Spectroscopic analysis of drug-nucleic acid interactions

Synthesis and Photophysics of Water-Soluble Psoralens with Red-Shifted Absorption

8-Methoxypsoralen (8-MOP) serves as a PUVA (psoralen + UV-A) agent in the treatment of certain skin diseases. Derivatives of 8-MOP with cationic aromatic substituents at the five positions were synthesized and characterized by steady-state, femtosecond and nanosecond spectroscopy as well as cyclic voltammetry. The aromatic substituents' positive charge increases the water solubility and the affinity toward intercalation into DNA. The aromatic substituents were supposed to lower the psoralen S₁ energy and thereby suppress a photo-induced electron transfer (PET) with guanine-bearing DNA. Such a suppression of this PET is expected to increase the propensity of psoralens to photo-addition to DNA. For derivatives bearing methylpyridinium residues, femtosecond spectroscopy revealed an intramolecular PET occurring on the picosecond time scale. This PET precludes the population of the triplet state. As triplet states are the precursor state for the photo-addition to DNA, their intermolecular PET renders these derivatives ineffective in terms of PUVA. For two derivatives bearing trimethylphenylammonium moieties, such an intramolecular PET does not occur and the triplet state is populated. Surprisingly, these compounds also exhibit no PUVA activity. Based on these findings, implications for further optimization of PUVA agents are discussed.

Tracing the Photoaddition of Pharmaceutical Psoralens to DNA

The psoralens 8-methoxypsoralen (8-MOP), 4,5',8-trimethylpsoralen (TMP) and 5-methoxypsoralen (5-MOP) find clinical application in PUVA (psoralen + UVA) therapy. PUVA treats skin diseases like psoriasis and atopic eczema. Psoralens target the DNA of cells. Upon photo-excitation psoralens bind to the DNA base thymine. This photo-binding was studied using steady-state UV/Vis and IR spectroscopy as well as nanosecond transient UV/Vis absorption. The experiments show that the photo-addition of 8-MOP and TMP involve the psoralen triplet state and a biradical intermediate. 5-MOP forms a structurally different photo-product. Its formation could not be traced by the present spectroscopic technique.

Role of hydroxyl groups in the B-ring of flavonoids in stabilization of the Hoogsteen paired third strand of Poly(U).Poly(A)*Poly(U) triplex

We have reported the interaction of two flavonoids namely quercetin (Q) and morin (M) with double stranded poly(A).poly(U) (herein after A.U) and triple stranded poly(U).poly(A)*poly(U) (herein after U.A*U, dot represents the Watson-Crick and asterisk represents Hoogsteen base pairing respectively) in this article. It has been observed that relative positions of hydroxyl groups on the B-ring of the flavonoids affect the stabilization of RNA. The double strand as well as the triple strand of RNA-polymers become more stabilized in presence of Q, however both the duplex and triplex remain unaffected in presence of M. The presence of catechol moiety on the B-ring of Q is supposed to be responsible for the stabilization. Moreover, after exploiting a series of biophysical experiments, it has been found that, triple helical RNA becomes more stabilized over its parent duplex in presence of Q. Fluorescence quenching, viscosity measurement and helix melting results establish the fact that Q binds with both forms of RNA through the mode of intercalation while M does not bind at all to either forms of RNA.

Effect of intercalator substituent and nucleotide sequence on the stability of DNA- and RNA-naphthalimide complexes

DNA intercalators are commonly used as anti-cancer and anti-tumor agents. As a result, it is imperative to understand how changes in intercalator structure affect binding affinity to DNA. Amonafide and mitonafide, two naphthalimide derivatives that are active against HeLa and KB cells in vitro, were previously shown to intercalate into DNA. Here, a systematic study was undertaken to change the 3-substituent on the aromatic intercalator 1,8-naphthalimide to determine how 11 different functional groups with a variety of physical and electronic properties affect binding of the naphthalimide to DNA and RNA duplexes of different sequence compositions and lengths. Wavelength scans, NMR titrations, and circular dichroism were used to investigate the binding mode of 1,8-naphthalimide derivatives to short synthetic DNA. Optical melting experiments were used to measure the change in melting temperature of the DNA and RNA duplexes due to intercalation, which ranged from 0 to 19.4°C. Thermal stabilities were affected by changing the substituent, and several patterns and idiosyncrasies were identified. By systematically varying the 3-substituent, the binding strength of the same derivative to various DNA and RNA duplexes was compared. The binding strength of different derivatives to the same DNA and RNA sequences was also compared. The results of these comparisons shed light on the complexities of site specificity and binding strength in DNA-intercalator complexes. For example, the consequences of adding a 5'-TpG-3' or 5'-GpT-3' step to a duplex is dependent on the sequence composition of the duplex. When added to a poly-AT duplex, naphthalimide binding was enhanced by 5.6-11.5°C, but when added to a poly-GC duplex, naphthalimide binding was diminished by 3.2-6.9°C.

