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1.
Angew Chem Int Ed Engl ; : e202408581, 2024 Jul 16.
Artículo en Inglés | MEDLINE | ID: mdl-39012206

RESUMEN

A first example of a mitochondrial G-quadruplex (mitoG4s) targeted Ru(II) photooxidant complex is reported. The complex, Ru-TAP-PDC3 induces photodamage toward guanine quadruplexes (G4s) located in the mitochondrial genome under hypoxic and normoxic conditions. Ru-TAP-PDC3 shows high affinity for mitoG4s and localises within mitochondria of live HeLa cells. Immunolabelling with anti-G4 antibody, BG4, confirms Ru-TAP-PDC3 associates with G4s within the mitochondria of fixed cells. The complex induces depletion of mtDNA in live cells under irradiation at 405 nm, confirmed by loss of PicoGreen signal from mitochondria. Biochemical studies confirm this process induces apoptosis. The complex shows low dark toxicity and an impressive phototoxicity index (PI) of >89 was determined in Hela under very low intensity irradiation, 5 J/cm2. The phototoxicity is thought to operate through both Type II singlet oxygen and Type III pathways depending on normoxic or hypoxic conditions from live cell imaging and plasmid DNA cleavage. Overall, we demonstrate targeting mitoG4s and mtDNA with a photooxidant is a potent route to achieving apoptosis under hypoxic conditions that can be extended to phototherapy.

2.
J Med Virol ; 96(6): e29692, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38804172

RESUMEN

To achieve a virological cure for hepatitis B virus (HBV), innovative strategies are required to target the covalently closed circular DNA (cccDNA) genome. Guanine-quadruplexes (G4s) are a secondary structure that can be adopted by DNA and play a significant role in regulating viral replication, transcription, and translation. Antibody-based probes and small molecules have been developed to study the role of G4s in the context of the human genome, but none have been specifically made to target G4s in viral infection. Herein, we describe the development of a humanized single-domain antibody (S10) that can target a G4 located in the PreCore (PreC) promoter of the HBV cccDNA genome. MicroScale Thermophoresis demonstrated that S10 has a strong nanomolar affinity to the PreC G4 in its quadruplex form and a structural electron density envelope of the complex was determined using Small-Angle X-ray Scattering. Lentiviral transduction of S10 into HepG2-NTCP cells shows nuclear localization, and chromatin immunoprecipitation coupled with next-generation sequencing demonstrated that S10 can bind to the HBV PreC G4 present on the cccDNA. This research validates the existence of a G4 in HBV cccDNA and demonstrates that this DNA secondary structure can be targeted with high structural and sequence specificity using S10.


Asunto(s)
ADN Circular , ADN Viral , G-Cuádruplex , Virus de la Hepatitis B , Anticuerpos de Dominio Único , Humanos , Virus de la Hepatitis B/genética , Virus de la Hepatitis B/inmunología , ADN Circular/genética , ADN Viral/genética , Células Hep G2 , Anticuerpos de Dominio Único/genética , Anticuerpos de Dominio Único/inmunología , Anticuerpos de Dominio Único/química , Genoma Viral , Regiones Promotoras Genéticas , Replicación Viral , Hepatitis B/virología
3.
Int J Biol Macromol ; 268(Pt 2): 131811, 2024 May.
Artículo en Inglés | MEDLINE | ID: mdl-38677694

RESUMEN

It is estimated that 15 % of couples at reproductive age worldwide suffer from infertility, approximately 50 % of cases are caused by male factors. Significant progress has been made in the diagnosis and treatment of male infertility through assisted reproductive technology and molecular genetics methods. However, there is still inadequate research on the underlying mechanisms of gene regulation in the process of spermatogenesis. Guanine-quadruplexes (G4s) are a class of non-canonical secondary structures of nucleic acid commonly found in genomes and RNAs that play important roles in various biological processes. Interestingly, the DEAH-box helicase 36 (DHX36) displays high specificity for the G4s which can unwind both DNA G4s and RNA G4s enzymatically and is highly expressed in testis, thereby regulating multiple cellular functions including transcription, pre-mRNA splicing, translation, telomere maintenance, genomic stability, and RNA metabolism in development and male infertility. This review provides an overview of the roles of G4s and DHX36 in reproduction and development. We mainly focus on the potential role of DHX36 in male infertility. We also discuss possible future research directions regarding the mechanism of spermatogenesis mediated by DHX36 through G4s in spermatogenesis-related genes and provide new targets for gene therapy of male infertility.


