Contributions of a long side chain to the binding affinity of an anthracene derivative to DNA

Systematic studies on the DNA binding of a new anthracene derivative, carrying a 1,8-octyldiamine side chain, were carried out. Calorimetric, spectroscopic, and helix melting studies show that the side chain, consisting of eight methylene groups, enhances the binding constant by a factor of approximately 35 when compared to the binding of a probe lacking the long side chain. Furthermore, the enthalpy of binding of the long-chain derivative to calf thymus DNA (Delta H = 4.1 +/- 0.1 kcal/mol) is far greater than the sum of the enthalpy changes associated with the binding of the probe lacking the long side chain, and the enthalpy for the binding of 1,8-octyldiamine.2HCl. Strong synergistic effects, therefore, are seen with the long-chain derivative. Spectroscopic data indicate bathochromism, strong hypochromism, and quenching of anthryl fluorescence when the above ligand binds to calf thymus DNA. Fluorescence energy transfer studies and circular dichroism data strongly suggest intercalation of the anthryl ring system. The binding stabilizes the double helix, and the helix melting temperature is increased from 78 degrees C to >90 degrees C. The binding to DNA is reversible, depended on the ionic strength, and the major binding mode was suppressed at high ionic strengths and a new mode begins to dominate binding. Substitution of the anthracene ring with 1,8-octyldiamine chain provided a simple method to enhance the binding constant by nearly a factor of 35.     

Spectroscopic identification of binding modes of anthracene probes and DNA sequence recognition

The binding properties of two anthracene derivatives with calf thymus DNA (CT DNA), poly(dA-dT), and poly(dG) x poly(dC) are reported. One contained bulky, cyclic cationic substituents at the 9 and 10 positions, and the other carried acylic, branched, cationic substituents. Binding of the probes to the DNA was examined by calorimetry, spectroscopy and helix melting studies. The cyclic derivative indicated exothermic binding, strong hypochromism, bathochromism, positive induced circular dichroism (CD, 300-400 nm), significant unwinding of the helix, large increases in the helix melting temperature, strong but negative linear dichroism (LD, 300-400 nm) and considerable stabilization of the helix. In contrast, the acyclic analog indicated thermoneutral binding, smaller hypochromism, no bathochromism, very weak induced CD, and no change in the helix melting temperature with any of the DNA polymers. A sharp distinction between the binding properties of the two probes is indicated, and both have intrinsic binding constants of approximately 10(6) M(-1) for the three polymers. However, when the ionic strength of the medium was lowered (10 mM NaCl), the absorption as well as CD spectral changes associated with the binding of the acyclic derivative corresponded with those of the cyclic derivative. The acyclic derivative showed large preference (10-fold) for poly(dG) x poly(dC) over poly(dA-dT), whereas the cyclic analog showed no preference. The characteristic spectroscopic signatures of the two distinct binding modes of these probes will be helpful in deciphering the interaction of other anthracene derivatives with DNA.     

DNA binding hydroxyl radical probes

The hydroxyl radical is the primary mediator of DNA damage by the indirect effect of ionizing radiation. It is a powerful oxidizing agent produced by the radiolysis of water and is responsible for a significant fraction of the DNA damage associated with ionizing radiation. There is therefore an interest in the development of sensitive assays for its detection. The hydroxylation of aromatic groups to produce fluorescent products has been used for this purpose. We have examined four different chromophores, which produce fluorescent products when hydroxylated. Of these, the coumarin system suffers from the fewest disadvantages. We have therefore examined its behavior when linked to a cationic peptide ligand designed to bind strongly to DNA.     

