Conformation Of Adducts Research Articles

Interactions with DNA Models of the Oxaliplatin Analog (cis-1,3-DACH)PtCl2.

It is generally accepted that adjacent guanine residues in DNA are the primary target for platinum antitumor drugs and that differences in the conformations of the Pt-DNA adducts can play a role in their antitumor activity. In this study, we investigated the effect of the carrier ligand cis-1,3-diaminocyclohexane (cis-1,3-DACH) upon formation, stability, and stereochemistry of the (cis-1,3-DACH)PtG2 and (cis-1,3-DACH)Pt(d(GpG)) adducts (G = 9-EthlyGuanine, guanosine, 5'- and 3'-guanosine monophosphate; d(GpG) = deoxyguanosil(3'-5')deoxyguanosine). A peculiar feature of the cis-1,3-DACH carrier ligand is the steric bulk of the diamine, which is asymmetric with respect to the Pt-coordination plane. The (cis-1,3-DACH)Pt(5'GMP)2 and (cis-1,3-DACH)Pt(3'GMP)2 adducts show preference for the ΛHT and ∆HT conformations, respectively (HT stands for Head-to-Tail). Moreover, the increased intensity of the circular dichroism signals in the cis-1,3-DACH derivatives with respect to the analogous cis-(NH3)2 species could be a consequence of the greater bite angle of the cis-1,3-DACH carrier ligand with respect to cis-(NH3)2. Finally, the (cis-1,3-DACH)Pt(d(GpG)) adduct is present in two isomeric forms, each one giving a pair of H8 resonances linked by a NOE cross peak. The two isomers were formed in comparable amounts and had a dominance of the HH conformer but with some contribution of the ΔHT conformer which is related to the HH conformer by having the 3'-G base flipped with respect to the 5'-G residue.

Ozone-assisted low temperature oxidation of indene: An experimental and computational study

Elucidating the oxidation chemistry of polycyclic aromatic hydrocarbons (PAHs) aids in understanding the degradation reaction processes of PAHs, as well as their competitive roles in PAH growth. In this work, ozone-assisted oxidation of indene, the smallest prototype PAH molecule, was investigated in an atmospheric jet stirred reactor at 400–550 K. Ab initio quantum chemistry calculations were conducted to characterize the oxidation kinetics of indene and interpret the experimental observations. Fingerprint oxidation products including 2-(2-oxoethyl) benzoic acid, 2-(formylmethyl) benzaldehyde, 1,2-indanedione and 1-indanone were identified by synchrotron vacuum ultraviolet photoionization mass spectrometry. The initial C9H8O3 adduct resulting from O3-addition to indene exhibits high instability and is primarily detected as 2-(2-oxoethyl)benzoic acid following ozonolysis reactions. Minor amounts of vinylhydroperoxide were also observed as isomeric products of the C9H8O3 adduct. Theoretical calculations indicate that indene ozonolysis is highly structure-dependent, where the conformation of the C9H8O3 adduct determines the configuration of the resulting Criegee intermediates (CI). The distinctive reaction pathways introduced by the bifunctionalized characteristics of indene-derived large CIs are emphasized in this study. syn-Configuration CI features more conversion pathways compared to anti-CI due to the interaction between CI functionality and the neighboring aldehyde group, among which the bicyclic ring-closure reaction yielding secondary ozonide is most favored. The dioxirane intermediates generated from anti-CIs can undergo the Crossed Acid-forming channel to yield the target acid products, which provides an alternative way for dioxirane conversion. Further theoretical analyses demonstrate that ozonolysis is not the exclusive mechanism for indene oxidation under O3-assisted conditions. Instead, it is accompanied by low-temperature reactions initiated by OH/O2, leading to key products such as 2-(formylmethyl) benzaldehyde and 1-indanone. The present work aims to unravel the elusive chemistry involved in the O3-initiated oxidation of indene, providing new insights into the distinctive kinetics introduced by large bifunctionalized CIs in the ozonolysis of structurally similar PAHs.

Exploring the electronic and steric effects on the dimerization of intramolecular frustrated Lewis pairs: a comparison between aminoboranes and aminoalanes.

