RESUMEN
Leveraging the fluorescence enhancement effect of the G-triplex (G3)/thioflavin T (ThT) catalyzed by the adjacent double-stranded DNA positioned at the 5' terminus of the G3, the G3-specific oligonucleotide (G3MB6) was utilized to facilitate the rapid detection of mercury (Hg(II)) through thymine-Hg(II)-thymine (T-Hg(II)-T) interactions. G3MB6 adopted a hairpin structure in which partially complementary strands could be disrupted with the presence of Hg(II). It prompted the formation of double-stranded DNA by T-Hg(II)-T, inducing the unbound single strand of G3MB6 to spontaneously form a parallel G3 structure, producing a solid fluorescence signal by ThT. Conversely, fluorescence was absent without Hg(II), since no double strand and formation of G3 occurred. The fluorescence intensity of G3MB6 exhibited a positive correlation with Hg(II) concentrations from 17.72 to 300 nM (R2 = 0.9954), boasting a notably low quality of limitation (LOQ) of 17.72 nM. Additionally, it demonstrated remarkable selectivity for detecting Hg(II). Upon application to detect Hg(II) in milk samples, the recovery rates went from 100.3% to 103.2%.
Asunto(s)
ADN , Mercurio , Mercurio/análisis , Mercurio/química , ADN/química , Animales , Espectrometría de Fluorescencia/métodos , Conformación de Ácido Nucleico , Timina/química , Técnicas Biosensibles/métodos , Leche/químicaRESUMEN
Polycyclic aromatic hydrocarbons (PAHs) are potent inhibitors of DNA that can induce genetic damage, abnormal gene expression, and metabolic disorders upon interfacing with biological macromolecules. However, the mechanism of their interactions with DNA remains elusive. Therefore, this study selected three representative PAHs, including phenanthrene (Phen), pyrene (Pyre), and benzo[a]pyrene (B[a]P), and explored their binding mechanisms with the double-strand DNA (dsDNA) from different species, including 1J1V (Escherichia coli), 6J5B (Arabidopsis thaliana), and 6Q1V (Homo sapiens). The results revealed that binding between PAHs and dsDNA occurred in the groove via van der Waals forces and π-π stacking, with the carboxyl oxygen atom of the thymine (T)-base within dsDNA being the key binding site. This result was further confirmed by the spectroscopic experiments, where significant changes in the peak of the T-base were observed after PAHs-dsDNA binding. More interestingly, the total binding energies of Pyre with the three dsDNA were -138.800 kJ/mol (Pyre-1J1V), -105.523 kJ/mol (Pyre-6J5B), and -127.567 kJ/mol (Pyre-6Q1V), respectively, all of which were higher than those of Phen and B[a]P. This suggests that that Pyre has the strongest dsDNA binding ability. Additionally, analysis of the thermodynamic parameters indicated that the interactions between the three PAHs and dsDNA were exothermic reactions. In contrast, the Pyre-dsDNA interaction predominantly involved van der Waals forces and hydrogen bonding due to the enthalpy change (∆H) < 0 and entropy change (∆S) < 0, while the Phen-dsDNA and B[a]P-dsDNA interactions predominantly involved hydrophobic forces due to ∆H > 0 and ∆S > 0. Furthermore, Pyre caused local distortion of dsDNA, which was more pronounced under atomic force microscopy (AFM). In summary, this study has unveiled a new phenomenon of binding between PAHs and dsDNA. This sheds light on the carcinogenic potential and environmental impacts of PAHs pollution.