Design, synthesis and anticancer activity of oxoaporphine alkaloid derivatives

A series of new oxoaporphine derivatives were synthesized and their inhibitory activity of topoisomerase I, cytotoxicity and DNA-binding properties were studied. Oxoaporphine can strongly inhibit topoisomerase I at concentrations of 5-50 µM and the cytotoxicity of the derivatives are more potent than their lead compound. Hypochromism, broadening and red shift in the absorption spectra were observed when these compounds bind to calf thymus DNA (CT DNA). These spectral characteristics were consistent with the intercalative binding of these compounds.

Magneto-structural correlation, antioxidant, DNA interaction and growth inhibition activities of new chloro-bridged phenolate complexes

The consistent stability constants as well as antioxidant, DNA interaction and cytotoxicity efficacy of chloro-bridged complexes have been established.

Enthused research on DNA-binding and DNA-cleavage aptitude of mixed ligand metal complexes

Five new Mn(II), Co(II), Ni(II), Cu(II) and Zn(II) mixed ligand complexes have been synthesized using a Schiff base precursor (obtained by the condensation of N-(4-aminophenyl)acetamide and 4-chlorobenzaldehyde) as main ligand and 1,10-phenanthroline as co-ligand. They have been characterized by microanalytical data, IR, UV-Vis, magnetic moment values, conductivity and electrochemical measurements. The spectral data reveal that all the complexes exhibit octahedral geometry. The high electrical conductance of the complexes supports their electrolytic nature. The monomeric nature of the complexes has been assessed from their magnetic susceptibility values. These complexes are better antimicrobial active agents than the free ligands. DNA (CT) binding properties of these complexes have been explored by UV-Vis., viscosity measurements, cyclic voltammetry, and differential pulse voltammetry measurements. The oxidative cleavage activity of the complexes has been studied using supercoiled pUC19 DNA by gel electrophoresis. The experimental results show that the complexes are good intercalators.

Unprocessed viral DNA could be the primary target of the HIV-1 integrase inhibitor raltegravir

Integration of HIV DNA into host chromosome requires a 3'-processing (3'-P) and a strand transfer (ST) reactions catalyzed by virus integrase (IN). Raltegravir (RAL), commonly used in AIDS therapy, belongs to the family of IN ST inhibitors (INSTIs) acting on IN-viral DNA complexes (intasomes). However, studies show that RAL fails to bind IN alone, but nothing has been reported on the behaviour of RAL toward free viral DNA. Here, we assessed whether free viral DNA could be a primary target for RAL, assuming that the DNA molecule is a receptor for a huge number of pharmacological agents. Optical spectroscopy, molecular dynamics and free energy calculations, showed that RAL is a tight binder of both processed and unprocessed LTR (long terminal repeat) ends. Complex formation involved mainly van der Waals forces and was enthalpy driven. Dissociation constants (Kds) revealed that RAL affinity for unbound LTRs was stronger than for bound LTRs. Moreover, Kd value for binding of RAL to LTRs and IC50 value (half concentration for inhibition) were in same range, suggesting that RAL binding to DNA and ST inhibition are correlated events. Accommodation of RAL into terminal base-pairs of unprocessed LTR is facilitated by an extensive end fraying that lowers the RAL binding energy barrier. The RAL binding entails a weak damping of fraying and correlatively of 3'-P inhibition. Noteworthy, present calculated RAL structures bound to free viral DNA resemble those found in RAL-intasome crystals, especially concerning the contacts between the fluorobenzyl group and the conserved 5'C(4)pA(3)3' step. We propose that RAL inhibits IN, in binding first unprocessed DNA. Similarly to anticancer drug poisons acting on topoisomerases, its interaction with DNA does not alter the cut, but blocks the subsequent joining reaction. We also speculate that INSTIs having viral DNA rather IN as main target could induce less resistance.

