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1.
Nature ; 613(7942): 187-194, 2023 01.
Artigo em Inglês | MEDLINE | ID: mdl-36544021

RESUMO

R-loops are RNA-DNA-hybrid-containing nucleic acids with important cellular roles. Deregulation of R-loop dynamics can lead to DNA damage and genome instability1, which has been linked to the action of endonucleases such as XPG2-4. However, the mechanisms and cellular consequences of such processing have remained unclear. Here we identify a new population of RNA-DNA hybrids in the cytoplasm that are R-loop-processing products. When nuclear R-loops were perturbed by depleting the RNA-DNA helicase senataxin (SETX) or the breast cancer gene BRCA1 (refs. 5-7), we observed XPG- and XPF-dependent cytoplasmic hybrid formation. We identify their source as a subset of stable, overlapping nuclear hybrids with a specific nucleotide signature. Cytoplasmic hybrids bind to the pattern recognition receptors cGAS and TLR3 (ref. 8), activating IRF3 and inducing apoptosis. Excised hybrids and an R-loop-induced innate immune response were also observed in SETX-mutated cells from patients with ataxia oculomotor apraxia type 2 (ref. 9) and in BRCA1-mutated cancer cells10. These findings establish RNA-DNA hybrids as immunogenic species that aberrantly accumulate in the cytoplasm after R-loop processing, linking R-loop accumulation to cell death through the innate immune response. Aberrant R-loop processing and subsequent innate immune activation may contribute to many diseases, such as neurodegeneration and cancer.


Assuntos
Citoplasma , DNA , Reconhecimento da Imunidade Inata , Ácidos Nucleicos Heteroduplexes , Estruturas R-Loop , RNA , Humanos , Apoptose , Citoplasma/imunologia , Citoplasma/metabolismo , DNA/química , DNA/imunologia , DNA Helicases/genética , DNA Helicases/metabolismo , Genes BRCA1 , Enzimas Multifuncionais/genética , Enzimas Multifuncionais/metabolismo , Mutação , Neoplasias , Ácidos Nucleicos Heteroduplexes/química , Ácidos Nucleicos Heteroduplexes/imunologia , Estruturas R-Loop/imunologia , RNA/química , RNA/imunologia , RNA Helicases/genética , RNA Helicases/metabolismo , Ataxias Espinocerebelares/genética
2.
Int J Mol Sci ; 21(20)2020 Oct 21.
Artigo em Inglês | MEDLINE | ID: mdl-33096752

RESUMO

Certain G-quadruplex forming guanine-rich oligonucleotides (GROs), including AS1411, are endowed with cancer-selective antiproliferative activity. They are known to bind to nucleolin protein, resulting in the inhibition of nucleolin-mediated phenomena. However, multiple nucleolin-independent biological effects of GROs have also been reported, allowing them to be considered promising candidates for multi-targeted cancer therapy. Herein, with the aim of optimizing AS1411 structural features to find GROs with improved anticancer properties, we have studied a small library of AS1411 derivatives differing in the sequence length and base composition. The AS1411 derivatives were characterized by using circular dichroism and nuclear magnetic resonance spectroscopies and then investigated for their enzymatic resistance in serum and nuclear extract, as well as for their ability to bind nucleolin, inhibit topoisomerase I, and affect the viability of MCF-7 human breast adenocarcinoma cells. All derivatives showed higher thermal stability and inhibitory effect against topoisomerase I than AS1411. In addition, most of them showed an improved antiproliferative activity on MCF-7 cells compared to AS1411 despite a weaker binding to nucleolin. Our results support the hypothesis that the antiproliferative properties of GROs are due to multi-targeted effects.


Assuntos
Antineoplásicos/química , Antineoplásicos/farmacologia , Aptâmeros de Nucleotídeos/química , Ácidos Nucleicos Heteroduplexes/química , Oligodesoxirribonucleotídeos/química , Antineoplásicos/farmacocinética , Apoptose/efeitos dos fármacos , Aptâmeros de Nucleotídeos/farmacologia , Dicroísmo Circular , DNA Topoisomerases Tipo I/metabolismo , Desoxirribonucleases/metabolismo , Ensaios de Seleção de Medicamentos Antitumorais/métodos , Estabilidade de Medicamentos , Feminino , Transferência Ressonante de Energia de Fluorescência , Humanos , Células MCF-7 , Espectroscopia de Ressonância Magnética , Oligodesoxirribonucleotídeos/farmacologia , Fosfoproteínas/metabolismo , Proteínas de Ligação a RNA/metabolismo , Ressonância de Plasmônio de Superfície , Timina/química , Inibidores da Topoisomerase I/química , Inibidores da Topoisomerase I/farmacologia , Nucleolina
3.
Biochem J ; 477(18): 3567-3582, 2020 09 30.
Artigo em Inglês | MEDLINE | ID: mdl-32886094

