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1.
Angew Chem Int Ed Engl ; : e202407838, 2024 Jun 11.
Artigo em Inglês | MEDLINE | ID: mdl-38860437

RESUMO

The inherent chiral structures of DNA serve as attractive scaffolds to construct DNA hybrid catalysts for valuable enantioselective transformations. Duplex and G-quadruplex DNA-based enantioselective catalysis has made great progress, yet novel design strategies of DNA hybrid catalysts are highly demanding and atomistic analysis of active centers is still challenging. DNA i-motif structures could be finely tuned by different cytosine-cytosine base pairs, providing a new platform to design DNA catalysts. Herein, we found that a human telomeric i-motif DNA containing cytosine-silver(I)-cytosine (C-Ag+-C) base pairs interacting with Cu(II) ions (i-motif DNA(Ag+)/Cu2+) could catalyze Diels-Alder reactions with full conversions and up to 95% enantiomeric excess. As characterized by various physicochemical techniques, the presence of Ag+ is proved to replace the protons in hemiprotonated cytosine-cytosine (C:C+) base pairs and stabilize the DNA i-motif to allow the acceptance of Cu(II) ions. The i-motif DNA(Ag+)/Cu2+ catalyst shows about 8-fold rate acceleration compared with DNA and Cu2+. Based on DNA mutation experiments, thermodynamic studies and density function theory calculations, the catalytic center of Cu(II) ion is proposed to be located in a specific loop region via binding to one nitrogen-7 atom of an unpaired adenine and two phosphate-oxygen atoms from nearby deoxythymidine monophosphate and deoxyadenosine monophosphate, respectively.

2.
Anal Chem ; 96(26): 10835-10840, 2024 Jul 02.
Artigo em Inglês | MEDLINE | ID: mdl-38889097

RESUMO

G-quadruplex (G4) DNA is considered as a prospective therapeutic target due to its potential biological significance. To understand G4 biological roles and function, a G4-specific fluorescent probe is necessary. However, it is difficult for versatile G4 to precisely recognize without perturbing their folding dynamics. Herein, we reported that flavone P0 can be a fluorescent probe for G4 DNA-specific recognition and have developed a highly selective detection of K+ ion by dimeric G4/P0 system. When comparing various nucleic acid structures, including G4, i-motif, ss/ds-DNA, and triplex, an apparent fluorescence enhancement is observed in the presence of G4 DNA for 85-fold, but only 8-fold for non-G4 DNA. Furthermore, based on fluorescent probe of flavone P0 for G4 DNA screening, the noncovalent dimeric G4/P0 system is exploited as a K+ sensor, that selectively responds to K+ with a 513-fold fluorescence enhancement and a detection range for K+ ion concentration from 0 to 500 mM. This K+ sensor also has a remarkably anti-interference ability for other metal cations, especially for a high concentration of Na+. These results have demonstrated that flavone P0 is an efficient tool for monitoring G-quadruplex DNA and endows flavone P0 with bioanalytical and medicinal applications.


Assuntos
DNA , Flavonas , Corantes Fluorescentes , Quadruplex G , Potássio , Flavonas/química , Corantes Fluorescentes/química , Potássio/química , Potássio/análise , DNA/química , Espectrometria de Fluorescência
3.
Chem Commun (Camb) ; 60(9): 1172-1175, 2024 Jan 25.
Artigo em Inglês | MEDLINE | ID: mdl-38193540

RESUMO

We found that under oxidative stress conditions, the coexistence of human telomeric DNA (HT-DNA) and a copper-terpyridine metallodrug can accelerate dopamine oxidation. The unwinding of HT-DNA from a duplex to cytosine-rich (C-rich) and guanine-rich (G-rich) single strands promotes dopamine oxidation in a general order of C-rich > G-rich > duplex. Along with dopamine oxidation, HT-DNA also undergoes severe damage.