Tuning the DNA binding modes of an anthracene derivative with salt

The DNA binding properties of an anthracene derivative with substituents at the 9 and 10 positions, carrying four positive charges, are examined in calorimetric, spectroscopic and photocleavage studies. Isothermal titration calorimetric data indicated exothermic binding of the ligand to calf thymus DNA with a binding constant of (1.4 ± 0.5) × 10⁵ M⁻¹ and this value is much greater than binding of similar monocationic derivatives. The values for the other binding parameters were, ΔH = −3.5 ± 0.4 kcal/mol; ΔS = 11.6 ± 1.6 cal/mol K, and a binding site size of ∼4 base pairs. Absorption spectral studies indicated small, but significant red shifts in the vibronic bands, and ∼70% of hypochromism. The binding plots indicated bi-phasic binding of the ligand. At higher ionic strengths, the red shifts in the absorption spectra were abolished but significant hypochromism persisted.Excitation and sensitized fluorescence spectral studies indicated weak energy transfer from the DNA bases to the ligand. Further more, energy transfer was reduced substantially at higher ionic strengths. Strong induced circular dichroism bands are noted, in the 300–400 nm region, and these are most likely dominated by the contributions from the groove bound form as well as the intercalated chromophore. Helix melting studies indicated improvement in the helix stability, and substantial increase in the melting temperature (ΔT_m > 17 °C). Differential scanning calorimetric data, on the other hand, indicated only minor improvements in the thermodynamic parameters. Irradiation of a mixture of the ligand (2 μM) and supercoiled pUC18 DNA (20 μM, @374 nm) resulted in the efficient formation of nicked circular DNA (>90%) in an hour. The data indicated at least two distinct binding modes, and one of these persisted at high ionic strengths (375 mM NaCl). Substitution at 9 and 10 positions of the anthracene ring system with positively charged residues resulted in multiple binding modes, and these are resolvable in ionic strength studies.     

Thermodynamic integration to predict host-guest binding affinities

An alchemical free energy method with explicit solvent molecular dynamics simulations was applied as part of the blind prediction contest SAMPL3 to calculate binding free energies for seven guests to an acyclic cucurbit-[n]uril host. The predictions included determination of protonation states for both host and guests, docking pose generation, and binding free energy calculations using thermodynamic integration. We found a root mean square error (RMSE) of 3.6 kcal mol(-1) from the reference experimental results, with an R(2) correlation of 0.51. The agreement with experiment for the largest contributor to this error, guest 6, is improved by 1.7 kcal mol(-1) when a periodicity-induced free energy correction is applied. The corrections for the other ligands were significantly smaller, and altogether the RMSE was reduced by 0.4 kcal mol(-1). We link properties of the host-guest systems during simulation to errors in the computed free energies. Overall, we show that charged host-guest systems studied here, initialized in unconfirmed docking poses, present a challenge to accurate alchemical simulation methods.     

Relative binding affinities of alkali metal cations to

The binding affinity and selectivity of a new ionophore, [1(8)]starand (1), toward alkali metal cations in methanol were examined through NMR titration experiments and free energy perturbation (FEP) and molecular dynamics simulations. The preference was determined to be K(+) > Rb(+) > Cs(+) > Na(+) > Li(+) in both FEP simulations and NMR experiments. The FEP simulation results were able to predict the relative binding free energies with errors less than 0.13 kcal/mol, except for the case between Li(+) and Na(+). The cation selectivity was rationalized by analyzing the radial distribution functions of the M-O and M-C distances of free metal cations in methanol and those of metal-ionophore complexes in methanol.     

A thermodynamic investigation into the binding properties of DNA functionalized gold nanoparticle probes and molecular fluorophore probes

We report the first quantitative analysis of the oligonucleotide binding thermodynamics for DNA functionalized gold nanoparticle probes and compare our findings to molecular fluorophore probes on a sequence-for-sequence basis. With proper design, nanoparticle probes show significantly increased binding over molecular fluorophore probes under identical conditions. This is significant because probe binding strength directly influences detection sensitivity limits.     

Stereocontrolled synthesis of anthracene β-C-ribosides: fluorescent probes for photophysical studies of DNA

Effective, stereocontrolled syntheses of the 1-anthracenyl and 2-anthrancenyl β-C-2′-deoxyribosides are reported and were based on a diastereofacialselective, palladium-catalyzed glycosidation of the corresponding protected (4S,5R)-4-hydroxy-5-(hydroxymethyl)dihydrofuran.     

Evaluation of relative DNA binding affinities of anthrapyrazoles by electrospray ionization mass spectrometry

Binding interactions of a new series of anthrapyrazoles (APs) with DNA were evaluated by electrospray ionization mass spectrometry (ESI-MS). Relative binding affinities were estimated from the ESI-MS data based on the fraction of bound DNA for DNA/anthrapyrazole mixtures, and they show a correlation to the shift in melting point of the DNA measured from a previous study. Minimal sequence specificity was observed for the series of anthrapyrazoles. Upon collisionally activated dissociation of the duplex/anthrapyrazole complexes, typically ejection of the ligand was the dominant pathway for most of the complexes. However, for complexes containing AP2 or mitoxantrone, strand separation with the ligand remaining on one of the single strands was observed, indicative of a different binding mode or stronger binding.     

