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1.
J Phys Chem B ; 128(11): 2640-2651, 2024 Mar 21.
Artigo em Inglês | MEDLINE | ID: mdl-38452253

RESUMO

2-Aminopurine (2AP) is the most widely used fluorescent nucleobase analogue in DNA and RNA research. Its unique photophysical properties and sensitivity to environmental changes make it a useful tool for understanding nucleic acid dynamics and DNA-protein interactions. We studied the effect of ions present in commonly used buffer solutions on the excited-state photophysical properties of 2AP. Fluorescence quenching was negligible for tris(hydroxymethyl)aminomethane (TRIS), but significant for phosphate, carbonate, 3-(N-morpholino) propanesulfonic acid (MOPS), and 4-(2-hydroxyethyl)-1-piperazineethanesulfonic acid (HEPES) buffers. Results indicate that the two tautomers of 2AP (7H, 9H) are quenched by phosphate ions to different extents. Quenching by the H2PO4- ion is more pronounced for the 7H tautomer, while the opposite is true for the HPO42- ion. For phosphate ions, the results of the time-resolved fluorescence study cannot be explained using a simple collisional quenching mechanism. Instead, results are consistent with transient interactions between 2AP and the phosphate ions. We postulate that excited-state interactions between the 2AP tautomers and an H-bond acceptor (phosphate and carbonate) result in significant quenching of the singlet-excited state of 2AP. Such interactions manifest in biexponential fluorescence intensity decays with pre-exponential factors that vary with quencher concentration, and downward curvatures of the Stern-Volmer plots.


Assuntos
2-Aminopurina , DNA , 2-Aminopurina/química , Fluorescência , DNA/química , Carbonatos , Fosfatos , Espectrometria de Fluorescência/métodos
2.
Anal Methods ; 16(4): 576-582, 2024 01 25.
Artigo em Inglês | MEDLINE | ID: mdl-38189219

RESUMO

Reversible structural changes in DNA nanomachines have great potential in the field of bioanalysis. Here, we demonstrate an assembly strategy for quencher-free and tunable DNA tweezers based on 2-aminopurine (2-AP), avoiding the tedious fluorescence labelling step. The conformational state of the tweezers could be controlled by specific oligonucleotides (fuel or anti-fuel). Taking advantage of the local environmental sensitivity of 2-AP, the structural changes of the tweezers were easily tracked, and multiple cyclic switching of the tweezers between the open and closed states was achieved. In addition, the influence of oligonucleotide structure on the fluorescence properties of 2-AP was deeply explored. We figured out that the fluorescence of 2-AP was highly quenched by the base-stacking of natural bases in DNA oligonucleotides. Moreover, by comprehensively regulating the type of bases surrounding the inserted 2-AP site, a sensitive fluorescence response towards dynamic change can be obtained. This principle of quencher-free nanodevices based on 2-AP provides a convenient method for monitoring the structural changes of DNA nanomachines.


Assuntos
2-Aminopurina , DNA , 2-Aminopurina/química , Fluorescência , DNA/química , Oligonucleotídeos/química , Sequência de Bases
3.
Biotechnol Bioeng ; 121(4): 1384-1393, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38151965

RESUMO

2,6-diaminopurine (Z), a naturally occurring noncanonical nucleotide base found in bacteriophages, enhances DNA hybridization by forming three hydrogen bonds with thymine (T). These distinct biochemical characteristics make it particularly valuable in applications that rely on the thermodynamics of DNA hybridization. However, the practical use of Z-containing oligos is limited by their high production cost and the challenges associated with their synthesis. Here, we developed an efficient and cost-effective approach to synthesize Z-containing oligos of high quality based on an isothermal strand displacement reaction. These newly synthesized Z-oligos are then employed as toehold-blockers in an isothermal genotyping assay designed to detect rare single nucleotide variations (SNV). When compared with their counterparts containing the standard adenine (A) base, the Z-containing blockers significantly enhance the accuracy of identifying SNV. Overall, our innovative methodology in the synthesis of Z-containing oligos, which can also be used to incorporate other unconventional and unnatural bases into oligonucleotides, is anticipated to be adopted for diverse applications, including genotyping, biosensing, and gene therapy.


