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1.
Nucleic Acids Res ; 51(6): 2931-2949, 2023 04 11.
Article in English | MEDLINE | ID: mdl-36869664

ABSTRACT

Bacterial nucleotide excision repair (NER), mediated by the UvrA, UvrB and UvrC proteins is a multistep, ATP-dependent process, that is responsible for the removal of a very wide range of chemically and structurally diverse DNA lesions. DNA damage removal is performed by UvrC, an enzyme possessing a dual endonuclease activity, capable of incising the DNA on either side of the damaged site to release a short single-stranded DNA fragment containing the lesion. Using biochemical and biophysical approaches, we have probed the oligomeric state, UvrB- and DNA-binding abilities and incision activities of wild-type and mutant constructs of UvrC from the radiation resistant bacterium, Deinococcus radiodurans. Moreover, by combining the power of new structure prediction algorithms and experimental crystallographic data, we have assembled the first model of a complete UvrC, revealing several unexpected structural motifs and in particular, a central inactive RNase H domain acting as a platform for the surrounding domains. In this configuration, UvrC is maintained in a 'closed' inactive state that needs to undergo a major rearrangement to adopt an 'open' active state capable of performing the dual incision reaction. Taken together, this study provides important insight into the mechanism of recruitment and activation of UvrC during NER.


Subject(s)
Bacterial Proteins , DNA Repair , Deinococcus , Endodeoxyribonucleases , Bacterial Proteins/metabolism , DNA Damage , DNA Helicases/metabolism , DNA, Bacterial/metabolism , Endodeoxyribonucleases/metabolism , Escherichia coli/genetics
2.
J Am Chem Soc ; 145(10): 5970-5981, 2023 Mar 15.
Article in English | MEDLINE | ID: mdl-36866828

ABSTRACT

Nonpyrophoric aminophosphines reacted with indium(III) halides in the presence of zinc chloride have emerged as promising phosphorus precursors in the synthesis of colloidal indium phosphide (InP) quantum dots (QDs). Nonetheless, due to the required P/In ratio of 4:1, it remains challenging to prepare large-sized (>5 nm), near-infrared absorbing/emitting InP QDs using this synthetic scheme. Furthermore, the addition of zinc chloride leads to structural disorder and the formation of shallow trap states inducing spectral broadening. To overcome these limitations, we introduce a synthetic approach relying on the use of indium(I) halide, which acts as both the indium source and reducing agent for aminophosphine. The developed zinc-free, single-injection method gives access to tetrahedral InP QDs with an edge length > 10 nm and narrow size distribution. The first excitonic peak is tunable from 450 to 700 nm by changing the indium halide (InI, InBr, InCl). Kinetic studies using phosphorus NMR reveal the coexistence of two reaction pathways, the reduction of transaminated aminophosphine by In(I) and via redox disproportionation. Etching the surface of the obtained InP QDs at room temperature with in situ-generated hydrofluoric acid (HF) leads to strong photoluminescence (PL) emission with a quantum yield approaching 80%. Alternatively, surface passivation of the InP core QDs was achieved by low-temperature (140 °C) ZnS shelling using the monomolecular precursor zinc diethyldithiocarbamate. The obtained InP/ZnS core/shell QDs that emit in a range of 507-728 nm exhibit a small Stokes shift (110-120 meV) and a narrow PL line width (112 meV at 728 nm).

3.
Chemistry ; 28(35): e202200734, 2022 Jun 21.
Article in English | MEDLINE | ID: mdl-35441438

ABSTRACT

Combining the selectivity of G-quadruplex (G4) ligands with the spatial and temporal control of photochemistry is an emerging strategy to elucidate the biological relevance of these structures. In this work, we developed six novel V-shaped G4 ligands that can, upon irradiation, form stable covalent adducts with G4 structures via the reactive intermediate, quinone methide (QM). We thoroughly investigated the photochemical properties of the ligands and their ability to generate QMs. Subsequently, we analyzed their specificity for various topologies of G4 and discovered a preferential binding towards the human telomeric sequence. Finally, we tested the ligand ability to act as photochemical alkylating agents, identifying the covalent adducts with G4 structures. This work introduces a novel molecular tool in the chemical biology toolkit for G4s.