Asunto(s)
ARN Helicasas DEAD-box , G-Cuádruplex , Infertilidad Masculina , Espermatogénesis , Masculino , Humanos , ARN Helicasas DEAD-box/metabolismo , ARN Helicasas DEAD-box/genética , ARN Helicasas DEAD-box/química , Infertilidad Masculina/genética , Espermatogénesis/genética , Animales , ARN/genética , ARN/metabolismo
4.
Elife ; 122024 Feb 23.
Artículo en Inglés | MEDLINE | ID: mdl-38391174

RESUMEN

The dynamic interplay between guanine-quadruplex (G4) structures and pathogenicity islands (PAIs) represents a captivating area of research with implications for understanding the molecular mechanisms underlying pathogenicity. This study conducted a comprehensive analysis of a large-scale dataset from reported 89 pathogenic strains of bacteria to investigate the potential interactions between G4 structures and PAIs. G4 structures exhibited an uneven and non-random distribution within the PAIs and were consistently conserved within the same pathogenic strains. Additionally, this investigation identified positive correlations between the number and frequency of G4 structures and the GC content across different genomic features, including the genome, promoters, genes, tRNA, and rRNA regions, indicating a potential relationship between G4 structures and the GC-associated regions of the genome. The observed differences in GC content between PAIs and the core genome further highlight the unique nature of PAIs and underlying factors, such as DNA topology. High-confidence G4 structures within regulatory regions of Escherichia coli were identified, modulating the efficiency or specificity of DNA integration events within PAIs. Collectively, these findings pave the way for future research to unravel the intricate molecular mechanisms and functional implications of G4-PAI interactions, thereby advancing our understanding of bacterial pathogenicity and the role of G4 structures in pathogenic diseases.


Asunto(s)
G-Cuádruplex , Islas Genómicas , Islas Genómicas/genética , Bacterias/genética , ADN , Virulencia/genética , Escherichia coli/genética , Genoma Bacteriano
5.
Plant J ; 118(1): 124-140, 2024 Apr.
Artículo en Inglés | MEDLINE | ID: mdl-38113339

RESUMEN

As in many other organisms, tRNA-derived RNAs (tDRs) exist in plants and likely have multiple functions. We previously showed that tDRs are present in Arabidopsis under normal growth conditions, and that the ones originating from alanine tRNAs are the most abundant in leaves. We also showed that tDRs Ala of 20 nt produced from mature tRNAAla (AGC) can block in vitro protein translation. Here, we report that first, these tDRs Ala (AGC) can be found within peculiar foci in the cell that are neither P-bodies nor stress granules and, second, that they assemble into intermolecular RNA G-quadruplex (rG4) structures. Such tDR Ala rG4 structures can specifically interact with an Arabidopsis DEA(D/H) RNA helicase, the DExH1 protein, and unwind them. The rG4-DExH1 protein interaction relies on a glycine-arginine domain with RGG/RG/GR/GRR motifs present at the N-terminal extremity of the protein. Mutations on the four guanine residues located at the 5' extremity of the tDR Ala abolish its rG4 structure assembly, association with the DExH1 protein, and foci formation, but they do not prevent protein translation inhibition in vitro. Our data suggest that the sequestration of tDRs Ala into rG4 complexes might represent a way to modulate accessible and functional tDRs for translation inhibition within the plant cell via the activity of a specific RNA helicase, DExH1.


