LIGHT-INDUCED FREE RADICALS IN ORIENTED DNA-PROFLAVINE COMPLEXES

Abstract— Oriented wet DNA-proflavine complexes were illuminated with visible light, Λ > 395 nm, at 77 K, in the presence or absence of oxygen. The electron paramagnetic resonance spectra at 77 K and low microwave power (3 μ W) indicated formation of anionic free radicals in thymine and cationic free radicals, probably in guanine, identical to those induced by y rays at 77 K in similar samples of pure DNA.
The free-radical formation rate showed a quadratic dependence on light intensity, indicating a biphotonic mechanism. The proflavine triplet spectrum was observed during illumination. If the exciting light includes wavelengths below 390 nm, significant amounts of hydrogen addition radicals in thymine are found.     

Preparation of nanoparticles by reducing intermediate radicals formed in sonolytical pyrolysis of surfactants

Metal nanoparticles with a narrow size distribution could be prepared by sonolysis of aqueous solutions of metal cations in the presence of surfactants such as sodium dodecyl sulfate, polyethylene glycol monostearate, etc. The role of the surfactans is not only to stabilize formed particles, but also to produce reductive radicals in pyrolysis or hydrogen abstraction of OH radicals from surfactants. Particles with a smaller size could be obtained in a faster reduction rate with dilute metal cations concentration. Pt(IV) is consecutively reduced in two steps to Pt(0)via Pt(II). By comparing the sonolytical reduction withγ-ray radiolysis, two kinds of organic reducing radicals are proposed to contribute to the reduction. One (R_ab) is an intermediate radical which is produced by hydrogen abstraction of OH radical from surfactant and effective only on the reduction of Pt(II) to Pt(0). The other (R_py) is also an intermediate radical which is produced by thermal decomposition of surfactant at the interface between the cavity and bulk solution and effective on the reduction of Pt(IV) to Pt(II).     

Interaction Between DNA and Some Salicylic Acid Derivatives and Characterization of Their DNA Targets

A nanofiber polypyrrole (PPy) film was electrochemically deposited on a Pt electrode and used for immobilization of single‐stranded DNA (ssDNA) and investigation of hybridization events. Then, the interaction of DNA with four salicylic acid (SA) derivatives was studied with electrochemical methods. The oxidation peak of guanine was decreased by increasing the concentrations of salicylic acid derivatives. The binding constants of these compounds with four different sequences of DNA including different percentages of guanine‐cytosine and adenine‐thymine bases were calculated and it was clarified that sequences with higher percentage of adenine‐thymine bases have a higher binding constant in their interaction with SA derivatives.     

Oligonucleotide cross-linking with copper ions. Spectral and quantum chemical study

Copper(II) complexes with synthetic oligonucleotides consisting of repeating adenine–thymine and guanine–cytosine complementary base pairs have been studied by UV spectroscopy and simulated by DFT quantum chemical calculations at the B3LYP/6-311G++(d,p) level of theory with inclusion of solvation (hydration) effects. The obtained data suggest selective interaction of copper(II) ions with guanine–cytosine complementary pairs, followed by DNA cross-linking at those sites.     

Structural basis for bifunctional zinc(II) macrocyclic complex recognition of thymine bulges in DNA

The zinc(II) complex of 1-(4-quinoylyl)methyl-1,4,7,10-tetraazacyclododecane (cy4q) binds selectively to thymine bulges in DNA and to a uracil bulge in RNA. Binding constants are in the low-micromolar range for thymine bulges in the stems of hairpins, for a thymine bulge in a DNA duplex, and for a uracil bulge in an RNA hairpin. Binding studies of Zn(cy4q) to a series of hairpins containing thymine bulges with different flanking bases showed that the complex had a moderate selectivity for thymine bulges with neighboring purines. The dissociation constants of the most strongly bound Zn(cy4q)-DNA thymine bulge adducts were 100-fold tighter than similar sequences with fully complementary stems or than bulges containing cytosine, guanine, or adenine. In order to probe the role of the pendent group, three additional zinc(II) complexes containing 1,4,7,10-tetraazacyclododecane (cyclen) with aromatic pendent groups were studied for binding to DNA including 1-(2-quinolyl)methyl-1,4,7,10-tetraazacyclododecane (cy2q), 1-(4-biphenyl)methyl-1,4,7,10-tetraazacyclododecane (cybp), and 5-(1,4,7,10-tetraazacyclododecan-1-ylsulfonyl)-N,N-dimethylnaphthalen-1-amine (dsc). The Zn(cybp) complex binds with moderate affinity but little selectivity to DNA hairpins with thymine bulges and to DNA lacking bulges. Similarly, Zn(dsc) binds weakly both to thymine bulges and hairpins with fully complementary stems. The zinc(II) complex of cy2q has the 2-quinolyl moiety bound to the Zn(II) center, as shown by (1)H NMR spectroscopy and pH-potentiometric titrations. As a consequence, only weak (500 μM) binding is observed to DNA with no appreciable selectivity. An NMR structure of a thymine-bulge-containing hairpin shows that the thymine is extrahelical but rotated toward the major groove. NMR data for Zn(cy4q) bound to DNA containing a thymine bulge is consistent with binding of the zinc(II) complex to the thymine N3(-) and stacking of the quinoline on top of the thymine. The thymine-bulge bound zinc(II) complex is pointed into the major groove, and there are interactions with the guanine positioned 5' to the thymine bulge.     