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ADN , Hidrocarburos Policíclicos Aromáticos , Timina , Timina/química , Humanos , Arabidopsis/metabolismo , Escherichia coli , Fenantrenos , Pirenos/químicaRESUMEN
DNA glycosidic bond cleavage may induce cancer under the ultraviolet (UV) effect. Yet, the mechanism of glycosidic bond cleavage remains unclear and requires more detailed clarification. Herein, quantum chemical studies on its photoinduced mechanism are performed using a 5'-thymidine monophosphate (5'-dTMPH) model. In this study, four possible paths were examined to study the glycosidic bond cleavage. The results showed that, upon excitation, the electronic transition from the π bonding to π antibonding orbitals of the thymine ring leads to the damage of the thymine ring. Afterwards, the glycosidic bond is cleaved. At first, the doublet ground state (GS) path of glycosidic bond cleavage widely studied by other groups is caused by free electron generated by photoirradiation, with a kinetically feasible energy barrier of ~23 kcal/mol. Additionally, then, the other three paths were proposed that also might cause the glycosidic bond cleavage. The first one is the doublet excited state (ES) path, triggered by free electron along with UV excitation, which can result in a very-high-energy barrier ~49 kcal/mol that is kinetically unfavorable. The second one is the singlet ES path, induced by direct UV excitation, which assumes DNA is directly excited by UV light, which features a very low-energy barrier ~16 kcal/mol that is favored in kinetics. The third one is the triplet ES path, from the singlet state via intersystem crossing (ISC), which refers to a feasible ~27 kcal/mol energy barrier. This study emphasizes the pivotal role of the DNA glycosidic bond cleavage by our proposed direct UV excitation (especially singlet ES path) in addition to the authorized indirect free-electron-induced path, which should provide essential insights to future mechanistic comprehension and novel anti-cancer drug design.
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Timina , Rayos Ultravioleta , Timina/química , Glicósidos/química , Teoría Cuántica , Nucleótidos/química , ADN/química , Modelos Moleculares , Procesos Fotoquímicos , Electrones , TermodinámicaRESUMEN
The stability of the human telomere G-quadruplex (G4) is directly linked to cancer disease. The human telomere is mostly associated with the flanking nucleobases, which can affect the stability of G4. Hence, in this study, the effect of the flanking nucleobases in the context of their chemical nature, number, and position on the structure and stability of G4 has been investigated in varying concentrations of KCl mimicking the normal and cancer KCl microenvironments. The addition of flanking nucleobases does not alter the G4 topology. However, the presence of merely a single flanking nucleobase destabilizes the telomeric G4. This destabilizing effect is more prominent for thymine than adenine flanking nucleobase, probably due to the formation of the intermolecular G4 topology by thymine. Interestingly, the change in the stability of the telomeric G4 in the presence of thymine flanking nucleobase is sensitive to the concentration of KCl relevant to the normal and cancerous microenvironments, in contrast to adenine. Flanking nucleobases have a greater impact at the 5' end compared to the 3' end, particularly noticeable in KCl concentrations resembling the normal microenvironment rather than the cancerous one. These findings indicate that the effect of the flanking nucleobases on telomeric G4 is different in the KCl salt relevant to normal and cancerous microenvironments. This study may be helpful in attaining molecular-level insight into the role of G4 in telomeric length regulation under normal and cancerous KCl salt conditions.
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G-Cuádruplex , Cloruro de Potasio , Telómero , Humanos , Telómero/química , Cloruro de Potasio/química , Timina/químicaRESUMEN
Rare tautomeric forms of nucleobases can lead to Watson-Crick-like (WC-like) mispairs in DNA, but the process of proton transfer is fast and difficult to detect experimentally. NMR studies show evidence for the existence of short-time WC-like guanine-thymine (G-T) mispairs; however, the mechanism of proton transfer and the degree to which nuclear quantum effects play a role are unclear. We use a B-DNA helix exhibiting a wGT mispair as a model system to study tautomerization reactions. We perform ab initio (PBE0/6-31G*) quantum mechanical/molecular mechanical (QM/MM) simulations to examine the free energy surface for tautomerization. We demonstrate that while the ab initio QM/MM simulations are accurate, considerable sampling is required to achieve high precision in the free energy barriers. To address this problem, we develop a QM/MM machine learning potential correction (QM/MM-ΔMLP) that is able to improve the computational efficiency, greatly extend the accessible time scales of the simulations, and enable practical application of path integral molecular dynamics to examine nuclear quantum effects. We find that the inclusion of nuclear quantum effects has only a modest effect on the mechanistic pathway but leads to a considerable lowering of the free energy barrier for the GT*âG*T equilibrium. Our results enable a rationalization of observed experimental data and the prediction of populations of rare tautomeric forms of nucleobases and rates of their interconversion in B-DNA.