A 5'-cap for DNA probes binding RNA target strands

Detecting short RNA strands with high fidelity at any of the bases of their sequence, including the termini, can be challenging, since fraying, wobbling, and refolding all compete with canonical base pairing. We performed a search for 5'-substituents of oligodeoxynucleotides that increase base pairing fidelity at the terminus of duplexes with RNA target strands. From a total of over 70 caps, differing in stacking moiety and linker, a phosphodiester-linked sequence of the residues of L-prolinol, glycine, and oxolinic acid, dubbed ogOA, was identified as a 5'-cap that stabilizes any of the four canonical base pairs, with ΔT(m) values of up to +13.1 °C for an octamer. At the same time, the cap increases discrimination against any of the 12 possible terminal mismatches, including mismatches that are more stable than their perfectly matched counterparts in the control duplex, such as A:A. A probe with the cap also showed increased selectivity in the detection of two closely related microRNAs, let7c and let7a, with a ΔT(m) value of 9.2 °C. Melting curves also yielded thermodynamic data that shed light on the uniformity of molecular recognition in the sequence space of DNA:DNA and DNA:RNA duplexes. Hybridization probes with fidelity-enhancing caps should find applications in the individual and parallel detection of biologically active RNA species.     

Water-soluble organic dppz analogues--tuning DNA binding affinities, luminescence, and photo-redox properties

Three new water-soluble dppz derivatives are reported, one of which binds to DNA with an affinity comparable to any mononuclear metal complex and also displays a high selectivity for GC sites.     

The radical anions and the electron affinities of perfluorinated benzene,naphthalene and anthracene

Although benzene and naphthalene do not have electron affinities in the conventional sense, perfluorobenzene and perfluoronaphthalene have nonzero electron affinities. Theoretical methods extensively calibrated with experiment for the prediction of electron affinities (EAs) predict the EAs of perfluorobenzene, perfluoronaphthalene and perfluoroanthracene as 0.69, 1.02 and 1.84 eV, respectively. A rough estimate of 2.39 eV is made for the electron affinity of perfluorotetracene. Thus the perfluoro polycyclic aromatic hydrocarbons (PAHs) are predicted to be effective electron acceptors.     

Photophysics of aminoxanthone derivatives and their application as binding probes for DNA

Xanthones with amino substituents were synthesized to diminish the photoreactivity of the xanthone chromophore with DNA, with the objective of using these molecules to study their binding dynamics with DNA. The aminoxanthones showed a strong solvatochromic effect on their singlet and triplet excited-state photophysics, where polar solvents led to a decrease of the energies for the excited states. Quenching of the triplet excited states by nitrite anions was used to determine the binding dynamics, and a residence time in the microsecond time domain was estimated for the bound 2-aminoxanthone with DNA. The quenching experiments performed showed that this methodology will not be applicable to study the binding dynamics of a wide variety of guests with DNA.     

A study of the distribution of the hydroxyethyl groups in hydroxyethylstarch

Literature information on the study of the distribution of hydroxyethyl groups in hydroxyethylated starch is discussed. The structures of the polymeric components of starch (amylose and amylopectin) have no influence on the distribution of hydroxyethyl groups in hydroxyethylstarch. This distribution scarcely changes with a variation in the degree of substitution from 0.1 to 1.0. However, there is a change with an appreciable lowering of the degree of substitution to 0.03 or with a rise in it to 2.0. A preferential substitution of hydroxyethyl groups at C-2 of the anhydroglucose unit of starch is observed, as has been established by all authors. A substantial influence on the distribution of hydroxyethyl and hydroxypropyl groups is exerted by the conditions of performing the chemical modification of starch by treating it with ethylene oxide or propylene oxide. A variation in these conditions permits a fundamental change in the distribution of substituting groups at C-2, C-3, and C-6 of the anhydroglucose unit.Central Scientific-Research Institute of Hematology and Blood Transfusion, Ministry of Health of the USSR, Moscow. Translated from Khimiya Prirodnykh Soedinenii, No. 1, pp. 22–28, January–February, 1980.     