Methylation of DNA bases by methyl free radicals: mechanism of formation of C8-methylguanine

The C8-methylguanine (C8mG) lesions are reported to be produced in vivo due to methylation of guanine base of DNA by methyl free (·CH₃) radicals derived from the carcinogen 1,2-dimethylhydrazines and tert-butylhydroperoxide. It is believed that C8mG lesions can induce G to T and G to C transversion mutations and deletions. However, the mechanisms of reactions of ·CH₃ radicals with DNA bases leading to formation of C8mG and other methylated DNA bases and their biological implications are not properly understood. In the present contribution, we have carried out density functional theory (DFT) calculations to ascertain the various stable methylated derivatives of all the four DNA bases that are formed by the attack of ·CH₃ radicals on DNA bases as well as to understand the mechanism of formation of C8mG due to reaction of ·CH₃ radicals with the C8 site of guanine. Our calculations reveal that ·CH₃ radical would form stable methylated products at the C8 sites of purine bases (guanine and adenine) and at the C5 and C6 sites of pyrimidine bases (cytosine and thymine) by directly attacking to bases. The C8mG is the most stable. This is in agreement with experimental observation. Further, we have found that in absence of any external agents, the C8mG is formed preferably by direct addition of a ·CH₃ radical to the C8 site of guanine followed by abstraction of the H8 hydrogen atom by another ·CH₃ radical. The barrier energies for these two steps are found to be 18.16 (18.73) and 16.05 (18.54) kcal/mol, respectively, as determined at the M06-2X/6-311+G(d,p) level of theory in gas phase (aqueous media). Thus, the present study explains the mechanism of formation of C8mG.     

Electrospray ionization mass spectrometric study of purine base-cisplatin complexes

By mixing cisplatin (cis-diamminedichloroplatinum(II)) with purine base the following ions have been obtained under electrospray ionization conditions: [A+Pt(NH3)2 Cl]+, [A+PtNH3Cl]+, [G+Pt(NH3)2 Cl]+ and [G+PtNH3)Cl]+. Their collision-induced dissociation led to the loss of NH3 and HCl and formation of the protonated base. The last process is strongly favoured for adenine over guanine. It confirms that, analogously as for DNA, formation of the guanine-cisplatin complex is favoured over that of the adenine complex and, as a consequence, it suggests that the mass spectrometric study of nucleic base complexes with platinum may provide some information on the interactions of DNA with other platinum drugs. The loss of NH3 accompanied by that of CO from the guanine ring has experimentally confirmed the presence of a strong hydrogen bond between the NH3 molecule and the O=C6 moiety of guanine found by theoretical calculations.     

Hydrogen-abstracted adenine-thymine radicals with interesting transferable properties

The formation of radicals on DNA bases through various pathways can lead to harmful structural alterations. Such processes are of interest for preventing alteration of healthy DNA and, conversely, to develop more refined methods for inhibiting the replication of unwanted mutagenic DNA. In the present work, we explore theoretically the energetic and structural properties of the nine possible neutral radicals formed via hydrogen abstraction from the adenine-thymine base pair. The lowest energy radical is formed by loss of a hydrogen atom from the methyl group of thymine. The next lowest energy radicals, lying 8 and 9 kcal mol-1 higher than the global minimum, are those in which hydrogens are removed from the two nitrogens that would join the base pair to 2-deoxyribose in double-stranded DNA. The other six radicals lie between 16 and 32 kcal mol-1 higher in energy. Unlike the guanine-cytosine base pair, adenine-thymine (A-T) exhibits only minor structural changes upon hydrogen abstraction, with all A-T derived radicals maintaining planarity. Moreover, the energetic ordering for the radicals of the two isolated bases (adenine and thymine) is preserved upon formation of the base pair, though with a wider spread of energies. Even more significantly, the energetic interleaving of the (A-H)*-T and A-(T-H)* radicals is correctly predicted from the X-H bond dissociation energies of the isolated adenine and thymine. This suggests that the addition of the hydrogen-bonded complement base only marginally affects the bond energies.     