Assuntos
2-Aminopurina/análogos & derivados , DNA , Nucleotídeos , Genótipo , Hibridização de Ácido Nucleico , DNA/química
4.
Int J Mol Sci ; 24(24)2023 Dec 12.
Artigo em Inglês | MEDLINE | ID: mdl-38139210

RESUMO

The synthesis and characterization of the multicomponent crystals formed by 2,2'-thiodiacetic acid (H2tda) and 2,6-diaminopurine (Hdap) or N9-(2-hydroxyethyl)adenine (9heade) are detailed in this report. These crystals exist in a salt rather than a co-crystal form, as confirmed by single crystal X-ray diffractometry, which reflects their ionic nature. This analysis confirmed proton transfer from the 2,2'-thiodiacetic acid to the basic groups of the coformers. The new multicomponent crystals have molecular formulas [(H9heade+)(Htda-)] 1 and [(H2dap+)2(tda2-)]·2H2O 2. These were also characterized using FTIR, 1H and 13C NMR and mass spectroscopies, elemental analysis, and thermogravimetric/differential scanning calorimetry (TG/DSC) analyses. In the crystal packing the ions interact with each other via O-H⋯N, O-H⋯O, N-H⋯O, and N-H⋯N hydrogen bonds, generating cyclic hydrogen-bonded motifs with graph-set notation of R22(16), R22(10), R32(10), R33(10), R22(9), R32(8), and R42(8), to form different supramolecular homo- and hetero-synthons. In addition, in the crystal packing of 2, pairs of diaminopurinium ions display a strong anti-parallel π,π-stacking interaction, characterized by short inter-centroids and interplanar distances (3.39 and 3.24 Å, respectively) and a fairly tight angle (17.5°). These assemblies were further analyzed energetically using DFT calculations, MEP surface analysis, and QTAIM characterization.


Assuntos
Adenina , Prótons , 2-Aminopurina
5.
J Phys Chem B ; 127(37): 7858-7871, 2023 09 21.
Artigo em Inglês | MEDLINE | ID: mdl-37698525

RESUMO

Novel fluorescent nucleic acid base analogues (FBAs) with improved optical properties are needed in a variety of biological applications. 2-Amino-6-chloro-8-vinylpurine (2A6Cl8VP) is structural analogue of two existing highly fluorescent FBAs, 2-aminopurine (2AP) and 8-vinyladenine (8VA), and can therefore be expected to have similar base pairing as well as better optical properties compared to its counterparts. In order to determine the absorption and fluorescence properties of 2A6Cl8VP, as a first step, we used TD-DFT calculations and the polarizable continuum model for simulating the solvents and computationally predicted absorption and fluorescence maxima. To test the computational predictions, we also synthesized 2A6Cl8VP and measured its UV/vis absorbance, fluorescence emission, and fluorescence lifetime. The computationally predicted absorbance and fluorescence maxima of 2A6Cl8VP are in reasonable agreement to the experimental values and are significantly redshifted compared to 2AP and 8VA, allowing for its specific excitation. The fluorescence quantum yield of 2A6Cl8VP, however, is significantly lower than those of 2AP and 8VA. Overall, 2A6Cl8VP is a novel fluorescent nucleobase analogue, which can be useful in studying structural, biophysical, and biochemical applications.


Assuntos
2-Aminopurina , Purinas , Biofísica , Corantes
6.
Anal Methods ; 15(34): 4243-4251, 2023 08 31.
Artigo em Inglês | MEDLINE | ID: mdl-37592315

