Spectral and conformational analysis of deoxyadenosine adducts derived from syn- and anti-Dibenzo[a,l]pyrene diol epoxides: fluorescence studies

On the impact of the molecule structure in chemical carcinogenesis

Cancer is as a highly complex and multifactorial disease responsible for the death of hundreds of thousands of people in the western countries every year. Since cancer is clonal and due to changes at the level of the genetic material, viruses, chemical mutagens and other exogenous factors such as short-waved electromagnetic radiation that alter the structure of DNA are among the principal causes. The focus of this present review lies on the influence of the molecular structure of two well-investigated chemical carcinogens from the group of polycyclic aromatic hydrocarbons (PAHs), benzo[a]pyrene (BP) and dibenzo[a,l]pyrene (DBP). Although there is only one additional benzo ring present in the latter compound, DBP exerts much stronger genotoxic and carcinogenic effects in certain tumor models as compared to BP. Actually, DBP has been identified as the most potent tumorigen among all carcinogenic PAHs tested to date. The genotoxic effects of both compounds investigated in mammalian cells in culture or in animal models are described. Comparison of enzymatic activation, DNA binding levels of reactive diol-epoxide metabolites, efficiency of DNA adduct repair and mutagenicity provides some clues on why this compound is about 100-fold more potent in inducing tumors than BP. The data published during the past 20 years support and strengthen the idea that compound-inherent physicochemical parameters, along with inefficient repair of certain kinds of DNA lesions formed upon metabolic activation, can be considered as strong determinants for high carcinogenic potency of a chemical.

The characterization of (±)-anti-benzo[a]pyrene diolepoxide–DNA adducts and (±)-anti-dibenzo[a,l]pyrene diolepoxide–DNA adducts in the same DNA sample using solid-matrix phosphorescence

Solid-matrix phosphorescence (SMP) spectra and lifetimes were used to characterize the (+/-)-anti-benzo[a]pyrene diolepoxide [(+/-)-anti-B[a]PDE] and (+/-)-anti-dibenzo[a,l]pyrene diolepoxide [(+/-)-anti-DB[a,l]PDE] bonded to the same sample of DNA. SMP spectra and lifetimes were also acquired for two samples of DNA that had only (+/-)-anti-B[a]PDE or (+/-)-anti-DB[a,l]PDE bonded to the individual samples of DNA. A detailed comparison of the SMP properties was made among the three samples of DNA. The SMP excitation spectra for the (+/-)-anti-B[a]PDE-DNA and the (+/-)-anti-DB[a,l]PDE-DNA adducts were very similar. However, the SMP emission spectra of the two DNA adduct systems were very dissimilar with a major emission band for the (+/-)-anti-B[a]PDE-DNA adducts appearing at 613 nm and for the (+/-)-anti-DB[a,l]PDE-DNA adducts a major band was at 558 nm. It was possible to selectively use SMP emission wavelengths and obtain a SMP excitation of spectrum of the (+/-)-anti-DB[a,l]PDE-DNA adducts in the dual adducted DNA sample without the (+/-)-anti-B[a]PDE-DNA adducts emitting SMP. In addition, it was shown that the SMP emission spectrum of the dual adducted DNA sample could be used to detect both adduct systems in the modified DNA sample. It was demonstrated that the SMP lifetimes could be effectively employed to characterize the dual adducted DNA sample. For example, the SMP decay curve for the (+/-)-anti-DB[a,l]PDE-DNA adducts could be acquired without any SMP emission from the (+/-)-anti-B[a]PDE-DNA adducts. Also, ln(SMP intensity) versus time plots were very useful in characterizing the dual adducted DNA sample.