带电组氨酸侧链与DNA碱基间非键作用强度的理论研究

采用MP2方法和6-31+G(d,p)基组优化得到了带有一个正电荷的组氨酸侧链与4个DNA碱基间形成的18个氢键复合物的气相稳定结构, 从文献中获取了组氨酸侧链与DNA碱基间形成的12个堆积和T型复合物的气相稳定结构, 使用包含基组重叠误差(BSSE)校正的MP2方法和aug-cc-pVTZ基组及密度泛函理论M06-2X-D3方法和aug-cc-pVDZ基组计算了这些复合物的结合能. 研究结果表明, 包含BSSE校正的M06-2X-D3方法和aug-cc-pVDZ基组能够给出较准确的结合能; 气相条件下, 组氨酸侧链与同种DNA碱基间的离子氢键作用明显强于堆积作用和T型作用, 组氨酸侧链最易通过离子氢键与胞嘧啶C和鸟嘌呤G作用形成氢键复合物, 组氨酸与胞嘧啶C和鸟嘌呤G间的T型作用强于与腺嘌呤A和胸腺嘧啶T间的离子氢键作用; 水相条件下, 组氨酸侧链与同种DNA碱基间的离子氢键作用仍明显强于堆积作用和T型作用, 组氨酸侧链更易与胞嘧啶C和鸟嘌呤G相互作用形成氢键复合物, 但是最强的组氨酸侧链与胞嘧啶C间的T型作用明显弱于与腺嘌呤A和胸腺嘧啶T间的离子氢键作用, 说明水相条件下组氨酸侧链与DNA碱基间主要通过离子氢键作用形成氢键复合物.     

UV-induced free radicals in oriented DNA.

Abstract— Samples of oriented DNA containing 30% water were UV-irradiated at 77 K and investigated by electron paramagnetic resonance (EPR). The EPR spectra recorded in directions parallel and perpendicular to the DNA fibre direction showed that at low UV doses the induced free radicals are very similar to those induced by γ-irradiation at the same temperature. The γ-induced free radicals have previously been analysed and found to consist mainly of anionic free radicals on thymine and cationic free radicals on guanine. At higher UV doses or by suitable annealing of the samples given a low UV dose, significant amounts of hydrogen-addition radicals on thymine were observed. The quantum yield of free radical formation for irradiation at 300nm ± 10nm was estimated to 10^--⁴. We also made a quantitative determination of the UV-induced free radicals inside an optically effective volume of the sample. The following free radical induction frequencies at 77 K were estimated: γ-rays: 2 × 10^--¹² free radicals per rad per dalton and UV (300nm): 6 × 10^--¹² free radicals per J/m² per dalton.     

AN EPR STUDY OF π-CATION RADICALS IN DINUCLEOSIDE PHOSPHATES AND DNA PRODUCED BY PHOTOIONIZATION

In this work we have produced the π-cation radicals of a number of nucleotides, dinucleoside phosphates, and DNA in aqueous glasses (8M NaCIO₄) by photoionization and investigated these species by EPR spectroscopy. Results found for nucleotides and dinucleoside phosphates containing one type of DNA base, e.g. TpT, GpG, or dApdA, were used in the analysis of spectra found for mixed dinucleoside phosphates, e.g. TpdG. For TpdG and TpdA in neutral glasses photoionization takes place from the purine base and no transfer of charge to the pyrimidine base is found. In basic conditions both the adenine and thymine π-cations are observed in TpdA. In both neutral and basic conditions the results found for mixed dinucleoside phosphates containing guanine show that the guanine cation is formed preferentially by photolysis. This result was found to extend to DNA. Photolysis of DNA in 8M NaC1O₄ produced principally the guanine cation. Computer simulations using parameters determined by other workers from a study of γ-irradiated oriented DNA closely match the spectrum found in this work attributed to the guanine cation in dinucleoside phosphates and DNA. This work thus confirms the presence of the guanine cation in γ-irradiated DNA.     

