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1.
Int J Mol Sci ; 22(16)2021 Aug 19.
Artigo em Inglês | MEDLINE | ID: mdl-34445637

RESUMO

DNA is a polymeric macromolecule that can display a variety of backbone conformations. While the classical B-DNA is a right-handed double helix, Z-DNA is a left-handed helix with a zig-zag orientation. The Z conformation depends upon the base sequence, base modification and supercoiling and is considered to be transient. To determine whether the presence of Z-DNA can be detected immunochemically, the binding of monoclonal and polyclonal anti-Z-DNA antibodies to a panel of natural DNA antigens was assessed by an ELISA using brominated poly(dG-dC) as a control for Z-DNA. As these studies showed, among natural DNA tested (Micrococcus luteus, calf thymus, Escherichiacoli, salmon sperm, lambda phage), micrococcal (MC) DNA showed the highest binding with both anti-Z-DNA preparations, and E. coli DNA showed binding with the monoclonal anti-DNA preparation. The specificity for Z-DNA conformation in MC DNA was demonstrated by an inhibition binding assay. An algorithm to identify propensity to form Z-DNA indicated that DNA from Mycobacterium tuberculosis could form Z-DNA, a prediction confirmed by immunoassay. Together, these findings indicate that anti-Z-DNA antibodies can serve as probes for the presence of Z-DNA in DNA of various species origin and that the content of Z-DNA varies significantly among DNA sources.


Assuntos
Anticorpos Monoclonais/metabolismo , Especificidade de Anticorpos , DNA Forma Z/metabolismo , Escherichia coli/imunologia , Micrococcus luteus/imunologia , Placenta/imunologia , Espermatozoides/imunologia , Animais , Anticorpos Monoclonais/imunologia , DNA Forma Z/química , DNA Forma Z/imunologia , Escherichia coli/metabolismo , Feminino , Humanos , Masculino , Micrococcus luteus/metabolismo , Conformação de Ácido Nucleico , Placenta/metabolismo , Gravidez , Salmão , Ovinos , Especificidade da Espécie , Espermatozoides/metabolismo
2.
Molecules ; 26(16)2021 Aug 12.
Artigo em Inglês | MEDLINE | ID: mdl-34443469

RESUMO

The classical genetic code maps nucleotide triplets to amino acids. The associated sequence composition is complex, representing many elaborations during evolution of form and function. Other genomic elements code for the expression and processing of RNA transcripts. However, over 50% of the human genome consists of widely dispersed repetitive sequences. Among these are simple sequence repeats (SSRs), representing a class of flipons, that under physiological conditions, form alternative nucleic acid conformations such as Z-DNA, G4 quartets, I-motifs, and triplexes. Proteins that bind in a structure-specific manner enable the seeding of condensates with the potential to regulate a wide range of biological processes. SSRs also encode the low complexity peptide repeats to patch condensates together, increasing the number of combinations possible. In situations where SSRs are transcribed, SSR-specific, single-stranded binding proteins may further impact condensate formation. Jointly, flipons and patches speed evolution by enhancing the functionality of condensates. Here, the focus is on the selection of SSR flipons and peptide patches that solve for survival under a wide range of environmental contexts, generating complexity with simple parts.


Assuntos
DNA Forma Z/química , DNA Forma Z/genética , Evolução Molecular , Conformação de Ácido Nucleico , Proteínas/química , Proteínas/genética , Animais , Códon , DNA Forma Z/metabolismo , Genética , Humanos , Repetições de Microssatélites/genética , Proteínas/metabolismo
3.
Int J Mol Sci ; 22(14)2021 Jul 19.
Artigo em Inglês | MEDLINE | ID: mdl-34299306

RESUMO

It is now difficult to believe that a biological function for the left-handed Z-DNA and Z-RNA conformations was once controversial. The papers in this Special Issue, "Z-DNA and Z-RNA: from Physical Structure to Biological Function", are based on presentations at the ABZ2021 meeting that was held virtually on 19 May 2021 and provide evidence for several biological functions of these structures. The first of its kind, this international conference gathered over 200 scientists from many disciplines to specifically address progress in research involving Z-DNA and Z-RNA. These high-energy left-handed conformers of B-DNA and A-RNA are associated with biological functions and disease outcomes, as evidenced from both mouse and human genetic studies. These alternative structures, referred to as "flipons", form under physiological conditions, regulate type I interferon responses and induce necroptosis during viral infection. They can also stimulate genetic instability, resulting in adaptive evolution and diseases such as cancer. The meeting featured cutting-edge science that was, for the most part, unpublished. We plan for the ABZ meeting to reconvene in 2022.


