UV spectra of adenine methyl and glycosyl derivatives and their transformation induced by amino acid carboxylic groups

UV absorption spectra of adenine, adenosine and their methyl derivatives were studied in dimethylsuloxide (DMSO). Considerable changes in UV spectra of adenine under methylation at the 1 and 3 positions, and adenosine under methylation at the 1 position attested the essential structural reconstruction of adenine purine ring. Ade and m6Ade were shown to form complexes with deprotonated carboxylic group of amino acids (carboxylate-ion) through two H-bonds involving amino group and N7H imino group, tautomeric transition N9H-->N7H being initiated namely by interaction with carboxylate-ion. Considerable changes in UV spectra of m1Ade, m1A, and m3Ade under interaction with neutral carboxylic group of amino acids were interpreted as a result of proton transfer from amino acid to the base.     

Recognition modes of hypoxanthine,xanthine and their derivatives by amino acid carboxylic group: UV spectroscopic and quantum chemical data

UV absorption spectra of Hyp, Xan, their nucleosides and methyl derivatives were studied in anhydrous dimethylsuloxide and the changes in these spectra on the interactions with neutral and deprotonated carboxylic groups of amino acids were traced. By the semiempirical quantum-chemical method MNDO/H it was shown, that interaction with carboxylate-ion fixes Hyp as the rare N7H enolic tautomer and converts Xan into its N9H diketo tautomeric form with a probable admixture of the N7H O6-enolic form. Significant changes in the UV spectra of Xan, m3Xan, m9Xan and X under interaction with carboxylate-ion are determined by essential contribution to complex formation of proton transfer from bases to ligands, m9Xan and X proving to be slightly protonated even by the solvent. The methylation of the N7 position in m7I and m7X was established to result in the practical absence of their interactions with carboxylate-ion and initiation of a new ability of forming complex with the neutral carboxylic group. Substitution of the C8H group by N in 8-azaXan does not change the interaction specificity of the base with two forms of carboxylic group.     

Specific interactions of isoguanine with the neutral and deprotonated carboxylic group of amino acids: results of model quantum chemical calculations

The MNDO/H quantum chemical calculations performed in order to estimate energetic features of the isoguanine (isoGua) prototropic tautomers complexes with acetic acid and its carboxylate-ion (models of neutral and deprotonated forms of amino acid carboxylic group) demonstrate ability of the latter to induce the N9H-->N7H tautomeric transition in the base, being characteristic to other purine bases as well. By contrast, the neutral carboxylic group forms the most stable complex with the ground-state isoGua tautomer N3HN9H.     

Deprotonated carboxylic group of amino acids transforms adenine into its rare prototropic tautomers

By UV spectroscopic data for anhydrous DMSO solutions and ab initio HF/6-31G** calculations in vacuum it was shown for the first time that deprotonated amino acid carboxylic group is able to change tautomeric state of a nucleotide base, exactly to convert the N9H ground-state prototropic tautomer of adenine into the N7H and N1H rare ones.     

Specific interaction of isocytosine and amino acid carboxylic group shifts the base tautomeric equilibrium

By 1H NMR, UV and IR spectroscopies in anhydrous DMSO and quantum-chemical calculations by MNDO/H in vacuum specific interactions of isocytosine with neutral and deprotonated carboxylic groups of amino acids were investigated. In vacuum interaction with carboxylate ion provokes in isoCyt transition from the ground-state enolic form to the high energy N3H-keto tautomer. In DMSO keto tautomer N3H of isoCyt is stabilized but interactions with carboxylate ion essentially shifts equilibrium to enolic form. Neutral carboxylic group forms the most stable complex with the ground-state enolic tautomer in vacuum but in DMSO it proves to shift the keto(N3H)-enolic equilibrium to the right.     