RESUMO

Simple, rapid, and highly sensitive methods for single-stranded nucleic acid detection are of great significance in clinical testing. Meanwhile, common methods are inseparable from the participation of enzymes, which greatly increases their complexity. Herein, an enzyme-free and sensitive method combining HCR and CHA is established to detect single-stranded nucleic acid. A target induces the auxiliary hairpin strands to open their secondary structure, exposing partial sequences that can trigger catalytic hairpin assembly (CHA) and hybridization chain reactions (HCR), respectively. To avoid additional signaling substances, 2-aminopurines (which fluoresces differently in double-stranded DNA and G-quadruplex) are modified in the substrate chains of CHA and HCR. Compared with methods that adopt CHA or HCR alone, the sensitivity of this method is increased by nearly 10 times. Moreover, this method can effectively improve the specific recognition of the target. To "turn on" the method, two regions that can pair with H5 and H6 are required. Taking foot-and-mouth disease virus (FMDV) as the object, this method can specifically detect FMDV to 2.78 × 101 TCID50. Although the sensitivity is not as good as RT-qPCR, it owns the advantages of simplicity and speed. We think this method can be used for the primary screening of FMDV, and has application potential in some grassroots.


Assuntos
Vírus da Febre Aftosa , Ácidos Nucleicos , Animais , Hibridização de Ácido Nucleico , Hibridização Genética , 2-Aminopurina , Catálise
7.
Molecules ; 28(15)2023 Aug 06.
Artigo em Inglês | MEDLINE | ID: mdl-37570884

RESUMO

Rheumatoid arthritis (RA) remains one of the most prevalent autoimmune diseases worldwide. Janus kinase 3 (JAK3) is an essential enzyme for treating autoimmune diseases, including RA. Molecular modeling techniques play a crucial role in the search for new drugs by reducing time delays. In this study, the 3D-QSAR approach is employed to predict new JAK3 inhibitors. Two robust models, both field-based with R2 = 0.93, R = 0.96, and Q2 = 87, and atom-based with R2 = 0.94, R = 0.97, and Q2 = 86, yielded good results by identifying groups that may readily direct their interaction. A reliable pharmacophore model, DHRRR1, was provided in this work to enable the clear characterization of chemical features, leading to the design of 13 inhibitors with their pIC50 values. The DHRRR1 model yielded a validation result with a ROC value of 0.87. Five promising inhibitors were selected for further study based on an ADMET analysis of their pharmacokinetic properties and covalent docking (CovDock). Compared to the FDA-approved drug tofacitinib, the pharmaceutical features, binding affinity and stability of the inhibitors were analyzed through CovDock, 300 ns molecular dynamics simulations, free energy binding calculations and ADMET predictions. The results show that the inhibitors have strong binding affinity, stability and favorable pharmaceutical properties. The newly predicted molecules, as JAK3 inhibitors for the treatment of RA, are promising candidates for use as drugs.


Assuntos
2-Aminopurina , Antirreumáticos , Desenho Assistido por Computador , Desenho de Fármacos , Janus Quinase 3 , Inibidores de Janus Quinases , 2-Aminopurina/análogos & derivados , 2-Aminopurina/farmacologia , Inibidores de Janus Quinases/química , Inibidores de Janus Quinases/farmacologia , Janus Quinase 3/antagonistas & inibidores , Relação Quantitativa Estrutura-Atividade , Piperidinas/química , Piperidinas/farmacologia , Pirimidinas/química , Pirimidinas/farmacologia , Artrite Reumatoide/tratamento farmacológico , Antirreumáticos/química , Antirreumáticos/farmacologia , Farmacóforo
8.
J Mol Endocrinol ; 71(3)2023 10 01.
Artigo em Inglês | MEDLINE | ID: mdl-37522854