RESUMO

Recombination activating genes (RAGs), consisting of RAG1 and RAG2 have ability to perform spatially and temporally regulated DNA recombination in a sequence specific manner. Besides, RAGs also cleave at non-B DNA structures and are thought to contribute towards genomic rearrangements and cancer. The nonamer binding domain of RAG1 binds to the nonamer sequence of the signal sequence during V(D)J recombination. However, deletion of NBD did not affect RAG cleavage on non-B DNA structures. In the present study, we investigated the involvement of other RAG domains when RAGs act as a structure-specific nuclease. Studies using purified central domain (CD) and C-terminal domain (CTD) of the RAG1 showed that CD of RAG1 exhibited high affinity and specific binding to heteroduplex DNA, which was irrespective of the sequence of single-stranded DNA, unlike CTD which showed minimal binding. Furthermore, we show that ZnC2 of RAG1 is crucial for its binding to DNA structures as deletion and point mutations abrogated the binding of CD to heteroduplex DNA. Our results also provide evidence that unlike RAG cleavage on RSS, central domain of RAG1 is sufficient to cleave heteroduplex DNA harbouring pyrimidines, but not purines. Finally, we show that a point mutation in the DDE catalytic motif is sufficient to block the cleavage of CD on heteroduplex DNA. Therefore, in the present study we demonstrate that the while ZnC2 module in central domain of RAG1 is required for binding to non-B DNA structures, active site amino acids are important for RAGs to function as a structure-specific nuclease.


Assuntos
Proteínas de Homeodomínio/química , Ácidos Nucleicos Heteroduplexes/química , Motivos de Aminoácidos , Proteínas de Ligação a DNA/química , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Células HEK293 , Proteínas de Homeodomínio/genética , Proteínas de Homeodomínio/metabolismo , Humanos , Proteínas Nucleares/química , Proteínas Nucleares/genética , Proteínas Nucleares/metabolismo , Ácidos Nucleicos Heteroduplexes/genética , Ácidos Nucleicos Heteroduplexes/metabolismo , Domínios Proteicos , Relação Estrutura-Atividade , Recombinação V(D)J
4.
Nucleic Acids Res ; 47(15): 7798-7808, 2019 09 05.
Artigo em Inglês | MEDLINE | ID: mdl-31372639

RESUMO

Homologous recombination is a fundamental process in all living organisms that allows the faithful repair of DNA double strand breaks, through the exchange of DNA strands between homologous regions of the genome. Results of three decades of investigation and recent fruitful observations have unveiled key elements of the reaction mechanism, which proceeds along nucleofilaments of recombinase proteins of the RecA family. Yet, one essential aspect of homologous recombination has largely been overlooked when deciphering the mechanism: while ATP is hydrolyzed in large quantity during the process, how exactly hydrolysis influences the DNA strand exchange reaction at the structural level remains to be elucidated. In this study, we build on a previous geometrical approach that studied the RecA filament variability without bound DNA to examine the putative implication of ATP hydrolysis on the structure, position, and interactions of up to three DNA strands within the RecA nucleofilament. Simulation results on modeled intermediates in the ATP cycle bring important clues about how local distortions in the DNA strand geometries resulting from ATP hydrolysis can aid sequence recognition by promoting local melting of already formed DNA heteroduplex and transient reverse strand exchange in a weaving type of mechanism.


Assuntos
Trifosfato de Adenosina/química , DNA de Cadeia Simples/química , DNA/química , Recombinação Homóloga , Ácidos Nucleicos Heteroduplexes/química , Recombinases Rec A/química , Trifosfato de Adenosina/metabolismo , Bactérias/genética , Bactérias/metabolismo , Sítios de Ligação , DNA/genética , DNA/metabolismo , Quebras de DNA de Cadeia Dupla , DNA de Cadeia Simples/genética , DNA de Cadeia Simples/metabolismo , Hidrólise , Simulação de Dinâmica Molecular , Conformação de Ácido Nucleico , Ácidos Nucleicos Heteroduplexes/genética , Ácidos Nucleicos Heteroduplexes/metabolismo , Ligação Proteica , Conformação Proteica , Recombinases Rec A/genética , Recombinases Rec A/metabolismo
5.
Analyst ; 144(16): 4917-4924, 2019 Aug 21.
Artigo em Inglês | MEDLINE | ID: mdl-31313769