Assuntos
Cobre , Dopamina , Humanos , DNA/metabolismo , Oxirredução , Guanina , Citosina , Dano ao DNA
4.
Biochemistry ; 60(48): 3707-3713, 2021 12 07.
Artigo em Inglês | MEDLINE | ID: mdl-34757721

RESUMO

G-quadruplex (G4) ligand-induced DNA damage has been involved in many physiological functions of cells. Herein, cationic porphyrin (TMPyP4)-mediated DNA oxidation damage was investigated aiming at mitochondrial G4 DNA (mt9438) and its structural analogue of the thrombin-binding aptamer (TBA). TMPyP4 is found to stabilize TBA G4 but destabilize mt9438. For two resulting DNA-TMPyP4 assemblies, the distinct light-induced singlet oxygen (1O2) generation and the subsequent DNA damage were found. For mt9438-TMPyP4, a slower 1O2-induced DNA damage takes place and results in the formation of DNA aggregation. In contrast, 1O2 tends to promote DNA unfolding in a relatively faster rate for TBA-TMPyP4. Despite of such distinct DNA damage behavior, UV resonance Raman spectra reveal that for both mt9438-TMPyP4 and TBA-TMPyP4 the DNA damage commonly stems from the guanine-specific oxidation. Our results clearly indicate that the ligand-mediated DNA damage is strongly dependent on the initial interplay between DNA and the ligand.


Assuntos
Aptâmeros de Nucleotídeos/química , Quadruplex G/efeitos dos fármacos , Estresse Oxidativo/efeitos dos fármacos , Porfirinas/química , Aptâmeros de Nucleotídeos/genética , Cátions/química , Cátions/farmacologia , Dano ao DNA/efeitos dos fármacos , Ligantes , Porfirinas/genética , Porfirinas/farmacologia
5.
Chem Sci ; 12(22): 7918-7923, 2021 May 11.
Artigo em Inglês | MEDLINE | ID: mdl-34168845

RESUMO

The assembly of DNA with metal-complex cofactors can form promising biocatalysts for asymmetric reactions, although catalytic performance is typically limited by low enantioselectivities and stereo-control remains a challenge. Here, we engineer G-quadruplex-based DNA biocatalysts for an asymmetric cyclopropanation reaction, achieving enantiomeric excess (eetrans) values of up to +91% with controllable stereoinversion, where the enantioselectivity switches to -72% eetrans through modification of the Fe-porphyrin cofactor. Complementary circular dichroism, nuclear magnetic resonance, and fluorescence titration experiments show that the porphyrin ligand of the cofactor participates in the regulation of the catalytic enantioselectivity via a synergetic effect with DNA residues at the active site. These findings underline the important role of cofactor modification in DNA catalysis and thus pave the way for the rational engineering of DNA-based biocatalysts.

6.
Anal Chem ; 93(18): 6907-6912, 2021 05 11.
Artigo em Inglês | MEDLINE | ID: mdl-33929188

RESUMO

Potassium ion (K+) plays a crucial role in biological systems, such as maintaining cellular processes and causing diseases. However, specifically, the detection of K+ is extremely challenging because of the coexistence of the chemically similar ion of Na+ under physiological conditions. In this work, a K+ specific biosensor is constructed on the basis of a dimerized G-quadruplex (GQ) DNA, which is promoted by K+, and the enzymatic activity of the resulting DNAzyme depends on the concentration of the K+. The K+ in a 1-200 mM concentration range can be selectively detected by visual color, UV-Vis absorbance or fluorescence even if the concentration of the accompanying Na+ is up to 140 mM at an ambient condition up to 45 °C. In addition, this system can also be used to selectively detect NH4+ in a 5-200 mM concentration range. This dimerized DNAzyme offers a new type of biosensor with a potential application in the biological system.


Assuntos
Técnicas Biossensoriais , DNA Catalítico , Quadruplex G , DNA Catalítico/metabolismo , Hemina , Íons , Potássio
7.
Cerebellum ; 20(4): 584-595, 2021 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-33555544