RESUMO

Placenta synthesizes hormones that play a vital role in adapting maternal physiology and supporting fetal growth. This study aimed to explore the link between progesterone, a key steroid hormone produced by placenta, and mitochondrial fission and protein kinase R through the use of chemical inhibition in trophoblasts subjected to endotoxin lipopolysaccharide and double-stranded RNA analog polyinosinic:polycytidylic acid stress. Expressions of protein kinase R, dynamin-related protein 1, mitochondrial fission protein 1, and heat shock protein 60 were determined by applying lipopolysaccharide and polyinosinic:polycytidylic acid to BeWo trophoblast cells. Next, cells were treated with protein kinase R inhibitor 2-aminopurine and mitochondrial division inhibitor 1 to examine changes in progesterone levels and expression levels of proteins and mRNAs involved in progesterone biosynthesis. Last, effect of 2-aminopurine on mitochondrial fission was determined by immunoblotting and quantitative PCR (qPCR). Mitochondrial structural changes were also examined by transmission electron microscopy. Lipopolysaccharide and polyinosinic:polycytidylic acid stimulation induced mitochondrial fission and activated protein kinase R but decreased heat shock protein 60 levels and progesterone synthesis. Chemical inhibition of mitochondrial fission elevated progesterone synthesis and protein and mRNA levels of genes involved in progesterone biosynthesis. Inhibition of protein kinase R with 2-aminopurine prevented lipopolysaccharide and polyinosinic:polycytidylic acid induced mitochondrial fission and increased progesterone biosynthesis. Use of chemical inhibitors to treat placental stress caused by pathogens has potential to stabilize the production of progesterone. The study reveals that inhibiting mitochondrial fragmentation and reducing activity of stress kinase protein kinase R in syncytiotrophoblasts leads to an increase in progesterone synthesis when exposed to lipopolysaccharide and polyinosinic:polycytidylic acid.


Assuntos
Placenta , Progesterona , Gravidez , Feminino , Humanos , Placenta/metabolismo , Progesterona/metabolismo , Dinâmica Mitocondrial/fisiologia , Lipopolissacarídeos/farmacologia , 2-Aminopurina/metabolismo , 2-Aminopurina/farmacologia , Chaperonina 60/metabolismo , Proteínas Quinases/metabolismo , Poli C/metabolismo , Poli C/farmacologia
9.
Analyst ; 148(11): 2482-2492, 2023 May 30.
Artigo em Inglês | MEDLINE | ID: mdl-37159025

RESUMO

Target double-stranded DNA (dsDNA) or single-stranded DNA (ssDNA) can activate the trans-cleavage activity of the CRISPR/Cas12a, cutting the surrounding non-target ssDNA arbitrarily. In a typical CRISPR/Cas12a system, this non-target ssDNA, with a fluorescent tag and its quencher incorporated at both ends (ssDNA-FQ), is usually used as the reporter. Here, a 2-aminopurine probe (T-pro 4), made by inserting four 2-APs in non-target ssDNA, was screened for using as a reporter in the CRISPR/Cas12a system. Compared with ssDNA-FQ, each 2-AP probe is cleaved by the activated CRISPR/Cas12a system, multi-unit signals are generated. Therefore, the CRISPR/Cas12a system using the 2-AP probe as a reporter may be more sensitive than the CRISPR/Cas12a system which uses ssDNA-FQ as the reporter. We achieved ssDNA detection at as little as 10-11 M using the 2-AP probe as the reporter in the CRISPR/Cas12a system. Compared to the CRISPR/Cas12a system using ssDNA-FQ as the reporter, its sensitivity increased by an order of magnitude. Furthermore, the method that combines PCR and the 2-AP-probe-mediated CRISPR/Cas12a system can detect goat pox virus (GTPV) down to 8.35 × 10-2 copies per µL, 10 times lower than the method that combines PCR and the ssDNA-FQ-mediated CRISPR/Cas12a system. These results indicate that the CRISPR/Cas12a system using the screened 2-AP probe as a reporter has potential in highly sensitive detection of viruses.


Assuntos
2-Aminopurina , Técnicas Biossensoriais , Sistemas CRISPR-Cas/genética , DNA de Cadeia Simples/genética , Corantes , Reação em Cadeia da Polimerase
10.
J Phys Chem Lett ; 14(18): 4313-4321, 2023 May 11.
Artigo em Inglês | MEDLINE | ID: mdl-37130045

RESUMO

The level of interest in probing the strength of noncovalent interactions in DNA duplexes is high, as these weak forces dictate the range of suprastructures the double helix adopts under different conditions, in turn directly impacting the biological functions and industrial applications of duplexes that require making and breaking them to access the genetic code. However, few experimental tools can measure these weak forces embedded within large biological suprastructures in the native solution environment. Here, we develop experimental methods for detecting the presence of a single noncovalent interaction [a hydrogen bond (H-bond)] within a large DNA duplex in solution and measure its formation enthalpy (ΔHf). We report that introduction of a H-bond into the TC2═O group from the noncanonical nucleobase 2-aminopurine produces an expected decrease ∼10 ± 0.76 cm-1 (from ∼1720 cm-1 in Watson-Crick to ∼1710 cm-1 in 2-aminopurine), which correlates with an enthalpy of ∼0.93 ± 0.066 kcal/mol for this interaction.