RESUMO

MicroRNAs (miRNAs) are attractive candidates for biomarkers for early cancer diagnosis, and play vital roles in physiological and pathological processes. In this work, we developed a colorimetric and fluorescent dual-mode sensor for miRNA detection based on the optical properties of gold nanoparticles (AuNPs) and the duplex-specific nuclease (DSN)-assisted signal amplification technique. In brief, FAM labelled hairpin probes (HPs) were immobilized on AuNPs, and fluorescence was efficiently quenched by the vicinity of the fluorophores to the AuNPs surface. In the presence of target miRNAs, the HPs could specifically hybridize with miRNAs and the DNA strand in the DNA/RNA heteroduplexes could be subsequently hydrolyzed by DSN. As a result, numbers of fluorophores were released into the solution, resulting in obvious fluorescence signal recovery. Meanwhile, the target miRNAs were able to participate in other hybridization reactions. With the DSN-assisted signal amplification technique, lots of gold nanoparticles were produced with short-chain DNA on their surface, which could aggregate in salt solution and result in a colorimetric detection. The proposed dual-mode strategy offers a sensitive, accurate and selective detection method for miRNAs. One reason is that the stem of the HPs was elaborately designed to avoid hydrolyzation by DSN under optimal conditions, which ensures a relatively low background and high sensitivity. The other is that the dual-mode strategy is more beneficial for enhancing the accuracy and reproducibility of the measurements. Moreover, the unique selective-cutting ability and single-base mismatch differentiation capability of the DSN also give rise to a satisfactory selectivity. This demonstrated that the developed method could quantitatively detect miR-21 down to 50 pM with a linear calibration range from 50 pM to 1 nM, and the analytical assay of target miRNAs in cell lysate samples revealed its great potential for application in biomedical research and clinical diagnostics.


Assuntos
Corantes/química , Endonucleases/química , Ouro/química , Nanopartículas Metálicas/química , MicroRNAs/análise , Técnicas Biossensoriais/métodos , Linhagem Celular , Colorimetria , DNA/química , Humanos , Limite de Detecção , Técnicas de Amplificação de Ácido Nucleico/métodos , Conformação de Ácido Nucleico , Ácidos Nucleicos Heteroduplexes/química , Hibridização de Ácido Nucleico , Reprodutibilidade dos Testes , Sensibilidade e Especificidade , Espectrometria de Fluorescência
6.
J Cell Biochem ; 120(12): 19915-19924, 2019 12.
Artigo em Inglês | MEDLINE | ID: mdl-31318096

RESUMO

Argonaute-2 (AGO2), a member of the Argonaute family, is the only member possessing catalytic and RNA silencing activity. In here, a molecular dynamics (MDs) simulation was performed using the crystal structure of human AGO2 protein complex with miR-20a. miR-20a is involved with various kind of biological process like heart and lung development, oncogenic process, etc. In precise, MD simulation was carried out with AGO2 protein complex with wild type, two mutant sites and four mutant sites in guided microRNA (miRNA). It has been noted that root-mean-square deviation (RMSD) of atomic positions of nucleic acid for wild type and two mutant sites guided miRNA has the same pattern of fluctuations, which stabilizes around 0.27 nm after 2 ns. Cα atom of AGO2 protein in the complex shows that this complex with wild type and two mutant site mutation duplex has a stable RMSD value after 20 ns, ranging between 0.14 and 0.21 nm. From the root-mean-square fluctuation (RMSF), we observed an increased pattern of fluctuations for the atoms of four mutant complex of AGO2-miR-20a complex. This increased RMSF of non-mutated nucleic acids is contributed by U-A bond breaking at the site of the nucleotide of U2 of guided miRNA, as observed from the duplex structure taken at different time steps of the simulation. Superimposed structure of the miRNA-mRNA duplex for the three complexes depicts that the three miRNA-mRNA duplexes are stable during the simulation. Current work demonstrates the possible correlations between the conformational changes of this AGO2-miR-20a duplex structure and the interactions of different atoms.


Assuntos
Proteínas Argonautas/química , MicroRNAs/química , Proteínas Argonautas/metabolismo , Humanos , MicroRNAs/metabolismo , Modelos Moleculares , Simulação de Dinâmica Molecular , Mutação , Ácidos Nucleicos Heteroduplexes/química , RNA Mensageiro
7.
J Vet Sci ; 20(3): e23, 2019 May.
Artigo em Inglês | MEDLINE | ID: mdl-31161741

RESUMO

The clustered regularly interspaced short palindrome repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system is a versatile genome editing tool with high efficiency. A guide sequence of 20 nucleotides (nt) is commonly used in application of CRISPR/Cas9; however, the relationship between the length of the guide sequence and the efficiency of CRISPR/Cas9 in porcine cells is still not clear. To illustrate this issue, guide RNAs of different lengths targeting the EGFP gene were designed. Specifically, guide RNAs of 17 nt or longer were sufficient to direct the Cas9 protein to cleave target DNA sequences, while 15 nt or shorter guide RNAs had loss-of-function. Full-length guide RNAs complemented with mismatches also showed loss-of-function. When the shortened guide RNA and target DNA heteroduplex (gRNA:DNA heteroduplex) was blocked by mismatch, the CRISPR/Cas9 would be interfered with. These results suggested the length of the gRNA:DNA heteroduplex was a key factor for maintaining high efficiency of the CRISPR/Cas9 system rather than weak bonding between shortened guide RNA and Cas9 in porcine cells.