RESUMO

Accumulating evidence demonstrates that the cerebellum is involved in a variety of cognitive functions. Recently, impaired auditory-motor integration for vocal control has been identified in patients with cerebellar degeneration, characterized by abnormally enhanced vocal compensations for pitch perturbations. However, the causal relationship between the cerebellum and auditory feedback during vocal production remains unclear. By applying anodal transcranial direct current stimulation (a-tDCS) over right cerebellum, the present study investigated cerebellar contributions to auditory-motor processing of feedback errors during vocal pitch regulation. Twenty young adults participated in a frequency-altered-feedback (FAF) task, in which they vocalized vowel sounds and heard their voice unexpectedly pitch-shifted by ± 50 or ± 200 cents. Active or sham cerebellar a-tDCS was applied either prior to or during the FAF task. Compensatory vocal responses to pitch perturbations were measured and compared across the conditions. Active cerebellar a-tDCS led to significantly larger and slower vocal compensations for pitch perturbations than sham stimulation. Moreover, this modulatory effect was observed regardless of the timing of cerebellar a-tDCS as well as the size and direction of the pitch perturbation. These findings provide the first causal evidence that the cerebellum is essentially involved in auditory feedback control of vocal production. Enhanced and slowed vocal compensations caused by cerebellar a-tDCS may be related to its inhibition on the prefrontal cortex that exerts inhibitory control over vocal compensation behavior, suggesting the importance of the cerebrocerebellar connections in this feedback control process.


Assuntos
Estimulação Transcraniana por Corrente Contínua , Voz , Cerebelo , Retroalimentação , Retroalimentação Sensorial/fisiologia , Humanos , Voz/fisiologia , Adulto Jovem
9.
Chem Sci ; 11(33): 8846-8853, 2020 Aug 12.
Artigo em Inglês | MEDLINE | ID: mdl-34123138

RESUMO

While many protein enzymes exert their functions through multimerization, which improves both selectivity and activity, this has not yet been demonstrated for other naturally occurring catalysts. Here, we report a multimerization effect applied to catalytic DNAs (or DNAzymes) and demonstrate that the enzymatic efficiency of G-quadruplexes (GQs) in interaction with the hemin cofactor is remarkably enhanced by homodimerization. The resulting non-covalent dimeric GQ-DNAzyme system provides hemin with a structurally defined active site in which both the cofactor (hemin) and the oxidant (H2O2) are activated. This new biocatalytic system efficiently performs peroxidase- and peroxygenase-type biotransformations of a broad range of substrates, thus providing new perspectives for biotechnological application of GQs.

10.
Angew Chem Int Ed Engl ; 59(9): 3444-3449, 2020 02 24.
Artigo em Inglês | MEDLINE | ID: mdl-31825550

RESUMO

The diverse secondary structures of nucleic acids are emerging as attractive chiral scaffolds to construct artificial metalloenzymes (ArMs) for enantioselective catalysis. DNA-based ArMs containing duplex and G-quadruplex scaffolds have been widely investigated, yet RNA-based ArMs are scarce. Here we report that a cyclic dinucleotide of c-di-AMP and Cu2+ ions assemble into an artificial metalloribozyme (c-di-AMP⋅Cu2+ ) that enables catalysis of enantioselective Friedel-Crafts reactions in aqueous media with high reactivity and excellent enantioselectivity of up to 97 % ee. The assembly of c-di-AMP⋅Cu2+ gives rise to a 20-fold rate acceleration compared to Cu2+ ions. Based on various biophysical techniques and density function theory (DFT) calculations, a fine coordination structure of c-di-AMP⋅Cu2+ metalloribozyme is suggested in which two c-di-AMP form a dimer scaffold and the Cu2+ ion is located in the center of an adenine-adenine plane through binding to two N7 nitrogen atoms and one phosphate oxygen atom.


Assuntos
Reação de Cicloadição , Fosfatos de Dinucleosídeos/química , Água/química , Catálise , Cobre/química , Teoria da Densidade Funcional , Dimerização , Fosfatos de Dinucleosídeos/metabolismo , Quadruplex G , Cinética , Metaloproteínas/química , Metaloproteínas/metabolismo , Estereoisomerismo , Especificidade por Substrato
11.
J Phys Chem B ; 123(37): 7794-7800, 2019 09 19.
Artigo em Inglês | MEDLINE | ID: mdl-31335146

