Independent generation of the 5-hydroxy-5,6-dihydrothymidin-6-yl radical and its reactivity in dinucleoside monophosphates

Hydroxyl radical is a major reactive oxygen species produced by gamma-radiolysis of water or Fenton reaction. It attacks pyrimidine bases and gives the 5-hydroxy-5,6-dihydropyrimidin-6-yl radical as the major product. Here we report the synthesis of all four stereoisomers of 5-hydroxy-6-phenylthio-5,6-dihydrothymidine (T*), which, upon 254 nm UV irradiation, give rise to the 5-hydroxy-5,6-dihydrothymidin-6-yl radical (I). We also incorporated the photolabile radical precursors into dinucleoside monophosphates d(GT*) and d(TT*) and characterized major products resulting from the 254-nm irradiation of these dinucleoside monophosphates. Our results showed that, under anaerobic conditions, the most abundant product emanating from the 254-nm irradiation of d(GT*) and d(TT*) is an abasic site lesion. Products with the thymine portion being modified to thymine glycol and 5-hydroxy-5,6-dihydrothymine were also observed. In addition, we demonstrated that radical I can attack the C8 carbon atom of its 5' neighboring guanine and give rise to a novel cross-link lesion. Moreover, LC-MS/MS results showed that gamma-radiation of d(GT) under anaerobic condition yielded the same type of cross-link lesions.     

Formation of 5-Hydroxy-5,6-Dihydrothymidine and cis-5,6-Dihydroxy-5,6-Dihydrothymidine in the Radiolysis of N2O-Saturated Aqueous Solutions of Thymidine, Thymidine 5"-Monophosphate, and DNA

The yields of formation of 5-hydroxy-5,6-dihydrothymidine and cis-5,6-dihydroxy-5,6-dihydrothymidine in the radiolysis of thymidine, thymidine 5"-monophosphate, and DNA in N₂O-saturated aqueous solutions were measured in order to study the mechanism of nucleic acid radiolysis. The above compounds were found to be main radiolysis products upon irradiation of thymidine and thymidine 5"-monophosphate. However, these compounds were formed in very low yields upon irradiation of DNA, and they amounted to less than 2% of the degradation yield of DNA thymine. The yield of the 5-hydroxythymidin-6-yl radical was evaluated by determining the amount of 5-hydroxy-5,6-dihydrothymidine formed in the radiolysis of the above compounds in the presence of cysteamine.     

Metallobleomycin-mediated cleavage of DNA not involving a threading-intercalation mechanism.

The DNA cleavage properties of metallobleomycins conjugated to three solid supports were investigated using plasmid DNA, relaxed covalently closed circular DNA, and linear duplex DNA as substrates. Cleavage of pBR322 and pSP64 plasmid DNAs by Fe(II).BLM A(5)-CPG-C(2) was observed with efficiencies not dissimilar to that obtained using free Fe(II).BLM A(5). Similar results were observed following Fe(II).BLM A(5)-CPG-C(2)-mediated cleavage of a relaxed plasmid, a substrate that lacks ends or negative supercoiling capable of facilitating strand separation. BLMs covalently tethered to solid supports, including Fe(II).BLM A(5)-Sepharose 4B, Fe(II).BLM A(5)-CPG-C(6), and Fe(II).BLM A(5)-CPG-C(2), cleaved a 5'-(32)P end labeled linear DNA duplex with a sequence selectivity identical to that of free Fe(II).BLM A(5); cleavage predominated at 5'-G(82)T(83)-3' and 5'-G(84)T(85)-3'. To verify that these results could also be obtained using other metallobleomycins, supercoiled plasmid DNA and a linear DNA duplex were employed as substrates for Co(III).BLM A(5)-CPG-C(2). Free green Co(III).BLM A(5) was only about 2-fold more efficient than green Co(III).BLM A(5)-CPG-C(2) in effecting DNA cleavage. A similar result was obtained using Cu(II).BLM A(5)-CPG-C(2) + dithiothreitol. In addition, the conjugated Co.BLM A(5) and Cu.BLM A(5) cleaved the linear duplex DNA with a sequence selectivity identical to that of the respective free metalloBLMs. Interestingly, when supercoiled plasmid DNA was used as a substrate, conjugated Fe.BLM A(5) and Co.BLM A(5) were both found to produce Form III DNA in addition to Form II DNA. The formation of Form III DNA by conjugated Fe.BLM A(5) was assessed quantitatively. When corrected for differences in the intrinsic efficiencies of DNA cleavage by conjugated vs free BLMs, conjugated Fe.BLM A(5) was found to produce Form III DNA to about the same extent as the respective free Fe.BLM A(5), arguing that this conjugated BLM can also effect double-strand cleavage of DNA. Although previous evidence supporting DNA intercalation by some metallobleomycins is convincing, the present evidence indicates that threading intercalation is not a requirement for DNA cleavage by Fe(II).BLM A(5), Co(III).BLM A(5), or Cu(I).BLM A(5).     