Effect of carboxylate and Na ions on the tautomeric status of 9-methylguanine

Interactions of 9-methylguanine (m9Gua) with carboxylate ion of acetic acid (CH3COO-) and Na+ were studied by 1H NMR spectroscopy and ab initio quantum chemical calculations of the B3LYP/6-31++G(d,p) and B3LYP/6-311++G(d,p) levels of theory. Changes in the m9Gua 1H NMR spectrum in the presence of the equimolar amount of sodium acetate (NaAc), which in anhydrous DMSO dissociates to CH3COO- and Na+, were interpreted as a consequence of a complex formation of m9Gua in the amino-keto-N1H tautomeric form (m9GuaN1H) with carboxylate ions via two H-bonds involving amino and N1H-imino protons. Quantum chemical calculations of interactions of the m9GuaN1H ground-state tautomer and the m9GuaN3H high energy one with relative energy 20.01 kcal/mol show that the ground state tautomer forms the ground-state complex CH3COO-:mgGuaN1H, by 5.57 kcal/mol more stable than the CH3COO-:m9GuaN3H complex, and coordination of Na+ with the O6 and N7 atoms reduces this energy difference to 2.57 kcal/mol. Such a coordination of Na+ with tautomer m9GuaN3H therewith decreases its relative energy only to 13.31 kcal/mol. Non-additivity of the two ligands contributions to the 8-times reduction of the relative energy of the high energy tautomer in the CH3COO-:m9GuaN3H:Na+(O6,N7) triple complex was concluded, the role of CH3COO- being dominant. Besides, coordination with Na+ resulted in an iminoproton transfer from the base to CH3COO- in the triple complexes of both tautomers, according to calculations in vacuum. Biological significance of the results is noticed.     

Guanine-derived radicals: dielectric constant-dependent stability and UV/Vis spectral properties: a DFT study

Upon successive deprotonation of the guanine radical cation, various neutral radicals and radical anions can be formed. Their relative stability and UV/Vis absorption spectra have been calculated by DFT in the vacuum and in aqueous solution. Good agreement with experimental data is obtained when solvent effects are taken into account. The experimental observation that in the nucleosides deprotonation of the guanine radical cation occurs at N1 (formation of N1G(*)) in water and at N2 (formation of N2G(*)) in single crystals is now explained by a strong effect of the dielectric constant of the environment on their stability. While SCRF=PCM and CPCM (Gaussian 03) describe the trend, SCRF=DPCM (Gaussian 98) even shows the crossover from N2G(*) to N1G(*) at high dielectric constant. A crossover of the preferred deprotonation site is also given by the nucleoside itself. While for the gas phase a deprotonation at N2 is calculated to be favored over that at N1, the reverse is found for an aqueous environment (in agreement with the experiment). The radical anions of guanine, N9N1G(*)(-) and N9N2G(*)(-), are very similar in energy, but a comparison of the experimental and calculated UV/Vis spectra allows us to identify the experimentally observed intermediate clearly as N9N1G(*)(-).     

Identification of guanine and adenine adducts in DNA alkylated by dibromodulcitol in vitro and in vivo

DNA reacted with dibromodulcitol in neutral solution yielded 3- and 7-alkyl substituted purines after hydrolysis at neutral pH-value at 37°C. The alkylated products were identified by mass spectrometry and by comparison of their UV absorption spectra and chromatographic properties on thin-layer chromatography (TLC) and various columns with those of the corresponding galactitylpurine derivatives obtained by synthetic route from alkylation of the appropriate nucleic bases or nucleosides. The labelled alkylpurines occurring in DNA of Yoshida tumour cells treated with [³H]dibromodulcitol in vivo were also indentified by co-chromatography of labelled DNA hydrolysate with synthetic 3- and 7-alkyl substituted purines. On the basis of the same chromatographic behaviour 3-(1-deoxy-3,6-anhydrogalactit-1-yl)adenine, 7-(1-deoxygalactit-1-yl)guanine, 7-(1-deoxy-3,6-anhydrogalactit-1-yl)guanine and 1,6-di(guanin-7-yl)-1,6-dideoxygalactitol were identified as main alkylated products in tumor cell DNA after in vivo treatment with dibromodulcitol.     

9-(Phosphonoalkyl)guanine derivatives as substrates or inhibitors of guanylate kinase.