RESUMO

Phosphorylation of glucose is the prime step in sugar metabolism and energy storage. Two key glucose phosphates are involved, that is, glucose 6-phosphate (G6P) and α-glucose 1-phosphate (αG1P). The chiral conformation of glucose, G6P, and αG1P plays an essential role in enzyme-mediated conversions. However, few techniques were able to give a direct view of the conformational changes from glucose to G6P and αG1P. Here, Raman optical activity (ROA) was used to elucidate the stereochemical evolution of glucose upon phosphorylation. ROA was found to be extremely sensitive to different phosphorylation sites. A characteristic ROA marker of (+)980 cm-1, originated from the phosphate group symmetric stretching vibration, is observed for αG1P with phosphorylation at chiral C1, while no corresponding ROA signal for G6P with phosphorylation at achiral C6 is observed. Phosphorylation-induced gauch-gauch (gg)/gauch-trans (gt) rotamer distribution changes can be sensitively probed by the sign of the ROA band around 1460 cm-1. A positive ROA band at 1465 cm-1 of glucose corresponds to a higher gt ratio, while a negative band at 1455 cm-1 of G6P suggests a dominant gg population, and the disappearance of this ROA band for αG1P indicates a nearly balanced gg/gt distribution. Meanwhile, the phosphorylation at C6 and C1 could cause dramatic reduction of the conformational flexibility of the adjacent C4-OH and C2-OH, respectively. These stereochemical changes revealed by ROA spectra offer a structural basis on the understanding of sugar phosphorylation from the perspective of chirality.


Assuntos
Glucose/metabolismo , Configuração de Carboidratos , Glucose/química , Rotação Ocular , Fosforilação , Análise Espectral Raman , Estereoisomerismo
12.
Sensors (Basel) ; 20(1)2019 Dec 30.
Artigo em Inglês | MEDLINE | ID: mdl-31906035

RESUMO

The widespread application of networks is providing a better platform for the development of society and technology. With the expansion of the scope of network applications, many issues need to be solved. Among them, the maximization of utility and the improvement of security have attracted much attention. Many existing attacks mean the network faces security challenges. The concept of trust should be considered to address these security issues. Meanwhile, the utility of the network, including efficiency, profit, welfare, etc., are concerns that should be maximized. Over the past decade, the concepts of game and trust have been introduced to various types of networks. However, there is a lack of research effort on several key points in distributed networks, which are critical to the information transmission of distributed networks, such as expelling malicious nodes quickly and accurately and finding equilibrium between energy assumption and high transmission rate. The purpose of this paper is to give a holistic overview of existing research on trust and game theory in networks. We analyzed that network utility can be maximized in terms of effectiveness, profits, and security. Moreover, a possible research agenda is proposed to promote the application and development of game theory and trust for improving security and maximizing utility.

13.
Nucleic Acids Res ; 46(18): 9264-9275, 2018 10 12.
Artigo em Inglês | MEDLINE | ID: mdl-30184167

RESUMO

G-quadruplexes are unusual DNA and RNA secondary structures ubiquitous in a variety of organisms including vertebrates, plants, viruses and bacteria. The folding topology and stability of intramolecular G-quadruplexes are determined to a large extent by their loops. Loop permutation is defined as swapping two or three of these regions so that intramolecular G-quadruplexes only differ in the sequential order of their loops. Over the past two decades, both length and base composition of loops have been studied extensively, but a systematic study on the effect of loop permutation has been missing. In the present work, 99 sequences from 21 groups with different loop permutations were tested. To our surprise, both conformation and thermal stability are greatly dependent on loop permutation. Loop permutation actually matters as much as loop length and base composition on G-quadruplex folding, with effects on Tm as high as 17°C. Sequences containing a longer central loop have a high propensity to adopt a stable non-parallel topology. Conversely, sequences containing a short central loop tend to form a parallel topology of lower stability. In addition, over half of interrogated sequences were found in the genomes of diverse organisms, implicating their potential regulatory roles in the genome or as therapeutic targets. This study illustrates the structural roles of loops in G-quadruplex folding and should help to establish rules to predict the folding pattern and stability of G-quadruplexes.