Assuntos
Sistemas CRISPR-Cas/genética , Edição de Genes , Ácidos Nucleicos Heteroduplexes/genética , RNA Guia de Cinetoplastídeos/genética , Animais , Pareamento Incorreto de Bases/genética , Linhagem Celular , Edição de Genes/normas , Genes erbB-1/genética , Ácidos Nucleicos Heteroduplexes/química , RNA Guia de Cinetoplastídeos/química , Suínos
8.
Chem Commun (Camb) ; 55(48): 6827-6830, 2019 Jun 11.
Artigo em Inglês | MEDLINE | ID: mdl-31106806

RESUMO

We develop a new fluorescent method for sensitive detection of long noncoding RNAs (lncRNAs) on the basis of duplex-specific nuclease-actuated cyclic enzymatic repairing-mediated signal amplification. This method exhibits high sensitivity with a detection limit of 0.081 fM, and it can accurately detect the endogenous lncRNA HOTAIR in cancer cells, providing a new approach to study the physiological function of lncRNAs in human diseases.


Assuntos
Técnicas de Amplificação de Ácido Nucleico/métodos , Ácidos Nucleicos Heteroduplexes/química , RNA Longo não Codificante/análise , Linhagem Celular , Linhagem Celular Tumoral , Endonucleases/química , Corantes Fluorescentes/química , Humanos , Limite de Detecção , Sensibilidade e Especificidade
9.
Mol Cell ; 73(3): 398-411, 2019 02 07.
Artigo em Inglês | MEDLINE | ID: mdl-30735654

RESUMO

During transcription, the nascent RNA strand can base pair with its template DNA, displacing the non-template strand as ssDNA and forming a structure called an R-loop. R-loops are common across many domains of life and cause DNA damage in certain contexts. In this review, we summarize recent results implicating R-loops as important regulators of cellular processes such as transcription termination, gene regulation, and DNA repair. We also highlight recent work suggesting that R-loops can be problematic to cells as blocks to efficient transcription and replication that trigger the DNA damage response. Finally, we discuss how R-loops may contribute to cancer, neurodegeneration, and inflammatory diseases and compare the available next-generation sequencing-based approaches to map R-loops genome wide.


Assuntos
Núcleo Celular/fisiologia , DNA/genética , Genoma , Instabilidade Genômica , Ácidos Nucleicos Heteroduplexes/genética , RNA/genética , Animais , DNA/química , DNA/metabolismo , Dano ao DNA , Reparo do DNA , Regulação da Expressão Gênica , Humanos , Conformação de Ácido Nucleico , Ácidos Nucleicos Heteroduplexes/química , Ácidos Nucleicos Heteroduplexes/metabolismo , RNA/química , RNA/metabolismo , Relação Estrutura-Atividade , Transcrição Gênica
10.
Biochemistry ; 57(48): 6662-6668, 2018 12 04.
Artigo em Inglês | MEDLINE | ID: mdl-30406989

RESUMO

RNA helicase A (RHA) as a member of the DExH/D-box subgroup of helicase superfamily II is involved in virtually all aspects of RNA metabolism. It exhibits robust RNA helicase activity in vitro. However, little is known about the molecular and physical determinants for RHA substrate recognition and RHA translocation along the nucleic acids. Here, our nondenaturing polyacrylamide gel electrophoresis (PAGE)-based unwinding assays of chemical and structural modified substrates indicate that RHA translocates efficiently along the 3' overhang of RNA, but not DNA, with a requirement of covalent continuity. Ribose-phosphate backbone lesions on both strands of the nucleic acids, especially on the 3' overhang of the loading strand, affect RHA unwinding significantly. Furthermore, RHA requires RNA on the 3' overhang which directly or indirectly connects with the duplex region to mediate productive unwinding. Collectively, these findings propose a basic mechanism of the substrate determinants for RHA backbone tracking during duplex unwinding.


Assuntos
RNA Helicases DEAD-box/metabolismo , Proteínas de Neoplasias/metabolismo , Conformação de Ácido Nucleico , RNA/química , RNA/metabolismo , Sequência de Bases , DNA/química , DNA/genética , DNA/metabolismo , Humanos , Cinética , Modelos Biológicos , Ácidos Nucleicos Heteroduplexes/química , Ácidos Nucleicos Heteroduplexes/genética , Ácidos Nucleicos Heteroduplexes/metabolismo , RNA/genética , Proteínas Recombinantes/metabolismo , Especificidade por Substrato
11.
Bioconjug Chem ; 29(4): 1025-1029, 2018 04 18.
Artigo em Inglês | MEDLINE | ID: mdl-29505242

RESUMO

Two highly specific biomolecular recognition events, nucleic acid duplex hybridization and DNA-peptide recognition in the minor groove, were coalesced in a miniature ensemble for the first time by covalently attaching a natural AT-hook peptide motif to nucleic acid duplexes via a 2'-amino-LNA scaffold. A combination of molecular dynamics simulations and ultraviolet thermal denaturation studies revealed high sequence-specific affinity of the peptide-oligonucleotide conjugates (POCs) when binding to complementary DNA strands, leveraging the bioinformation encrypted in the minor groove of DNA duplexes. The significant cooperative DNA duplex stabilization may pave the way toward further development of POCs with enhanced affinity and selectivity toward target sequences carrying peptide-binding genetic islands.