Subject(s)
G-Quadruplexes , Indolequinones , Alkylating Agents/chemistry , Humans , Ligands
4.
Anal Bioanal Chem ; 414(6): 2029-2040, 2022 Mar.
Article in English | MEDLINE | ID: mdl-35066600

ABSTRACT

As the support of all living kingdoms' genetic information, the integrity of the DNA biomolecule must be preserved. To that goal, cells have evolved specific DNA repair pathways to thwart a large diversity of chemical substances and radiations that alter the DNA structure and lead to the development of pathologies such as cancers or neurodegenerative diseases. When dysregulated, activity rates of various actors of DNA repair can play a key role in carcinogenesis as well as in drugs resistance or hypersensitivity mechanisms. For the last 10 years, new complementary treatments have aimed at targeting specific enzymes responsible for such resistances. It is therefore crucial for biomedical research and clinical diagnosis to develop fast and sensitive tools able to measure the activity rate of DNA repair enzymes. In this work, a new assay for measuring enzymatic activities using microbeacons (µBs) is expounded. µB refers to microsphere functionalized by hairpin-shaped nucleic acid probes containing a single site-specific lesion in the stem and modified with chromophores. Following the processing of the lesion by the targeted protein, µB is cleaved and either lights off (signal-off strategy) or on (signal-on), depending on the use of fluorescent or profluorescent probes, respectively. After an optimization phase of the assay, we reported the combined analysis of restriction enzyme, AP-endonuclease, and DNA N-glycosylase by real-time monitoring followed by a flow cytometry measurement. As proofs of concept, we demonstrated the potential of the biosensor for highlighting DNA repair inhibitors and discriminating cell lines from their enzymatic activities.


Subject(s)
Biosensing Techniques , DNA Repair , DNA/chemistry , Flow Cytometry
5.
Org Biomol Chem ; 18(10): 1892-1899, 2020 03 11.
Article in English | MEDLINE | ID: mdl-31960874

ABSTRACT

Branched oligonucleotides containing a biologically relevant DNA lesion, dCyd341, which involves an interstrand crosslink between a cytosine base on one strand and a ribose moiety on the opposite strand, were prepared in a single automated solid-phase synthesis. For this, we first prepared the phosphoramidite analogue of dCyd341 bearing an orthogonal levulinyl protecting group. Then, following the synthesis of the first DNA strand containing dCyd341, the levulinic group was removed and the synthesis was then continued from the free base hydroxyl group at the branching point, using traditional phosphoramidites. The synthesized oligonucleotides were fully characterized by MALDI-TOF/MS and were enzymatically digested, and the presence of the lesion was confirmed by HPLC-MS/MS and the sequence was finally controlled upon exonuclease digestion followed by MALDI-TOF/MS analysis. The developed strategy was successfully employed for the preparation of several short linear and branched oligonucleotides containing the aforementioned lesion.


Subject(s)
DNA Damage , Oligodeoxyribonucleotides/chemical synthesis , Oligodeoxyribonucleotides/genetics , Solid-Phase Synthesis Techniques
6.
Nucleic Acids Res ; 46(5): 2417-2431, 2018 03 16.
Article in English | MEDLINE | ID: mdl-29361132

