug located at different sites in the groove (pairwise RMSD 4.3-12.6 A) we arrive at three very similar structures (pairwise RMSD 0.80-1.34 A) representing one converged binding site at the centre of the AATT tract. Two of the three structures show the tetrahydropyrimidinium ring to be suitably positioned for an -NH to adenine N3 hydrogen bond suggesting that electrostatic interactions may play an important role in the enhanced affinity as well as imparting additional A-T specificity. The NMR data show that the pyrimidinium NH interaction is dynamic since signal averaging from the two sides of the ring indicate rapid rotations in the bound form.

Solution structure and dynamics of the A-T tract DNA decamer duplex d(GGTAATTACC)2: implications for recognition by minor groove binding drugs.

The structure of the DNA decamer duplex d(GGTAATTACC)(2) has been determined using NMR distance restraints and molecular dynamics simulations of 500 ps to 1 ns in aqueous solution at 300 K. Using both canonical A and canonical B starting structures [root-mean-square deviation (RMSD) 4.6 A; 1 A=10(-10) m], with and without experimental restraints, we show that all four simulations converge to a similar envelope of final conformations with B-like helical parameters (pairwise RMSD 1.27-2.03 A between time-averaged structures). While the two restrained simulations reach a stable trajectory after 300-400 ps, the unrestrained trajectories take longer to equilibrate. We have analysed the dynamic aspects of these structures (sugar pucker, helical twist, roll, propeller twist and groove width) and show that the minor groove width in the AATT core of the duplex fluctuates significantly, sampling both wide and narrow conformations. The structure does not have the highly pre-organized narrow minor groove generally regarded as essential for recognition and binding by small molecules, suggesting that ligand binding carries with it a significant component of 'induced-fit'. Our simulations show that there are significant differences in structure between the TpA step (where p=phosphate) and the ApA and ApT steps, where a large roll into the major groove at the TpA step appears to be an important factor in widening the minor groove at this position.

Molecular recognition between a new pentacyclic acridinium salt and DNA sequences investigated by optical spectroscopic techniques, proton nuclear magnetic resonance spectroscopy, and molecular modeling.

A pentacyclic acridine, 1H-2,3-dihydroindolizino[7,6,5-kl]acridinium chloride (1), related in structure to tetra- and pentacyclic marine natural products, has previously been shown to induce apoptosis in breast and non-small-cell lung tumor cell lines and shows significant differences in biological potency and antitumor profile from other intercalating agents based on the acridine framework. We report on the molecular recognition of the acridinium salt with DNA, quantified by optical spectroscopic methods, and have compared these results with the clinical agent amsacrine (m-AMSA). The results point to an intercalative association between 1 and G-C-rich sequences of DNA. We have synthesized a hexamer duplex d(ACGCGT)2, presenting two potential 5'-CpG recipient sites, and have investigated in detail by NMR and molecular modeling methods the orientational preferences of 1, particularly with regard to the pyrrolidine ring system. On the basis of the intermolecular nuclear Overhauser effect (NOE) data, four possible intercalation models were considered; no single model produced a significantly better fit than any of the others. The best fit to the experimental data was obtained by considering a dynamic equilibrium between the different intercalated orientations with the drug maximizing pi-overlap with the G-C base pairs at the intercalation site. We found little evidence for any degree of groove specificity imparted by the pyrrolidine ring. If these simulations have biological relevance they suggest that, at most, the agent induces only a transitory hot spot in the DNA which, evidently, is sufficient to be sensed by damage-recognition mechanisms of the cell.