Theoretical studies on the binding affinities of β-cyclodextrin to small molecules and monosaccharides

Equilibrium geometries and electronic structures of complexes between β-cyclodextrin (β-CD) and some small molecules as well as monosaccharides were investigated by Austin Model 1 (AM1) to obtain binding energy of the complexes. It was indicated that β-CD could bind the structurally similar solvent molecules and monosaccharides because of the negative binding energy of the complexes, and especially could show the chiral binding ability to monosaccharides with more hydroxyl groups, due to its chiral characteristics. The complexes were stabilized by the hydrogen bonding between β-CD and guests. Based on the AM1 optimized geometries, the IR spectra were calculated by AM1 method. Vibration frequencies of O-H bonds in the guests were red-shifted owing to the weakening of the O-H bonds with the formation of the complexes.     

Electron affinities of the DNA and RNA bases.

Adiabatic electron affinities (AEAs) for the DNA and RNA bases are predicted by using a range of density functionals with a double-zeta plus polarization plus diffuse (DZP++) basis set in an effort to bracket the true EAs. Although the AEAs exhibit moderate fluctuations with respect to the choice of functional, systematic trends show that the covalent uracil (U) and thymine (T) anions are bound by 0.05-0.25 eV while the adenine (A) anion is clearly unbound. The computed AEAs for cytosine (C) and guanine (G) oscillate between small positive and negative values for the three most reliable functional combinations (BP86, B3LYP, and BLYP), and it remains unclear if either covalent anion is bound. AEAs with B3LYP/TZ2P++ single points are 0.19 (U), 0.16 (T), 0.07 (G), -0.02 (C), and -0.17 eV (A). Favorable comparisons are made to experimental estimates extrapolated from photoelectron spectra data for the complexes of the nucleobases with water. However, experimental values scaled from liquid-phase reduction potentials are shown to overestimate the AEAs by as much as 1.5 eV. Because the uracil and thymine covalent EAs are in energy ranges near those of their dipole-bound counterparts, preparation and precise experimental measurement of the thermodynamically stable covalent anions may prove challenging.     

The binding of pyrene and other probes to CD polymers

The binding interactions of commercial epichlorohydrin (EP)-linked CD polymers (CDPs) with pyrene and p-substituted phenols are compared with those of the respective CD monomers for these probes. Shifts in pK_a for the phenols are consistent with a more open site on the CDPs than the CDs. The relative affinity for pyrene exhibited by -CDP is estimated by a competition experiment with pyrene / -CD binding. Spectral studies on synthesized EP-linked sucrose polymers are employed to gain insight into the role of glyceryl-linker units in guest binding.     

Luminescence properties of PPV derivatives carrying anthracene pendent groups

Photo- (PL) and electroluminescence (EL) properties of three different PPV derivatives carrying the 9,10-diphenylanthracene units are compared. One (polymer 1 ) of the polymers contains the 9,10-diphenylanthracene structure as an integral part of the main chain, but the other two have it as the pendent group attached to the main chain through either oxyethyleneoxy (polymer 2 ) or oxyhexamethyleneoxy (polymer 3 ) spacer. Polymers 1 and 2 exhibit very similar PL and EL spectra that are more or less of superimposed feature of the spectra from the backbones and the anthracene pendents. In contrast, polymer 3 shows an EL spectrum that is completely different from its PL spectrum. Whereas the PL spectrum of polymer 3 appears to be a combination of the spectra from the main chain and the pendents, as for polymer 1 and 2 , the EL spectrum of polymer 3 , however, looks as if the lights were emitted only from the backbone. This difference is explained in terms of excited state electronic interactions between the main chain and the pendents.     

Synthesis,characterization, and DNA binding of two copper(II) complexes as DNA fluorescent probes

[Cu(DAPT)₂Cl]Cl·H₂O and [Cu(DBM)(DAPT)Cl] [DAPT = 2,4-diamine-6-(pyrazin-2-yl)-1,3,5-triazine] were synthesized and characterized by IR and UV spectroscopy, elemental analysis, TG–DTA, molar conductivity, and LC–MS. The interaction with calf thymus DNA (ct-DNA) of the two complexes has been studied using UV spectra, fluorescent spectra, cyclic voltammetry, and viscosity measurements. The complexes interact with ct-DNA through classical intercalation. Fluorescence intensity changes of 1 and 2 in the absence and presence of ct-DNA have been investigated for quantitative determination of ct-DNA with the limit of detection of 3.8 and 7.7 ng mL^?1, respectively. From the result, the two complexes are potentially sensitive DNA fluorescent probes.