Electrochemical DNA sensor based on methylene blue functionalized polythiophene as a hybridization indicator

A polythiophene functionalized with methylene blue (PMT-MB) was synthesized and used as an indicator for electrochemical oligonucleotides (ODNs) hybridization detection. After hybridization with complementary ODNs, the current signal of PMT-MB increased, which illustrated that PMT-MB can effectively recognize complementary ODN targets as an indicator. Compared to MB, PMT-MB showed much better resistance to the concentration change of buffer solution. In all buffer solutions tested, the hybridization always resulted in the increased current signal of PMT-MB due to the electrostatic interaction. While, when MB was used as an indicator, the inconsistent current response was obtained after the hybridization. When high concentration of buffer solution was used for accumulation, the hybridization resulted in the decreased current signal, while at the low concentrations, the current signal increased. The interaction between PMT-MB and dsODNs was also studied by UV-vis spectroscopy.

Synthesis and DNA Binding/Cleavage of Mononuclear Copper(II) Phenanthroline/Bipyridine Proline Complexes

The complexes [Cu(II)(phen)(L-Pro)(H2O)]+ ClO4(-) (1; phen = 1,10-phenanthroline) and [Cu(II)(bipy)(L-Pro)(H2O)]+ ClO4(-) (2; bipy = 2,2'-bipyridine) were synthesized and characterized by IR, magnetic susceptibility, UV/VIS, EPR, ESI-MS, elemental analysis, and theoretical calculations. The metal center was found in a square-pyramidal geometry. UV/VIS, thermal-denaturation, and fluorescence-spectroscopic studies were conducted to assess the interaction of the complexes with CT-DNA. An intercalative mode of binding was found, with intrinsic binding constants (Kb) of 3.86x10(3) and 4.6x10(3) M(-1) and Stern-Volmer quenching constants (K) of 0.15 and 0.11 for 1 and 2, respectively. Interestingly, none of the Cu(II) complexes was able to cleave pUC-19 DNA, which is attributed to the absence of a Pro amide H-atom and inhibition of the formation of an OH radical from the axially coordinated H2O molecule.

Mixed-Ligand Copper(II)–Phenanthroline–Dipeptide Complexes: Synthesis, Characterization, and DNA-Cleavage Properties

The mixed-ligand complexes [Cu(II)(HisLeu)(phen)](+) (1) and [Cu(II)(HisSer)(phen)](+) (2; phen=1,10-phenanthroline) were synthesized and characterized. The intercalative interaction of the Cu(II) complexes with calf-thymus DNA (CT-DNA) was probed by UV/VIS and fluorescence titration, as well as by thermal-denaturation experiments, and the intrinsic binding constants (K(b)) for the complexes with 1 and 2 were 4.2x10(3) and 4.9x10(3) M(-1), resp. Both complexes were found to be efficient catalysts for the hydrolytic cleavage of plasmid pUC19 DNA, as tested by gel electrophoresis, converting the DNA from the supercoiled to the nicked-circular form at rate constants of 1.32 and 1.40 h(-1) for 1 and 2, resp.

Ternary Nickel(II) Complexes as Hydrolytic DNA-Cleavage Agents

A series of small model complexes made from Ni(II) and the ligands ethylenediamine (en), histamine (hist), and histidylleucine (HisLeu) were prepared and studied as potential hydrolytic DNA-cleavage agents. The stability constants and species-distribution curves for these complexes were determined as a function of pH. The 1 : 1 : 1 ternary complexes [Ni(II)(en)(HisLeu)] (1) and [Ni(II)(hist)(HisLeu)] (2) were the only major species present at the physiologically relevant pH of 6-7, as further corroborated by ESI-MS analysis. The complex geometries of 1 and 2 were analyzed by UV/VIS experiments and molecular dynamics (MD) simulations. Both ternary complexes were found to intercalate with DNA, as shown by UV/VIS, thermal-denaturation, and fluorescence-titration studies with ethidium bromide (EB). The intrinsic binding constants (K(b)) for the bound complexes 1DNA and 2DNA were determined as 150 and 290, resp. Gel-electrophoresis experiments revealed that 1 and 2 cleave supercoiled (type-I) to nicked-circular (type-II) DNA at physiological pH, with rate constants of 0.64 and 0.75 h(-1), resp. A tentative mechanism for this hydrolytic cleavage is proposed.

