Inhibition of the thermally driven B to Z transition by intercalating drugs

Calculation of hydrodynamic properties for G-quadruplex nucleic acid structures from in silico bead models

Nucleic acids enriched in guanine bases can adopt unique quadruple helical tertiary structures known as G-quadruplexes. G-quadruplexes have emerged as attractive drug targets as many G-quadruplex-forming sequences have been discovered in functionally critical sites within the human genome, including the telomere, oncogene promoters, and mRNA processing sites. A single G-quadruplex-forming sequence can adopt one of many folding topologies, often resulting in a lack of a single definitive atomic-level resolution structure for many of these sequences and a major challenge to the discovery of G-quadruplex-selective small molecule drugs. Low-resolution techniques employed to study G-quadruplex structures (e.g., CD spectroscopy) are often unable to discern between G-quadruplex structural ensembles, while high-resolution techniques (e.g., NMR spectroscopy) can be overwhelmed by a highly polymorphic system. Hydrodynamic bead modeling is an approach to studying G-quadruplex structures that could bridge the gap between low-resolution techniques and high-resolution molecular models. Here, we present a discussion of hydrodynamic bead modeling in the context of studying G-quadruplex structures, highlighting recent successes and limitations to this approach, as well as an example featuring a G-quadruplex structure formed from the human telomere. This example can easily be adapted to the investigation of any other G-quadruplex-forming sequences.

Binding and oxidative cleavage studies of DNA by mixed ligand Co(III) and Ni(II) complexes of quinolo [3,2-b]benzodiazapine and 1,10-phenanthroline

Two mixed ligand complexes of the type [M(phen)(2)(qbdp)](PF(6))n.xH(2)O where M = Co(III) and Ni(II), qbdp = quinolo[3,2-b] benzodiazepine and phen = 1,10-phenanthroline, n = 3 or 2, x = 2 or 3 have been synthesized and characterized by employing analytical and spectral methods. The DNA binding property of the complexes with calf thymus-DNA has been investigated by using absorption spectra, viscosity measurements as well as thermal denaturation studies. The absorption spectral results indicate that the Co(III) and Ni(II) complexes intercalate between the base pairs of the DNA tightly with intrinsic DNA binding constant of 6.4 x 10(4) and 4.8 x 10(4) M(-1) in Tris HCl buffer containing 50 mM NaCl, respectively. The large enhancement in the relative viscosity of DNA on binding to the quinolo [3,2-b] benzodiazepine supports the proposed DNA binding modes. The complexes on reaction with super coiled (SC) DNA shows nuclease activity.

Synthesis, crystal structure, cytotoxic activity and DNA-binding properties of the copper (II) and zinc (II) complexes with 1-[3-(2-pyridyl)pyrazol-1-ylmethyl]naphthalene

A new ligand L, 1-[3-(2-pyridyl)pyrazol-1-ylmethyl]naphthalene, and its two metal complexes, [Cu(L)3](ClO4)2 (1) and [Zn(L)3](ClO4)2(H2O)2 (2), have been synthesized and characterized. The crystal structure of complex 1 was determined by single crystal X-ray diffraction, which crystallized in monoclinic, space group P2(1)/n with unit cell parameters, a = 12.710(4) angstroms, b = 12.135(3) angstroms, c = 33.450(9) angstroms, beta = 93.281(5) degrees and Z = 4. The Cu atom was six-coordinated to N(1), N(2), N(4), N(5), N(7) and N(8) from three L ligands and formed a slightly distorted octahedral geometry. Complexes 1 and 2, and ligand L were subjected to biological tests in vitro using three different cancer cell lines (HL-60, BGC-823 and MDA-MB-435). Complex 1 showed significant cytotoxic activity against three cancer cell lines. The interactions of complexes 1 and 2, and ligand L with calf thymus DNA were then investigated by thermal denaturation, viscosity measurements and spectrophotometric methods. The experimental results indicated that complexes 1 and 2 bound to DNA by intercalative mode via the ligand L. The intrinsic binding constants of complexes 1 and 2, and ligand L with DNA were 1.8 x 10(4), 5.4 x 10(3) and 2.76 x 10(3) M(-1), respectively.

Preferential binding of quinolones to DNA with alternating G, C / A, T sequences: a spectroscopic study