ABSTRACT

Poly(ADP-ribose) polymerases (PARPs) act as DNA break sensors and catalyze the synthesis of polymers of ADP-ribose (PAR) covalently attached to acceptor proteins at DNA damage sites. It has been demonstrated that both mammalian PARP1 and PARP2 PARylate double-strand break termini in DNA oligonucleotide duplexes in vitro. Here, we show that mammalian PARP2 and PARP3 can PARylate and mono(ADP-ribosyl)ate (MARylate), respectively, 5'- and 3'-terminal phosphate residues at double- and single-strand break termini of a DNA molecule containing multiple strand breaks. PARP3-catalyzed DNA MARylation can be considered a new type of reversible post-replicative DNA modification. According to DNA substrate specificity of PARP3 and PARP2, we propose a putative mechanistic model of PARP-catalyzed strand break-oriented ADP-ribosylation of DNA termini. Notably, PARP-mediated DNA ADP-ribosylation can be more effective than PARPs' auto-ADP-ribosylation depending on the DNA substrates and reaction conditions used. Finally, we show an effective PARP3- or PARP2-catalyzed ADP-ribosylation of high-molecular-weight (∼3-kb) DNA molecules, PARP-mediated DNA PARylation in cell-free extracts and a persisting signal of anti-PAR antibodies in a serially purified genomic DNA from bleomycin-treated poly(ADP-ribose) glycohydrolase-depleted HeLa cells. These results suggest that certain types of complex DNA breaks can be effectively ADP-ribosylated by PARPs in cellular response to DNA damage.


Subject(s)
Cell Cycle Proteins/metabolism , DNA Breaks , DNA/metabolism , Poly(ADP-ribose) Polymerases/metabolism , Adenosine Diphosphate Ribose/metabolism , DNA/chemistry , DNA Adducts/metabolism , DNA Breaks, Double-Stranded , HeLa Cells , Humans , Phosphates/metabolism , Substrate Specificity
7.
Nucleic Acids Res ; 45(19): 11193-11212, 2017 Nov 02.
Article in English | MEDLINE | ID: mdl-28977421

ABSTRACT

Ribonucleoside 5'-monophosphates (rNMPs) are the most common non-standard nucleotides found in DNA of eukaryotic cells, with over 100 million rNMPs transiently incorporated in the mammalian genome per cell cycle. Human ribonuclease (RNase) H2 is the principal enzyme able to cleave rNMPs in DNA. Whether RNase H2 may process abasic or oxidized rNMPs incorporated in DNA is unknown. The base excision repair (BER) pathway is mainly responsible for repairing oxidized and abasic sites into DNA. Here we show that human RNase H2 is unable to process an abasic rNMP (rAP site) or a ribose 8oxoG (r8oxoG) site embedded in DNA. On the contrary, we found that recombinant purified human apurinic/apyrimidinic endonuclease-1 (APE1) and APE1 from human cell extracts efficiently process an rAP site in DNA and have weak endoribonuclease and 3'-exonuclease activities on r8oxoG substrate. Using biochemical assays, our results provide evidence of a human enzyme able to recognize and process abasic and oxidized ribonucleotides embedded in DNA.


Subject(s)
DNA-(Apurinic or Apyrimidinic Site) Lyase/metabolism , DNA/metabolism , Ribonuclease H/metabolism , Ribonucleotides/metabolism , Binding Sites/genetics , DNA/genetics , DNA Repair , DNA-(Apurinic or Apyrimidinic Site) Lyase/genetics , HeLa Cells , Humans , Kinetics , Models, Genetic , Oxidation-Reduction , Protein Binding , Recombinant Proteins/metabolism , Ribonuclease H/genetics , Ribonucleotides/genetics , Substrate Specificity
8.
Nucleic Acids Res ; 44(19): 9279-9295, 2016 Nov 02.
Article in English | MEDLINE | ID: mdl-27471034

ABSTRACT

Poly(ADP-ribose) polymerases (PARPs/ARTDs) use nicotinamide adenine dinucleotide (NAD+) to catalyse the synthesis of a long branched poly(ADP-ribose) polymer (PAR) attached to the acceptor amino acid residues of nuclear proteins. PARPs act on single- and double-stranded DNA breaks by recruiting DNA repair factors. Here, in in vitro biochemical experiments, we found that the mammalian PARP1 and PARP2 proteins can directly ADP-ribosylate the termini of DNA oligonucleotides. PARP1 preferentially catalysed covalent attachment of ADP-ribose units to the ends of recessed DNA duplexes containing 3'-cordycepin, 5'- and 3'-phosphate and also to 5'-phosphate of a single-stranded oligonucleotide. PARP2 preferentially ADP-ribosylated the nicked/gapped DNA duplexes containing 5'-phosphate at the double-stranded termini. PAR glycohydrolase (PARG) restored native DNA structure by hydrolysing PAR-DNA adducts generated by PARP1 and PARP2. Biochemical and mass spectrometry analyses of the adducts suggested that PARPs utilise DNA termini as an alternative to 2'-hydroxyl of ADP-ribose and protein acceptor residues to catalyse PAR chain initiation either via the 2',1″-O-glycosidic ribose-ribose bond or via phosphodiester bond formation between C1' of ADP-ribose and the phosphate of a terminal deoxyribonucleotide. This new type of post-replicative modification of DNA provides novel insights into the molecular mechanisms underlying biological phenomena of ADP-ribosylation mediated by PARPs.