Fabrication of Unimolecular Double-stranded DNA Microarrays on Solid Surfaces for Probing DNA-Protein/Drug Interactions

We present a novel method for fabricating unimolecular double-stranded DNA microarrays on solid surfaces, which were used to probe sequence-specific DNA/protein interactions. For manufacturing the unimolecular double-stranded DNA microarrays, two kinds of special single-stranded oligonucleotides, constant oligonucleotide and target oligonucleotide, were chemically synthesized. The constant oligonucleotides with internal aminated dT were used to capture and immobilize the target oligonucleotides onto the solid surface, and also to provide a primer for later enzymatic extension reactions, while target oligonucleotides took the role of harbouring DNA-binding sites of DNA-binding proteins. The variant target oligonucleotides were annealed and ligated with the constant oligonucleotides to form the new unimolecular oligonucleotides for microspotting. The prepared unimolecular oligonucleotides were microspotted on aldehyde-derivatized glass slides to make partial-dsDNA microarrays. Finally, the partial-dsDNA microarrays were converted into a unimolecular complete-dsDNA microarray by a DNA polymerase extension reaction. The efficiency and accuracy of the polymerase synthesis were demonstrated by the fluorescent-labeled dUTP incorporation in the enzymatic extension reaction and the restriction endonuclease digestion of the fabricated unimolecular complete-dsDNA microarray. The accessibility and specificity of the sequence-specific DNA-binding proteins binding to the immobilized unimolecular dsDNA probes were demonstrated by the binding of Cy3 labeled NF-κB (p50·p50) to the unimolecular dsDNA microarray. This unimolecular dsDNA microarray provides a general technique for high-throughput DNA-protein or DNA-drugs interactions.

Effect of primary and secondary structure of oligodeoxyribonucleotides on the fluorescent properties of conjugated dyes

We studied fluorescence intensity, polarization and lifetime of some commonly used fluorophores conjugated to oligodeoxyribonucleotides with different primary and secondary structures. We found that fluorescence intensity can increase or decrease upon hybridization of the labeled strand to its complement depending on the sequence and position of the fluorophore. Up to 10-fold quenching of the fluorescence upon hybridization was observed when the dye moiety was attached close to the 3' end and the 3'-terminal base was either dG or dC. No quenching upon hybridization was observed when the dye was positioned within the same sequence context but close to the 5' end. The presence of a dG overhang quenches the fluorescence less efficiently than a blunt end dG-dC or dC-dG base pair. When located internally in the double strand, the dG-dC base pair does not affect the fluorescence of the nearby dye. Guanosine in a single-stranded oligonucleotide quenches the fluorescence of nearby dye by <2-fold. Upon duplex formation, this quenching is eliminated and the fluorescence increases. This increase can only be detected when the fluorophore is located at least 6 nt from the terminal dG-dC base pair. The change of fluorescence polarization upon duplex formation inversely correlates with the change of intensity. Fluorescein conjugated to a single-stranded oligonucleotide or a duplex undergoes a bi-exponential decay with approximately 4 and approximately 1 ns lifetimes.

Spectroscopic studies of interaction of chlorobenzylidine with DNA

Electronic absorbance and fluorescence titrations are used to probe the interaction of chlorobenzylidine with DNA. The binding of chlorobenzylidine to DNA results in hypochromism, a small shift to a longer wavelength in the absorption spectra, and emission quenching in the fluorescence spectra. These spectral characteristics suggest that chlorobenzylidine binds to DNA by an intercalative mode. This conclusion is reinforced by fluorescence polarization measurements. Scatchard plots constructed from fluorescence titration data give a binding constant of 1.3 x 10(5) M(-1) and a binding site size of 10 base pairs. This indicates that chlorobenzylidine has a high affinity with DNA. The intercalative interaction is exothermic with a Van't Hoff enthalpy of -143 kJ/mol. This result is obtained from the temperature dependence of the binding constant. The interaction of chlorobenzylidine with DNA is affected by the pH value of the solution. The binding constant has its maximum at pH 3.0. Upon binding to DNA, the fluorescence from chlorobenzylidine is quenched efficiently by the DNA bases and the fluorescence intensity tends to be constant at high concentrations of DNA when the binding is saturated. The Stern-Volmer quenching constant obtained from the linear quenching plot is 1.6 x 10(4) M(-1) at 25 degrees C. The measurements of the fluorescence lifetime and the dependence of the quenching constant on the temperature indicate that the fluorescence quenching process is static. The fluorescence lifetime of chlorobenzylidine is 1.9 +/- 0.4 ns.