The dimerization of intramolecular aminoborane and aminoalane frustrated Lewis pairs was investigated using density functional theory. We systematically varied the substituents to gradually increase their bulkiness, including H, CH3, t-Bu, Ph, and Mes groups. Starting from the most stable conformer of the monomers, a frustrated Lewis pair or classic Lewis adduct, we studied the dimerization process for all systems, revealing significant variations in the Gibbs free energy. Dimerization was favored in four aminoboranes and six aminoalanes, depending on the specific combinations of substituents. Applying an energy decomposition analysis, we found that the preparation energy of the monomers and the non-orbital interactions between them are the primary contributors to the observed energetic differences, showing a clear linear relationship. Additionally, we analyzed the electronic effects by increasing the acidity of the Lewis acid, observing a shift toward endergonic and exergonic directions in aminoboranes and aminoalanes, respectively. This shift was attributed to the stabilization of a classic Lewis adduct. This study underscores three crucial factors influencing dimer formation: (i) substituent size, (ii) stabilization of the classic Lewis adduct conformation, and (iii) covalent radii of the Lewis centers. Understanding these factors is essential for designing FLPs and preventing unwanted dimerization that could affect their catalytic performance in H2 activation processes.

Structure-Dependent Mechanism of Organophosphate Release from Albumin and Butyrylcholinesterase Adducts When Exposed to Fluoride Ion: A Comprehensive In Silico Study.

The most favorable targets for retrospectively determining human exposure to organophosphorus pesticides, insecticides, retardants, and other industrial organophosphates (OPs) are adducts of OPs with blood plasma butyrylcholinesterase (BChE) and human serum albumin (HSA). One of the methods for determining OP exposure is the reactivation of modified BChE using a concentrated solution of KF in an acidic medium. It is known that under the action of fluoride ion, OPs or their fluoroanhydrides can be released not only from BChE adducts but also from the adducts with albumin; however, the contribution of albumin to the total pool of released OPs after plasma treatment with KF has not yet been studied. The efficiency of OP release can be affected by many factors associated with the experimental technique, but first, the structure of the adduct must be taken into account. We report a comparative analysis of the structure and conformation of organophosphorus adducts on HSA and BChE using molecular modeling methods and the mechanism of OP release after fluoride ion exposure. The conformational analysis of the organophosphorus adducts on HSA and BChE was performed, and the interaction of fluoride ions with modified proteins was studied by molecular dynamics simulation. The geometric and energy characteristics of the studied adducts and their complexes with fluoride ion were calculated using molecular mechanics and semiempirical approaches. The structural features of modified HSA and BChE that can affect the efficiency of OP release after fluoride ion exposure were revealed. Using the proposed approach, the expediency of using KF for establishing exposure to different OPs, depending on their structure, can be assessed.

Inhibition of E. coli RecQ Helicase Activity by Structurally Distinct DNA Lesions: Structure—Function Relationships

DNA helicase unwinding activity can be inhibited by small molecules and by covalently bound DNA lesions. Little is known about the relationships between the structural features of DNA lesions and their impact on unwinding rates and processivities. Employing E.coli RecQ helicase as a model system, and various conformationally defined DNA lesions, the unwinding rate constants kobs = kU + kD, and processivities P = (kU/(kU + kD) were determined (kU, unwinding rate constant; kD, helicase-DNA dissociation rate constant). The highest kobs values were observed in the case of intercalated benzo[a]pyrene (BP)-derived adenine adducts, while kobs values of guanine adducts with minor groove or base-displaced intercalated adduct conformations were ~10-20 times smaller. Full unwinding was observed in each case with the processivity P = 1.0 (100% unwinding). The kobs values of the non-bulky lesions T(6-4)T, CPD cyclobutane thymine dimers, and a guanine oxidation product, spiroiminodihydantoin (Sp), are up to 20 times greater than some of the bulky adduct values; their unwinding efficiencies are strongly inhibited with processivities P = 0.11 (CPD), 0.062 (T(6-4)T), and 0.63 (Sp). These latter observations can be accounted for by correlated decreases in unwinding rate constants and enhancements in the helicase DNA complex dissociation rate constants.

Structure and Conformation of Novel BODIPY Ugi Adducts.