Assuntos
2-Aminopurina , DNA , Temperatura , Conformação de Ácido Nucleico , Ligação de Hidrogênio , Termodinâmica , DNA/química , Análise Espectral
11.
Methods Mol Biol ; 2651: 105-113, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36892762

RESUMO

The left-handed Z-DNA is surrounded by right-handed canonical B-DNA, and thus the junction between B- and Z-DNA has been occurred during temporal Z-DNA formation in the genome. The base extrusion structure of the BZ junction may help detect Z-DNA formation in DNAs. Here we describe the BZ junction structural detection by using 2-aminopurine (2AP) fluorescent probe. BZ junction formation can be measured in solution by this method.


Assuntos
DNA de Forma B , DNA Forma Z , DNA/genética , 2-Aminopurina/química , Replicação do DNA , Conformação de Ácido Nucleico
12.
Methods Mol Biol ; 2568: 13-23, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-36227559

RESUMO

Structural analyses of large, complex noncoding RNAs continue to lag behind their rapid discovery and functional descriptions. Site-specifically incorporated, minimally invasive fluorescent probes such as 2-aminopurine (2AP) and pyrrolo-cytosine (PyC) have provided essential complementary information about local RNA structure, conformational dynamics, and interactions. Here I describe a protocol that benchmarks and correlates local RNA conformations with their respective fluorescence lifetimes, as a general technique that confers key advantages over fluorescence intensity-based methods. The observation that fluorescence lifetimes are more sensitive to local structures than sequence contexts suggests broad utility across diverse RNA and ribonucleoprotein systems.


Assuntos
2-Aminopurina , RNA , 2-Aminopurina/química , Fluorescência , Corantes Fluorescentes/química , Conformação de Ácido Nucleico , RNA/química , Ribonucleoproteínas , Espectrometria de Fluorescência/métodos
13.
Org Lett ; 24(33): 6111-6116, 2022 08 26.
Artigo em Inglês | MEDLINE | ID: mdl-35973215

RESUMO

We report a simple, postsynthetic strategy for synthesis of oligonucleotides containing 2,6-diaminopurine nucleotides and 2-aminoadenine conjugates using 2-fluoro-6-amino-adenosine. The strategy allows introduction of 2,6-diaminopurine and other 2-amino group-containing ligands. The strongly electronegative 2-fluoro deactivates 6-NH2 obviating the need for any protecting group on adenine, and simple aromatic nucleophilic substitution of fluorine makes reaction with aqueous NH3 or R-NH2 feasible at the 2-position.


Assuntos
2-Aminopurina , Oligonucleotídeos , 2-Aminopurina/análogos & derivados , Adenina
14.
J Hazard Mater ; 440: 129712, 2022 10 15.
Artigo em Inglês | MEDLINE | ID: mdl-35952430

RESUMO

Based on the high recognition ability and flexible programmability of GR5 DNAzyme, two fluorescent biosensors were engineered for amplified detection of Pb2+ via incorporating Ti3C2TX MXenes and embedding 2-aminopurine (2-AP), respectively. The quencher-required approach relied on the DNA affinity and fluorescence quenching ability of Ti3C2TX MXenes. Benefiting from the low background signal modulated by Ti3C2TX MXenes, the sensitive determination of Pb2+ was achieved in the linear range of 0.2-10 ng mL-1 with the limit of detection (LOD) of 0.05 ng mL-1. The quencher-free approach combined the fluorescent trait of 2-AP embedded in DNA structure, and the RNA cleavage-propelled digestion process of Exonuclease I (Exo I) for signal amplification, indicating the sensitive detection of Pb2+ with the LOD as low as 0.02 ng mL-1 in the linear range of 0.1-10 ng mL-1. Both DNAzyme assays exhibited simple procedures, favorable specificity, rapid analysis, and satisfactory application in standard reference materials (lead in drinking water) and spiked water samples. The two fluorescent biosensors established in this work would not only provide theoretic fundament for DNA adsorption of Ti3C2TX MXenes and the design of 2-AP-embedded DNAzyme assays, but also hold a great potential for on-site monitoring of lead pollution in water samples.