Interaction of bis(ethylene)tin(bis(salicylidene)ethylenediamine) with DNA

The fluorescence spectral characteristics and interaction of bis(ethylene)tin(bis(salicylidene)ethylenediamine) [Et2Sn(salen)] with DNA are described. The polarity of the solvent has a strong effect on the fluorescence characteristics of Et2Sn(salen). Et2Sn(salen) bound to DNA showed a marked decrease in the fluorescence intensity with a bathochromic shift of the excitation and emission peaks. A hypochromism in the UV absorption spectra was also observed. KI quenching and competitive binding to DNA between Et2Sn(salen) and ethidium bromide (EB) were studied in connection with other experimental observations to show that the interactive model between Et2Sn(salen) and DNA is an intercalative one. The pH and salt effect on the fluorescence properties was also investigated. The intrinsic binding constant was estimated to be 1.071 x 10(5) mol L(-1) in base pairs and the binding site number is 1.98, respectively. A linear relationship between F/F0 and the concentration of calf thymus DNA covers 5.1 x 10(-6) - 2.41 x 10(-4) mol L(-1), which can be utilized for determining traces of calf thymus DNA with a detection limit of 1.1 x 10(-7) mol L(-1) in base pairs.

DNA binding studies of a solvatochromic fluorescence probe 3-methoxybenzanthrone

A fluorescence probe of 3-methoxybenzanthrone (MBA) exhibits significant solvatochromic characteristics correlated with the polarity of solvents. The interaction of the solvatochromic fluorescence probe with calf thymus DNA (ct-DNA) has been investigated. In the presence of ct-DNA the fluorescence of MBA is strongly quenched with a blue-shift of emission peak and a hypochromism in absorption spectra. The absorption spectra, fluorescence quenching and fluorescence polarization experiments show that the MBA molecule as an intercalator is inserted into the base-stacking domain of the ct-DNA double helix, and the interaction of the nucleobases with the MBA molecule causes quenching of fluorescence and hypochromism in the absorption spectra. The intrinsic binding constant and the binding site number were determined to be 1.70 x 10(5) mol l-1 in base pairs and six, respectively. The I0/I versus [ct-DNA] plot shows linear relationship in the range covering 4.3 x 10(-7)-1.02 x 10(-4) mol l-1 in base pairs which can be used for ct-DNA determination. The limit of detection was found to be 4.3 x 10(-7) mol l-1 in base pairs (0.5 microgram ml-1).

Synthetic DNA minor groove-binding drugs

In this review, both cationic and neutral synthetic ligands that bind in the minor groove of DNA are discussed. Certain bis-distamycins and related lexitropsins show activities against human immunodeficiency virus (HIV)-1 and HIV-2 at low nanomolar concentrations. DAPI binds strongly to AT-containing polymers and is located in the minor groove of DNA. DAPI intercalates in DNA sequences that do not contain at least three consecutive AT bp. Berenil can also exhibit intercalative, as well as minor groove binding, properties depending on sequence. Furan-containing analogues of berenil play an important role in their activities against Pneumocystis carinii and Cryptosporidium parvuam infections in vivo. Pt(II)-berenil conjugates show a good activity profile against HL60 and U-937 human leukemic cells. Pt-pentamidine shows higher antiproliferative activity against small cell lung, non-small cell lung, and melanoma cancer cell lines compared with many other tumor cell lines. trans-Butenamidine shows good anti-P. carinii activity in rats. Pentamidine is used against P. carinii pneumonia in individuals infected with HIV who are at high risk from this infection. A comparison of the cytotoxic potencies of adozelesin, bizelesin, carzelesin, cisplatin, and doxorubicin indicates that adozelesin is a potent analog of CC-1065. Naturally occurring pyrrolo[2,1-c][l,4]benzodiazepines such as anthramycin have a 2- to 3-bp sequence specificity, but a synthetic PBD dimer spans 6 bp, actively recognizing a central 5'-GATC sequence. The crosslinking efficiency of PBD dimers is much greater than that of other major groove crosslinkers, such as cisplatin, melphalan, etc. Neothramycin is used clinically for the treatment of superficial carcinoma of the bladder.