Two novel BODIPY‐Ugi (boron dipyrromethene) adducts exhibit peculiar room temperature (T=20 °C) H‐1 NMR spectra in that several protons located at the aromatic aniline‐type ring are lost in the baseline. This observation revealed the existence of a dynamic conformational process where rotation around the C−N bond is hindered. Variable‐temperature H‐1 and C‐13 NMR spectroscopic analysis confirmed this conclusion; that is, low‐temperature spectra show distinct signals for all four aromatic protons below coalescence, whereas average signals are recorded above coalescence (T=+120 °C). Particularly interesting was the rather large difference in chemical shifts for the ortho protons below coalescence, Δδ=1.45 ppm, which was explained based on DFT computational analysis. Indeed, the calculated lowest‐energy gas‐phase conformation of the BODIPY Ugi adducts locates one half of the aniline‐type ring in the shielding anisotropic cone of the bridge phenyl ring in the BODIPY segment. This is in contrast to the solid‐state conformation established by X‐ray diffraction analysis that shows a nearly parallel arrangement of the aromatic rings, probably induced by crystal packing forces.

Structural features of DNA polymerases β and λ in complex with benzo[a]pyrene-adducted DNA cause a difference in lesion tolerance

DNA polymerases β (Pol β) and λ (Pol λ) belong to one structural family (X family) and possess the same enzymatic activities. Nonetheless, these enzymes have differences in their catalytic efficiency and specificity. We have previously reported that these enzymes can bypass bulky benzo[a]pyrene–DNA adducts via translesion synthesis during gap-filling reactions, although efficiency and specificity are dependent on the reaction conditions and adduct conformation. In the present study, we analyzed structural features of Pols β and λ complexed with a gapped DNA duplex containing either cis- or trans-benzo[a]pyrene-diol epoxide-N2-dG (BP-dG) using molecular dynamics simulations. It was found that the most pronounced structural difference lies in the positioning of the trans-BP-dG residue relative to secondary structures of the protein; this dissimilarity may explain the differences between Pols β and λ in gap-filling/translesion synthesis. In the case of Pol β, trans-BP-dG turned out to be positioned parallel to the α-helix and β-sheet. In the Pol λ complex, trans-BP-dG is perpendicular to the α-helix. This difference persisted throughout the molecular dynamics trajectory. Selectivity for the BP-dG isomers remained after a deletion of noncatalytic domains of Pol λ. Modeling of Pol λ or β complexes with cis-BP-dG–containing DNA in the presence of Mn2+ either at both metal-binding sites or at the catalytic site only revealed that for both enzymes, the model of the complex containing both Mg2+ and Mn2+ is stabler than that containing two Mn2+ ions. This observation may reflect a shared property of these enzymes: the preference for Mn2+ in terms of catalysis and for Mg2+ regarding triphosphate coordination during the translesion reaction.

Theoretical Study of Light-Induced Crosslinking Reaction Between Pyrimidine DNA Bases and Aromatic Amino Acids

Low-lying electronic excited states and their relaxation pathways as well as energetics of the crosslinking reaction between uracil as a model system for pyrimidine-type building blocks of DNA and RNA and benzene as a model system for aromatic groups of tyrosine (Tyr) and phenylalanine (Phe) amino acids have been studied in the framework of density functional theory. The equilibrium geometries of the ground and electronic excited states as well as the crossing points between the potential energy surfaces of the uracil–benzene complex were computed. Based on these results, different relaxation pathways of the electronic excited states that lead to either back to the initial geometry configuration or the dimerization between the six-membered rings of the uracil–benzene complex have been identified, and the energetic conditions for their occurrence are discussed. It can be concluded that the DNA–protein crosslinking reaction can be induced by the external electromagnetic field via the dimerization reaction between the six-membered rings of the uracil–benzene pair at the electronic excited-state level of the complex. In the case of the uracil–phenol complex, the configuration of the cyclic adduct (dimerized) conformation is less likely to be formed.

Conformational Landscape, Chirality Recognition and Chiral Analyses: Rotational Spectroscopy of Tetrahydro-2-Furoic Acid⋅⋅⋅Propylene Oxide Conformers.