Assuntos
Técnicas Biossensoriais , DNA Catalítico , Água Potável , 2-Aminopurina/análise , Técnicas Biossensoriais/métodos , DNA/química , DNA Catalítico/química , Água Potável/análise , Chumbo/análise , Limite de Detecção , Clivagem do RNA
15.
J Phys Chem Lett ; 13(34): 8010-8018, 2022 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-35984918

RESUMO

RNA plays a critical role in many biological processes, and the structures it adopts are intimately linked to those functions. Among many factors that contribute to RNA folding, van der Waals interactions between adjacent nucleobases stabilize structures in which the bases are stacked on top of one another. Here, we utilize fluorescence-detected circular dichroism spectroscopy (FDCD) to investigate base-stacking heterogeneity in RNA labeled with the fluorescent adenine analogue 2-aminopurine (2-AP). Comparison of standard (transmission-detected) CD and FDCD spectra reveals that in dinucleotides, 2-AP fluorescence is emitted almost exclusively by unstacked molecules. In a trinucleotide, some fluorescence is emitted by a population of stacked and highly quenched molecules, but more than half originates from a minor ∼10% population of unstacked molecules. The combination of FDCD and standard CD measurements reveals the prevalence of stacked and unstacked conformational subpopulations as well as their relative fluorescence quantum yields.


Assuntos
2-Aminopurina , RNA , 2-Aminopurina/química , Dicroísmo Circular , Conformação de Ácido Nucleico , RNA/química , Espectrometria de Fluorescência
16.
Neurotherapeutics ; 19(4): 1381-1400, 2022 07.
Artigo em Inglês | MEDLINE | ID: mdl-35655111

RESUMO

Double-stranded RNA (dsRNA)-activated kinase (PKR) is an important component in inflammation and immune dysfunction. However, the role of PKR in neuropathic pain remains unclear. Here, we showed that lumbar 5 spinal nerve ligation (SNL) led to a significant increase in the level of phosphorylated PKR (p-PKR) in both the dorsal root ganglia (DRG) and spinal dorsal horn. Images of double immunofluorescence staining revealed that p-PKR was expressed in myelinated A-fibers, unmyelinated C-fibers, and satellite glial cells in the DRG. In the dorsal horn, p-PKR was located in neuronal cells, astrocytes, and microglia. Data from behavioral tests showed that intrathecal (i.t.) injection of 2-aminopurine (2-AP), a specific inhibitor of PKR activation, and PKR siRNA prevented the reductions in PWT and PWL following SNL. Established neuropathic pain was also attenuated by i.t. injection of 2-AP and PKR siRNA, which started on day 7 after SNL. Prior repeated i.t. injections of PKR siRNA prevented the SNL-induced degradation of IκBα and IκBß in the cytosol and the nuclear translocation of nuclear factor κB (NF-κB) p65 in both the DRG and dorsal horn. Moreover, the SNL-induced increase in interleukin-1ß (IL-1ß), interleukin-6 (IL-6), and tumor necrosis factor-alpha (TNF-α) production was diminished by this treatment. Collectively, these results suggest that peripheral nerve injury-induced PKR activation via NF-κB signaling-regulated expression of proinflammatory cytokines in the DRG and dorsal horn contributes to the pathogenesis of neuropathic pain. Our findings suggest that pharmacologically targeting PKR might be an effective therapeutic strategy for the treatment of neuropathic pain.