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Emparejamiento Base , Guanina , Aprendizaje Automático , Simulación de Dinámica Molecular , Protones , Teoría Cuántica , Timina , Guanina/química , Timina/química , ADN/química , TermodinámicaRESUMEN
Novel hollow AuAg nanoboxes (AuAg NBs) were designed for an innovative electrochemiluminescence (ECL) sensor to ultrasensitively detect Pb2+ and Hg2+ with the aid of DNAzyme and "thymine-Hg2+-thymine" ("T-Hg2+-T") structure. AuAg NBs are employed as an excellent surface plasma resonance (SPR) source, as well as an effective coreaction accelerator for the CoNi NFs/S2O82- system to greatly improve ECL performance. To detect Pb2+, the DNAzyme catalyzes the cleavage of ribonucleic acid targets into numerous small nucleic acid fragments, leading to an ECL signal. When Hg2+ is added, the thymine-thymine (T-T) mismatches of the Hg2+ aptamer bind Hg2+ to form the "T-Hg2+-T" structure, which not only inhibits the SPR process but also produces a large steric hindrance, thus quenching the ECL signal and allowing quantification of Hg2+. The novel ECL sensor quantifies Pb2+ in the range of 0.1 fM to 0.1 µM with a limit of detection of 0.07 fM and Hg2+ in the range of 10 pM to 1 µM with a LOD of 4.07 pM.
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Técnicas Biosensibles , ADN Catalítico , Oro , Plomo , Mediciones Luminiscentes , Mercurio , Plata , Mercurio/análisis , Oro/química , Técnicas Biosensibles/métodos , Plomo/análisis , Plomo/química , ADN Catalítico/química , ADN Catalítico/metabolismo , Plata/química , Técnicas Electroquímicas/métodos , Resonancia por Plasmón de Superficie , Nanopartículas del Metal/química , Límite de Detección , Timina/químicaRESUMEN
One of the most recent advances in the genome editing field has been the addition of "TALE Base Editors", an innovative platform for cell therapy that relies on the deamination of cytidines within double strand DNA, leading to the formation of an uracil (U) intermediate. These molecular tools are fusions of transcription activator-like effector domains (TALE) for specific DNA sequence binding, split-DddA deaminase halves that will, upon catalytic domain reconstitution, initiate the conversion of a cytosine (C) to a thymine (T), and an uracil glycosylase inhibitor (UGI). We developed a high throughput screening strategy capable to probe key editing parameters in a precisely defined genomic context in cellulo, excluding or minimizing biases arising from different microenvironmental and/or epigenetic contexts. Here we aimed to further explore how target composition and TALEB architecture will impact the editing outcomes. We demonstrated how the nature of the linker between TALE array and split DddAtox head allows us to fine tune the editing window, also controlling possible bystander activity. Furthermore, we showed that both the TALEB architecture and spacer length separating the two TALE DNA binding regions impact the target TC editing dependence by the surrounding bases, leading to more restrictive or permissive editing profiles.
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Citosina , Edición Génica , Timina , Edición Génica/métodos , Humanos , Citosina/metabolismo , Citosina/química , Timina/metabolismo , Timina/química , Efectores Tipo Activadores de la Transcripción/metabolismo , Efectores Tipo Activadores de la Transcripción/genética , ADN/metabolismo , ADN/genética , Células HEK293RESUMEN
Experimental methods to determine transition temperatures for individual base pair melting events in DNA duplexes are lacking despite intense interest in these thermodynamic parameters. Here, we determine the dimensions of the thymine (T) C2âO stretching vibration when it is within the DNA duplex via isotopic substitutions at other atomic positions in the structure. First, we determined that this stretching state was localized enough to specific atoms in the molecule to make submolecular scale measurements of local structure and stability in high molecular weight complexes. Next, we develop a new isotope-edited variable temperature infrared method to measure melting transitions at various locations in a DNA structure. As an initial test of this "sub-molecular scale thermometer", we applied our T13C2 difference infrared signal to measure location-dependent melting temperatures (TmL) in a DNA duplex via variable temperature attenuated total reflectance Fourier transform infrared (VT-ATR-FTIR) spectroscopy. We report that the TmL of a single Watson-Crick A-T base pair near the end of an A-T rich sequence (poly T) is â¼34.9 ± 0.7°C. This is slightly lower than the TmL of a single base pair near the middle position of the poly T sequence (TmL â¼35.6±0.2°C). In addition, we also report that the TmL of a single Watson-Crick A-T base pair near the end of a 50% G-C sequence (12-mer) is â¼52.5 ± 0.3°C, which is slightly lower than the global melting Tm of the 12-mer sequence (TmL â¼54.0±0.9°C). Our results provide direct physical evidence for end fraying in DNA sequences with our novel spectroscopic methods.