A chiral adduct formed between a chiral carboxylic acid, tetrahydro-2-furoic acid (THFA), and a chiral ester, propylene oxide (PO), was investigated using rotational spectroscopy and DFT calculations. Isolated THFA exists dominantly as three different conformers: I, II, and III in a jet, with I and II taking on the trans-COOH configuration and III having the cis-COOH configuration. We utilized CREST, a conformational ensemble space exploration tool, to identify the possible conformations of the binary adduct, THFA⋅⋅⋅PO. Subsequent DFT geometry optimizations predicted about two hundred homochiral and heterochiral binary structures with 28 low energy structures within an energy window of 15 kJ mol-1 . A rich broadband rotational spectrum was obtained with a mixture of trace amounts of THFA+PO in neon in a supersonic jet expansion. Six THFA⋅⋅⋅PO conformers were identified experimentally. Kinetically favored binary products which contain trans-COOH I dominate among the observed conformers, while thermodynamically more stable adducts were also detected. Detailed analyses of the structures of the observed conformers show interesting chirality-controlled structural preferences. Such non-covalently bound chiral contact pairs are the foundation of chiral-tag rotational spectroscopy, an exciting new analytical application of rotational spectroscopy for determination of enantiomeric excess. Enantiomeric excess analyses were performed and the results are discussed.

Unveiling the coexistence of cis- and trans-isomers in the hydrolysis of ZrO2: A coupled DFT and high-resolution photoelectron spectroscopy study.

High-resolution anion photoelectron spectroscopy of the ZrO3H2 - and ZrO3D2 - anions and complementary electronic structure calculations are used to investigate the reaction between zirconium dioxide and a single water molecule, ZrO2 0/- + H2O. Experimental spectra of ZrO3H2 - and ZrO3D2 - were obtained using slow photoelectron velocity-map imaging of cryogenically cooled anions, revealing the presence of two dissociative adduct conformers and yielding insight into the vibronic structure of the corresponding neutral species. Franck-Condon simulations for both the cis- and trans-dihydroxide structures are required to fully reproduce the experimental spectrum. Additionally, it was found that water-splitting is stabilized more by ZrO2 than TiO2, suggesting Zr-based catalysts are more reactive toward hydrolysis.

Predictable Selectivity in Remote C-H Oxidation of Steroids: Analysis of Substrate Binding Mode.

Predictability is a key requirement to encompass late-stage C-H functionalization in synthetic routes. However, prediction (and control) of reaction selectivity is usually challenging, especially for complex substrate structures and elusive transformations such as remote C(sp3 )-H oxidation, as it requires distinguishing a specific C-H bond from many others with similar reactivity. Developed here is a strategy for predictable, remote C-H oxidation that entails substrate binding to a supramolecular Mn or Fe catalyst followed by elucidation of the conformation of the host-guest adduct by NMR analysis. These analyses indicate which remote C-H bonds are suitably oriented for the oxidation before carrying out the reaction, enabling prediction of site selectivity. This strategy was applied to late-stage C(sp3 )-H oxidation of amino-steroids at C15 (or C16) positions, with a selectivity tunable by modification of catalyst chirality and metal.

Structural and biochemical analyses of the LdtMt2-panipenem adduct provide new insights into the effect of the 1-β-methyl group on carbapenems

Tuberculosis has attracted increased attention worldwide due to its high morality and its resistance to treatment with traditional antibacterial drugs. The l,d-transpeptidase LdtMt2 confers resistance to traditional β-lactams and is considered a target for anti-Tuberculosis treatment. Carbapenems are proposed to inhibit Mycobacterium tuberculosis by repressing the activity of LdtMt2. The interaction mechanisms between LdtMt2 and carbapenems have been revealed by LdtMt2-carbapenem adduct structures along with various biochemical assays. Interestingly, the lack of the 1-β-methyl group in imipenem may be related to its high binding ability to LdtMt2. However, there is limited evidence on the interaction mode of LdtMt2 and panipenem, another carbapenem lacking the 1-β-methyl group. Herein, we identified the biochemical features of panipenem binding to LdtMt2. We further suggest that the presence of the 1-β-methyl group in carbapenems is indeed related to the ligand affinity of LdtMt2 and that the presence of the Y308 and Y318 residues in LdtMt2 stabilized the conformation of the LdtMt2-carbepenem adduct. Our research provides a structural basis for the development of novel carbapenems against L,D-transpeptidases.