Several 9-(phosphonoalkyl)guanines (Gua(CH2)nCH2-PO3H2; n = 4-6) and 9-(difluorophosphonoalkyl)guanines (Gua(CH2)nCF2PO3H2; n = 3-7) were studied as potential substrates and inhibitors of guanylate kinase. These compounds are inhibitors of the enzyme except 9-(5-phosphonopentyl)guanine (n = 4) which is a substrate with an efficiency of phosphorylation of about 0.3% that of GMP, as estimated from the Vmax/Km ratios. The phosphonate and difluorophosphonate derivatives with n = 5 produce optimal inhibition. These two compounds have similar affinity, both being competitive inhibitors with respect to GMP and noncompetitive inhibitors with respect to ATP. pH-dependence studies indicate that the dianionic rather than the monoanionic form of these compounds bind to the enzyme. The lack of phosphorylation of 9-(5,5-difluoro-5-phosphonopentyl)guanine by guanylate kinase is explained by the decreased nucleophilic character of the oxygen atoms of the phosphonate group rather than by inadequate binding to the GMP-binding site.     

Reaction of acid-activated mitomycin C with calf thymus DNA and model guanines: elucidation of the base-catalyzed degradation of N7-alkylguanine nucleosides

Mitomycin C (MC, 1) forms covalent adducts under acidic activating conditions (pH approximately 4) with deoxyguanosine, d(GpC), and guanine residues of calf thymus DNA. In the case of deoxyguanosine, five adducts arise from a common precursor, N7-(2' beta, 7'-diaminomitosen-1'-yl)-2'-deoxyguanosine (10a; not isolated), which hydrolyzes spontaneously via two pathways: scission of the glycosidic bond to form N7-(2' beta, 7'-diaminomitosen-1' alpha-yl)guanine (5) and its 1' beta-isomer (6) and imidazolium ring opening to generate three 2,6-diamino-4-hydroxy-5-(N-formyl-2' beta, 7'-diaminomitosen-1' beta-yl)pyrimidine (FAPyr) derivatives that are substituted at N6 by isomeric 2'-deoxyribose units [i.e., 1' beta-furanose (7), 1' alpha-furanose (8), and 1' beta-pyranose (9)]. The structures of 5-9 were determined by spectroscopic methods. The same five adducts were obtained from d(GpC), but only the guanine adducts 5 and 6 were formed in DNA. Adducts 7-9 interconvert during high-performance liquid chromatography (HPLC). The unexpected isomerization of the deoxyribose moiety of the initially formed 1' beta-furanose adduct 7 to those of 8 and 9 occurs upon imidazolium ring opening, as discerned by the course of imidazolium cleavage of the simple models N7-ethyl- and N7-methylguanosine and N7-methyl-2'-deoxyguanosine. All ring-opened N7-alkylguanosine derivatives studied here exist as a mixture of distinct N-formyl rotamers, manifested by multiple interconverting peaks on HPLC and in the 1H NMR spectra. In the UV spectra of such derivatives, a new and diagnostic maximum at 218 nm (at pH 7) is observed. Acid-activated MC is found to alkylate preferentially the Gua-N7 position in deoxyguanosine or d(GpC), in contrast to reductively activated MC, which preferentially alkylates the Gua-N2 position. This finding is explained by the different electronic structures of acid- and reduction-activated MC. In DNA, the N7 specificity of acid-activated MC is partially offset by steric factors.     

Xanthosine and xanthine. Substrate properties with purine nucleoside phosphorylases, and relevance to other enzyme systems.

Substrate properties of xanthine (Xan) and xanthosine (Xao) for purine nucleoside phosphorylases (PNP) of mammalian origin have been reported previously, but only at a single arbitrarily selected pH and with no kinetic constants. Additionally, studies have not taken into account the fact that, at physiological pH, Xao (pKa = 5.7) is a monoanion, while Xan (pKa = 7.7) is an equilibrium mixture of the neutral and monoanionic forms. Furthermore the monoanionic forms, unlike those of guanosine (Guo) and inosine (Ino), and guanine (Gua) and hypoxanthine (Hx), are still 6-oxopurines. The optimum pH for PNP from human erythrocytes and calf spleen with both Xao and Xan is in the range 5-6, whereas those with Guo and Gua, and Ino and Hx, are in the range 7-8. The pH-dependence of substrate properties of Xao and Xan points to both neutral and anionic forms as substrates, with a marked preference for the neutral species. Both neutral and anionic forms of 6-thioxanthine (pKa = 6.5 +/- 0.1), but not of 2-thioxanthine (pKa = 5.9 +/- 0.1), are weaker substrates. Phosphorolysis of Xao to Xan by calf spleen PNP at pH 5.7 levels off at 83% conversion, due to equilibrium with the reverse synthetic pathway (equilibrium constant 0.05), and not by product inhibition. Replacement of Pi by arsenate led to complete arsenolysis of Xao. Kinetic parameters are reported for the phosphorolytic and reverse synthetic pathways at several selected pH values. Phosphorolysis of 200 micro m Xao by the human enzyme at pH 5.7 is inhibited by Guo (IC50 = 10 +/- 2 micro m), Hx (IC50 = 7 +/- 1 micro m) and Gua (IC50 = 4.0 +/- 0.2 micro m). With Gua, inhibition was shown to be competitive, with Ki = 2.0 +/- 0.3 micro m. By contrast, Xao and its products of phosphorolysis (Xan and R1P), were poor inhibitors of phosphorolysis of Guo, and Xan did not inhibit the reverse reaction with Gua. Possible modes of binding of the neutral and anionic forms of Xan and Xao by mammalian PNPs are proposed. Attention is directed to the fact that the structural properties of the neutral and ionic forms of XMP, Xao and Xan are also of key importance in many other enzyme systems, such as IMP dehydrogenase, some nucleic acid polymerases, biosynthesis of caffeine and phosphoribosyltransferases.     