Assuntos
DNA Forma Z/química , Conformação de Ácido Nucleico , RNA/química , Animais , DNA Forma Z/genética , DNA Forma Z/metabolismo , Humanos , Camundongos , RNA/genética , RNA/metabolismo
4.
Int J Mol Sci ; 22(7)2021 Mar 29.
Artigo em Inglês | MEDLINE | ID: mdl-33805331

RESUMO

Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion spectroscopy is commonly used for quantifying conformational changes of protein in µs-to-ms timescale transitions. To elucidate the dynamics and mechanism of protein binding, parameters implementing CPMG relaxation dispersion results must be appropriately determined. Building an analytical model for multi-state transitions is particularly complex. In this study, we developed a new global search algorithm that incorporates a random search approach combined with a field-dependent global parameterization method. The robust inter-dependence of the parameters carrying out the global search for individual residues (GSIR) or the global search for total residues (GSTR) provides information on the global minimum of the conformational transition process of the Zα domain of human ADAR1 (hZαADAR1)-DNA complex. The global search results indicated that a α-helical segment of hZαADAR1 provided the main contribution to the three-state conformational changes of a hZαADAR1-DNA complex with a slow B-Z exchange process. The two global exchange rate constants, kex and kZB, were found to be 844 and 9.8 s-1, respectively, in agreement with two regimes of residue-dependent chemical shift differences-the "dominant oscillatory regime" and "semi-oscillatory regime". We anticipate that our global search approach will lead to the development of quantification methods for conformational changes not only in Z-DNA binding protein (ZBP) binding interactions but also in various protein binding processes.


Assuntos
Adenosina Desaminase/química , DNA de Forma B/química , DNA Forma Z/química , Modelos Moleculares , Proteínas de Ligação a RNA/química , Adenosina Desaminase/metabolismo , Algoritmos , DNA de Forma B/metabolismo , DNA Forma Z/metabolismo , Proteínas de Ligação a DNA/química , Proteínas de Ligação a DNA/metabolismo , Humanos , Espectroscopia de Ressonância Magnética , Conformação Proteica , Proteínas de Ligação a RNA/metabolismo , Termodinâmica
5.
Mol Immunol ; 129: 86-93, 2021 01.
Artigo em Inglês | MEDLINE | ID: mdl-33221042

RESUMO

Macrophages play a crucial role in host innate immune defense against infection and tissue injury. Macrophages are highly plastic cells and their subtypes have been characterized as M1 (also termed classically activated) and M2 (alternatively activated). Although the M1/M2 paradigm has been well documented, less is known regarding the role of macrophage activation/polarization in inflammation-associated necrotic cell death. To address this gap in current knowledge, we prepared bone marrow-derived macrophages, induced them to M1 or M2 subtypes, and then investigated the expression of necroptosis signaling molecules and macrophage subtype-dependent responses to different necroptosis inducers. We found that necroptosis effector mixed lineage kinase domain-like protein (MLKL) and the key necroptosis regulator Z-DNA/RNA binding protein 1 were predominantly induced in M1 but not M2 macrophages. Interestingly, the protein but not mRNA levels of receptor-interacting protein kinase-3 (RIPK3) were also upregulated in M1 macrophages. We further found that macrophage necrotic cell death, the releases of lactate dehydrogenase and dead cell proteases as well as MLKL phosphorylation at Ser345 in response to various necroptosis inducers were greatly augmented in M1 but not M2 macrophages, and the accelerated effects were blocked by two structurally distinct specific RIPK3 inhibitors GSK872 or GSK843. Thus, our findings demonstrate that M1 but not M2 subtypes of macrophages are more susceptible to inflammation-related lytic cell death in an RIPK3 kinase activity-dependent manner.