Assuntos
Neuralgia , Traumatismos dos Nervos Periféricos , Ratos , Animais , Gânglios Espinais , Traumatismos dos Nervos Periféricos/complicações , Traumatismos dos Nervos Periféricos/metabolismo , Interleucina-1beta/metabolismo , Fator de Necrose Tumoral alfa/metabolismo , RNA de Cadeia Dupla/metabolismo , RNA de Cadeia Dupla/farmacologia , RNA de Cadeia Dupla/uso terapêutico , Inibidor de NF-kappaB alfa/metabolismo , NF-kappa B/metabolismo , Interleucina-6/metabolismo , Proteínas Quinases/metabolismo , RNA Interferente Pequeno/genética , RNA Interferente Pequeno/metabolismo , 2-Aminopurina/metabolismo , 2-Aminopurina/farmacologia , 2-Aminopurina/uso terapêutico , Hiperalgesia/metabolismo , Ratos Sprague-Dawley , Neuralgia/tratamento farmacológico , Corno Dorsal da Medula Espinal/metabolismo
17.
ACS Chem Biol ; 17(7): 1672-1676, 2022 07 15.
Artigo em Inglês | MEDLINE | ID: mdl-35700389

RESUMO

2,6-Diaminopurine (Z) is a naturally occurring adenine (A) analog that bacteriophages employ in place of A in their genetic alphabet. Recent discoveries of biogenesis pathways of Z in bacteriophages have stimulated substantial research interest in this DNA modification. Here, we systematically examined the effects of Z on the efficiency and fidelity of DNA transcription. Our results showed that Z exhibited no mutagenic yet substantial inhibitory effects on transcription mediated by purified T7 RNA polymerase and by human RNA polymerase II in HeLa nuclear extracts and in human cells. A structurally related adenine analog, 2-aminopurine (2AP), strongly blocked T7 RNA polymerase but did not impede human RNA polymerase II in vitro or in human cells, where no mutant transcript could be detected. The lack of mutagenic consequence and the presence of a strong blockage effect of Z on transcription suggest a role of Z in transcriptional regulation. Z is also subjected to removal by transcription-coupled nucleotide-excision repair (TC-NER), but not global-genome NER in human cells. Our findings provide new insight into the effects of Z on transcription and its potential biological functions.


Assuntos
2-Aminopurina , RNA Polimerase II , 2-Aminopurina/análogos & derivados , 2-Aminopurina/farmacologia , DNA , Reparo do DNA , Humanos , RNA Polimerase II/metabolismo , Transcrição Gênica
18.
Chembiochem ; 23(12): e202200127, 2022 06 20.
Artigo em Inglês | MEDLINE | ID: mdl-35468257

RESUMO

Glucose is the most important analyte for biosensors. Recently a DNA aptamer was reported allowing binding-based detection. However, due to a relatively weak binding affinity, it is difficult to perform binding assays to understand the property of this aptamer. In this work, we replaced the only adenine base in the aptamer binding pocket with a 2-aminopurine (2AP) and used fluorescence spectroscopy to study glucose binding. In the selection buffer, glucose increased the 2AP fluorescence with a Kd of 15.0 mM glucose, which was comparable with the 10 mM Kd previously reported using the strand displacement assay. The binding required two Na+ ions or one Mg2+ that cannot be replaced by Li+ or K+ . The binding was weaker at higher temperature and its van't Hoff plot indicated enthalpy-driven binding. While other monosaccharides failed to achieve saturated binding even at high concentrations, two glucose-containing disaccharides, namely trehalose and sucrose, reached a similar fluorescence level as glucose although with over 10-fold higher Kd values. Detection limits in both the selection buffer (0.9 mM) and in artificial interstitial fluids (6.0 mM) were measured.