Robust incision of Benoz[a]pyrene-7,8-dihyrodiol-9,10-epoxide-DNA adducts by a recombinant thermoresistant interspecies combination UvrABC endonuclease system

Prokaryotic DNA repair nucleases are useful reagents for detecting DNA lesions. UvrABC endonuclease, encoded by the UvrA, UvrB, and UvrC genes can incise DNA containing bulky nucleotide adducts and intrastrand cross-links. UvrA, UvrB, and UvrC were cloned from Bacillus caldotenax (Bca)and UvrC from Thermatoga maritima (Tma), and recombinant proteins were overexpressed in and purified from Escherichia coli. Incision activities of UvrABC composed of all Bca-derived subunits (UvrABC(Bca)) and an interspecies combination UvrABC composed of Bca-derived UvrA and UvrB and Tma-derived UvrC (UvrABC(Tma)) were compared on benoz[a]pyrene-7,8-dihyrodiol-9,10-epoxide (BPDE)-adducted substrates. Both UvrABC(Bca) and UvrABC(Tma) specifically incised both BPDE-adducted plasmid DNAs and site-specifically modified 50-bp oligonucleotides containing a single (+)-trans- or (+)-cis-BPDE adduct. Incision activity was maximal at 55-60 degrees C. However, UvrABC(Tma) was more robust than UvrABC(Bca) with 4-fold greater incision activity on BPDE-adducted oligonucleotides and 1.5-fold greater on [(3)H]BPDE-adducted plasmid DNAs. Remarkably, UvrABC(Bca) incised only at the eighth phosphodiester bond 5' to the BPDE-modified guanosine. In contrast, UvrABC(Tma) performed dual incision, cutting at both the fifth phosphodiester bond 3' and eighth phosphodiester bond 5' from BPDE-modified guanosine. BPDE adduct stereochemistry influenced incision activity, and cis adducts on oligonucleotide substrates were incised more efficiently than trans adducts by both UvrABC(Bca) and UvrABC(Tma). UvrAB-DNA complex formation was similar with (+)-trans- and (+)-cis-BPDE-adducted substrates, suggesting that UvrAB binds both adducts equally and that adduct configuration modifies UvrC recognition of the UvrAB-DNA complex. The dual incision capabilities and higher incision activity of UvrABC(Tma) make it a robust tool for DNA adduct studies.

Solid-matrix fluorescence quenching of benzo[e]pyrene and (+/-)-anti-dibenzo[a, l]pyrene diolepoxide-DNA adducts

The solid-matrix fluorescence (SMF) quenching of benzo[e]pyrene and (+/-)-anti-dibenzo[a, l]pyrene-11,12-diol-13,14-epoxide ((+/-)-antiDB[a, l]PDE)-DNA adducts with thallium nitrate (TlNO(3)) and sodium iodide (NaI) was examined and several SMF quenching models were developed. The SMF quenching data for B[e]P with either TlNO(3) or NaI fit a two-independent-binding-site model. However, the SMF quenching of (+/-)-anti-DB[a, l]PDE-DNA adducts with TlNO(3) fits a sphere of action model, but quenching with NaI was modeled with the two-independent-binding-site model. The data were compared with earlier SMF quenching data for 7,8,9,10-tetrahydroxytetrahydro-benzo[a]pyrene (tetrol I-1) and (+/-)-anti-benzo[a]pyrene-trans-7,8-dihydrodiol-9,10-epoxide ((+/-)-anti-BPDE)DNA adducts. The interpretation of the SMF quenching data for the (+/-)-anti-DB[a, l]PDE-DNA adducts was distinctively different than the interpretation of the SMF quenching data for the (+/-)-antiBPDE-DNA adducts. This initial study shows that SMF quenching has the potential to characterize polycyclic aromatic hydrocarbonDNA adducts with different numbers of aromatic rings. In addition, the data indicated that external and intercalated DNA adducts interacted with heavy-atom salts in dissimilar fashions. The new SMF methodology developed is useful for the characterization of both polycyclic aromatic hydrocarbon-DNA adducts and metabolites from polycyclic aromatic hydrocarbons.