Assuntos
Morte Celular/fisiologia , Macrófagos/metabolismo , Proteína Serina-Treonina Quinases de Interação com Receptores/metabolismo , Animais , Benzotiazóis/farmacologia , Morte Celular/efeitos dos fármacos , Células Cultivadas , DNA Forma Z/metabolismo , Inflamação/metabolismo , L-Lactato Desidrogenase/metabolismo , Ativação de Macrófagos/efeitos dos fármacos , Ativação de Macrófagos/fisiologia , Macrófagos/efeitos dos fármacos , Camundongos , Camundongos Endogâmicos C57BL , Necroptose/efeitos dos fármacos , Necroptose/fisiologia , Fosforilação/efeitos dos fármacos , Fosforilação/fisiologia , Proteínas Quinases/metabolismo , Quinolinas/farmacologia , Células RAW 264.7 , RNA Mensageiro/metabolismo , Proteínas de Ligação a RNA/metabolismo , Transdução de Sinais/efeitos dos fármacos , Transdução de Sinais/fisiologia , Regulação para Cima/efeitos dos fármacos , Regulação para Cima/fisiologia
6.
Anal Chem ; 92(21): 14452-14458, 2020 11 03.
Artigo em Inglês | MEDLINE | ID: mdl-33085464

RESUMO

The SWI/SNF complex is a highly conserved chromatin remodeling complex and can hydrolyze ATP by its catalytic subunit BRG1 or BRM to reconstruct the chromatin. To investigate whether this ATP-dependent chromatin remodeling could affect the DNA conformation, we therefore regulated (knocked down or overexpressed) BRG1/BRM in the cells and applied Fourier transform infrared (FTIR) spectroscopy to probe DNA conformational changes. As a result, we found that BRG1/BRM was indeed associated with the DNA conformational changes, in which knockdown of BRG1/BRM reduced Z-DNA conformation, while overexpression of BRG1/BRM enhanced Z-DNA conformation. This Z-DNA conformational transformation was also verified using the Z-DNA-binding proteins. Therefore, this work has provided a direct analytical tool to probe Z-DNA transformation upon ATP-dependent chromatin remodeling.


Assuntos
Montagem e Desmontagem da Cromatina , DNA Forma Z/química , Conformação de Ácido Nucleico , Espectroscopia de Infravermelho com Transformada de Fourier , Trifosfato de Adenosina/metabolismo , Linhagem Celular Tumoral , DNA Helicases/deficiência , DNA Helicases/genética , DNA Forma Z/metabolismo , Técnicas de Silenciamento de Genes , Humanos , Proteínas Nucleares/deficiência , Proteínas Nucleares/genética , Fatores de Transcrição/deficiência , Fatores de Transcrição/genética
7.
Biochem Biophys Res Commun ; 533(3): 417-423, 2020 12 10.
Artigo em Inglês | MEDLINE | ID: mdl-32972754

RESUMO

Structural transformation of the canonical right-handed helix, B-DNA, to the non-canonical left-handed helix, Z-DNA, can be induced by the Zα domain of the human RNA editing enzyme ADAR1 (hZαADAR1). To characterize the site-specific preferences of binding and structural changes in DNA containing the 2'-O-methyl guanosine derivative (mG), titration of the imino proton spectra and chemical shift perturbations were performed on hZαADAR1 upon binding to Z-DNA. The structural transition between B-Z conformation as the changing ratio between DNA and protein showed a binding affinity of the modified DNA onto the Z-DNA binding protein similar to wild-type DNA or RNA. The chemical shift perturbation results showed that the overall structure and environment of the modified DNA revealed DNA-like properties rather than RNA-like characteristics. Moreover, we found evidence for two distinct regimes, "Z-DNA Sensing" and "Modification Sensing", based on the site-specific chemical shift perturbation between the DNA (or RNA) binding complex and the modified DNA-hZαADAR1 complex. Thus, we propose that modification of the sugar backbone of DNA with 2'-O-methyl guanosine promotes the changes in the surrounding α3 helical structural segment as well as the non-perturbed feature of the ß-hairpin region.


Assuntos
Adenosina Desaminase/química , DNA de Forma B/química , DNA Forma Z/química , Proteínas de Ligação a RNA/química , Adenosina Desaminase/metabolismo , DNA/química , DNA de Forma B/metabolismo , DNA Forma Z/metabolismo , Guanosina/química , Humanos , Modelos Moleculares , Ressonância Magnética Nuclear Biomolecular , Domínios Proteicos , Proteínas de Ligação a RNA/metabolismo
8.
Nat Neurosci ; 23(6): 718-729, 2020 06.
Artigo em Inglês | MEDLINE | ID: mdl-32367065

RESUMO

DNA forms conformational states beyond the right-handed double helix; however, the functional relevance of these noncanonical structures in the brain remains unknown. Here we show that, in the prefrontal cortex of mice, the formation of one such structure, Z-DNA, is involved in the regulation of extinction memory. Z-DNA is formed during fear learning and reduced during extinction learning, which is mediated, in part, by a direct interaction between Z-DNA and the RNA-editing enzyme Adar1. Adar1 binds to Z-DNA during fear extinction learning, which leads to a reduction in Z-DNA at sites where Adar1 is recruited. Knockdown of Adar1 leads to an inability to modify a previously acquired fear memory and blocks activity-dependent changes in DNA structure and RNA state-effects that are fully rescued by the introduction of full-length Adar1. These findings suggest a new mechanism of learning-induced gene regulation that is dependent on proteins that recognize alternate DNA structure states, which are required for memory flexibility.