Density functional theory study on the interaction between keto-9H guanine and aspartic acid

A theoretical study was performed using density functional theory (DFT) to investigate hydrogen bonding interactions in signature complexes formed between keto-9H guanine (Gua) and aspartic acid (Asp) at neutral pH. Optimized geometries, binding energies and the theoretical IR spectra of guanine, aspartic acid and their corresponding complexes (Gua-Asp) were calculated using the B3LYP method and the 6-31+G(d) basis set. Stationary points found to be at local minima on the potential energy surface were verified by second derivative harmonic vibrational frequency calculations at the same level of theory. AIM theory was used to analyze the hydrogen bonding characteristics of these DNA base complex systems. Our results show that the binding motif for the most stable complex is strikingly similar to a Watson-Crick motif observed in the guanine-cytosine base pair. We have found a range of hydrogen bonding interactions between guanine and aspartic acid in the six complexes. This was further verified by theoretical IR spectra of ω(C-H---O-H) cm⁻¹ stretches for the Gua-Asp complexes. The electron density plot indicates strong hydrogen bonding as shown by the 2p _z dominant HOMO orbital character.     

Experimental and theoretical study of energetics of complex formation between nucleic acid bases and the bases with amide group.

A number of nucleic acid base pairs and complexes between the bases and the amide group of acrylamide have been studied experimentally by using mass spectrometry and theoretically by the method of atom-atom potential function calculations. It has been found from temperature dependencies of peak intensities in mass spectra of m2.2.9(3) Gua.m1Ura, m9 Ade.m1Cyt, m2.2.9(3) Gua.m1Gua.m1Cyt pairs that enthalpy values, delta H, of the complex formation are equal to 14.2 +/- 1.1, 13.5 +/- 1.3 and 16.4 +/- 1.4 kcal/M, respectively, and those of acrylamide with m1.3(2) Ura and m1Thy corresponds to 9.7 +/- 1.0 and 6.8 +/- 0.6 kcal/M. There is a good agreement of the experimental data with calculations when taking into account both the amino-oxo and the amino-hydroxy tautomeric forms of guanine. A combined use of the data allows us to determine the energy, the modes of interaction and the structure of the complexes. The results are discussed in connection with the modelling of molecular structure of biopolymers by the method of classical potential functions, protein-nucleic acids recognition and fidelity of nucleic acids biosynthesis.     

Fluorescence studies of calf spleen purine nucleoside phosphorylase (PNP) complexes with guanine and 9-deazaguanine

Interactions of trimeric calf spleen purine nucleoside phosphorylase (PNP) with guanine (Gua) and its analogue, 9-deazaguanine (9-deaza-Gua), were studied by means of the steady-state fluorescence. The aim was to test the hypothesis that the enzyme stabilizes the anionic form of purine, inferred previously from the unusual increase of fluorescence observed after binding of guanine by calf spleen PNP. We have found that the dissociation constants obtained form titration experiments are in fact pH-independent in the range 7.0-10.25 for both PNP/Gua and PNP/9-deaza-Gua complexes. In particular, at pH 7.0 we found Kd = 0.12 +/- 0.02 micro M for Gua and 0.16 +/- 0.01 micro M for 9-deaza-Gua, while at the conditions where there is more than 40% of the anionic form the respective values were Kd = 0.15 +/- 0.01 micro M for Gua (pH 9.0) and 0.25 +/- 0.02 micro M for 9-deaza-Gua (pH 10.25). Hence, the enzyme does not prefer binding of anionic forms of these ligands in respect to the neutral ones. This result questions the involvement of the anionic forms in the reaction catalyzed by trimeric PNPs, and contradicts the hypothesis of a strong hydrogen bond formation between the enzyme Asn 243 residue and the purine N7 position.     