Subject(s)
DNA Breaks, Double-Stranded , DNA/genetics , DNA/metabolism , Poly(ADP-ribose) Polymerases/metabolism , Animals , Catalysis , DNA Adducts , Humans , Hydrolysis , Mice , NAD/metabolism , Poly (ADP-Ribose) Polymerase-1/metabolism , Protein Binding , Substrate Specificity
9.
Langmuir ; 33(44): 12785-12792, 2017 11 07.
Article in English | MEDLINE | ID: mdl-29035542

ABSTRACT

The detection of small molecules impacts various fields; however, their small size and low concentration are usually the cause of limitations in their detection. Thus, the need for biosensors with appropriate probes and signal amplification strategies is required. Aptamers are appropriate probes selected specifically against small targets such as adenosine. The possibility to split aptamers in parts led to original amplification strategies based on sandwich assays. By combining the self-assembling of oligonucleotide dimers with split-aptamer dangling ends and a surface plasmon resonance imaging technique, we developed an original amplification approach based on linear chain formation in the presence of the adenosine target. In this article, on the basis of sequence engineering, we analyzed its performance and the effect of the probe grafting density on the length of the chains formed at the surface of the biosensor.


Subject(s)
Adenosine/chemistry , Aptamers, Nucleotide , Biosensing Techniques , Polymers , Surface Plasmon Resonance
10.
J Biol Chem ; 290(23): 14610-7, 2015 Jun 05.
Article in English | MEDLINE | ID: mdl-25903131

ABSTRACT

Oxidatively generated guanine radical cations in DNA can undergo various nucleophilic reactions including the formation of C8-guanine cross-links with adjacent or nearby N3-thymines in DNA in the presence of O2. The G*[C8-N3]T* lesions have been identified in the DNA of human cells exposed to oxidative stress, and are most likely genotoxic if not removed by cellular defense mechanisms. It has been shown that the G*[C8-N3]T* lesions are substrates of nucleotide excision repair in human cell extracts. Cleavage at the sites of the lesions was also observed but not further investigated (Ding et al. (2012) Nucleic Acids Res. 40, 2506-2517). Using a panel of eukaryotic and prokaryotic bifunctional DNA glycosylases/lyases (NEIL1, Nei, Fpg, Nth, and NTH1) and apurinic/apyrimidinic (AP) endonucleases (Apn1, APE1, and Nfo), the analysis of cleavage fragments by PAGE and MALDI-TOF/MS show that the G*[C8-N3]T* lesions in 17-mer duplexes are incised on either side of G*, that none of the recovered cleavage fragments contain G*, and that T* is converted to a normal T in the 3'-fragment cleavage products. The abilities of the DNA glycosylases to incise the DNA strand adjacent to G*, while this base is initially cross-linked with T*, is a surprising observation and an indication of the versatility of these base excision repair proteins.


Subject(s)
DNA Repair , DNA/chemistry , Oligonucleotides/chemistry , Base Sequence , DNA/metabolism , DNA Glycosylases/metabolism , HeLa Cells , Humans , Molecular Sequence Data , Oligonucleotides/metabolism , Oxidation-Reduction
11.
Chem Res Toxicol ; 29(11): 1796-1809, 2016 11 21.
Article in English | MEDLINE | ID: mdl-27676238