Asunto(s)
Arabidopsis , G-Cuádruplex , Arabidopsis/genética , ARN Helicasas/genética , ARN , ARN de Transferencia
6.
Biomolecules ; 13(11)2023 11 11.
Artículo en Inglés | MEDLINE | ID: mdl-38002321

RESUMEN

Cationic liposomes, specifically 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP) liposomes, serve as successful carriers for guanine-quadruplex (G4) structure-based cytosine-guanine oligodeoxynucleotides (CpG ODNs). The combined benefits of CpG ODNs forming a G4 structure and a non-viral vector carrier endow the ensuing complex with promising adjuvant properties. Although G4-CpG ODN-DOTAP complexes show a higher immunostimulatory effect than naked G4-CpG ODNs, the effects of the complex composition, especially charge ratios, on the production of the pro-inflammatory cytokines interleukin (IL)-6 and interferon (IFN)-α remain unclear. Here, we examined whether charge ratios drive the bifurcation of cytokine inductions in human peripheral blood mononuclear cells. Linear CpG ODN-DOTAP liposome complexes formed micrometer-sized positively charged agglomerates; G4-CpG ODN-DOTAP liposome complexes with low charge ratios (0.5 and 1.5) formed ~250 nm-sized negatively charged complexes. Notably, low-charge-ratio (0.5 and 1.5) complexes induced significantly higher IL-6 and IFN-α levels simultaneously than high-charge-ratio (2 and 2.5) complexes. Moreover, confocal microscopy indicated a positive correlation between the cellular uptake of the complex and amount of cytokine induced. The observed effects of charge ratios on complex size, surface charge, and affinity for factors that modify cellular-uptake, intracellular-activity, and cytokine-production efficiency highlight the importance of a rational complex design for delivering and controlling G4-CpG ODN activity.


Asunto(s)
Liposomas , Propano , Humanos , Liposomas/química , Propano/farmacología , Leucocitos Mononucleares , Citocinas , Oligodesoxirribonucleótidos/farmacología , Oligodesoxirribonucleótidos/química , Interleucina-6/farmacología , Interferón-alfa/farmacología
7.
Chemphyschem ; 24(16): e202300264, 2023 08 15.
Artículo en Inglés | MEDLINE | ID: mdl-37318900

RESUMEN

The complexes of G-quadruplex forming DNA thrombin binding aptamers (TBA) and polyamidoamine dendrimers (PAMAM) were studied with the aim to form a model targeted drug delivery system. Hydrodynamic diameter, zeta potential and melting temperature (Tm ) were investigated by dynamic light scattering and UV-VIS spectrophotometry. Non-covalent adsorption by means of electrostatic interaction between positively charged amino groups of dendrimers (+) and negatively charged phosphate groups of aptamers (-) has driven the formation of aggregates. The size of complexes was in the range of 0.2-2 µm and depended on the type of dispersant, charge ratio (+/-) and temperature. Raising the temperature increased the polydispersity, new smaller size distributions were observed indicating the G-quadruplex unfolding. The melting transition temperature of TBA aptamer was affected by the presence of amino-terminated PAMAM rather than carboxylated succinic acid PAMAM-SAH dendrimer, thus supporting the electrostatic nature of interaction that disturbed denaturation of target-specific quadruplex aptamer structure.


Asunto(s)
Aptámeros de Nucleótidos , Dendrímeros , Dendrímeros/química , Dispersión Dinámica de Luz , Espectrofotometría
8.
Retrovirology ; 20(1): 10, 2023 05 30.
Artículo en Inglés | MEDLINE | ID: mdl-37254203

RESUMEN

BACKGROUND: Once integrated in the genome of infected cells, HIV-1 provirus is transcribed by the cellular transcription machinery. This process is regulated by both viral and cellular factors, which are necessary for an efficient viral replication as well as for the setting up of viral latency, leading to a repressed transcription of the integrated provirus. RESULTS: In this study, we examined the role of two parameters in HIV-1 LTR promoter activity. We identified DNA topoisomerase1 (TOP1) to be a potent repressor of this promoter and linked this repression to its catalytic domain. Additionally, we confirmed the folding of a Guanine quadruplex (G4) structure in the HIV-1 promoter and its repressive effect. We demonstrated a direct interaction between TOP1 and this G4 structure, providing evidence of a functional relationship between the two repressive elements. Mutations abolishing G4 folding affected TOP1/G4 interaction and hindered G4-dependent inhibition of TOP1 catalytic activity in vitro. As a result, HIV-1 promoter activity was reactivated in a native chromatin environment. Lastly, we noticed an enrichment of predicted G4 sequences in the promoter of TOP1-repressed cellular genes. CONCLUSIONS: Our results demonstrate the formation of a TOP1/G4 complex on the HIV-1 LTR promoter and its repressive effect on the promoter activity. They reveal the existence of a new mechanism of TOP1/G4-dependent transcriptional repression conserved between viral and human genes. This mechanism contrasts with the known property of TOP1 as global transcriptional activator and offers new perspectives for anti-cancer and anti-viral strategies.