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Emparejamiento Base , ADN , Timina , Temperatura de Transición , ADN/química , Timina/química , Espectroscopía Infrarroja por Transformada de Fourier , Espectrofotometría Infrarroja/métodos , Conformación de Ácido Nucleico , TemperaturaRESUMEN
Sequencing the DNA nucleobases is essential in the diagnosis and treatment of many diseases related to human genes. In this article, the encapsulation of DNA nucleobases with some of the important synthesized chiral (7, 6), (8, 6), and (10, 8) carbon nanotubes were investigated. The structures were modeled by applying density functional theory based on tight binding method (DFTB) by considering semi-empirical basis sets. Encapsulating DNA nucleobases on the inside of CNTs caused changes in the electronic properties of the selected chiral CNTs. The results confirmed that van der Waals (vdW) interactions, π-orbitals interactions, non-bonded electron pairs, and the presence of high electronegative atoms are the key factors for these changes. The result of electronic parameters showed that among the CNTs, CNT (8, 6) is a suitable choice in sequencing guanine (G) and cytosine (C) DNA nucleobases. However, they are not able to sequence adenine (A) and thymine (T). According to the band gap energy engineering approach and absorption energy, the presence of G and C DNA nucleobases decreased the band gap energy of CNTs. Hence selected CNTs suggested as biosensor substrates for sequencing G and C DNA nucleobases.
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ADN , Guanina , Nanotubos de Carbono , Nanotubos de Carbono/química , ADN/química , Guanina/química , Teoría Funcional de la Densidad , Adenina/química , Citosina/química , Timina/química , Análisis de Secuencia de ADN/métodos , Electrones , Modelos Moleculares , HumanosRESUMEN
Uracil-thymine dehydrogenase (UTDH), which catalyzes the irreversible oxidation of uracil to barbituric acid in oxidative pyrimidine metabolism, was purified from Rhodococcus erythropolis JCM 3132. The finding of unusual stabilizing conditions (pH 11, in the presence of NADP+ or NADPH) enabled the enzyme purification. The purified enzyme was a heteromer consisting of three different subunits. The enzyme catalyzed oxidation of uracil to barbituric acid with artificial electron acceptors such as methylene blue, phenazine methosulfate, benzoquinone, and α-naphthoquinone; however, NAD+, NADP+, flavin adenine dinucleotide, and flavin mononucleotide did not serve as electron acceptors. The enzyme acted not only on uracil and thymine but also on 5-halogen-substituted uracil and hydroxypyrimidine (pyrimidone), while dihydropyrimidine, which is an intermediate in reductive pyrimidine metabolism, and purine did not serve as substrates. The activity of UTDH was enhanced by cerium ions, and this activation was observed with all combinations of substrates and electron acceptors.