ABSTRACT

The hyperthermophilic archaeon Thermococcus gammatolerans can resist huge doses of γ-irradiation, up to 5.0 kGy, without loss of viability. The potential to withstand such harsh conditions is probably due to complementary passive and active mechanisms, including repair of damaged chromosomes. In this work, we documented the formation and repair of oxidative DNA lesions in T. gammatolerans. The basal level of the oxidized nucleoside, 8-oxo-2'-deoxyguanosine (8-oxo-dGuo), was established at 9.2 (± 0.9) 8-oxo-dGuo per 106 nucleosides, a higher level than those usually measured in eukaryotic cells or bacteria. A significant increase in oxidative damage, i.e., up to 24.2 (± 8.0) 8-oxo-dGuo/106 nucleosides, was measured for T. gammatolerans exposed to a 5.0 kGy dose of γ-rays. Surprisingly, the yield of radiation-induced modifications was lower than those previously observed for human cells exposed to doses corresponding to a few grays. One hour after irradiation, 8-oxo-dGuo levels were significantly reduced, indicating an efficient repair. Two putative base excision repair (BER) enzymes, TGAM_1277 and TGAM_1653, were demonstrated both by proteomics and transcriptomics to be present in the cells without exposure to ionizing radiation. Their transcripts were moderately upregulated after gamma irradiation. After heterologous production and purification of these enzymes, biochemical assays based on electrophoresis and MALDI-TOF (matrix-assisted laser desorption ionization-time of flight) mass spectrometry indicated that both have a ß-elimination cleavage activity. TGAM_1653 repairs 8-oxo-dGuo, whereas TGAM_1277 is also able to remove lesions affecting pyrimidines (1-[2-deoxy-ß-d-erythro-pentofuranosyl]-5-hydroxyhydantoin (5-OH-dHyd) and 1-[2-deoxy-ß-d-erythro-pentofuranosyl]-5-hydroxy-5-methylhydantoin (5-OH-5-Me-dHyd)). This work showed that in normal growth conditions or in the presence of a strong oxidative stress, T. gammatolerans has the potential to rapidly reduce the extent of DNA oxidation, with at least these two BER enzymes as bodyguards with distinct substrate ranges.


Subject(s)
DNA Damage , DNA Repair , DNA, Archaeal/chemistry , Radiation Tolerance , Thermococcus/genetics , Oxidation-Reduction , Proteomics , Transcriptome
12.
Analyst ; 141(22): 6208-6216, 2016 Oct 24.
Article in English | MEDLINE | ID: mdl-27704075

ABSTRACT

DNA is under continuous assault by environmental and endogenous reactive oxygen and alkylating species, inducing the formation of mutagenic, toxic and genome destabilizing nucleobase lesions. Due to the implications of such genetic alterations in cell death, aging, inflammation, neurodegenerative diseases and cancer, many efforts have been devoted to developing assays that aim at analyzing DNA repair activities from purified enzymes or cell extracts. The present work deals with the conception and application of a new, miniaturized and parallelized on surface-DNA biosensor to measure base excision repair (BER) activities. Such a bio-analytical tool was built by using the "click chemistry" approach to immobilize, on a glass slide, fluorescent stem-loop DNA probes, which contain a specific nucleobase lesion. The performance of this new high-throughput DNA repair analysis technology was determined by detecting uracil N-glycosylase and AP-endonuclease activities from purified enzymes or in cell extracts. The applications of this device were extended to analyze, in cell extracts, the ability of two inhibitors (Uracil glycosylase inhibitor (Ugi) and methoxyamine (MX)) to block the excision of uracil and the cleavage of AP sites, respectively. Altogether, our results show that this new fluorescent DNA microarray platform provides an easy, rapid and robust method for detecting DNA N-glycosylase and AP-endonuclease activities and evaluating the effects of BER inhibitors in a multiplexed fashion.