Photoelectrochemical determination of Hg(II) via dual signal amplification involving SPR enhancement and a folding-based DNA probe

The authors describe a highly sensitive and selective photoelectrochemical (PEC) assay for mercury(II) ions. It is based on a dual signal amplification strategy. The first enhancement results from the surface plasmon resonance (SPR) of Au@Ag nanoparticles (NPs) absorbed on MoS₂ nanosheets. Here, the injection of hot electrons of Au@Ag NPs into MoS₂ nanosheets produces a strong photocurrent, while background signals are strongly reduced. The second enhancement results from the use of a thymine rich ct-DNA aptamer attached to the Au@Ag-MoS₂ nanohybrid. The DNA specifically binds Hg(II) ions to form thymine-Hg(II)-thymine (T-Hg-T) complexes. This leads to the formation of a hairpin-shaped dsDNA structure. The use of a CdSe quantum dot label at the terminal end of the ct-DNA further facilitates electron–hole separation. The photocurrent of the detector is measured as a function of Hg(II) concentration at a bias voltage of 0.1 V and under irradiation of 430 nm light. Due to the two-fold amplification strategy presented here, the linear range extends from 10 pmol·L^?1 to 100 nmol·L^?1, with a detection limit of 5 pmol·L^?1 (at S/N?=?3).

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Graphical Abstract The injection of hot electrons of Au@Ag into MoS₂ produces a strong photocurrent, and the formation of thymine-Hg(II)-thymine further facilitates electron–hole separation by CdSe. This dual signal amplification strategy is used to detect Hg(II) ions via a photoelectrochemical assay.

     

Transfer of stereochemical information in a minimal self-replicating system

[structure: see text]. The rational design, synthesis, and characterization of a minimal self-replicating system based on a 1,3-dipolar cycloaddition between a nitrone and a maleimide is presented. The importance of molecular recognition in this system is demonstrated using a competitive inhibitor. Doping experiments demonstrate that only one of the two diastereoisomeric products of the cycloaddition reaction is capable of acting as an efficient template for its own formation, accelerating the reaction between the nitrone and maleimide and controlling the stereochemical outcome of the reaction.     

DNA Interactions of a Dinuclear Ruthenium(II) Complex Bridged by 1,3-bis(1,10-phenanthroline[5,6-d]imidazol-2-yl)benzene

A novel dinuclear ruthenium(II) complex [(phen)₂Ru(mbpibH₂)Ru(phen)₂]⁴⁺ [phen = 1,10-phenanthroline; mbpibH₂ = 1,3-bis(1,10-phenanthroline[5,6-d]imidazol-2-yl)-benzene] has been synthesized and characterized. The DNA-binding behavior of this complex has been studied by spectroscopic and viscosity measurements. Results suggest that the dinuclear ruthenium(II) complex intercalates into DNA base pairs via its bridging moiety. It has also been found that the dinuclear ruthenium(II) complex displays the enantiopreferential DNA-binding after equilibrium dialysis.     

Ultra-selective and sensitive DNA detection by a universal apurinic/apyrimidinic probe-based endonuclease IV signal amplification system

A novel signal amplification system that is applicable to any DNA sequence of interest has been developed by using a combination of apurinic/apyrimidinic probe and endonuclease IV. The system allows rapid, highly selective and sensitive detection of target DNA sequences at very low concentrations (10 fmol) or low abundance levels (1%).     