Synthesis and spectral studies on platinum complexes with mono- and bidentate N-donor organic ligands

Platinum(II) complexes of types PtLX₂, PtL₂X₂, PtLX″ and the Pt(IV) complexes PtLXY (where L = mono- or bidentate organic ligand containing nitrogen donor atoms; X = Cl or Br; X′ = oxalate or malonate and Y = Br) have been synthesized and characterized from their elemental analysis, IR and X-ray photoelectron spectral data. The Pt 4f_7/2 binding energies indicate that 1,8-naphthalene-diamine ligand is a better donor of electron density to the metal than other ligands studied here. The Cl 2p_3/2 binding energies in the square planar Pt(II) complexes are observed in the range 198.8 ± 0.8 eV. The ν (PtCl) vibrations (ca 335 and 320 cm^?1) corresponding to two cis-Cl ligands were observed in the IR spectra.The extent of the interaction between cis-dichloro-bis-(theophylline)platinum(II) with calf thymus DNA has beenstudied. The UV difference spectra resulting from aquated Pt^II(theoph)₂-DNA interaction exhibit bands at 282 and 292 nm attributable to the change in the electron distribution of the base moieties induced by binding with platinum and due to the loss of base stacking. Melting profiles for the DNA samples treated with Pt-complex showed decrease in the melting temperature. Binding of the guanine residues of the DNA, involving probably (N7)-0(6) positions to the metal is implied.     

Reaction force analysis of the effect of Mg(II) on the 1,3 intramolecular hydrogen transfer in thymine

The 1,3 intramolecular hydrogen transfer reaction in free thymine and in Mg(II)-thymine have been studied at the density functional theory level. The mechanism of intramolecular proton transfer in these systems emerges from the analysis of the reaction force profile along the reaction path; it is rationalized in terms of structural and electronic reorganizations that take place during the chemical transformation. Results show that the presence of Mg(II) monocoordinated to thymine activates the hydrogenic motion by inducing structural and electronic changes in the molecular backbone. In the metallic complex, it is found that the hydrogen transfer is followed by a relaxation process that facilitates the metal cation migration to form a bicoordinated complex.     

Reactions of OH* and eaq − with uracil and thymine in the presence of Cu(II) ions in dilute aqueous solutions: A pulse radiolysis study

The reactions of OH^* and e_aq ^? adducts of uracil and thymine with Cu(II) ions in aqueous solutions were followed by pulse radiolysis. The transient absorption spectra of the OH^* adducts of uracil when followed in the presence of Cu(II) ions show growth in absorption at wavelengths 420 and 350 nm at 15 μs and 65 μs after the pulse respectively. Similar transient absorption spectra of thymine showed growth in absorption at wavelengths 390 and 320 nm at 38 μs and 65 μs after the pulse respectively. The rates of electron transfer from the OH^* adducts of uracil and thymine to various Cu(II) compounds when monitored at 360 nm lie between 10⁶ and 10⁸ mol^?1 dm³ s^?1 this implies that the electron transfer process is not an efficient process. Low rate constants coupled with the spectral changes suggest formation of a radical copper adduct which decays by water insertion to give cis-glycols as the major product. The electron transfer from the electron adducts of uracil and thymine to various copper(II) compounds takes place more efficiently (rate constants of the order of 10⁸ and 10⁹ mol^?1 dm³ s^?1) compared with that from the OH^* adducts. The t-butanol radicals formed on scavenging the OH^* radicals also produce adducts with Cu(I) ions which are formed on oxidation of the electron adducts by Cu(II) ions. This adduct has absorption around 400 nm both in the case of uracil and thymine.     

DFT and MP2 investigations on the hydrogen bonding interaction between 5,6-dihydrothymine and dna bases: A, C, G, T

5,6-Dihydrothymine (DHT) is a nucleobase lesion induced by the action of ionizing radiation on thymine residue in DNA. In this work, we present the hydrogen bonding base pairs involving 5,6-dihydrothymine bound to four bases in DNA: adenine (A), cytosine (C), guanine (G), and thymine (T). Full geometry optimizations are performed for the studied complexes by the B3LYP method. Interaction energies are corrected for the basis set superposition error, using the full Boys-Bernardi counterpoise correction scheme. Hydrogen bonding patterns of these base pairs are characterized using NBO and AIM analysis. According to the calculated binding energies and structural parameters, the stability of the base pairs decrease in the following order: DHT:G ～ DHT:A > DHT:C > DHT:T.     

Reactions of carbamyl radicals: intramolecular hydrogen abstraction reactions

ω-Phenylalkyl-N-methylcarbarnyl radicals undergo intermolecular addition to 3,3-dinethylbut-l-ene in preference to intramolecular hydrogen abstraction. Methyl N-(ω-phenylalkyl) carbanyl radicals and methyl N-pentylcarbamyi radicals readily abstract hydrogen through a six membered transition state or a seven membered transition state if the hydrogen is beniylic. The selectivities are interpreted in terms of the electrophilicity of the radical and the stereo-electronic requirements of hydrogen abstraction reactions.     