Fullerene–1,4-dioxane adducts: a DFT study of the structural features and molecular properties

Using the PBE/3ζ density functional theory method, we have computationally studied fullerene–1,4-dioxane adducts, which were recently synthesized in sonochemical reaction of C60/C70 with ethylene glycol in the presence of NaOH. We have found the preference of the boat conformations of C60 and C70 adducts with 1,4-dioxane over the chair ones. Fullerene–dioxane adducts have the dipole moments of 2.5–3.0 D and band gaps narrower as compared with original C60/C70. Adducts ab-, cc1-, and cc2-C72H4O2 are revealed higher stability than their regioisomers. Herewith, cc-adducts have the lower mean polarizabilities that corresponds to the experimental observation of the cc-functionalization of the C70 fullerene core. All adducts have the nonzero anisotropies of polarizability higher than the values of starting C60 and C70. The lowest anisotropy corresponds to cc1-C72H4O2 that makes this compound promising for organic solar cells.

Molecular Dynamics Study of One-Base Deletion Duplexes Containing the Major DNA Adduct Formed by Ochratoxin A: Effects of Sequence Context and Adduct Ionization State on Lesion Site Structure and Mutagenicity.

Ochratoxin A (OTA) is a ubiquitous food toxin associated with chronic nephropathy in humans and renal carcinogenicity in rodents. The mutational spectra of cells exposed to OTA reveal that one-base deletions comprise the largest percentage (73%) of the total mutations that occur upon OTA exposure. To contribute toward understanding the prevalence of OTA-induced one-base deletion mutations, the present work uses molecular dynamics (MD) simulations to analyze the conformational preferences of one-base deletion duplexes containing OT-G, the major OTA adduct (addition product) at the C8-site of guanine. Specifically, the influence of OT-G in four possible ionization states and three sequence contexts (G1, G2 and G3 in the NarI (5'-G1G2CG3CC-3'), a prokaryotic mutational hotspot sequence) on the structure of the adducted DNA is investigated. Our data reveal that the damaged helices are stable in two (B-type (B) and stacked (S)) conformations that are structurally similar to those adopted by common N-linked C8-guanine lesions. However, the adduct ionization state and sequence context affect the degree of helical distortion and the B/S conformational heterogeneity, which will impact the lesion repair and replication outcomes. This finding correlates with the experimentally reported tissue-specific mutagenicity of OTA exposure. Furthermore, regardless of the adduct conformation, ionization state, or sequence context, more stable lesion-site interactions and lack of disruption of the flanking base pairs in the one-base deletion duplexes compared to the corresponding two-base deletion helices rationalize the greater abundance of OTA induced one-base deletions. Overall, our work provides valuable structural insights that help explain the experimentally observed mutagenicity associated with OTA.

In Vitro interaction between yeast frataxin and superoxide dismutases: Influence of mitochondrial metals

BackgroundFriedreich's ataxia results from a decreased expression of the nuclear gene encoding the mitochondrial protein, frataxin. Frataxin participates in the biosynthesis of iron-sulfur clusters and heme cofactors, as well as in iron storage and protection against oxidative stress. How frataxin interacts with the antioxidant defence components is poorly understood. MethodsTherefore, we have investigated by kinetic, thermodynamic and modelling approaches the molecular interactions between yeast frataxin (Yfh1) and superoxide dismutases, Sod1 and Sod2, and the influence of Yfh1 on their enzymatic activities. ResultsYfh1 interacts with cytosolic Sod1 with a dissociation constant, Kd = 1.3 ± 0.3 μM, in two kinetic steps. The first step occurs in the 200 ms range and corresponds to the Yfh1-Sod1 interaction, whereas the second is slow and is assumed to be a change in the conformation of the protein-protein adduct. Furthermore, computational investigations confirm the stability of the Yfh1-Sod1 complex. Yfh1 forms two protein complexes with mitochondrial Sod2 with 1:1 and 2:1 Yfh1/Sod2 stoichiometry (Kd1 = 1.05 ± 0.05 and Kd2 = 6.6 ± 0.1 μM). Furthermore, Yfh1 increases the enzymatic activity of Sod1 while slightly affecting that of Sod2. Finally, the stabilities of the protein-protein adducts and the effect of Yfh1 on superoxide dismutase activities depend on the nature of the mitochondrial metal. ConclusionsThis work confirms the participation of Yfh1 in cellular defence against oxidative stress.