Assuntos
DNA/química , Quadruplex G , Conformação de Ácido Nucleico , Termodinâmica , Algoritmos , Sequência de Bases , Dicroísmo Circular
14.
Chembiochem ; 19(20): 2233-2240, 2018 10 18.
Artigo em Inglês | MEDLINE | ID: mdl-30070000

RESUMO

Interactions of copper(II)-bipyridine cofactors and thioanisole substrate with human telomeric G-quadruplex DNA were studied by UV/Vis absorption, circular dichroism, and fluorescence quenching titration. Three copper(II)-bipyridine complexes are equivalently anchored to the G-quadruplex scaffold at all five fluorescently labeled sites. Thioanisole interacts with the DNA architecture at both the second loop and 3' terminus in the absence or presence of copper(II)-bipyridine complexes. These nonspecificities in the weak interactions of CuII complexes and thioanisole with G-quadruplex might explain why DNA only affords a modest enantioselectivity in the oxidation of thioanisole. These findings provide insights toward the construction of highly enantioselective DNA-based catalysts.


Assuntos
2,2'-Dipiridil , Complexos de Coordenação/química , Cobre , DNA , Sulfetos , 2,2'-Dipiridil/química , 2,2'-Dipiridil/metabolismo , Catálise , Dicroísmo Circular/métodos , Cobre/química , Cobre/metabolismo , DNA/química , DNA/metabolismo , Quadruplex G , Humanos , Oxirredução , Espectrometria de Fluorescência/métodos , Especificidade por Substrato , Sulfetos/química , Sulfetos/metabolismo , Telômero
15.
Biochimie ; 146: 20-27, 2018 Mar.
Artigo em Inglês | MEDLINE | ID: mdl-29158004

RESUMO

DNAzymes have been widely used in biosensors, asymmetric synthesis and pharmaceuticals. Typically, metal cofactor and substrate interact with DNA by supramolecular interactions in DNAzyme based asymmetric catalysis. However, binding positions of cofactor and substrate with DNA scaffold are not well understood, which is an obstacle to reveal the assembly and catalysis mechanisms of DNAzyme. Herein, we report a method of site-specific fluorescence quenching titration to elucidate the assembly and catalysis processes of a G-quadruplex based Diels-Alderase DNAzyme. Titration data indicate that cofactor Cu(II)-terpyridine stacked atop 5' and 3' external G-quartets with high and low binding affinities respectively, and induced the G-quadruplex to form a hybrid-1 topology. Substrate azachalcone interacted with 3' quartet exclusively, implicating that asymmetric Diels-Alder cycloaddition may occur at 3' G-quartet. In addition, enzyme kinetic analyses show that activity and enantioselectivity of the DNAzyme were substantially preserved after attaching the fluorophores. Overall, site-specific fluorescence quenching is a concise and efficient approach to probe the assembly processes of DNAzyme.


Assuntos
Chalcona/metabolismo , Coenzimas/metabolismo , Cobre/metabolismo , DNA Catalítico/química , DNA Catalítico/metabolismo , Quadruplex G , Cinética , Espectrometria de Fluorescência , Especificidade por Substrato
16.
Appl Spectrosc ; 71(9): 2211-2217, 2017 Sep.
Artigo em Inglês | MEDLINE | ID: mdl-28574281

RESUMO

Developing a high-sensitivity Raman optical activity (ROA) spectrometer has been regarded as one of the great challenges in chiral science and technology. Herein, we report our recent progress on the development of a short-wavelength ROA (sw-ROA) spectrometer with the excitation line at 457 nm, which shows obviously improved signal-to-noise (S/N) ratio compared with the currently available 532 nm ROA spectrometer. This could be ascribed to the fifth-power of frequency dependence for ROA intensity together with the potential advantage of avoiding fluorescence for most molecules. The required laser power at the sample for being able to obtain a reliable ROA spectrum is less than 150 milliwatts (mW) for most samples. In the case of neat S-α-pinene sample, the ROA signal can be acquired with the laser power at sample as low as 5 mW with the total exposure time of 5 min. The concentration of S-α-pinene sample can be reduced to 10% (v/v) by diluting with ethanol. These results demonstrate the great potential of sw-ROA (457 nm) working with decreased laser power, shortened acquisition time, and lower sample concentration. The applicability of sw-ROA (457 nm) has also been demonstrated by measuring representative chiral samples, including carbohydrates, amino acids, protein in aqueous solution, and chiral organic molecule in organic solvents.