Asunto(s)
VIH-1 , Humanos , VIH-1/genética , Guanina , Factores de Transcripción/genética , Cromatina , Duplicado del Terminal Largo de VIH/genética , Transcripción Genética
9.
Anal Chim Acta ; 1253: 341098, 2023 May 01.
Artículo en Inglés | MEDLINE | ID: mdl-36965991

RESUMEN

Sensitive and accurate determination of tumor-derived exosomes from complicated biofluids is an important prerequisite for early tumor diagnosis through exosome-based liquid biopsy. Herein, a label-free fluorescence immunoassay protocol for ultrasensitive detection of exosomes was developed by engineering substantial dimerized guanine-quadruplex (Dimer-G4) signal units via in situ cutting-mediated exponential rolling circle amplification (CM-ERCA). First, exosomes were captured and enriched via immunomagnetic separation. Then, molecular recognition was built by the formation of antibody-aptamer sandwich immunocomplex through the specific binding of the designed aptamer-primers with the targeted exosomes. The accuracy of exosome detection was significantly improved by the specific recognition of two typical exosomal protein markers simultaneously. Eventually, in situ CM-ERCA was triggered by a perfect match between the multifunctional circular DNA template and the aptamer-primer on exosomal surface. Amplicons of CM-ERCA loaded with Dimer-G4 were exponentially accumulated during continuous cyclic amplification, dramatically lighting up the thioflavin T (ThT) and generating substantial Dimer-G4 signal units. As a result, ultrasensitive detection of exosomes with the detection limit down to 2.4 × 102 particles/mL was achieved due to the fluorescence enhancement of substantial Dimer-G4 signal units, which is ahead of most of available fluorescence-based methods reported currently. In addition, the intense fluorescence emission and favorable anti-interference of the proposed immunoassay supports identification of exosomes direct in human serums, overcoming the limitations of conventional G4/ThT in serum analysis and revealing its potential for exosome-based liquid biopsy.


Asunto(s)
Aptámeros de Nucleótidos , Técnicas Biosensibles , Exosomas , Neoplasias , Humanos , Exosomas/química , Aptámeros de Nucleótidos/química , Neoplasias/metabolismo , Técnicas Biosensibles/métodos , Límite de Detección
10.
Autophagy ; 19(7): 1901-1915, 2023 07.
Artículo en Inglés | MEDLINE | ID: mdl-36740766

RESUMEN

Guanine-quadruplex structures (G4) are unusual nucleic acid conformations formed by guanine-rich DNA and RNA sequences and known to control gene expression mechanisms, from transcription to protein synthesis. So far, a number of molecules that recognize G4 have been developed for potential therapeutic applications in human pathologies, including cancer and infectious diseases. These molecules are called G4 ligands. When the biological effects of G4 ligands are studied, the analysis is often limited to nucleic acid targets. However, recent evidence indicates that G4 ligands may target other cellular components and compartments such as lysosomes and mitochondria. Here, we summarize our current knowledge of the regulation of lysosome by G4 ligands, underlying their potential functional impact on lysosome biology and autophagic flux, as well as on the transcriptional regulation of lysosomal genes. We outline the consequences of these effects on cell fate decisions and we systematically analyzed G4-prone sequences within the promoter of 435 lysosome-related genes. Finally, we propose some hypotheses about the mechanisms involved in the regulation of lysosomes by G4 ligands.


Asunto(s)
Autofagia , G-Cuádruplex , Humanos , Ligandos , ADN/metabolismo , Guanina
11.
J Mol Cell Biol ; 14(11)2023 04 06.
Artículo en Inglés | MEDLINE | ID: mdl-36484653

RESUMEN

Spermatogenesis is a highly complex developmental process that typically consists of mitosis, meiosis, and spermiogenesis. DNA/RNA helicase DHX36, a unique guanine-quadruplex (G4) resolvase, plays crucial roles in a variety of biological processes. We previously showed that DHX36 is highly expressed in male germ cells with the highest level in zygotene spermatocytes. Here, we deleted Dhx36 in advanced germ cells with Stra8-GFPCre and found that a Dhx36 deficiency in the differentiated spermatogonia leads to meiotic defects and abnormal spermiogenesis. These defects in late stages of spermatogenesis arise from dysregulated transcription of G4-harboring genes, which are required for meiosis. Thus, this study reveals that Dhx36 plays crucial roles in late stages of spermatogenesis.