Assuntos
DNA/química , Oligonucleotídeos/química , Peptídeos/química , Sítios de Ligação , Ligação de Hidrogênio , Simulação de Dinâmica Molecular , Conformação de Ácido Nucleico , Ácidos Nucleicos Heteroduplexes/química , Estudo de Prova de Conceito , Conformação Proteica
12.
Int J Nanomedicine ; 12: 5013-5022, 2017.
Artigo em Inglês | MEDLINE | ID: mdl-28761341

RESUMO

miRNAs have emerged as new biomarkers for the detection of a wide variety of cancers. By employing duplex-specific nuclease for signal amplification and gold nanoparticles (AuNPs) as the carriers of detection probes, a novel electrochemical assay of miRNAs was performed. The method is based on conversion of the well-known colorimetric assay into electrochemical analysis with enhanced sensitivity. DNA capture probes immobilized on the electrode surface and ferrocene (Fc)-labeled DNA detection probes (denoted "Fc-DNA-Fc") presented in the solution induced the assembly of positively charged AuNPs on the electrode surface through the electrostatic interaction. As a result, a large number of Fc-DNA-Fc molecules were attached on the electrode surface, thus amplifying the electrochemical signal. When duplex-specific nuclease was added to recycle the process of miRNA-initiated digestion of the immobilized DNA probes, Fc-DNA-Fc-induced assembly of AuNPs on the electrode surface could not occur. This resulted in a significant fall in the oxidation current of Fc. The current was found to be inversely proportional to the concentration of miRNAs in the range of 0-25 fM, and a detection limit of 0.1 fM was achieved. Moreover, this work presents a new method for converting colorimetric assays into sensitive electrochemical analyses, and thus would be valuable for design of novel chemical/biosensors.


Assuntos
Colorimetria/métodos , Técnicas Eletroquímicas/métodos , MicroRNAs/análise , Nanopartículas/química , Técnicas Biossensoriais/métodos , Sondas de DNA/química , Eletrodos , Compostos Ferrosos/química , Ouro/química , Humanos , Limite de Detecção , Metalocenos , MicroRNAs/sangue , MicroRNAs/química , Ácidos Nucleicos Heteroduplexes/química , Sensibilidade e Especificidade
13.
J Biol Chem ; 291(19): 10006-20, 2016 May 06.
Artigo em Inglês | MEDLINE | ID: mdl-26975377

RESUMO

The human primosome, a 340-kilodalton complex of primase and DNA polymerase α (Polα), synthesizes chimeric RNA-DNA primers to be extended by replicative DNA polymerases δ and ϵ. The intricate mechanism of concerted primer synthesis by two catalytic centers was an enigma for over three decades. Here we report the crystal structures of two key complexes, the human primosome and the C-terminal domain of the primase large subunit (p58C) with bound DNA/RNA duplex. These structures, along with analysis of primase/polymerase activities, provide a plausible mechanism for all transactions of the primosome including initiation, elongation, accurate counting of RNA primer length, primer transfer to Polα, and concerted autoregulation of alternate activation/inhibition of the catalytic centers. Our findings reveal a central role of p58C in the coordinated actions of two catalytic domains in the primosome and ultimately could impact the design of anticancer drugs.


Assuntos
DNA Polimerase I/química , DNA Primase/química , DNA/química , Complexos Multienzimáticos/química , Ácidos Nucleicos Heteroduplexes/química , DNA/biossíntese , DNA Polimerase I/metabolismo , DNA Primase/metabolismo , Humanos , Complexos Multienzimáticos/metabolismo , Ácidos Nucleicos Heteroduplexes/metabolismo
14.
Curr Drug Targets ; 16(14): 1650-9, 2015.
Artigo em Inglês | MEDLINE | ID: mdl-26601722