MP2 study on the hydrogen bonding interaction between 5-hydroxy-5-methylhydantoin and DNA bases: A,C, G,T

The 5-hydroxy-5-methylhydantoin (5-OH-5-Me-dHyd) is a nucleobase lesion induced by the action of ionizing radiation on thymine residue in DNA. In this study, we present the hydrogen bonding base pairs involving 5-OH-5-Me-dHyd bound to the four bases in DNA: adenine (A), cytosine (C), guanine (G), and thymine (T). Full geometry optimizations have been performed for the studied complexes by MP2 method. The interaction energies were corrected for the basis-set superposition error (BSSE), using the full Boys–Bernardi counterpoise correction scheme. Hydrogen bonding patterns of these base pairs were characterized using NBO analysis and AIM analysis. According to the calculated binding energies and structural parameters, the stability of the base pairs decrease in the following order: 5-OH-5-Me-dHyd:G>5-OH-5-Me-dHyd:A>5-OH-5-Me -dHyd:C~5-OH-5-Me-dHyd:T.     

MP2 study on the hydrogen-bonding interaction between 5-hydroxymethyl-uracil and DNA bases: A,C, G,T

The 5-hydroxymethyl-uracil (HmU) is a product of oxidative attack on the methyl group of thymine in DNA. In this work, we present the hydrogen bonding complexes formation involving HmU bound to the four bases in DNA: adenine (A), cytosine (C), guanine (G), and thymine (T). Full geometry optimizations have been performed for the studied complexes by MP2 method. The interaction energies were corrected for the basis-set superposition error (BSSE), using the full Boys-Bernardi counterpoise correction scheme. Hydrogen bonding patterns of these base pairs were characterized using NBO analysis and AIM analysis. According to the calculated binding energies and structural parameters, the stability of the base pairs decrease in the following order: HmU:A > HmU:G > HmU:C > HmU:T.     

Fluorescence and electrochemical detection of pyrimidine/purine transversion by a ferrocenyl aminonaphthyridine derivative

A novel hydrogen bond-forming ligand for pyrimidine/purine transversion, which contains both a fluorescent naphthyridine moiety and a ferrocenyl group as an electrochemical indicator, is described. Hydrogen bond-mediated recognition for a target nucleobase at an abasic site in a DNA duplex is confirmed by both fluorescence and electrochemical measurements. The analysis by fluorescence titration reveals that the ligand shows significant fluorescent quenching upon formation of a 1 : 1 complex with the target nucleobase opposite the abasic site, and the selectivity is in the order of cytosine > thymine > adenine, guanine, reflecting the stability of the hydrogen bond formation.     

A third mode of DNA binding: Phosphate clamps by a polynuclear platinum complex

We describe a 1.2 A X-ray structure of a double-stranded B-DNA dodecamer (the Dickerson Dodecamer, DDD, [d(CGCGAATTCGCG)]2) associated with a cytotoxic platinum(II) complex, [{trans-Pt(NH3)2(NH2(CH2)6(NH3+)}2-mu-{trans-Pt(NH3)2(NH2(CH2)6NH2)2}] (TriplatinNC). TriplatinNC is a multifunctional DNA ligand, with three cationic Pt(II) centers, and directional hydrogen bonding functionalities, linked by flexible hydrophobic segments, but without the potential for covalent interaction. TriplatinNC does not intercalate nor does it bind in either groove. Instead, it binds to phosphate oxygen atoms and thus associates with the backbone. The three square-planar tetra-am(m)ine Pt(II) coordination units form bidentate N...O...N complexes with OP atoms, in a motif we call the Phosphate Clamp. The geometry is conserved among the 8 observed phosphate clamps in this structure. The interaction appears to prefer O2P over O1P atoms (frequency of interaction is O2P > O1P, base and sugar oxygens > N). The high repetition and geometric regularity of the motif suggests that this type of Pt(II) center can be developed as a modular nucleic acid binding device with general utility. TriplatinNC extends along the phosphate backbone, in a mode of binding we call "Backbone Tracking" and spans the minor groove in a mode of binding we call "Groove Spanning". Electrostatic forces appear to induce modest DNA bending into the major groove. This bending may be related to the direct coordination of a sodium cation by a DNA base, with unprecedented inner-shell (direct) coordination of penta-hydrated sodium at the O6 atom of a guanine.