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Oxidación-Reducción , Pirimidinas , Rhodococcus , Uracilo , Uracilo/metabolismo , Uracilo/química , Pirimidinas/metabolismo , Rhodococcus/enzimología , NADP/metabolismo , Azul de Metileno/metabolismo , Azul de Metileno/química , Barbitúricos/metabolismo , Barbitúricos/química , Benzoquinonas/metabolismo , Benzoquinonas/química , Proteínas Bacterianas/metabolismo , Proteínas Bacterianas/genética , Proteínas Bacterianas/química , Concentración de Iones de Hidrógeno , Timina/metabolismo , Timina/química , Especificidad por Sustrato , Metosulfato de Metilfenazonio/metabolismo , Metosulfato de Metilfenazonio/químicaRESUMEN
Gilvocarcin V (GV) is a natural antibiotic exhibiting excellent antitumor activities and remarkably low toxicity in near-ultraviolet or visible light-dependent treatment. Notwithstanding, the [2 + 2] cycloaddition reaction between GV and thymine has been proven to be the key for its function in photodynamic therapy, and crucial mechanistic details about such a reaction are poorly understood. In this study, the electronic relaxation pathways and photoaddition reaction are characterized by femto- to nanosecond time-resolved spectroscopy combined with quantum chemical calculation. Our results reveal that ultrafast intersystem crossing (<3 ps) leads to the population of a local triplet excited state in DNA-intercalated GV. Such a state can further induce the formation of a biradical state, which is identified as the important reactive precursor for photoaddition between GV and thymine. The overall photoaddition quantum efficiency is determined to be 11.57 ± 1.0%. These results are essential to the elucidation of the DNA photoaddition mechanism of C-aryl glycoside-based artificial photocytotoxic agents and could help further development of those medicines.
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Cumarinas , Glicósidos , Timina , Timina/química , ADN/química , AntibacterianosRESUMEN
In this work, we developed a novel label-free fluorescent sensor for the highly sensitive detection of mercury ions (Hg2+) based on the coordination chemistry of thymine-Hg2+-thymine (T-Hg2+-T) structures and the properties of CRISPR-Cas12a systems. Most notably, two T-rich sequences (a blocker and an activator) were designed to form stable double-stranded structures in the presence of Hg2+ via the T-Hg2+-T base pairing. The formation of T-T mismatched double-stranded DNA between the blocker and the activator prevented the cleavage of G-rich sequences by Cas12a, allowing them to fold into G-quadruplex-thioflavin T complexes, resulting in significantly enhanced fluorescence. Under the optimized conditions, the developed sensor showed an excellent response for Hg2+ detection in the linear range of 0.05 to 200 nM with a detection limit of 23 pM. Moreover, this fluorescent sensor exhibited excellent selectivity and was successfully used for the detection of Hg2+ in real samples of Zhujiang river water and tangerine peel, demonstrating its potential in environmental monitoring and food safety applications.
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Mercurio , Timina , Espectrometría de Fluorescencia/métodos , Timina/química , Sistemas CRISPR-Cas , Mercurio/química , Iones/químicaRESUMEN
Electron driven chemistry of biomolecules in aqueous phase presents the realistic picture to study molecular processes. In this study we have investigated the interactions of electrons with the DNA constituents in their aqueous phase in order to obtain the quantities useful for DNA damage assessment. We have computed the inelastic mean free path (IMFP), mass stopping power (MSP) and absorbed dose (D) for the DNA constituents (Adenine, Cytosine, Guanine, Thymine and Uracil) in the aqueous medium from ionisation threshold to 5000â eV. We have modified complex optical potential formalism to include band gap of the systems to calculate inelastic cross sections which are used to estimate these entities. This is the maiden attempt to report these important quantities for the aqueous DNA constituents. We have compared our results with available data in gas and other phase and have observed explicable accord for IMFP and MSP. Since these are the first results of absorbed dose (D) for these compounds, we have explored present results vis-a-vis dose absorption in water.
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Electrones , Timina , Timina/química , Uracilo/química , Citosina/química , ADN/química , Agua/químicaRESUMEN
Many prokaryotic Argonaute (pAgo) proteins act as programmable nucleases that use small guide DNAs for recognition and cleavage of complementary target DNA. Recent studies suggested that pAgos participate in cell defense against invader DNA and may also be involved in other genetic processes, including DNA replication and repair. The ability of pAgos to recognize specific targets potentially make them an invaluable tool for DNA manipulations. Here, we demonstrate that DNA-guided DNA-targeting pAgo nucleases from three bacterial species, DloAgo from Dorea longicatena, CbAgo from Clostridium butyricum and KmAgo from Kurthia massiliensis, can sense site-specific modifications in the target DNA, including 8-oxoguanine, thymine glycol, ethenoadenine and pyrimidine dimers. The effects of DNA modifications on the activity of pAgos strongly depend on their positions relative to the site of cleavage and are comparable to or exceed the effects of guide-target mismatches at corresponding positions. For all tested pAgos, the strongest effects are observed when DNA lesions are located at the cleavage position. The results demonstrate that DNA cleavage by pAgos is strongly affected by DNA modifications, thus making possible their use as sensors of DNA damage.