RESUMO

A new class of therapeutic agents with a high potential for the treatment of different socially relevant human diseases is represented by Nucleic Acid Based Drugs (NABD), including small interfering RNAs (siRNA), decoy oligodeoxynucleotides (decoy ODN) and antisense oligonucleotides (ASOs). Although NABD can be engineered to be specifically directed against virtually any target, their susceptibility to nuclease degradation and the difficulty of delivery into target tissues severely limit their use in clinical practice and require the development of an appropriate nanostructured delivery system. For delivery of NABD, Inulin (Inu), a natural, water soluble and biocompatible polysaccharide, was derivatized by Spermine (Spm), a flexible molecule with four amine groups that, having pKa values in the range between 8-11, is mainly in the protonated form at pH 7.4. The synthesis of related copolymers (Inu-Spm) was performed by a two step reaction, using a method termed Enhanced Microwave Synthesis (EMS) which has the advantage, compared to conventional microwave reaction, that high amount of energy can be applied to the reaction system, by administering microwave irradiation and simultaneously controlling the temperature in the reaction vessel with cooled air. The synthesized inulin derivatives were characterized by FT-IR spectra and (1)H-NMR. INU-Spm derivatives with a degree of derivatization of about 14 % mol/mol were obtained. These polycations were tested to evaluate their ability to form non covalent complexes with genetic material (polyplexes). Agarose gel retardation assays showed that the obtained copolymers are able to electrostatically interact with DNA duplex to form polyplexes at different c/p weight ratios. Moreover, light scattering studies, performed to analyze size and z-potential of polyplexes, evidenced that copolymers are able to interact with genetic material leading to the formation of nanoscaled systems. In addition, biocompatibility of polyplexes was demonstrated by performing cytotoxicity assays on a 16HBE cell line. Transfection studies, performed by using siRNA able to silence luciferase expression, demonstrate the efficiency of polyplexes to transfect the same cell line, with a reduction of luciferase expression to about 70%. These results encourage us to work with these copolymers to obtain an efficient and feasible inulin based NABD delivery system.


Assuntos
Inulina/análogos & derivados , Ácidos Nucleicos Heteroduplexes/química , Espermina/química , Linhagem Celular , Sobrevivência Celular/efeitos dos fármacos , Sistemas de Liberação de Medicamentos/métodos , Humanos , Inulina/química , Inulina/farmacologia , Micro-Ondas , Ácidos Nucleicos Heteroduplexes/farmacologia , Tamanho da Partícula , Poliaminas/química , Polieletrólitos , Espermina/farmacologia
15.
Nucleic Acids Res ; 43(5): 2499-512, 2015 Mar 11.
Artigo em Inglês | MEDLINE | ID: mdl-25690900

RESUMO

2-Thiouracil-containing nucleosides are essential modified units of natural and synthetic nucleic acids. In particular, the 5-substituted-2-thiouridines (S2Us) present in tRNA play an important role in tuning the translation process through codon-anticodon interactions. The enhanced thermodynamic stability of S2U-containing RNA duplexes and the preferred S2U-A versus S2U-G base pairing are appreciated characteristics of S2U-modified molecular probes. Recently, we have demonstrated that 2-thiouridine (alone or within an RNA chain) is predominantly transformed under oxidative stress conditions to 4-pyrimidinone riboside (H2U) and not to uridine. Due to the important biological functions and various biotechnological applications for sulfur-containing nucleic acids, we compared the thermodynamic stabilities of duplexes containing desulfured products with those of 2-thiouracil-modified RNA and DNA duplexes. Differential scanning calorimetry experiments and theoretical calculations demonstrate that upon 2-thiouracil desulfuration to 4-pyrimidinone, the preferred base pairing of S2U with adenosine is lost, with preferred base pairing with guanosine observed instead. Therefore, biological processes and in vitro assays in which oxidative desulfuration of 2-thiouracil-containing components occurs may be altered. Moreover, we propose that the H2U-G base pair is a suitable model for investigation of the preferred recognition of 3'-G-ending versus A-ending codons by tRNA wobble nucleosides, which may adopt a 4-pyrimidinone-type structural motif.


Assuntos
Pareamento de Bases , DNA/química , Guanina/química , Ácidos Nucleicos Heteroduplexes/química , RNA/química , Tiouracila/química , Adenina/química , Dicroísmo Circular , DNA/genética , Modelos Químicos , Modelos Moleculares , Conformação de Ácido Nucleico , Desnaturação de Ácido Nucleico , Ácidos Nucleicos Heteroduplexes/genética , RNA/genética , Termodinâmica , Tiouridina/análogos & derivados , Tiouridina/química
16.
FEBS J ; 282(1): 4-18, 2015 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-25327637

RESUMO

RAGs (recombination activating genes) are responsible for the generation of antigen receptor diversity through the process of combinatorial joining of different V (variable), D (diversity) and J (joining) gene segments. In addition to its physiological property, wherein RAG functions as a sequence-specific nuclease, it can also act as a structure-specific nuclease leading to genomic instability and cancer. In the present study, we investigate the factors that regulate RAG cleavage on non-B DNA structures. We find that RAG binding and cleavage on heteroduplex DNA is dependent on the length of the double-stranded flanking region. Besides, the immediate flanking double-stranded region regulates RAG activity in a sequence-dependent manner. Interestingly, the cleavage efficiency of RAGs at the heteroduplex region is influenced by the phasing of DNA. Thus, our results suggest that sequence, length and phase positions of the DNA can affect the efficiency of RAG cleavage when it acts as a structure-specific nuclease. These findings provide novel insights on the regulation of the pathological functions of RAGs.