Conformational Analysis of Drug-Like Molecules Bound to Proteins: An Extensive Study of Ligand Reorganization upon Binding

This paper describes a large-scale study on the nature and the energetics of the conformational changes drug-like molecules experience upon binding. Ligand strain energies and conformational reorganization were analyzed with different computational methods on 150 crystal structures of pharmaceutically relevant protein-ligand complexes. The common knowledge that ligands rarely bind in their lowest calculated energy conformation was confirmed. Additionally, we found that over 60% of the ligands do not bind in a local minimum conformation. While approximately 60% of the ligands were calculated to bind with strain energies lower than 5 kcal/mol, strain energies over 9 kcal/mol were calculated in at least 10% of the cases regardless of the method used. A clear correlation was found between acceptable strain energy and ligand flexibility, while there was no correlation between strain energy and binding affinity, thus indicating that expensive conformational rearrangements can be tolerated in some cases without overly penalizing the tightness of binding. On the basis of the trends observed, thresholds for the acceptable strain energies of bioactive conformations were defined with consideration of the impact of ligand flexibility. An analysis of the degree of folding of the bound ligands confirmed the general tendency of small molecules to bind in an extended conformation. The results suggest that the unfolding of hydrophobic ligands during binding, which exposes hydrophobic surfaces to contact with protein residues, could be one of the factors accounting for high reorganization energies. Finally, different methods for conformational analysis were evaluated, and guidelines were defined to maximize the prevalence of bioactive conformations in computationally generated ensembles.

On-line identification of 3,4-methylenedioxymethamphetamine in human urine by non-aqueous capillary electrophoresis-fluorescence spectroscopy at 77 K

The analytical profiles for 3,4-methylenedioxymethamphetamine (3,4-MDMA) and related amphetamines in urine samples are described for non-aqueous capillary electrophoresis-fluorescence spectroscopy. 3,4-MDMA was detected and identified on-line, using a cryogenic molecular fluorescence technique at 77 K. Under optimized conditions, baseline separation of the selected compounds was achieved in less than 12 min. Precision was evaluated by measuring the repeatability and intermediate precision of the migration times and corrected peak areas. The non-aqueous CE separation conditions and the spectral characteristics of 3,4-MDMA with respect to solvent and temperature effects are also discussed.

On-line identification of trans- and cis-resveratrol by nonaqueous capillary electrophoresis/fluorescence spectroscopy at 77 K

This work presents a novel method for the accurate determining trans- and cis-resveratrol (3,5,4'-trihydroxystilbene) by nonaqueous capillary electrophoresis/fluorescence spectroscopy at 77 K. The proposed method permits not only the separation of resveratrol isomers, but also ensures that on-line spectra are readily distinguishable and unambiguously assigned. The experimental results also indicate that the effect of nonaqueous capillary electrophoresis buffer and low-temperature technique increase the detection limit by more than 150-fold.

High-performance liquid chromatography interfaced with fluorescence line-narrowing spectroscopy for on-line analysis

We have demonstrated, for the first time, that high-performance liquid chromatography (HPLC) can be interfaced with fluorescence line-narrowing spectroscopy (FLNS) for on-line identification and characterization of analytes. Interfacing centered primarily on the design and construction of a novel liquid helium cryostat that accommodates variable-sized quartz tubes/capillaries suitable for HPLC as well as capillary electrophoresis/electrochromatography. In addition to the high spectral resolution afforded by FLNS, analyzing the separated components at 4.2 K minimizes photodegradation from the excitation source and provides indefinite detection times for signal averaging. The proof-of-principle for the HPLC-FLNS system is first demonstrated with a mixture of four structurally similar polycyclic aromatic hydrocarbons and then applied to the analysis of DNA adducts from mouse skin exposed to the carcinogen dibenzo[a,l]pyrene. With femtomole detection limits, HPLC-FLNS can be used for real-world analyses of complex mixtures.

Fluorescence line-narrowing detection in chromatography and electrophoresis

A review of the basic aspects of fluorescence line-narrowing spectroscopy (FLNS) and its coupling with thin-layer chromatography (TLC) and polyacrylamide gel electrophoresis (PAGE) for off-line high-resolution low temperature spectral characterization is discussed. This is followed by a description of the on-line interfacing of capillary electrophoresis (CE) and capillary electrochromatography (CEC) with FLN detection. CE/ CEC-FLNS instrumentation and its applications for spectral identification of closely related analytes are also presented. Future prospects of micro and capillary high performance liquid chromatography (HPLC) with on-line high-resolution low temperature spectroscopic identification are considered.