New Conformations of Acylation Adducts of Inhibitors of β-Lactamase from Mycobacterium tuberculosis.

Mycobacterium tuberculosis (Mtb), the main causative agent of tuberculosis (TB), is naturally resistant to β-lactam antibiotics due to the production of the extended spectrum β-lactamase BlaC. β-Lactam/β-lactamase inhibitor combination therapies can circumvent the BlaC-mediated resistance of Mtb and are promising treatment options against TB. However, still little is known of the exact mechanism of BlaC inhibition by the β-lactamase inhibitors currently approved for clinical use, clavulanic acid, sulbactam, tazobactam, and avibactam. Here, we present the X-ray diffraction crystal structures of the acyl-enzyme adducts of wild-type BlaC with the four inhibitors. The +70 Da adduct derived from clavulanate and the trans-enamine acylation adducts of sulbactam and tazobactam are reported. BlaC in complex with avibactam revealed two inhibitor conformations. Preacylation binding could not be observed because inhibitor binding was not detected in BlaC variants carrying a substitution of the active site serine 70 to either alanine or cysteine, by crystallography, ITC or NMR. These results suggest that the catalytic serine 70 is necessary not only for enzyme acylation but also for increasing BlaC affinity for inhibitors in the preacylation state. The structure of BlaC with the serine to cysteine mutation showed a covalent linkage of the cysteine 70 Sγ atom to the nearby amino group of lysine 73. The differences of adduct conformations between BlaC and other β-lactamases are discussed.

Influence of geometric isomerism on the binding of platinum anticancer agents with phospholipids.

Reported herein is a detailed NMR and DFT study of the interaction of the 15N-labelled dinuclear platinum anticancer compound [{cis-PtCl(NH3)2}2{μ-H2N(CH2)6NH2}]2+ (15N-1, 1,1/c,c) with 1,2-dihexanoyl-sn-glycero-3-phosphate (DHPA), as a comparison with an earlier study of the interaction of the same water-soluble phospholipid fragment with the geometric trans isomer (1,1/t,t). The reaction of 15N-1 with the sodium salt of DHPA was studied at 298 K, pH ∼ 5.6, by [1H,15N] HSQC 2D NMR spectroscopy. The NMR data, supported by DFT models, provide evidence that the monofunctional DHPA adduct of 15N-1 exists in two conformational forms, with different orientation of the (CH2)6 linker; one has an interaction between the unbound {PtN3Cl} moiety and the coordinated DHPA molecule. Similarly, two bifunctional adduct conformers are identified, in which one has an interaction between the phosphate groups of the two bound DHPA molecules. When compared to the previously reported reactions of 1,1/t,t with DHPA, equilibrium conditions of the 1,1/c,c reaction are reached more slowly (120 h), similar to the reaction with phosphate. The rate constant for the first step of DHPA binding (kL) is slightly lower (1.6 fold) for the cis-compared to the trans-isomer, whereas the rate constant for the reverse reaction is 4-fold lower, resulting in a much greater proportion of DHPA bound species at equilibrium.

Processing of N5-substituted formamidopyrimidine DNA adducts by DNA glycosylases NEIL1 and NEIL3