Independent generation and study of 5,6-Dihydro-2'-deoxyuridin-6-yl,a member of the major family of reactive intermediates formed in DNA from the effects of gamma-radiolysis

Nucleobase radicals are the major family of reactive intermediates formed when nucleic acids are exposed to gamma-radiolysis. Elucidation of their reactivity is complicated by the formation of multiple species randomly throughout the biopolymers. 5,6-Dihydro-2'-deoxyuridin-6-yl (1) was generated upon photolysis (350 nm) of the respective tert-butyl ketone (2). The radical abstracts hydrogen atoms from beta-mercaptoethanol (k = 8.8 +/- 0.5 x 10(6) M(-)(1) s(-)(1)) and 2,5-dimethyltetrahydrofuran (k = 31 +/- 2.5 M(-)(1) s(-)(1)). The latter was used as a model for the 2-deoxyribose component of DNA. The major product formed in the presence of O(2) was 6-hydroxy-5,6-dihydro-2'-deoxyuridine (11), which is believed to be formed directly from the peroxy precursor and not via elimination of superoxide. Small amounts of 2-deoxyribonolactone (13) were also formed under aerobic conditions. This product is believed to result from intramolecular hydrogen atom abstraction by the C6-peroxyl radical (14) and suggests that gamma-radiolysis may indirectly result in oxidation of the C1'-position of nucleotides, despite the inaccessibility of this hydrogen in duplex DNA.     

A photo-elutable and template-free isothermal amplification strategy for sensitive fluorescence detection of 5-formylcytosine in genomic DNA

5-Formylcytosine (5fC), as an important epigenetic modification, plays a vital role in diverse biological processes and multiple diseases by regulating gene expression. Owing to the extremely low abundance of 5fC in all mammalian tissues and high structural similarity with other cytosine derivatives, the precise and sensitive detection of 5fC is challenging. Herein, a photo-elutable and template-free isothermal amplification strategy has been proposed for the sensitive detection of 5fC in genomic DNA based on 5fC-specific biotinylation, enrichment, photocleavage, and terminal deoxynucleotidyl transferase (TdT)-assisted fluorescence signal amplification, which is termed 5fC-PTIAS. By introducing the highly specific chemolabeling and the one-step photoelution processes, this strategy possesses a minimal nonspecific background as well as a much higher amplification efficiency. With the high signal-to-noise ratio, this strategy can achieve the accurate quantification of 5fC in various biological samples including mouse brain, kidney, and liver, with a limit of detection (LOD) of 0.025‰ in DNA (S/N = 3). These results not only confirm the widespread distribution of 5fC but also indicate its significant variation in different tissues and ages. The bisulfite- and mass spectrometry-free strategy is highly sensitive, selective, and easily mastered, holding great promise in detecting other epigenetic modifications with much lower levels.     

5,6-二甲氧基-N-[(R)-4-甲氧基-2-(丙烯-2-基)-2,3-二氢苯并呋喃-5-基]-1,1a,2,7b-四氢环丙并[c]苯并吡喃-7b-基甲酰胺的合成与表征

鱼藤酮与氧硫叶立德反应得到关键中间体(5,6-二甲氧基-1,1a,2,7b-四氢环丙并[c]苯并吡喃-7b-基)[(R)-4-羟基-2-(丙烯-2-基)-2,3-二氢苯并呋喃-5-基]甲酮(2),2再通过醚化、肟化、贝克曼重排得到5,6-二甲氧基-N-[(R)-4-甲氧基-2-(丙烯-2-基)-2,3-二氢苯并呋喃-5-基]-1,1a,2,7b-四氢环丙并[c]苯并吡喃-7b-基甲酰胺(5),化合物的结构经1H NMR,MS和元素分析确认,采用单晶X射线衍射法确定化合物5的晶体结构.化合物5属于三斜晶系,P1空间群,晶胞参数:a=0.95772(5)nm,b=1.06591(6)nm,c=1.30112(7)nm,α=111.8460(10)°,β=109.8870(10)°,γ=93.0870°,V=1.13429(11)nm3,Z=2,Dc=1.281 g/cm3,μ(Mo Kα)=0.092 mm-1,F(000)=464.     