Assuntos
Adenosina Desaminase/metabolismo , Adenosina Desaminase/fisiologia , DNA Forma Z/fisiologia , Extinção Psicológica/fisiologia , Edição de RNA/fisiologia , Animais , DNA Forma Z/metabolismo , Medo , Aprendizagem/fisiologia , Camundongos , Córtex Pré-Frontal/metabolismo , RNA Interferente Pequeno/farmacologia
9.
Int J Mol Sci ; 21(8)2020 Apr 11.
Artigo em Inglês | MEDLINE | ID: mdl-32290457

RESUMO

The non-canonical structures of nucleic acids are essential for their diverse functions during various biological processes. These non-canonical structures can undergo conformational exchange among multiple structural states. Data on their dynamics can illustrate conformational transitions that play important roles in folding, stability, and biological function. Here, we discuss several examples of the non-canonical structures of DNA focusing on their dynamic characterization by NMR spectroscopy: (1) G-quadruplex structures and their complexes with target proteins; (2) i-motif structures and their complexes with proteins; (3) triplex structures; (4) left-handed Z-DNAs and their complexes with various Z-DNA binding proteins. This review provides insight into how the dynamic features of non-canonical DNA structures contribute to essential biological processes.


Assuntos
DNA/química , Espectroscopia de Ressonância Magnética , Conformação de Ácido Nucleico , Animais , DNA/metabolismo , DNA Forma Z/química , DNA Forma Z/metabolismo , Proteínas de Ligação a DNA/química , Proteínas de Ligação a DNA/metabolismo , Quadruplex G , Humanos , Ligantes , Espectroscopia de Ressonância Magnética/métodos , Estrutura Molecular , Ácidos Nucleicos/química , Motivos de Nucleotídeos , Ligação Proteica
10.
J Biol Chem ; 295(14): 4684-4695, 2020 04 03.
Artigo em Inglês | MEDLINE | ID: mdl-32107311

RESUMO

R-loop structures are a prevalent class of alternative non-B DNA structures that form during transcription upon invasion of the DNA template by the nascent RNA. R-loops form universally in the genomes of organisms ranging from bacteriophages, bacteria, and yeasts to plants and animals, including mammals. A growing body of work has linked these structures to both physiological and pathological processes, in particular to genome instability. The rising interest in R-loops is placing new emphasis on understanding the fundamental physicochemical forces driving their formation and stability. Pioneering work in Escherichia coli revealed that DNA topology, in particular negative DNA superhelicity, plays a key role in driving R-loops. A clear role for DNA sequence was later uncovered. Here, we review and synthesize available evidence on the roles of DNA sequence and DNA topology in controlling R-loop formation and stability. Factoring in recent developments in R-loop modeling and single-molecule profiling, we propose a coherent model accounting for the interplay between DNA sequence and DNA topology in driving R-loop structure formation. This model reveals R-loops in a new light as powerful and reversible topological stress relievers, an insight that significantly expands the repertoire of R-loops' potential biological roles under both normal and aberrant conditions.


Assuntos
DNA Super-Helicoidal/química , Estruturas R-Loop/fisiologia , Animais , Replicação do DNA , DNA Super-Helicoidal/metabolismo , DNA Forma Z/química , DNA Forma Z/metabolismo , Escherichia coli/genética , Instabilidade Genômica , Transcrição Genética
11.
Eur J Hum Genet ; 28(1): 114-117, 2020 01.
Artigo em Inglês | MEDLINE | ID: mdl-31320745