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Proteínas Argonautas , Proteínas Bacterianas , Proteínas Bacterianas/metabolismo , Proteínas Bacterianas/genética , Proteínas Bacterianas/química , Proteínas Argonautas/metabolismo , Proteínas Argonautas/genética , ADN/metabolismo , Daño del ADN , Guanina/metabolismo , Guanina/química , Guanina/análogos & derivados , Clostridium butyricum/metabolismo , Clostridium butyricum/genética , Timina/metabolismo , Timina/química , Timina/análogos & derivadosRESUMEN
Genomic DNA of the cyanophage S-2L virus is composed of 2-aminoadenine (Z), thymine (T), guanine (G), and cytosine (C), forming the genetic alphabet ZTGC, which violates Watson-Crick base pairing rules. The Z-base has an extra amino group on the two position that allows the formation of a third hydrogen bond with thymine in DNA strands. Here, we explored and expanded applications of this non-Watson-Crick base pairing in protein expression and gene editing. Both ZTGC-DNA (Z-DNA) and ZUGC-RNA (Z-RNA) produced in vitro show detectable compatibility and can be decoded in mammalian cells, including Homo sapiens cells. Z-crRNA can guide CRISPR-effectors SpCas9 and LbCas12a to cleave specific DNA through non-Watson-Crick base pairing and boost cleavage activities compared to A-crRNA. Z-crRNA can also allow for efficient gene and base editing in human cells. Together, our results help pave the way for potential strategies for optimizing DNA or RNA payloads for gene editing therapeutics and give insights to understanding the natural Z-DNA genome.
Asunto(s)
Emparejamiento Base , Sistemas CRISPR-Cas , ADN de Forma Z , Edición Génica , Humanos , ADN/genética , ADN/química , ADN de Forma Z/genética , Edición Génica/métodos , ARN/genética , ARN Guía de Sistemas CRISPR-Cas , Timina/químicaRESUMEN
Mercury (Hg2+) is a highly toxic element and can seriously affect human health. This work proposed a photoelectrochemical (PEC) sensor with a Z-scheme Fe2O3/CdS heterostructure and two thymine-rich DNA strands (DNA-1 and Au@DNA-2) for sensitive detection of Hg2+. The light excitation of the Fe2O3/CdS composite accelerated the electron transfer among Fe2O3, CdS, and the electrode to produce a stable photocurrent response. Upon the recognition of Hg2+ to thymine bases (T) in two DNA strands to form a stable T-Hg2+-T biomimetic structure, the photocurrent response increased with the increasing concentration of Hg2+ due to the opening of electronic transmission channels from Au nanoparticles to Fe2O3/CdS nanocomposite. Under the optimal conditions screened by the Box-Behnken experiments, the proposed PEC sensor showed excellent analytical performance for Hg2+ detection with high sensitivity, a detection limit of 0.20 pM at a signal-to-noise ratio of 3, high selectivity, a detectable concentration range of 1 pM-100 nM, and acceptable stability. The good recovery and low relative standard deviation for the analysis of Hg2+ in lake and tap water samples demonstrated the potential application of the designed Z-scheme Fe2O3/CdS heterostructure in the PEC detection of heavy metal ions.