Induced chirality in fisetin upon binding to serum albumin: experimental circular dichroism and TDDFT calculations

Theoretical absorption and electronic circular dichroism (ECD) spectra predicted via time-dependent density functional theory (TDDFT) calculations on the neutral and four anionic species of fisetin, an achiral flavonoid, were used to rationalize the experimental absorption and induced circular dichroism (ICD) spectra of the ligand upon binding to human serum albumin (HSA). On this basis, the mechanism responsible for the appearance of the ICD signal was ascribed to a distortion of the conformation of bound fisetin. Furthermore, comparison of the simulated and experimental spectra revealed that two fisetin species bind to HSA, namely, the neutral molecule and the anion deprotonated at the hydroxyl group in position 7, in a 1:1 ratio. The coupling of the theoretical results with the experimental absorption and ICD data allows identification of the flavonoid species that bind to the protein and evaluation of their conformation in the binding site.     

Fluorescence studies of calf spleen purine nucleoside phosphorylase (PNP) complexes with guanine and 9-deazaguanine

Interactions of trimeric calf spleen purine nucleoside phosphorylase (PNP) with guanine (Gua) and its analogue, 9-deazaguanine (9-deaza-Gua), were studied by means of the steady-state fluorescence. The aim was to test the hypothesis that the enzyme stabilizes the anionic form of purine, inferred previously from the unusual increase of fluorescence observed after binding of guanine by calf spleen PNP. We have found that the dissociation constants obtained form titration experiments are in fact pH-independent in the range 7.0-10.25 for both PNP/Gua and PNP/9-deaza-Gua complexes. In particular, at pH 7.0 we found K _d = 0.12 ± 0.02 μ M for Gua and 0.16 ± 0.01 μ M for 9-deaza-Gua, while at the conditions where there is more than 40% of the anionic form the respective values were K _d = 0.15 ± 0.01 μ M for Gua (pH 9.0) and 0.25 ± 0.02 μ M for 9-deaza-Gua (pH 10.25). Hence, the enzyme does not prefer binding of anionic forms of these ligands in respect to the neutral ones. This result questions the involvement of the anionic forms in the reaction catalyzed by trimeric PNPs, and contradicts the hypothesis of a strong hydrogen bond formation between the enzyme Asn 243 residue and the purine N(7) position.     

Reaction of trans-4-N-acetoxy-N-acetylaminostilbene with guanosine and deoxyguanosine in vitro: the primary reaction product at N2 of guanine yields different final adducts

The model ultimate carcinogen, trans-4-N-acetoxy-N-acetylaminostilbene (N-acetoxy-AAS), was reacted with guanosine (Guo) and deoxyguanosine (d-Guo) and the resulting adducts were purified by Sephadex LH-20 chromatography and HPLC for structure identification. A number of new adducts was identified by mass and 1H-NMR spectroscopy. The generation of all known adducts can now be explained by a common mechanism. The electrophile formed from the hydroxamic acid ester at C-beta reacts in a first step predominantly with N2 of guanine (Gua). The resulting quinone-imide intermediate reacts in a second step with either one of three nucleophiles: (1) predominantly with N3 of Gua to yield the previously described angular cyclic adducts ((5R,6R)/(5S,6S)-9-oxo-5,6,7,9-tetrahydro-imidazo(2,1-b)purines); (2) with N1 of Gua to yield linear cyclic adducts ((6R,7R)/(6S,7S)-9-oxo-5,6,7,9-tetrahydro-imidazo(1,2-a)purines); (3) with water to yield the open ring (1R,2R)/(1S,2S)-2-(N2'-guanyl)-1-hydroxyethanes. To some minor extent (1:8-1:9) the electrophile reacts first with N1 or N3 of guanine which leads to the formation of two pairs of the corresponding regioisomeric cyclic adducts. This reaction mechanism may also explain the formation of cross-links between different bases.     