Use of capillary electrophoresis in the study of ligand-DNA interactions

Free solution capillary electrophoresis (FSCE) has been used to separate two non-self-complementary 12mer oligonucleotide duplexes: d(AAATTATATTAT).d(ATAA-TATAATTT) and d(GGGCCGCGCCGC).d(GCGGCGCGGCCC). Titration of mixtures of the two oligonucleotides with model intercalators (ethidium bromide andactinomycin D) and minor groove binders (netropsin, Hoechst 33258 and distamycin) has shown the suitability of FSCE as a method to study the sequence selectivity of DNA binding agents. Binding data have shown cooperativity of binding for netropsin and Hoechst 33258 and have provided ligand:DNA binding ratios for all five compounds. Cooperativity of netropsin binding to a 12mer with two potential sites has been demonstrated for the first time. Ligands binding in the minor groove caused changes in migration time and peak shape which were significantly different from those caused by intercalators.

Selective DNA binding of (N-alkylamine)-substituted naphthalene imides and diimides to G+C-rich DNA

Alkylamine-substituted naphthalene imides and diimides bind DNA by intercalation and have applications as anticancer agents. The unique structures of these imides in which two adjacent carbonyl groups lie coplanar to an extended aromatic ring system allow the possibility of sequence-selective interactions between the intercalated chromophore and guanine amino groups situated in the DNA minor groove. The binding affinities of N-[3-(dimethylamino)propyl amine]-1,8-naphthalenedicarboxylic imide (N-DMPrNI) and N,N'-bis [3,3'-(dimethylamino)propylamine]-naphthalene-1,4,5,8-tetracarboxylic diimide (N-BDMPrNDI) for natural DNAs of differing base composition were determined spectroscopically and by equilibrium dialysis. In agreement with the above proposition, binding studies indicated that both the naphthalene imide and diimide strongly prefer to intercalate into steps containing at least one G:C base pair. The dependencies of association constants on DNA base composition are consistent with a requirement for one G:C pair in the binding site of the monomide, and two G:C pairs in binding sites of the diimide. These selectivities are comparable to or exceed that of actinomycin D, a classic G:C-selective drug. Protection footprinting with DNase I confirmed that the naphthalene monoiimide (N-DMPrNI) prefers to bind adjacent to G:C base pairs, with a most consistent preference for "mixed" steps containing both a G:C and an A:T pair, excepting GA:TC. Several 5'-CG-3' steps were also good binding sites as indicated by nuclease protection, but few GC:GC or GG:CC steps were protected. The naphthalene diimide inhibited DNase I digestion, but did not yield a footprint. The base recognition ability and versatile chemistry make naphthalene imides and diimides attractive building blocks for design of highly sequence-specific, DNA-directed drug candidates including conjugated oligonucleotides or oligopeptides.

Fluorescence characteristics of 5-carboxytetramethylrhodamine linked covalently to the 5' end of oligonucleotides: multiple conformers of single-stranded and double-stranded dye-DNA complexes

Fluorescence steady-state and lifetime experiments have been carried out on duplex and single-stranded DNA molecules labeled at the 5' ends with 5-carboxytetramethylrhodamine (TMRh). The temperature and ionic strength of the solutions were varied over large ranges. The results reveal at least three well-defined states of the TMRh-DNA molecules for the single-stranded as well as for the double-stranded DNA molecules. Two states are fluorescent, with lifetimes in the range of 0.5-1 ns and 2.5-3 ns. A third state of TMRh-DNA does not fluoresce (a dark species of TMRh-DNA). The distribution of the TMRh-DNA molecules among these three states is strongly temperature and ionic strength dependent. Estimates are made of some reaction parameters of the multistate model. The results are discussed in terms of the photophysics of TMRh, and consequences of the multiple conformers of TMRh-DNA for studies involving fluorescence studies with TMRh-labeled DNA are considered.