Asunto(s)
ARN Helicasas , ARN , Masculino , ADN/genética , ADN Helicasas/genética , Meiosis , ARN Helicasas/genética , Espermatocitos , Espermatogénesis/genética , Animales , Ratones
12.
Biomolecules ; 12(12)2022 12 13.
Artículo en Inglés | MEDLINE | ID: mdl-36551297

RESUMEN

Unmethylated cytosine-phosphate-guanosine oligodeoxynucleotides (CpG ODNs) induce inflammatory cytokines and type I interferons (IFNs) to activate the immune system. To apply CpG ODNs as vaccine adjuvants, the cellular uptake and stability of phosphodiester-based, non-modified ODNs require further improvement. Previously developed new CpG ODNs forming guanine-quadruplex (G4) structures showed higher nuclease resistance and cellular uptake than linear CpG ODNs; however, the complex formation of G4-CpG ODNs with antigen proteins is necessary for their application as vaccine adjuvants. In this study, we utilized a cationic polymer, ε-poly-L-lysine (ε-PLL), as a carrier for G4-CpG ODNs and antigen. The ε-PLL/G4-CpG ODN complex exhibited enhanced stability against nucleases. Cellular uptake of the ε-PLL/G4-CpG ODN complex positively correlated with the N/P ratio. In comparison to naked G4-CpG ODNs, the ε-PLL/G4-CpG ODN complex induced extremely high levels of interleukin (IL)-6, IL-12, and IFN-ß. Relative immune cytokine production was successfully tuned by N/P ratio modification. Mice with the ε-PLL/G4-CpG ODN/ovalbumin (OVA) complex showed increased OVA-specific immunoglobulin (Ig)G, IgG1, and IgG2c levels, whereas total IgE levels did not increase and weight gain rates were not affected. Therefore, ε-PLL can serve as a safe and effective phosphodiester-based, non-modified CpG ODN delivery system, and the ε-PLL/G4-CpG ODN/antigen complex is a highly promising candidate for vaccine adjuvants and can be further used in clinical research.


Asunto(s)
Adyuvantes Inmunológicos , Adyuvantes de Vacunas , Animales , Ratones , Adyuvantes Inmunológicos/farmacología , Adyuvantes Inmunológicos/química , Lisina , Formación de Anticuerpos , Guanina , Antígenos , Inmunoglobulina G , Fosfatos , Oligodesoxirribonucleótidos/química
13.
Viruses ; 14(11)2022 11 11.
Artículo en Inglés | MEDLINE | ID: mdl-36423103

RESUMEN

The integration of the HIV-1 genome into the host genome is an essential step in the life cycle of the virus and it plays a critical role in the expression, long-term persistence, and reactivation of HIV expression. To better understand the local genomic environment surrounding HIV-1 proviruses, we assessed the influence of non-canonical B-form DNA (non-B DNA) on the HIV-1 integration site selection. We showed that productively and latently infected cells exhibit different integration site biases towards non-B DNA motifs. We identified a correlation between the integration sites of the latent proviruses and non-B DNA features known to potently influence gene expression (e.g., cruciform, guanine-quadruplex (G4), triplex, and Z-DNA). The reactivation potential of latent proviruses with latency reversal agents also correlated with their proximity to specific non-B DNA motifs. The perturbation of G4 structures in vitro using G4 structure-destabilizing or -stabilizing ligands resulted in a significant reduction in integration within 100 base pairs of G4 motifs. The stabilization of G4 structures increased the integration within 300-500 base pairs from G4 motifs, increased integration near transcription start sites, and increased the proportion of latently infected cells. Moreover, we showed that host lens epithelium-derived growth factor (LEDGF)/p75 and cleavage and polyadenylation specificity factor 6 (CPSF6) influenced the distribution of integration sites near several non-B DNA motifs, especially G4 DNA. Our findings identify non-B DNA motifs as important factors that influence productive and latent HIV-1 integration and the reactivation potential of latent proviruses.