17.
Biochim Biophys Acta Gen Subj ; 1861(8): 1913-1920, 2017 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-28533132

RESUMO

The structures of DNA G-quadruplexes are essential for their functions in vivo and in vitro. Our present study revealed that sequential order of the three G-quadruplex loops, that is, loop transposition, could be a critical factor to determinate the G-quadruplex conformation and consequently improved the catalytic function of G-quadruplex based DNAzyme. In the presence of 100mM K+, loop transposition induced one of the G-quadruplex isomers which shared identical loops but differed in the sequential order of loops into a hybrid topology while the others into predominately parallel topologies. 1D NMR spectroscopy and mutation analysis suggested that the hydrogen bonding from loops residues with nucleotides in flanking sequences may be responsible for the stabilization of the different conformations. A well-known DNAzyme consisting of G-quadruplex and hemin (Ferriprotoporphyrin IX chloride) was chosen to test the catalytic function. We found that the loop transposition could enhance the reaction rate obviously by increasing the hemin binding affinity to G-quadruplex. These findings disclose the relations between the loop transposition, G-quadruplex conformation and catalytic function of DNAzyme.


Assuntos
Biocatálise , DNA Catalítico/fisiologia , Quadruplex G , Hemina/metabolismo , Ligação de Hidrogênio
18.
Chem Commun (Camb) ; 52(62): 9644-7, 2016 Jul 26.
Artigo em Inglês | MEDLINE | ID: mdl-27359255

RESUMO

Enantioselective sulfoxidation reaction is achieved for the first time by a DNA metalloenzyme assembled with the human telomeric G-quadruplex DNA and Cu(ii)-4,4'-bimethyl-2,2'-bipyridine complex, and the mixed G-quadruplex architectures are responsible for the catalytic enantioselectivity and activity.


Assuntos
Biocatálise , Quadruplex G , Metaloproteínas/metabolismo , Sulfóxidos/metabolismo , Humanos , Metaloproteínas/química , Estrutura Molecular , Estereoisomerismo , Sulfóxidos/química
19.
Chem Commun (Camb) ; 51(67): 13174-7, 2015 Aug 28.
Artigo em Inglês | MEDLINE | ID: mdl-26192472

RESUMO

We report that K(+) and NH4(+) present different allosteric activation for higher-order human telomeric G-quadruplex DNA metalloenzyme. The obtained major endo products of Diels-Alder reaction can be switched from one preferred configuration in K(+) media (up to 92% ee) to its mirror configuration in NH4(+) media (up to -90% ee).


Assuntos
Compostos de Amônio/química , DNA Catalítico/química , Quadruplex G , Potássio/química , Humanos , Íons/química , Estereoisomerismo
20.
Chembiochem ; 16(4): 618-24, 2015 Mar 02.
Artigo em Inglês | MEDLINE | ID: mdl-25676722

RESUMO

Short human telomeric (HT) DNA sequences form single G-quadruplex (G4 ) units and exhibit structure-based stereocontrol for a series of reactions. However, for more biologically relevant higher-order HT G4 -DNAs (beyond a single G4 unit), the catalytic performances are unknown. Here, we found that higher-order HT G4 -DNA copper metalloenzymes (two or three G4 units) afford remarkably higher enantioselectivity (>90 % ee) and a five- to sixfold rate increase, compared to a single G4 unit, for the Diels-Alder reaction. Electron paramagnetic resonance (EPR) and enzymatic kinetic studies revealed that the distinct catalytic function between single and higher-order G4 -DNA copper metalloenzymes can be attributed to different Cu(II) coordination environments and substrate specificity. Our finding suggests that, like protein enzymes and ribozymes, higher-order structural organization is crucial for G4 -DNA-based catalysis.


Assuntos
DNA/química , DNA/metabolismo , Quadruplex G , Sequência de Bases , Catálise , Cobre/metabolismo , Reação de Cicloadição , Humanos , Cinética , Metaloproteínas/metabolismo , Estereoisomerismo , Especificidade por Substrato
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