Assuntos
Proteínas de Ligação a DNA/química , Proteínas de Ligação a DNA/metabolismo , Proteínas de Homeodomínio/química , Proteínas de Homeodomínio/metabolismo , Proteínas Nucleares/química , Proteínas Nucleares/metabolismo , Ácidos Nucleicos Heteroduplexes/genética , Ácidos Nucleicos Heteroduplexes/metabolismo , Região 5'-Flanqueadora , Sequência de Bases , Sítios de Ligação , Proteínas de Ligação a DNA/genética , Desoxirribonucleases/química , Desoxirribonucleases/genética , Desoxirribonucleases/metabolismo , Genes RAG-1 , Células HEK293 , Proteínas de Homeodomínio/genética , Humanos , Proteínas Nucleares/genética , Conformação de Ácido Nucleico , Ácidos Nucleicos Heteroduplexes/química , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Recombinação V(D)J
17.
J Biol Chem ; 288(22): 16177-84, 2013 May 31.
Artigo em Inglês | MEDLINE | ID: mdl-23595992

RESUMO

Recent crystallographic analysis of p66/p51 human immunodeficiency virus (HIV) type 1 reverse transcriptase (RT) complexed with a non-polypurine tract RNA/DNA hybrid has illuminated novel and important contacts between structural elements at the C terminus of the noncatalytic p51 subunit and the nucleic acid duplex in the vicinity of the ribonuclease H (RNase H) active site. In particular, a short peptide spanning residues Phe-416-Pro-421 was shown to interact with the DNA strand, cross the minor groove of the helix, and then form Van der Waals contacts with the RNA strand adjacent to the scissile phosphate. At the base of the adjoining α-helix M', Tyr-427 forms a hydrogen bond with Asn-348, the latter of which, when mutated to Ile, is implicated in resistance to both nucleoside and non-nucleoside RT inhibitors. Based on our structural data, we analyzed the role of the p51 C terminus by evaluating selectively mutated p66/p51 heterodimers carrying (i) p51 truncations that encroach on α-M', (ii) alterations that interrupt the Asn-348-Tyr-427 interaction, and (iii) alanine substitutions throughout the region Phe-416-Pro-421. Collectively, our data support the notion that the p51 C terminus makes an important contribution toward hybrid binding and orienting the RNA strand for catalysis at the RNase H active site.


Assuntos
DNA Viral/química , Transcriptase Reversa do HIV/química , HIV-1/enzimologia , Ácidos Nucleicos Heteroduplexes/química , RNA Viral/química , Substituição de Aminoácidos , Domínio Catalítico , DNA Viral/genética , DNA Viral/metabolismo , Transcriptase Reversa do HIV/genética , Transcriptase Reversa do HIV/metabolismo , HIV-1/genética , Humanos , Hidrólise , Mutação de Sentido Incorreto , Ácidos Nucleicos Heteroduplexes/genética , Ácidos Nucleicos Heteroduplexes/metabolismo , Estrutura Secundária de Proteína , RNA Viral/genética , RNA Viral/metabolismo
18.
Cell Rep ; 2(4): 707-13, 2012 Oct 25.
Artigo em Inglês | MEDLINE | ID: mdl-23022487

RESUMO

The transcription activator-like (TAL) effector targets specific host promoter through its central DNA-binding domain, which comprises multiple tandem repeats (TALE repeats). Recent structural analyses revealed that the TALE repeats form a superhelical structure that tracks along the forward strand of the DNA duplex. Here, we demonstrate that TALE repeats specifically recognize a DNA-RNA hybrid where the DNA strand determines the binding specificity. The crystal structure of a designed TALE in complex with the DNA-RNA hybrid was determined at a resolution of 2.5 Å. Although TALE repeats are in direct contact with only the DNA strand, the phosphodiester backbone of the RNA strand is inaccessible by macromolecules such as RNases. Consistent with this observation, sequence-specific recognition of an HIV-derived DNA-RNA hybrid by an engineered TALE efficiently blocked RNase H-mediated degradation of the RNA strand. Our study broadens the utility of TALE repeats and suggests potential applications in processes involving DNA replication and retroviral infections.


Assuntos
Proteínas de Ligação a DNA/metabolismo , DNA/metabolismo , Ácidos Nucleicos Heteroduplexes/metabolismo , RNA/metabolismo , Sequência de Bases , Sítios de Ligação , Cristalografia por Raios X , DNA/química , Proteínas de Ligação a DNA/química , HIV/genética , Humanos , Ácidos Nucleicos Heteroduplexes/química , Estrutura Terciária de Proteína , RNA/química , Ribonuclease H/metabolismo , Sequências de Repetição em Tandem
19.
Biochemistry ; 51(25): 5187-97, 2012 Jun 26.
Artigo em Inglês | MEDLINE | ID: mdl-22646210