Subject(s)
Biosensing Techniques , DNA Repair , Oligonucleotide Array Sequence Analysis , Click Chemistry , DNA , DNA Probes , DNA-(Apurinic or Apyrimidinic Site) Lyase/metabolism , HeLa Cells , Humans , Uracil-DNA Glycosidase/metabolism
13.
Proc Natl Acad Sci U S A ; 110(39): E3695-703, 2013 Sep 24.
Article in English | MEDLINE | ID: mdl-24023064

ABSTRACT

Spontaneous hydrolytic deamination of cytosine to uracil (U) in DNA is a constant source of genome instability in cells. This mutagenic process is greatly enhanced at high temperatures and in single-stranded DNA. If not repaired, these uracil residues give rise to C → T transitions, which are the most common spontaneous mutations occurring in living organisms and are frequently found in human tumors. In the majority of species, uracil residues are removed from DNA by specific uracil-DNA glycosylases in the base excision repair pathway. Alternatively, in certain archaeal organisms, uracil residues are eliminated by apurinic/apyrimidinic (AP) endonucleases in the nucleotide incision repair pathway. Here, we characterized the substrate specificity of the major human AP endonuclease 1, APE1, toward U in duplex DNA. APE1 cleaves oligonucleotide duplexes containing a single U⋅G base pair; this activity depends strongly on the sequence context and the base opposite to U. The apparent kinetic parameters of the reactions show that APE1 has high affinity for DNA containing U but cleaves the DNA duplex at an extremely low rate. MALDI-TOF MS analysis of the reaction products demonstrated that APE1-catalyzed cleavage of a U⋅G duplex generates the expected DNA fragments containing a 5'-terminal deoxyuridine monophosphate. The fact that U in duplex DNA is recognized and cleaved by APE1 in vitro suggests that this property of the exonuclease III family of AP endonucleases is remarkably conserved from Archaea to humans. We propose that nucleotide incision repair may act as a backup pathway to base excision repair to remove uracils arising from cytosine deamination.


Subject(s)
DNA Repair , DNA/metabolism , Nucleotides/metabolism , Signal Transduction , Uracil/metabolism , Base Sequence , Biocatalysis , Cell Line , Cytosine/metabolism , DNA-(Apurinic or Apyrimidinic Site) Lyase/metabolism , Deamination , Humans , Kinetics , Methanosarcina/metabolism , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , Substrate Specificity , Sulfites , Thymine DNA Glycosylase/metabolism
14.
Biochem Biophys Res Commun ; 446(1): 341-6, 2014 Mar 28.
Article in English | MEDLINE | ID: mdl-24607898

ABSTRACT

Recent studies have demonstrated that the modified base 5-hydroxymethylcytosine (5-hmC) is detectable at various rates in DNA extracted from human tissues. This oxidative product of 5-methylcytosine (5-mC) constitutes a new and important actor of epigenetic mechanisms. We designed a DNA pull down assay to trap and identify nuclear proteins bound to 5-hmC and/or 5-mC. We applied this strategy to three cancerous cell lines (HeLa, SH-SY5Y and UT7-MPL) in which we also measured 5-mC and 5-hmC levels by HPLC-MS/MS. We found that the putative oncoprotein Zinc finger and BTB domain-containing protein 2 (ZBTB2) is associated with methylated DNA sequences and that this interaction is inhibited by the presence of 5-hmC replacing 5-mC. As published data mention ZBTB2 recognition of p21 regulating sequences, we verified that this sequence specific binding was also alleviated by 5-hmC. ZBTB2 being considered as a multifunctional cell proliferation activator, notably through p21 repression, this work points out new epigenetic processes potentially involved in carcinogenesis.


Subject(s)
DNA Methylation , DNA, Neoplasm/genetics , DNA, Neoplasm/metabolism , Repressor Proteins/metabolism , 5-Methylcytosine/metabolism , Cell Line, Tumor , CpG Islands , Cyclin-Dependent Kinase Inhibitor p21/metabolism , Cytosine/analogs & derivatives , Cytosine/metabolism , DNA, Neoplasm/chemistry , Epigenesis, Genetic , HeLa Cells , Humans , Protein Binding
15.
Electrophoresis ; 35(14): 1938-46, 2014 Jul.
Article in English | MEDLINE | ID: mdl-24659099