RESUMO

Variants in the human double-stranded RNA editing enzyme ADAR produce three well-characterized rare Mendelian Diseases: Dyschromatosis Symmetrica Hereditaria (OMIM: 127400), Aicardi-Goutières syndrome (OMIM: 615010) and Bilateral Striatal Necrosis/Dystonia. ADAR encodes p150 and p110 protein isoforms. p150 incorporates the Zα domain that binds left-handed Z-DNA and Z-RNA with high affinity through contact of highly conserved residues with the DNA and RNA double helix. In certain individuals, frameshift variants on one parental chromosome in the second exon of ADAR produce haploinsufficiency of p150 while maintaining normal expression of p110. In other individuals, loss of p150 expression from one chromosome allows mapping of Zα p150 variants from the other parental chromosome directly to phenotype. The analysis reveals that loss of function Zα variants cause dysregulation of innate interferon responses to double-stranded RNA. This approach confirms a biological role for the left-handed conformation in human disease, further validating the power of Mendelian genetics to deliver unambiguous answers to difficult questions. The findings reveal that the human genome encodes genetic information using both shape and sequence.


Assuntos
Adenosina Desaminase/genética , Alelos , Doenças Genéticas Inatas/genética , Doenças do Sistema Imunitário/genética , Proteínas de Ligação a RNA/genética , Adenosina Desaminase/química , Adenosina Desaminase/metabolismo , Sítios de Ligação , Sequência Conservada , DNA Forma Z/metabolismo , Mutação da Fase de Leitura , Humanos , Interferons/metabolismo , Mutação com Perda de Função , Fenótipo , Ligação Proteica , RNA de Cadeia Dupla/metabolismo , Proteínas de Ligação a RNA/química , Proteínas de Ligação a RNA/metabolismo
12.
Nucleic Acids Res ; 47(16): 8899-8912, 2019 09 19.
Artigo em Inglês | MEDLINE | ID: mdl-31361900

RESUMO

DNA mismatches are highly polymorphic and dynamic in nature, albeit poorly characterized structurally. We utilized the antitumour antibiotic CoII(Chro)2 (Chro = chromomycin A3) to stabilize the palindromic duplex d(TTGGCGAA) DNA with two G:G mismatches, allowing X-ray crystallography-based monitoring of mismatch polymorphism. For the first time, the unusual geometry of several G:G mismatches including syn-syn, water mediated anti-syn and syn-syn-like conformations can be simultaneously observed in the crystal structure. The G:G mismatch sites of the d(TTGGCGAA) duplex can also act as a hotspot for the formation of alternative DNA structures with a GC/GA-5' intercalation site for binding by the GC-selective intercalator actinomycin D (ActiD). Direct intercalation of two ActiD molecules to G:G mismatch sites causes DNA rearrangements, resulting in backbone distortion to form right-handed Z-DNA structures with a single-step sharp kink. Our study provides insights on intercalators-mismatch DNA interactions and a rationale for mismatch interrogation and detection via DNA intercalation.


Assuntos
Antibióticos Antineoplásicos/química , Cromomicina A3/química , DNA Forma Z/química , Dactinomicina/química , Substâncias Intercalantes/química , Oligodesoxirribonucleotídeos/química , Antibióticos Antineoplásicos/metabolismo , Pareamento Incorreto de Bases , Pareamento de Bases , Sequência de Bases , Sítios de Ligação , Cromomicina A3/metabolismo , Cristalização , Cristalografia por Raios X , DNA Forma Z/metabolismo , Dactinomicina/metabolismo , Humanos , Substâncias Intercalantes/metabolismo , Modelos Moleculares , Oligodesoxirribonucleotídeos/síntese química , Soluções
13.
Sci Rep ; 9(1): 5904, 2019 04 11.
Artigo em Inglês | MEDLINE | ID: mdl-30976048

RESUMO

RNA-binding proteins play a particularly important role in regulating gene expression in trypanosomes. A map of the network of protein complexes in Trypanosoma brucei uncovered an essential protein (Tb927.10.7910) that is postulated to be an RNA-binding protein implicated in the regulation of the mitochondrial post-transcriptional gene regulatory network by its association with proteins that participate in a multi-protein RNA editing complex. However, the mechanism by which this protein interacts with its multiple target transcripts remained unknown. Using sensitive database searches and experimental data, we identify Z-DNA-binding domains in T. brucei in the N- and C-terminal regions of Tb927.10.7910. RNA-binding studies of the wild-type protein, now referred to as RBP7910 (RNA binding protein 7910), and site-directed mutagenesis of residues important for the Z-DNA binding domains show that it preferentially interacts with RNA molecules containing poly(U) and poly(AU)-rich sequences. The interaction of RBP7910 with these regions may be involved in regulation of RNA editing of mitochondrial transcripts.