Xanthine, xanthosine and its nucleotides: solution structures of neutral and ionic forms, and relevance to substrate properties in various enzyme systems and metabolic pathways

The 6-oxopurine xanthine (Xan, neutral form 2,6-diketopurine) differs from the corresponding 6-oxopurines guanine (Gua) and hypoxanthine (Hyp) in that, at physiological pH, it consists of a approximately 1:1 equilibrium mixture of the neutral and monoanionic forms, the latter due to ionization of N(3)-H, in striking contrast to dissociation of the N(1)-H in both Gua and Hyp at higher pH. In xanthosine (Xao) and its nucleotides the xanthine ring is predominantly, or exclusively, a similar monoanion at physiological pH. The foregoing has, somewhat surprisingly, been widely overlooked in studies on the properties of these compounds in various enzyme systems and metabolic pathways, including, amongst others, xanthine oxidase, purine phosphoribosyltransferases, IMP dehydrogenases, purine nucleoside phosphorylases, nucleoside hydrolases, the enzymes involved in the biosynthesis of caffeine, the development of xanthine nucleotide-directed G proteins, the pharmacological properties of alkylxanthines. We here review the acid/base properties of xanthine, its nucleosides and nucleotides, their N-alkyl derivatives and other analogues, and their relevance to studies on the foregoing. Included also is a survey of the pH-dependent helical forms of polyxanthylic acid, poly(X), its ability to form helical complexes with a broad range of other synthetic homopolynucleotides, the base pairing properties of xanthine in synthetic oligonucleotides, and in damaged DNA, as well as enzymes involved in circumventing the existence of xanthine in natural DNA.     

Interaction of anticancer drug cisplatin with guanine: density functional theory and surface-enhanced Raman spectroscopy study

Surface-enhanced Raman spectroscopy (SERS) in a silver sol assisted by density functional theory (DFT) calculations is shown to be a promising tool in the characterization of platinum complexes and their interaction with nucleic acid bases. This is demonstrated using cisplatin and guanine as a model. The energies and geometric parameters of cisplatin, guanine, and their reaction products are calculated at Becke's nonlocal three parameter exchange and correlation functional and the Lee-Yang-Parr correlation functional level using the 6-31++G(d,p) basis set on the light elements and the effective core potential by Hay and Wadt on platinum. Available X-ray crystallography data are mostly in agreement with predictions within the experimental precision level, although Pt-N bond lengths tend to be systematically overestimated. The normal Raman spectrum of cisplatin is assigned. The SERS spectra of cisplatin and its reaction product with guanine are measured from 10(-6) M aqueous solution. The observed spectral changes in the SERS spectrum of guanine upon cisplatin binding are modeled by DFT calculations. The best agreement between theory and experiment is achieved when the adsorbed reaction product is assumed to be the 1:1 adduct cis-Pt(NH3)2ClG in which Pt is bound to N7 and guanine is deprotonated at N9.     

Interaction of echinomycin with guanine: electrochemistry and spectroscopy studies

The interaction of antitumor antibiotic, echinomycin (Echi) with guanine (Gua) was thoroughly investigated by adsorptive transfer stripping cyclic voltammetry, ultraviolet and visible adsorption spectra (UV/Vis) and Fourier-transform infrared spectroscopy (FTIR). Electrochemistry provided a simple tool for verifying the occurrence of interaction between Echi and Gua. Echi could be accumulated from the solution and give well-defined electrochemical signals in 0.1 M phosphate buffer solution (pH 7.0) only when Gua was present on the surface of the electrochemically pretreated glass carbon electrode (GCE), suggesting a strong binding of Echi to Gua. All the acquired spectral data showed that a new adduct between Echi and Gua was formed, and two pairs of adjacent intermolecular hydrogen bonds between the Ala backbone atoms in Echi and Gua (Ala-NH to Gua-N3 and Gua-NH2 to Ala-CO) played a dominating role in the interaction. Electrochemistry coupled with spectroscopy techniques could provide a relatively easy way to obtain useful insights into the molecular mechanism of drug-DNA interactions, which should be important in the development of new anticancer drugs with specific base recognition.