ABSTRACT

By using a fluorescent exonuclease assay, we reported unusual electrophoretic mobility of 5'-indocarbo-cyanine 5 (5'-Cy5) labelled DNA fragments in denaturing polyacrylamide gels. Incubation time and enzyme concentration were two parameters involved in the formation of 5'-Cy5-labelled degradation products, while the structure of the substrate was slightly interfering. Replacement of positively charged 5'-Cy5-labelled DNA oligonucleotides (DNA oligos) by electrically neutral 5'-carboxyfluorescein (5'-FAM) labelled DNA oligos abolished the anomalous migration pattern of degradation products. MS analysis demonstrated that anomalously migrating products were in fact 5'-labelled DNA fragments ranging from 1 to 8 nucleotides. Longer 5'-Cy5-labelled DNA fragments migrated at the expected position. Altogether, these data highlighted, for the first time, the influence of the mass/charge ratio of 5'-Cy5-labelled DNA oligos on their electrophoretic mobility. Although obtained by performing 3' to 5' exonuclease assays with the family B DNA polymerase from Pyrococcus abyssi, these observations represent a major concern in DNA technology involving most DNA degrading enzymes.


Subject(s)
Carbocyanines/chemistry , Electrophoresis, Polyacrylamide Gel/methods , Fluorescent Dyes/chemistry , Oligodeoxyribonucleotides/chemistry , DNA-Directed DNA Polymerase
16.
Chem Res Toxicol ; 27(6): 1011-8, 2014 Jun 16.
Article in English | MEDLINE | ID: mdl-24798911

ABSTRACT

The possibility to induce the formation of covalent cross-links between polyamines and guanine following one electron oxidation of double stranded DNA has been evaluated. For such a purpose, a strategy has been developed to chemically synthesize the polyamine-C8-guanine adducts, and efforts have been made to characterize them. Then, an analytical method, based on HPLC separation coupled through electrospray ionization to tandem mass spectrometry, has been setup for their detection and quantification. Using such a sensitive approach, we have demonstrated that polyamine-C8-guanine adducts could be produced with significant yields in double stranded DNA following a one-electron oxidation reaction induced by photosensitization. These adducts, involving either putrescine, spermine, or spermidine, are generated by the nucleophilic addition of primary amino groups of polyamines onto the C8 position of the guanine radical cation. Our data demonstrate that such a nucleophilic addition of polyamines is much more efficient than the addition of a water molecule that leads to 8-oxo-7,8-dihydroguanine formation.


Subject(s)
Cross-Linking Reagents/chemistry , DNA/chemistry , Electrons , Polyamines/chemistry , Animals , Cattle , Chromatography, High Pressure Liquid , DNA/isolation & purification , Molecular Structure , Oxidation-Reduction , Tandem Mass Spectrometry
17.
Org Biomol Chem ; 12(17): 2778-83, 2014 May 07.
Article in English | MEDLINE | ID: mdl-24668242

ABSTRACT

The interest in the functionalization of oligonucleotides with organic molecules has grown considerably over the last decade. In this work, we report on the synthesis and characterization of porphyrin-oligonucleotide hybrids containing one to four DNA strands (P1-P4). The hybrid P4, which inserts one porphyrin and four DNA fragments, was combined with gold nanoparticles and imaged by transmission electron microscopy.


Subject(s)
DNA/chemistry , Gold/chemistry , Metal Nanoparticles/chemistry , Oligonucleotides/chemistry , Porphyrins/chemistry , Magnetic Resonance Spectroscopy , Metal Nanoparticles/ultrastructure , Microscopy, Electron, Transmission , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization
18.
Adv Sci (Weinh) ; 11(16): e2306710, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38419268