Algorithmic Search for Mesomorphic Compounds in the Series of 4'-[(5,6-Dihydro-4-methyl-2H-pyran-5-yl)- amino]benzylidene-4-alkoxyanilines

A computer analysis of the relationship between the structure and mesomorphic activity and a search for potentially mesomorphic compounds in the series of azomethines containing a dihydropyranyl fragment, 4'-[(5,6-dihydro-4-methyl-2H-pyran-5-yl)amino]benzylidene-4-alkoxyanilines, were performed using the SARD (Structure Activity Relationship Design) system. The structural fragments exerting positive and negative effects on the manifestation of mesomorphism were revealed. The mesomorphic activity of the training structures and the extent of their similarity with the hypothetical standard of the activity were evaluated. The predictions show 70% agreement with the experiment.     

Development of a real-world direct interface for integrated DNA extraction and amplification in a microfluidic device

Integrated DNA extraction and amplification have been carried out in a microfluidic device using electro-osmotic pumping (EOP) for fluidic control. All the necessary reagents for performing both DNA extraction and polymerase chain reaction (PCR) amplification were pre-loaded into the microfluidic device following encapsulation in agarose gel. Buccal cells were collected using OmniSwabs [Whatman?, UK] and manually added to a chaotropic binding/lysis solution pre-loaded into the microfluidic device. The released DNA was then adsorbed onto a silica monolith contained within the DNA extraction chamber and the microfluidic device sealed using polymer electrodes. The washing and elution steps for DNA extraction were carried out using EOP, resulting in transfer of the eluted DNA into the PCR chamber. Thermal cycling, achieved using a Peltier element, resulted in amplification of the Amelogenin locus as confirmed using conventional capillary gel electrophoresis. It was demonstrated that the PCR reagents could be stored in the microfluidic device for at least 8 weeks at 4 °C with no significant loss of activity. Such methodology lends itself to the production of 'ready-to-use' microfluidic devices containing all the necessary reagents for sample processing, with many obvious applications in forensics and clinical medicine.     

Acid-Catalyzed Rearrangements of 5,6-exo-Epoxy-7-oxabicyclo[2.2.1]hept-2-yl Derivatives. Migratory Aptitudes of Acyl vs. Alkyl Groups in Wagner-Meerwein Transpositions

In the presence of HSO₃F/Ac₂O in CH₂CL₂, 2-exo- and 2-endo-cyano-5,6-exo-epoxy-7-oxabicyclo[2.2.1]hept-2-yl acetates ( 6a , b ) gave products derived from the epoxide-ring opening and a 1,2-shift of the unsubstituted alkyl group (σ bond C(3)–C(4)). In contrast, under similar conditions, the 5,6-exo-epoxy-7-oxabicyclo[2.2.1]heptan-2-one ( 6c ) gave 5-oxo-2-oxabicyclo[2.2.1]heptane-3,7-diyl diacetates 20 and 21 arising from the 1,2-shift of the acyl group. Acid treatment of 5,6-exo-epoxy-2,2-dimethoxy-7-oxabicyclo[2.2.1]heptane ( 6d ) and of 5,6-exo-epoxy-2,2-bis(benzyloxy)-7-oxabicyclo[2.2.1]heptane ( 6e ) gave minor products arising from epoxide-ring opening and the 1,2-shift of σ bond C(3)–C(4) and major products ( 25 , 29 ) arising from the 1,3-shift of a methoxy and benzyloxy group, respectively. Under similar conditions, 5,6-exo-epoxy-2,2-ethylenedioxy-7-oxabicyclo[2.2.1]heptane ( 6f ) gave 1,1-(ethylenedioxy)-2-(2-furyl)ethyl acetate ( 32 , major) and a minor product 33 , arising from the 1,2-shift of σ bond C(3)–C(4). The following order of migratory aptitudes for 1,2-shifts toward electron-deficient centers has been established: acyl > alkyl > alkyl α-substituted with inductive electron-withdrawing groups. This order is valid for competitive Wagner-Meerwein rearrangements involving equilibria between carbocation intermediates with similar exothermicities.     

Synthesis of a new tricyclic 3-(tetrazol-5-yl)pyridine system from 2-(azidomethyl)nicotinonitriles

2-Methyl-3-cyanopyridines were converted into the corresponding 2-azidomethyl derivatives, which then underwent an intramolecular cycloaddition reaction. A novel heterocyclic system containing a 3-(tetrazol-5-yl)pyridine unit was obtained in this way.