Assuntos
DNA Forma Z/metabolismo , Proteínas de Protozoários/metabolismo , RNA de Protozoário/metabolismo , Proteínas de Ligação a RNA/metabolismo , RNA/metabolismo , Trypanosoma brucei brucei/metabolismo , Sequência de Aminoácidos , DNA Forma Z/genética , Mutação Puntual , Domínios Proteicos , Proteínas de Protozoários/genética , RNA/genética , RNA de Protozoário/genética , Proteínas de Ligação a RNA/genética , Homologia de Sequência de Aminoácidos , Trypanosoma brucei brucei/genética
14.
Chem Res Toxicol ; 32(5): 899-909, 2019 05 20.
Artigo em Inglês | MEDLINE | ID: mdl-30821442

RESUMO

One response to oxidation of guanine (G) to 8-oxo-7,8-dihydroguanine (OG) in a gene promoter is regulation of mRNA expression suggesting an epigenetic-like role for OG. A proposed mechanism involves G oxidation within a potential G-quadruplex-forming sequence (PQS) in the promoter, enabling a structural shift from B-DNA to a G-quadruplex fold (G4). When OG was located in the coding vs template strand, base excision repair led to an on/off transcriptional switch. Herein, a G-rich, potential Z-DNA-forming sequence (PZS) comprised of a d(GC) n repeat was explored to determine whether oxidation in this motif was also a transcriptional switch. Bioinformatic analysis found 1650 PZSs of length >10 nts in the human genome that were overrepresented in promoters and 5'-UTRs. Studies in human cells transfected with a luciferase reporter plasmid in which OG was synthesized in a PZS context in the promoter found that a coding strand OG increased expression and a template strand OG decreased expression. The initial base excision repair product of OG, an abasic site (AP), was also found to yield similar expression changes as OG. Biophysical studies on model Z-DNA strands found OG favored a shift in the equilibrium to Z-DNA from B-DNA, while an AP disrupted Z-DNA to favor a hairpin, placing AP in the loop where it is a poor substrate for the endonuclease APE1. Overall, the impact of OG and AP in a PZS on gene expression was similar to that in a PQS but reduced in magnitude.


Assuntos
Adutos de DNA/metabolismo , DNA Forma Z/metabolismo , Expressão Gênica/fisiologia , Guanina/química , Regiões Promotoras Genéticas/fisiologia , Sequência de Bases , Linhagem Celular Tumoral , Adutos de DNA/química , Adutos de DNA/genética , DNA Forma Z/química , DNA Forma Z/genética , Quadruplex G , Genoma/fisiologia , Guanina/análogos & derivados , Humanos , Oxirredução , Estresse Oxidativo/genética
15.
Commun Biol ; 2: 7, 2019.
Artigo em Inglês | MEDLINE | ID: mdl-30729177

RESUMO

Left-handed Z-DNA/Z-RNA is bound with high affinity by the Zα domain protein family that includes ADAR (a double-stranded RNA editing enzyme), ZBP1 and viral orthologs regulating innate immunity. Loss-of-function mutations in ADAR p150 allow persistent activation of the interferon system by Alu dsRNAs and are causal for Aicardi-Goutières Syndrome. Heterodimers of ADAR and DICER1 regulate the switch from RNA- to protein-centric immunity. Loss of DICER1 function produces age-related macular degeneration, a different type of Alu-mediated disease. The overlap of Z-forming sites with those for the signal recognition particle likely limits invasion of primate genomes by Alu retrotransposons.


Assuntos
Doenças Autoimunes do Sistema Nervoso/genética , DNA Forma Z/genética , DNA Forma Z/metabolismo , Malformações do Sistema Nervoso/genética , Adenosina Desaminase/genética , Adenosina Desaminase/metabolismo , Elementos Alu/genética , Sequência de Aminoácidos , Animais , Sítios de Ligação , RNA Helicases DEAD-box/genética , DNA Forma Z/química , Humanos , Mutação com Perda de Função , Conformação de Ácido Nucleico , Ligação Proteica , RNA de Cadeia Dupla/metabolismo , Proteínas de Ligação a RNA/genética , Proteínas de Ligação a RNA/metabolismo , Ribonuclease III/genética
16.
Bioorg Med Chem ; 27(2): 364-369, 2019 01 15.
Artigo em Inglês | MEDLINE | ID: mdl-30545733

RESUMO

We synthesized several DNA oligonucleotides containing one or several 2'-O-methyl-8-methyl guanosine (m8Gm) and demonstrated that these oligonucleotides not only stabilize the Z-DNA with a wide range of sequences under low salt conditions but also possess high thermal stability. Using artificial nucleobase-containing oligonucleotides, we studied the interaction of the Zα domain with Z-DNA. Furthermore, we showed that the m8Gm-contained oligonucleotides allow to study the photochemical reaction of Z-DNA.