The binding of quinolones, nalidixic acid (Nal), oxolinic acid (Oxo) with double stranded polynucleotides was undertaken by using UV-melting, UV-Vis absorption, fluorescence and CD spectroscopic techniques. The binding of Nal or Oxo to the polynucleotides under low-salt buffer conditions were determined for poly (dA).(dT), poly [d(A-T)], poly (dG).(dC), poly [d(G-C)] and E. coli DNA. The fluorescence data were analyzed using a previously established two step mechanism with two different DNA-Drug complexes [Rajeswari et al., Biochemistry 26, 6825-31 (1987)]. The first complex [DN](1) with a binding constant K(1), is formed where the interactions are 'nonspecific' and complex [DN](2) with a binding constant K(2), is formed where the interactions are "specific" which involve (additional) hydrophobic type of interactions like 'stacking' of the drug and the overall association constant is represented as K(=K(1)K(2)). The order of binding for Nal and Oxo is: poly [d(G-C)] > poly [d(A- T)] > E. coli > poly (dG).(dC) > poly (dA).(dT). Interaction of quinolones seems to be preferential in the alternating G, C or A, T stretches of DNA than those of non-alternating. Within any alternating or non-alternating in DNA sequences the G, C rich sequences have distinctly greater binding than A, T sequences. The overall association constant data (K) reveal higher binding of Oxo to DNA compared to Nal to any given polynucleotide investigated; which also explains the higher antibacterial potency of Oxo. Changes in the absorption difference spectra and in circular dichroic spectra also manifest these results. As the melting temperatures of the polynucleotides were only marginally raised in presence of the quinolone, we rule out the possibility of 'classical intercalation' of the drug. Amino group of guanine facilitates the binding of quinolones and therefore has the greater binding with the DNA. However, poly (dG).(dC) is known to exist in 'A' conformation which is not adopted by quinolones as in the case of poly (dA).(dT). Present results suggest that Nal or Oxo bind to DNA in a non-classical fashion which is partially stacking in nature.

Study on the interactions between CuL(2) and Morin with DNA

Absorption, fluorescence spectral and viscometric studies have been carried out on the interaction of Morin (2',3,4',5,7-pentahydroxyflavone, ) and its Cu complex, CuL(2) x 2H(2)O [L=Morin (2'-OH group deprotonated), ] with calf thymus DNA. CuL(2) shows different spectral characteristics from that of Morin in the presence of DNA. Increasing fluorescence is seen for CuL(2) with DNA addition whereas decreased fluorescence is observed for Morin. Quenching fluorescence is observed for the DNA-EB system when CuL(2) is added whereas slightly quenched fluorescence is seen for the DNA-EB system with Morin addition. The relative viscosity of DNA and the DNA-EB system increases with the addition of CuL(2.) Hypochromism and a smaller shift are observed in the UV-visible spectra of CuL(2) in the presence of DNA and the denatured temperature of DNA is decreased in the presence of CuL(2). The above results suggested that Morin and CuL(2) can both bind to DNA, but the binding mode is different. The complex binds to DNA mainly by intercalation, while Morin binds in a nonintercalating mode.

Z-->B transition in poly[d(G-m5C)2] induced by interaction with 4',6-diamidino-2-phenylindole

The Z form of poly[d(G-m5C)2], in presence of Mg2+ ion, is found to be transformed into B form upon interaction with 4',6-diamidino-2-phenylindole (DAPI). The Z-->B transformation is complete at a mixing ratio of about 0.07 DAPI per DNA base pairs, i.e., each DAPI molecule may be related to the conversion of 6-7 base pairs. An interaction between DAPI and poly[d(G-m5C)2] in its Z form at low drug: DNA ratios is suggested from optical dichroism and time-resolved luminescence anisotropy results. The spectroscopic behaviour of DAPI indicates that the Z conformation of DNA does not provide normal binding sites for DAPI, such as groove or intercalation sites, but that the initial association may be of external nature.

9-aminoacridine inhibits the B-Z transition of poly(dA-dT)

9-Aminoacridine is the parent compound of a family of pharmacologically active model substances that bind to DNA through intercalation between base pairs. In the present study we show that 9-aminoacridine inhibits the B-to-Z isomerization of poly(dA-dT) in conditions that otherwise cause it to occur (5 M NaCl and 123 mM Ni(ClO4)2). Higher concentrations of Ni(ClO4)2 (155 mM) are able to induce the Z-form due to the disruption of the drug-polynucleotide interaction by the metal ion. Additionally, the dye reverses the Z-form in certain conditions. Thus, the data from this study indicate that 9-aminoacridine binds preferentially to the B-form of poly(dA-dT).

Inhibition of the B to Z transition in poly(dGdC).poly(dGdC) by covalent attachment of ethidium: kinetic studies

The photoaffinity analogue ethidium monoazide was used to prepare samples of poly(dGdC).poly(dGdC) containing covalently attached ethidium. The effects of both noncovalently and covalently bound ethidium on the kinetics of the NaCl-induced B to Z transition in poly(dGdC).poly(dGdC) was examined using absorbance and fluorescence spectroscopy to monitor the reaction. Covalently and noncovalently attached ethidium were equal in the extent to which they reduce the rate of the B to Z transition. By using fluorescence to selectively monitor the fate of noncovalently bound ethidium over the course of the transition, we found that ethidium completely dissociates as the reaction proceeds, but at a rate that lags behind the conversion of the polymer to the Z form. These experiments provide evidence for the redistribution of noncovalently bound ethidium over the course of the B to Z transition, leading to the development of biphasic reaction kinetics. The observed kinetics suggest that the primary effect of both covalently and noncovalently bound ethidium is on the nucleation step of the B to Z transition. The reduction in the rate of the B to Z transition by noncovalently or covalently bound ethidium may be quantitatively explained as resulting from the reduced probability of finding a drug-free length of helix long enough for nucleation to occur. As necessary ancillary experiments, the defined length deoxyoligonucleotides (dGdC)4, (dGdC)5, and (dGdC)6 were synthesized and used in kinetic experiments designed to determine the nucleation length of the B to Z transition, which was found to be 6 bp. The activation energy of the B to Z transition was demonstrated to be independent of the amount of covalently bound ethidium and was found to be 21.2 +/- 1.1 kcal mol-1. Covalent attachment of ethidium was observed to increase the rate of the reverse Z to B transition, presumably by locking regions of the polymer into a right-handed conformation and thereby providing nucleation sites from which the Z to B conversion may propagate.