RESUMO

The family 4 uracil-DNA glycosylase from the hyperthermophilic organism Archaeoglobus fulgidus (AFUDG) is responsible for the removal of uracil in DNA as the first step in the base excision repair (BER) pathway. AFUDG contains a large solvent-exposed peptide region containing an α helix and loop anchored on each end via ligation of two cysteine thiolates to a [4Fe-4S](2+) cluster. We propose that this region plays a similar role in DNA damage recognition as a smaller iron-sulfur cluster loop (FCL) motif in the structurally unrelated BER glycosylases MutY and Endonuclease III and therefore refer to this region as the "pseudo-FCL" in AFUDG. In order to evaluate the importance of this region, three positively charged residues (Arg 86, Arg 91, Lys 100) and the anchoring Cys residues (Cys 85, Cys 101) within this motif were replaced with alanine, and the effects of these replacements on uracil excision in single- and double-stranded DNA were evaluated. These results show that this region participates and allows for efficient recognition and excision of uracil within DNA. Notably, R86A AFUDG exhibited reduced activity for uracil removal only within double-stranded DNA, suggesting an importance in duplex disruption and extrusion of the base as part of the excision process. In addition, mutation of the [4Fe-4S](2+) cluster cysteine ligands at the ends of the pseudo-FCL to alanine reduced the uracil excision efficiency, suggesting the importance of anchoring the loop via coordination to the cluster. In contrast, K100A AFUDG exhibited enhanced uracil excision activity, providing evidence for the importance of the loop conformation and flexibility. Taken together, the results herein provide evidence that the pseudo-FCL motif is involved in DNA binding and catalysis, particularly in duplex DNA contexts. This work underscores the requirement of an ensemble of interactions, both distant and in proximity to the damaged site, for accurate and efficient uracil excision.


Assuntos
Proteínas Arqueais/química , Archaeoglobus fulgidus/enzimologia , Reparo do DNA , Proteínas Ferro-Enxofre/química , Uracila-DNA Glicosidase/química , Uracila/metabolismo , Motivos de Aminoácidos/genética , Sequência de Aminoácidos , Proteínas Arqueais/genética , Proteínas Arqueais/metabolismo , Archaeoglobus fulgidus/genética , Archaeoglobus fulgidus/metabolismo , Catálise , Reparo do DNA/genética , Proteínas Ferro-Enxofre/genética , Proteínas Ferro-Enxofre/metabolismo , Dados de Sequência Molecular , Família Multigênica , Ácidos Nucleicos Heteroduplexes/química , Ácidos Nucleicos Heteroduplexes/genética , Ácidos Nucleicos Heteroduplexes/metabolismo , Ligação Proteica/genética , Uracila-DNA Glicosidase/genética , Uracila-DNA Glicosidase/metabolismo
20.
J Biol Chem ; 287(11): 8126-34, 2012 Mar 09.
Artigo em Inglês | MEDLINE | ID: mdl-22267744

RESUMO

The Escherichia coli UvrD helicase is known to function in the mismatch repair and nucleotide excision repair pathways and has also been suggested to have roles in recombination and replication restart. The primary intermediate DNA structure in these two processes is the Holliday junction. UvrD has been shown to unwind a variety of substrates including partial duplex DNA, nicked DNA, forked DNA structures, blunt duplex DNA and RNA-DNA hybrids. Here, we demonstrate that UvrD also catalyzes the robust unwinding of Holliday junction substrates. To characterize this unwinding reaction we have employed steady-state helicase assays, pre-steady-state rapid quench helicase assays, DNaseI footprinting, and electron microscopy. We conclude that UvrD binds initially to the junction compared with binding one of the blunt ends of the four-way junction to initiate unwinding and resolves the synthetic substrate into two double-stranded fork structures. We suggest that UvrD, along with its mismatch repair partners, MutS and MutL, may utilize its ability to unwind Holliday junctions directly in the prevention of homeologous recombination. UvrD may also be involved in the resolution of stalled replication forks by unwinding the Holliday junction intermediate to allow bypass of the blockage.


Assuntos
DNA Helicases/metabolismo , DNA Bacteriano/metabolismo , DNA Cruciforme/metabolismo , Proteínas de Escherichia coli/metabolismo , Escherichia coli/enzimologia , Adenosina Trifosfatases/química , Adenosina Trifosfatases/genética , Adenosina Trifosfatases/metabolismo , Pegada de DNA/métodos , DNA Helicases/química , DNA Helicases/genética , DNA Bacteriano/química , DNA Bacteriano/genética , DNA Cruciforme/química , DNA Cruciforme/genética , Desoxirribonuclease I/química , Escherichia coli/genética , Proteínas de Escherichia coli/química , Proteínas de Escherichia coli/genética , Proteínas MutL , Proteína MutS de Ligação de DNA com Erro de Pareamento/química , Proteína MutS de Ligação de DNA com Erro de Pareamento/genética , Proteína MutS de Ligação de DNA com Erro de Pareamento/metabolismo , Ácidos Nucleicos Heteroduplexes/química , Ácidos Nucleicos Heteroduplexes/genética , Ácidos Nucleicos Heteroduplexes/metabolismo
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