Assuntos
DNA Forma Z/química , Guanosina/análogos & derivados , Guanosina/química , Oligodesoxirribonucleotídeos/química , DNA Forma Z/síntese química , DNA Forma Z/metabolismo , DNA Forma Z/efeitos da radiação , Proteínas de Fluorescência Verde/metabolismo , Oligodesoxirribonucleotídeos/síntese química , Oligodesoxirribonucleotídeos/metabolismo , Oligodesoxirribonucleotídeos/efeitos da radiação , Oxirredução , Ligação Proteica , Temperatura de Transição , Raios Ultravioleta
17.
Sci Rep ; 8(1): 14828, 2018 10 04.
Artigo em Inglês | MEDLINE | ID: mdl-30287873

RESUMO

Dimethyl sulfoxide (DMSO) is a small molecule with polar, aprotic and amphiphilic properties. It serves as a solvent for many polar and nonpolar molecules and continues to be one of the most used solvents (vehicle) in medical applications and scientific research. To better understand the cellular effects of DMSO within the concentration range commonly used as a vehicle (0.1-1.5%, v/v) for cellular treatments, we applied Attenuated Total Reflectance (ATR) Fourier Transform Infrared (FT-IR) spectroscopy to DMSO treated and untreated epithelial colon cancer cells. Both unsupervised (Principal Component Analysis-PCA) and supervised (Linear Discriminant Analysis-LDA) pattern recognition/modelling algorithms applied to the IR data revealed total segregation and prominent differences between DMSO treated and untreated cells at whole, lipid and nucleic acid regions. Several of these data were supported by other independent techniques. Further IR data analyses of macromolecular profile indicated comprehensive alterations especially in proteins and nucleic acids. Protein secondary structure analysis showed predominance of ß-sheet over α-helix in DMSO treated cells. We also observed for the first time, a reduction in nucleic acid level upon DMSO treatment accompanied by the formation of Z-DNA. Molecular docking and binding free energy studies indicated a stabilization of Z-DNA in the presence of DMSO. This alternate DNA form may be related with the specific actions of DMSO on gene expression, differentiation, and epigenetic alterations. Using analytical tools combined with molecular and cellular biology techniques, our data indicate that even at very low concentrations, DMSO induces a number of changes in all macromolecules, which may affect experimental outcomes where DMSO is used as a solvent.


Assuntos
Neoplasias do Colo/patologia , Dimetil Sulfóxido/metabolismo , Células Epiteliais/fisiologia , Algoritmos , Neoplasias do Colo/metabolismo , Simulação por Computador , DNA Forma Z/metabolismo , Células HCT116 , Humanos , Simulação de Acoplamento Molecular , Complexos Multiproteicos/metabolismo , Análise de Componente Principal , Conformação Proteica em alfa-Hélice , Conformação Proteica em Folha beta , Receptores de Reconhecimento de Padrão/metabolismo , Espectroscopia de Infravermelho com Transformada de Fourier
18.
Nucleic Acids Res ; 46(19): 10504-10513, 2018 11 02.
Artigo em Inglês | MEDLINE | ID: mdl-30184200

RESUMO

BZ junctions, which connect B-DNA to Z-DNA, are necessary for local transformation of B-DNA to Z-DNA in the genome. However, the limited information on the junction-forming sequences and junction structures has led to a lack of understanding of the structural diversity and sequence preferences of BZ junctions. We determined three crystal structures of BZ junctions with diverse sequences followed by spectroscopic validation of DNA conformation. The structural features of the BZ junctions were well conserved regardless of sequences via the continuous base stacking through B-to-Z DNA with A-T base extrusion. However, the sequence-dependent structural heterogeneity of the junctions was also observed in base step parameters that are correlated with steric constraints imposed during Z-DNA formation. Further, circular dichroism and fluorescence-based analysis of BZ junctions revealed that a base extrusion was only found at the A-T base pair present next to a stable dinucleotide Z-DNA unit. Our findings suggest that Z-DNA formation in the genome is influenced by the sequence preference for BZ junctions.