A variety of agents cause DNA base alkylation damage, including the known hepatocarcinogen aflatoxin B1 (AFB1) and chemotherapeutic drugs derived from nitrogen mustard (NM). The N7 site of guanine is the primary site of alkylation, with some N7-deoxyguanosine adducts undergoing imidazole ring-opening to stable mutagenic N5-alkyl formamidopyrimidine (Fapy-dG) adducts. These adducts exist as a mixture of canonical β- and unnatural α-anomeric forms. The β species are predominant in double-stranded (ds) DNA. Recently, we have demonstrated that the DNA glycosylase NEIL1 can initiate repair of AFB1-Fapy-dG adducts both in vitro and in vivo, with Neil1−/− mice showing an increased susceptibility to AFB1-induced hepatocellular carcinoma.Here, we hypothesized that NEIL1 could excise NM-Fapy-dG and that NEIL3, a closely related DNA glycosylase, could excise both NM-Fapy-dG and AFB1-Fapy-dG. Product formation from the reaction of human NEIL1 with ds oligodeoxynucleotides containing a unique NM-Fapy-dG followed a bi-component exponential function under single turnover conditions. Thus, two adduct conformations were differentially recognized by hNEIL1. The excision rate of the major form (∼13.0 min−1), presumed to be the β-anomer, was significantly higher than that previously reported for 5-hydroxycytosine, 5-hydroxyuracil, thymine glycol (Tg), and AFB1-Fapy-dG. Product generation from the minor form was much slower (∼0.4 min−1), likely reflecting the rate of conversion of the α anomer into the β anomer. Mus musculus NEIL3 (MmuNEIL3Δ324) excised NM-Fapy-dG from single-stranded (ss) DNA (turnover rate of ∼0.4 min−1), but not from ds DNA. Product formation from ss substrate was incomplete, presumably because of a substantial presence of the α anomer. MmuNEIL3Δ324 could not initiate repair of AFB1-Fapy-dG in either ds or ss DNA. Overall, the data suggest that both NEIL1 and NEIL3 may protect cells against cytotoxic and mutagenic effects of NM-Fapy-dG, but NEIL1 may have a unique role in initiation of base excision repair of AFB1-Fapy-dG.

Biochemical and biophysical characterization of ruthenation of BRCA1 RING protein by RAPTA complexes and its E3 ubiquitin ligase activity

RAPTA compounds, ([Ru(η6-arene)(PTA)Cl2], PTA = 1,3,5-triaza-7-phosphaadamantane), have been reported to overcome drug resistance in cisplatin resistant cells. However, the exact mechanism of these complexes is still largely unexplored. In this study, the interaction of some RAPTA compounds with the N-terminal fragment of the BRCA1 RING domain protein was investigated. The binding of the RAPTA compounds to the BRCA1 protein resulted in a release of Zn2+ ions in a dose and time dependent manner, as well as thermal alteration of ruthenated-BRCA1 proteins. Electron Transfer Dissociation (ETD) fragmentation mass spectrometry revealed the preferential binding sites of the RAPTA complexes on the BRCA1 zinc finger RING domain at a similar short peptide stretch, Cys24Lys25Phe26Cys27Met28Leu29 and Lys35 (residues 44–49 and 55 on full length BRCA1). Changes in the conformation and binding constants of ruthenium-BRCA1 adducts were established, resulting in inactivation of the RING heterodimer BRCA1/BARD1-mediated E3 ubiquitin ligase function. These findings could provide mechanistic insight into the mode of action of RAPTA complexes for on tested BRCA1 model protein.

Effect of conformation of the arylamine-DNA adduct on the sensitivity of [Ru(phen)2(dppz)]2 + complex

DNA damage by endogenous/exogenous chemicals and ionizing radiation results in the formation of abasic sites, alkylation products, oxidative lesions and covalent-DNA adducts. The covalent DNA adducts adopt different conformations that might lead to various types of mutations. In the present study, we investigated the interaction of different Ru(II) polypyridyl complex, [Ru(phen)2(dppz)]2+ (phen: 1,10-phenanthroline; dppz: dipyrido[3,2-a:2′,3′-c]phenazine) with oligonucleotide sequences containing either [N-(2′-deoxyguanosin-8-yl)-2-aminofluorene] (AF-dG) or [N-(2′-deoxyguanosin-8-yl)-2-acetylaminofluorene] (AAF-dG) adduct. The modification of the oligonucleotides with the arylamines was characterized by UV–visible and MALDI-TOF spectroscopy. The results of thermal denaturation studies of oligonucleotide with Ru(II) complex indicate that Ru(II) complex stabilize the arylamine adducts better than control oligonucleotide. The integrated luminescence intensity of the Ru(II) complex was increased two-fold in AAF-dG adduct compared to control while a reverse trend was observed with AF-dG adduct. The addition of quencher enhanced the luminescence ratio between AF-modified and control duplex by 1.5 fold compared to 3.6 to 6-fold in AAF-dG adduct. The results from this study demonstrate the role of conformational heterogeneity of the arylamine-dG adduct in the binding of the Ru(II) complex and also provides us insight on the development of new probes.