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Técnicas Biosensibles , Mercurio , Nanopartículas del Metal , Humanos , Mercurio/análisis , Oro/química , Nanopartículas del Metal/química , Timina/química , ADN/química , Límite de Detección , Técnicas ElectroquímicasRESUMEN
The short-range charge transfer of DNA base triplets has wide application prospects in bioelectronic devices for identifying DNA bases and clinical diagnostics, and the key to its development is to understand the mechanisms of short-range electron dynamics. However, tracing how electrons are transferred during the short-range charge transfer of DNA base triplets remains a great challenge. Here, by means of ab initio molecular dynamics and Ehrenfest dynamics, the nuclear-electron interaction in the thymine-adenine-thymine (TAT) charge transfer process is successfully simulated. The results show that the electron transfer of TAT has an oscillating phenomenon with a period of 10 fs. The charge density difference proves that the charge transfer proportion is as high as 59.817% at 50 fs. The peak position of the hydrogen bond fluctuates regularly between -0.040 and -0.056. The time-dependent Marcus-Levich-Jortner theory proves that the vibrational coupling between nucleus and electron induces coherent electron transfer in TAT. This work provides a real-time demonstration of the short-range coherent electron transfer of DNA base triplets and establishes a theoretical basis for the design and development of novel biological probe molecules.
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Electrones , Timina , Timina/química , Transporte de Electrón , Simulación de Dinámica Molecular , ADN/químicaRESUMEN
The detection of mercury ions (Hg2+) with an ultralow concentration is of great significance for the treatment of heavy metal pollution in industrial waste water and the monitoring of drinking water quality. In this study, a simple, sensitive, and portable surface acoustic wave (SAW) biosensor for the determination of Hg2+ concentration was developed. First, a DNA fragment with a specific binding capacity for Hg2+ was chemically adsorbed on to the sensitive region through forming Au-S bonds with the SAW biosensor. The DNA probe could then form a thymine-Hg2+-thymine (T-Hg2+-T) complex with strong affinity for Hg2+ after immersion in a test solution containing Hg2+, resulting in a significant change in the response frequency of the device. The linear detection range of the device was 10 pM to 1 nM, while the limit of detection (LOD) was as low as 6.3 pM. Furthermore, the SAW biosensor exhibited excellent selectivity to Hg2+ compared with that of interfering ions, e.g., Ag+, Ba2+, Cu2+, Zn2+, Mn2+, Fe3+, Ca2+, and Na+. The results provide a new strategy for the preparation of portable devices that can monitor toxic heavy metal ions with high sensitivity and selectivity.
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Técnicas Biosensibles , Mercurio , Timina/química , Oro/química , Mercurio/química , Técnicas Biosensibles/métodos , Iones/químicaRESUMEN
We report the occurrence of register-shifted structures in simulations of uracil-containing dsDNA. These occur when the 3' base vicinal to uracil is thymine in U:A base-paired DNA. Upon base flipping of uracil, this 3' thymine hydrogen bonds with the adenine across the uracil instead of its complementary base. The register-shifted structure is persistent and sterically blocks re-entry of uracil into the helix stack. Register shifting might be important for DNA repair since the longer exposure of the lesion in register-shifted structures could facilitate enzymatic recognition and repair.
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Timina , Uracilo , Uracilo/química , Timina/química , Uracil-ADN Glicosidasa/química , Daño del ADN , Reparación del ADN , ADN/químicaRESUMEN
In DNA, thymine typically forms hydrogen bonds with adenine to hold two complementary strands together and to preserve the genetic code. While thymine is typically absent in RNA, a thymine-thymine hydrogen bonding structure is reminiscent of the wobble region in tRNA recognition, where noncanonical base pairing can occur. This noncanonical base pairing can be applied to synthetic polymer systems, where thymine is free to hydrogen bond with itself. In this work, the natural hydrogen bonding capacity of thymine was used to produce silicone polymer systems designed to be cross-linked by hydrogen bonds. Backbone and end-group-modified silicones were synthesized with differing concentrations of thymine, which facilitated the cross-linking of the polymeric strands. Removing the hydrogen on N3âwhich is typically involved in hydrogen bondingâresulted in systems with similar viscosities to the starting material and that were devoid of any apparent cross-links. Differential scanning calorimetry (DSC) studies of the thymine-modified polymers displayed thermal absorptions and releases, indicative of bond breaking and reformation, around 100 and 60 °C, respectively. The cycle of bond breaking and formation could be repeated without any noticeable degradation of the chemical structure of the polymers. These polymeric materials could be readily recycled and remolded by heating them at 110 °C for 5 min, followed by cooling to room temperature, confirming their thermoplastic nature.