DNA minor groove accessibility in the nucleosome core deduced from specific interactions with DAPI

Equilibrium binding properties of DAPI for purified nucleosome cores were derived from fluorescence intensity enhancement. Both the affinity and the number of sites of the primary, minor groove binding are preserved with respect to the corresponding isolated DNA, suggesting that the capacity for specific interactions of the minor groove may well be exerted in chromatin.

Analysis of drug-DNA binding isotherms: a Monte Carlo approach

Monte Carlo simulations of neighbor exclusion models have been used to demonstrate the importance of collecting and fitting data over a wide range of saturation. Low saturation data are important for good estimates of the affinity K of a drug or protein for the lattice site. High saturation data are important for distinguishing between negatively cooperative and noncooperative binding modes. Neglect of negative cooperativity (omega < 1) has in general little effect on the estimation of K. The error is mostly absorbed by increasing the value of n. This kind of behavior was previously observed with the fitting of nonideal, monomer-dimer, ultracentrifugation data where variations in B, the second virial coefficient, and K2, the dimerization equilibrium constant, are highly correlated, thus making their individual determination difficult. Within experimental error the distinction between a noncooperative model [Eq. (1)] and a negatively cooperative model [Eq. (3) or (4) with omega < 1] may require additional evidence to justify the choice of one model over another. For example, for homogeneous lattices of synthetic deoxyoligonucleotides, n may be constrained with some validity, thus allowing a more accurate and precise determination of K and omega. In fact, n may be established independently, for example, by nuclear magnetic resonance (NMR) methods. However, the assumption of an integral value of n for natural DNA samples may not be valid because of sequence heterogeneity. Unconstrained fitting of negatively cooperative data to Eq. (4) will thus be a very difficult problem (Table V). At an experimental error of only 2.3%, n and K can be reasonably determined but with a large error in omega. Data from the final 20% of saturation are essential in extracting omega. This may in part explain the absence of more reports of negatively cooperative behavior in the literature. This analysis is independent of the systematic error that may be induced by the transformation of data to the Scatchard plot, or the omission of drug self-association, or the occurrence of wall binding by ligand, or variable point density, or non-Gaussian noise, or the occurrence of another mode of binding distinct from the models of McGhee and von Hippel. Each of these will introduce additional error, possibly biased error, in the parameters estimated; however, this does not obviate our conclusion. Even under these ideal circumstances there are serious limitations that must be considered when fitting neighbor exclusion model data. The direct fitting of absorbance data [to Eq. (2) or functions that incorporate other parameters] will also be sensitive to these considerations.

Probing intercalation and conformational effects of the anticancer drug 2-methyl-9-hydroxyellipticinium acetate in DNA fragments with circular dichroism

Circular dichroism was applied to the analysis of drug-DNA associations. With the octanucleotide d(TGACGTCA) (octanucleotide I), which is the cAMP-responsive element (CRE) in gene promoters and its reverse d(ACTGCAGT) (octanucleotide II), it was demonstrated that the anticancer polyaromatic agent celiptium intercalates into DNA base pairs with its long direction perpendicular to both the DNA-helix axis and the base-pair long axis and induces larger conformational changes in the CpG-containing octanucleotide I CRE than in its reverse-sequence octanucleotide II. It was concluded that CD is a powerful and sensitive technique to discriminate between drug-binding modes of DNA, to define the geometry of the chromophore inserted into base pairs and, finally, to measure sequence-dependent conformational changes induced by intercalation in DNA. We anticipate that these studies will contribute to a better understanding of the molecular bases that underlie the mechanism of action of those cytotoxic drugs which interfere with the DNA-nuclear-protein recognition.

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.

Fluorinated anthracyclines: interactions with DNA

Four fluorine containing derivatives of anthracyclines (daunomycin and adriamycin) were synthesised, and comprised C-13, 1,1,1-trifluoroethyl-hydrazones of each anthracycline, and C-14 4-F and 4-CF3-benzoate esters of adriamycin. All four derivatives intercalated into DNA in a manner similar to their parent anthracycline. The ester derivatives exhibited 3-4-fold higher binding affinity to DNA, and slower DNA dissociation kinetics than adriamycin. This stabilisation derives from additional contacts of the C-14 side chain to the DNA minor groove. The hydrazone derivatives showed lower binding affinity to DNA, and dissociated from DNA 3-4 times faster than the parent compound. The 19F resonance of the bound drug was broadened to 120 Hz and shifted 60 Hz downfield (0.32 ppm) relative to the sharp (7.5 Hz) peak of the free drug. These values imply a rapid exchange between the free and DNA bound forms (DNA lifetime greater than 5 ms), with the fluorine group residing in a hydrophobic region in close contact with the DNA minor groove. The 4-8 fold lesser specific potency of the ester derivatives supports the concept that DNA binding is an important factor, but not sole determinant of biological activity of these analogues.