Assuntos
2-Aminopurina , Aptâmeros de Nucleotídeos , 2-Aminopurina/química , Aptâmeros de Nucleotídeos/química , Fluorescência , Glucose , Íons , Conformação de Ácido Nucleico , Espectrometria de Fluorescência/métodos
19.
DNA Repair (Amst) ; 111: 103286, 2022 03.
Artigo em Inglês | MEDLINE | ID: mdl-35124371

RESUMO

DNA interstrand cross-links (ICLs) are lesions with a covalent bond formed between DNA strands. ICLs are extremely toxic to cells because they prevent the separation of the two strands, which are necessary for the genetic interpretation of DNA. ICLs are repaired via Fanconi anemia and replication-independent pathways. The formation of so-called unhooked repair intermediates via a dual strand incision flanking the ICL site on one strand is an essential step in nearly all ICL repair pathways. Recently, ICLs derived from endogenous sources, such as those from ubiquitous DNA lesions, abasic (AP) sites, have emerged as an important class of ICLs. Despite the earlier efforts in preparing AP-ICLs in high yield using nucleotide analogs, little information is available for preparing AP-ICL unhooked intermediates with varying lengths of overhangs. In this study, we devise a simple approach to prepare model ICL unhooked intermediates derived from AP sites. We exploited the alkaline lability of ribonucleotides (rNMPs) and the high cross-linking efficiency between an AP lesion and a nucleotide analog, 2-aminopurine, via reductive amination. We designed chimeric DNA/RNA substrates with rNMPs flanking the cross-linking residue (2-aminopurine) to facilitate subsequent strand cleavage under our optimized conditions. Mass spectrometric analysis and primer extension assays confirmed the structures of ICL substrates. The method is straightforward, requires no synthetic chemistry expertise, and should be broadly accessible to all researchers in the DNA repair community. For step-by-step descriptions of the method, please refer to the companion manuscript in MethodsX.


Assuntos
2-Aminopurina , Ribonucleotídeos , Reagentes de Ligações Cruzadas/química , DNA/metabolismo , Dano ao DNA , Reparo do DNA , Replicação do DNA
20.
Phys Chem Chem Phys ; 24(7): 4204-4211, 2022 Feb 16.
Artigo em Inglês | MEDLINE | ID: mdl-35119441

RESUMO

Ultraviolet radiation (UVR) from the sun is essential for the prebiotic syntheses of nucleotides, but it can also induce photolesions such as the cyclobutane pyrimidine dimers (CPDs) to RNA or DNA oligonucleotide in prebiotic Earth. 2,6-Diaminopurine (26DAP) has been proposed to repair CPDs in high yield under prebiotic conditions and be a key component in enhancing the photostability of higher-order prebiotic DNA structures. However, its electronic relaxation pathways have not been studied, which is necessary to know whether 26DAP could have survived the intense UV fluxes of the prebiotic Earth. We investigate the electronic relaxation mechanism of both 26DAP and its 2'-deoxyribonucleoside (26DAP-d) in aqueous solution using steady-state and femtosecond transient absorption measurements that are complemented with electronic-structure calculations. The results demonstrate that both purine derivatives are significantly photostable to UVR. It is shown that upon excitation at 287 nm, the lowest energy 1ππ* state is initially populated. The population then branches following two relaxation coordinates in the 1ππ* potential energy surface, which are identified as the C2- and C6-relaxation coordinates. The population following the C6-coordinate internally converts to the ground state nonradiatively through a nearly barrierless conical intersection within 0.7 ps in 26DAP or within 1.1 ps in 26DAP-d. The population that follows the C2-relaxation coordinate decays back to the ground state by a combination of nonradiative internal conversion via a conical intersection and fluorescence emission from the 1ππ* minimum in 43 ps and 1.8 ns for the N9 and N7 tautomers of 26DAP, respectively, or in 70 ps for 26DAP-d. Fluorescence quantum yields of 0.037 and 0.008 are determined for 26DAP and 26DAP-d, respectively. Collectively, it is demonstrated that most of the excited state population in 26DAP and 26DAP-d decays back to the ground state via both nonradiative and radiative relaxation pathways. This result lends support to the idea that 26DAP could have accumulated in large enough quantities during the prebiotic era to participate in the formation of prebiotic RNA or DNA oligomers and act as a key component in the protection of the prebiotic genetic alphabet.


Assuntos
Dímeros de Pirimidina , Raios Ultravioleta , 2-Aminopurina/análogos & derivados , Teoria Quântica , Análise Espectral
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