ABSTRACT

A copper-dependent self-cleaving DNA (DNAzyme or deoyxyribozyme) previously isolated by in vitro selection has been analyzed by a combination of Molecular Dynamics (MD) simulations and advanced Electron Paramagnetic Resonance (Electron Spin Resonance) EPR/ESR spectroscopy, providing insights on the structural and mechanistic features of the cleavage reaction. The modeled 46-nucleotide deoxyribozyme in MD simulations forms duplex and triplex sub-structures that flank a highly conserved catalytic core. The DNA self-cleaving construct can also form a bimolecular complex that has a distinct substrate and enzyme domains. The highly dynamic structure combined with an oxidative site-specific cleavage of the substrate are two key-aspects to elucidate. By combining EPR/ESR spectroscopy with selectively isotopically labeled nucleotides it has been possible to overcome the major drawback related to the "metal-soup" scenario, also known as "super-stoichiometric" ratios of cofactors versus substrate, conventionally required for the DNA cleavage reaction within those nucleic acids-based enzymes. The focus on the endogenous paramagnetic center (Cu2+) here described paves the way for analysis on mixtures where several different cofactors are involved. Furthermore, the insertion of cleavage reaction within more complex architectures is now a realistic perspective towards the applicability of EPR/ESR spectroscopic studies.


Subject(s)
Copper , DNA , Molecular Dynamics Simulation , Copper/chemistry , Electron Spin Resonance Spectroscopy/methods , DNA/chemistry , Nucleic Acid Conformation , DNA Cleavage , DNA, Catalytic/chemistry , DNA, Catalytic/metabolism , Ions/chemistry
19.
Protein Sci ; 33(1): e4849, 2024 Jan.
Article in English | MEDLINE | ID: mdl-38037490

ABSTRACT

The breast cancer susceptibility 1 (BRCA1) protein plays a pivotal role in modulating the transcriptional activity of the vital intrinsically disordered transcription factor MYC. In this regard, mutations of BRCA1 and interruption of its regulatory activity are related to hereditary breast and ovarian cancer (HBOC). Interestingly, so far, MYC's main dimerization partner MAX (MYC-associated factor X) has not been found to bind BRCA1 despite a high sequence similarity between both oncoproteins. Herein, we show that a potential reason for this discrepancy is the heterogeneous conformational space of MAX, which encloses a well-documented folded coiled-coil homodimer as well as a less common intrinsically disordered monomer state-contrary to MYC, which exists mostly as intrinsically disordered protein in the absence of any binding partner. We show that when the intrinsically disordered state of MAX is artificially overpopulated, the binding of MAX to BRCA1 can readily be observed. We characterize this interaction by nuclear magnetic resonance (NMR) spectroscopy chemical shift and relaxation measurements, complemented with ITC and SAXS data. Our results suggest that BRCA1 directly binds the MAX monomer to form a disordered complex. Though probed herein under biomimetic in-vitro conditions, this finding can potentially stimulate new perspectives on the regulatory network around BRCA1 and its involvement in MYC:MAX regulation.


Subject(s)
BRCA1 Protein , Basic Helix-Loop-Helix Leucine Zipper Transcription Factors , Humans , Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/chemistry , Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/metabolism , BRCA1 Protein/chemistry , BRCA1 Protein/metabolism , Calorimetry/methods , Intrinsically Disordered Proteins/chemistry , Intrinsically Disordered Proteins/metabolism , Nuclear Magnetic Resonance, Biomolecular , Proto-Oncogene Proteins c-myc/metabolism
20.
J Phys Chem Lett ; 14(44): 10032-10038, 2023 Nov 09.
Article in English | MEDLINE | ID: mdl-37906734

ABSTRACT

Since the introduction of DNA-based architectures, in the past decade, DNA tetrahedrons have aroused great interest. Applications of such nanostructures require structural control, especially in the perspective of their possible functionalities. In this work, an integrated approach for structural characterization of a tetrahedron structure is proposed with a focus on the fundamental biophysical aspects driving the assembly process. To address such an issue, spin-labeled DNA sequences are chemically synthesized, self-assembled, and then analyzed by Continuous-Wave (CW) and pulsed Electron Paramagnetic Resonance (EPR) spectroscopy. Interspin distance measurements based on PELDOR/DEER techniques combined with molecular dynamics (MD) thus revealed unexpected dynamic heterogeneity and flexibility of the assembled structures. The observation of flexibility in these ordered 3D structures demonstrates the sensitivity of this approach and its effectiveness in accessing the main dynamic and structural features with unprecedented resolution.


Subject(s)
DNA , Molecular Dynamics Simulation , Electron Spin Resonance Spectroscopy/methods , Spin Labels , DNA/chemistry , Base Sequence
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