Differential scanning calorimetric study of the effect of intercalators and other kinds of DNA-binding drugs on the stepwise melting of plasmid DNA

The effect of intercalating drugs (the anthracycline group of antibiotics, ethidium bromide, actinomycin D) on stepwise melting of DNA was studied by differential scanning calorimetry (DSC). The DSC DNA melting profile of plasmid pJL3-TB5 DNA (5277 base-pairs in length) consists of seven peaks, and all the intercalators caused shifting of these peaks, particularly those formed at the high temperature ranges, to the higher temperature ranges in a characteristic manner depending upon the binding strength of the drug. The analysis of the anthracycline group of antibiotics, such as aclacinomycin A, daunomycin, adriamycin and pyrarubicin, indicates that the difference in binding is due to the sugar moiety at position O-7 of the chromophore in these antibiotics. Analysis on the basis of the helix-coil transition theory suggests that the anthracycline group of antibiotics interact preferentially with the 5'-CG-3' sequences. The effect of various DNA-binding drugs other than intercalators on stepwise melting of DNA was then studied by DSC. The representative drugs examined were distamycin A, peplomycin, cis-dichlorodiamine-platinum(II) (cis-DDP or cis-Platin) and mitomycin C, which differ in their mode of interaction with DNA; namely, minor groove binding, strand cleavage and intrastrand or interstrand cross-linking. Distamycin A caused shifting of the DSC peaks at the low temperature ranges to a higher temperature range, whereas peplomycin and cis-DDP caused shifting of all the DSC peaks to form a broad peak at a lower temperature range, suggesting that the DSC DNA melting profiles are affected in a characteristic manner depending upon the interaction mode of the drug.

Biophysical chemistry of the daunomycin-DNA interaction

Daunomycin (daunorubicin) is a potent anticancer antibiotic that binds to DNA by the process of intercalation. Fundamental aspects of the physical chemistry of the daunomycin-DNA interaction are reviewed here, including the thermodynamics and kinetics of the binding reaction, and recent work that indicates that daunomycin binds preferentially to certain sites along the DNA lattice. The solution studies reviewed here combine with recent theoretical and crystallographic investigations to make the daunomycin-DNA interaction one of the best-characterized intercalation reactions. The molecular interactions that stabilize the daunomycin-DNA complex, and which contribute to its sequence preference, are discussed.

The G.C base-pair preference of 2-N-methyl 9-hydroxyellipticinium

Among the DNA-intercalating drugs in the ellipticinium series, 9-hydroxy derivatives elicit the highest antitumoral properties. In water these drugs display a very low fluorescence quantum yield. Replacement of H2O by D2O partially restores the fluorescence of the ellipticinium chromophore. The possibility that such a proton-exchange mechanism could be involved in a base-recognizing process at the DNA level (and therefore be responsible for some base preference) was examined by direct fluorescence titration in deuterated buffer and DNA/drug fluorescence energy transfer. These experimental approaches provide mutually consistent results showing that the 9-hydroxylated drug recognizes specific DNA sites that are not recognized by the non-hydroxylated drug. When compared to 2-N-methyl ellipticinium, the 2-N-methyl 9-hydroxyellipticinium presents: (1) higher binding constants for each DNA studied; (2) a base dependence of the fluorescence properties of the bound form (fluorescence increment upon DNA binding varying over 5-11); (3) a base dependence of its DNA affinity constants (1.1-3.3 x 10(6) M-1) and of its site size (exclusion parameters varying over 3.0-4.4); (4) a base dependence of its energy transfer from DNA bases. Analysis of the binding data suggests that the 9-hydroxyl group of 2-N-methyl ellipticinium is responsible for a G.C base-pair preference, the preferred binding site being a doublet sequence of two adjacent G.C which could be flanked either by a additional G.C base pair or by an A.T base pair.