Effect of intercalative binding compared to external binding on Z/B equilibrium of poly d(GMe5C) using fluorescent oxazolopyridocarbazoles as probes

Using the fluorimetric determination of the binding isotherms in combination with circular dichroism, we have investigated the effect of the binding of the intercalating chromophore oxazolopyridocarbazole (OPC) to poly d(GMe5C) on B/Z equilibrium, compared to the effect of the external binder OPC derivative pentyl-2-OPC. The intercalating OPC appears to be very efficient in reversing left-handed poly d(GMe5C) into the right-handed conformation, according to a cooperative mode. For each OPC molecule intercalated into the B form, 7 base pairs were switched from the Z to B conformation. In contrast, the binding of the external binder pentyl-OPC resulted in a limited Z to B transition, involving the switch of 1.4 base pairs from the Z to B conformation. Moreover, OPC appears much more efficient than pentyl-OPC in inhibiting both the extent and kinetics of the salt-induced B/Z transition. At low drug to DNA ratio (D/P = 1/50), a 7-fold and 1.5-fold inhibition of the B/Z transition kinetics occurs in the presence of OPC and pentyl-OPC, respectively. These features are discussed in terms of the difference existing between the entropic contribution in the DNA binding of intercalating agents, compared to external binders.

Structure and stability of Z* DNA

The structure and stability of the left handed Z* DNA aggregate was examined by spectroscopic methods and by electron microscopy. Poly(dGdC), upon heating in the presence of Mn++, forms a large aggregate which may be sedimented at 12,000 X g, with a circular dichroism spectrum characteristic of left handed DNA. Aggregation gives rise to turbidity changes at visible wavelengths, providing a convenient means of monitoring the transition in solution. The wavelength dependence of turbidity is consistent with the scattering behavior of a long thin rod. Electron microscopy shows that Z* DNA is a large fibrous structure of indeterminant length, with a uniform diameter of approximately 20 nm. The results obtained in solution and under the requisite conditions for electron microscopy are mutually consistent. Poly(dGdC) preparations with average lengths of 60, 240, 500, and 2000 base pairs all form Z* DNA. Poly(dGm5dC) forms Z* DNA in the presence of Mn++ without heating, but poly(dAdC)-poly(dGdT) and calf thymus DNA cannot be induced to the Z* form under any conditions tried. Kinetic studies, monitored by turbidity changes, provide evidence that the formation of Z* DNA proceeds by a nucleated condensation mechanism. Dissolution of the Z* aggregate results from the chelation of Mn++ or by the addition of the intercalator ethidium bromide. The allosteric conversion of Z* DNA to an intercalated, right handed form by ethidium is demonstrated by kinetic studies, equilibrium binding studies and circular dichroism spectroscopy. Electron microscopy provides a striking visualization of the dissolution of the Z* aggregate by ethidium.

Porphyrin induced Z to B conversion of poly(dG-dC)2 in ethanol

The water soluble porphyrins H2TMpyP-2, H2TMpyP-4, and CuTMpyP-4 are found to bind to Z-form poly(dG-dC)2 in 60% ethanol (v/v) and to facilitate the conversion of the polymer to the B form. Metalloporphyrins with axial ligands (MnTMpyP-4, ZnTMpyP-4) interact to some degree with the Z form, but do not lead to extensive conversion to the B form. The conversion of the Z form into the B form was determined by CD titration experiments, which were used to quantitate the fraction of poly(dG-dC)2 present in each conformation. Under all conditions each bound porphyrin molecule converts multiple base pairs from Z to B. The kinetics of porphyrin reactions with Z-poly(dG-dC)2 in 60% ethanol were measured using two different detection techniques. Stopped flow spectrophotometry was used to observe the time-dependent spectral changes associated with the porphyrins during the reaction. Time-dependent changes in the poly(dG-dC)2 conformation were observed directly using CD. The porphyrin absorbance changes under the conditions of these experiments have a much shorter half time (t1/2 approximately 0.1 to 2 sec) than the CD changes (t1/2 approximately 10 sec). Thus it could be determined that a complex with spectral characteristics similar to those of the porphyrin intercalated into B-form poly(dG-dC)2 is produced while the polymer is predominantly in the Z form.