Assuntos
Adenosina Desaminase/química , DNA de Forma B/química , DNA Forma Z/química , DNA/química , Conformação de Ácido Nucleico , Domínios Proteicos , Proteínas de Ligação a RNA/química , Adenosina Desaminase/genética , Adenosina Desaminase/metabolismo , Pareamento de Bases , Sequência de Bases , Dicroísmo Circular , Cristalografia por Raios X , DNA/genética , DNA/metabolismo , DNA de Forma B/genética , DNA de Forma B/metabolismo , DNA Forma Z/genética , DNA Forma Z/metabolismo , Humanos , Modelos Moleculares , Proteínas de Ligação a RNA/genética , Proteínas de Ligação a RNA/metabolismo
19.
Int J Mol Sci ; 19(4)2018 Apr 04.
Artigo em Inglês | MEDLINE | ID: mdl-29617273

RESUMO

Recognition of unusual left-handed Z-DNA by specific binding of small molecules is crucial for understanding biological functions in which this particular structure participates. Recent investigations indicate that zinc cationic porphyrin (ZnTMPyP4) is promising as a probe for recognizing Z-DNA due to its characteristic chiroptical properties upon binding with Z-DNA. However, binding mechanisms of the ZnTMPyP4/Z-DNA complex remain unclear. By employing time-resolved UV-visible absorption spectroscopy in conjunction with induced circular dichroism (ICD), UV-vis, and fluorescence measurements, we examined the binding interactions of ZnTMPyP4 towards B-DNA and Z-DNA. For the ZnTMPyP4/Z-DNA complex, two coexisting binding modes were identified as the electrostatic interaction between pyridyl groups and phosphate backbones, and the major groove binding by zinc(II) coordinating with the exposed guanine N7. The respective contribution of each mode is assessed, allowing a complete scenario of binding modes revealed for the ZnTMPyP4/Z-DNA. These interaction modes are quite different from those (intercalation and partial intercalation modes) for the ZnTMPyP4/B-DNA complex, thereby resulting in explicit differentiation between B-DNA and Z-DNA. Additionally, the binding interactions of planar TMPyP4 to DNA were also investigated as a comparison. It is shown that without available virtual orbitals to coordinate, TMPyP4 binds with Z-DNA solely in the intercalation mode, as with B-DNA, and the intercalation results in a structural transition from Z-DNA to B-ZNA. These results provide mechanistic insights for understanding ZnTMPyP4 as a probe of recognizing Z-DNA and afford a possible strategy for designing new porphyrin derivatives with available virtual orbitals for the discrimination of B-DNA and Z-DNA.


Assuntos
DNA/química , Metaloporfirinas/química , Conformação de Ácido Nucleico , DNA/metabolismo , DNA de Forma B/química , DNA de Forma B/metabolismo , DNA Forma Z/química , DNA Forma Z/metabolismo , Metaloporfirinas/metabolismo , Porfirinas/química , Porfirinas/metabolismo , Ligação Proteica , Análise Espectral
20.
Org Biomol Chem ; 16(13): 2198-2209, 2018 03 28.
Artigo em Inglês | MEDLINE | ID: mdl-29532848

RESUMO

Base modifications are known to affect the structure and function of DNA. C8-guanine adducts from various carcinogenic compounds have been shown to be potent Z-DNA inducers. Hence, it has been hypothesized that Z-DNA plays a role in cancer and other genetic diseases. In this comprehensive review, Z-DNA and the effect of prevalent C8-guanine adducts on the B-Z transition are addressed. The discoveries of Z-DNA binding proteins including ADAR1, E3L, DLM1, and PKZ have suggested the relevance of Z-DNA in living systems. In addition, increasing evidence on the Z-DNA connection to gene transcription and inhibition reveals potential biological functions of the left-handed DNA. Finally, C8-guanine adducts that promote Z-DNA formation can be used as a tool to explore the Z-DNA function and its role in carcinogenesis.


Assuntos
Adutos de DNA/metabolismo , DNA Forma Z/metabolismo , Guanina/química , Neoplasias/genética , Animais , Carcinógenos/química , Adutos de DNA/química , DNA Forma Z/química , DNA Forma Z/genética , Proteínas de Ligação a DNA/genética , Proteínas de Ligação a DNA/metabolismo , Regulação da Expressão Gênica/genética , Humanos
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