Asunto(s)
ADN Forma B , G-Cuádruplex , Infecciones por VIH , Seropositividad para VIH , VIH-1 , Humanos , VIH-1/genética , Motivos de Nucleótidos , Latencia del Virus , ADN , Provirus/genética
14.
Brain Sci ; 12(7)2022 Jun 30.
Artículo en Inglés | MEDLINE | ID: mdl-35884681

RESUMEN

Olduvai protein domains (also known as DUF1220 or NBPF) have undergone the greatest human-specific increase in the copy number of any coding region in the genome. Their repeat number was strongly associated with the evolutionary expansion of brain volumes, neuron counts and cognitive abilities, as well as with disorders of the autistic spectrum. Nevertheless, the domain function and cellular mechanisms underlying the positive selection of Olduvai DNA sequences in higher primates remain obscure. Here, I show that the inclusion of Olduvai exon doublets in mature transcripts is facilitated by a potent splicing enhancer that was created through duplication within the first exon. The enhancer is the strongest among the NBPF transcripts and further promotes the already high splicing activity of the unexpanded first exons of the two-exon domains, safeguarding the expanded Olduvai exon doublets in the mature transcriptome. The duplication also creates a predicted RNA guanine quadruplex that may regulate the access to spliceosomal components of the super-enhancer and influence the splicing of adjacent exons. Thus, positive Olduvai selection during primate evolution is likely to result from a combination of multiple targets in gene expression pathways, including RNA splicing.

15.
Chemistry ; 28(57): e202201824, 2022 Oct 12.
Artículo en Inglés | MEDLINE | ID: mdl-35791808

RESUMEN

We investigated the mechanisms leading to the specific recognition of Guanine Guadruplex (G4) by DARPins peptides, which can lead to the design of G4 s specific sensors. To this end we carried out all-atom molecular dynamic simulations to unravel the interactions between specific nucleic acids, including human-telomeric (h-telo), Bcl-2, and c-Myc, with different peptides, forming a DARPin/G4 complex. By comparing the sequences of DARPin with that of a peptide known for its high affinity for c-Myc, we show that the recognition cannot be ascribed to sequence similarity but, instead, depends on the complementarity between the three-dimensional arrangement of the molecular fragments involved: the α-helix/loops domain of DARPin and the G4 backbone. Our results reveal that DARPins tertiary structure presents a charged hollow region in which G4 can be hosted, thus the more complementary the structural shapes, the more stable the interaction.


Asunto(s)
G-Cuádruplex , Ácidos Nucleicos , Sitios de Unión de Anticuerpos , Proteínas de Repetición de Anquirina Diseñadas , Epítopos , Guanina/química , Humanos , Péptidos/química , Proteínas Proto-Oncogénicas c-bcl-2
16.
Nanomedicine ; 40: 102508, 2022 02.
Artículo en Inglés | MEDLINE | ID: mdl-34906721

RESUMEN

Guanine-quadruplex (G4) oligodeoxynucleotides (ODNs) that contain unmethylated cytosine-phosphate-guanine motifs (G4 CpG ODN) with phosphodiester backbones are safer than the phosphorothioate (PT)-modified CpG ODNs recently used as vaccine adjuvants. However, cellular uptake and the nuclease stability of G4 CpG ODNs are still insufficient, resulting in lower immunostimulatory activity than PT-modified CpG ODNs. We aimed to enhance the immunostimulatory properties of G4 CpG ODNs by complexing with the cationic liposome 1,2-dioleoyl-3-trimethylammonium-propane (DOTAP). The complex acquired nuclease resistance and improved cellular uptake. The immunostimulatory activity of the G4 CpG ODN-DOTAP lipoplexes was enhanced to a level comparable to that of PT-modified ODNs. In addition, the lipoplexes based on unmodified G4 CpG ODNs demonstrated CpG motif-specific immunostimulant activity, although PT-modified ODNs lacking the CpG motif could activate human immune cells. Interestingly, G4 CpG ODN-DOTAP lipoplexes induced interferon-α production in a loop-length dependent manner.


Asunto(s)
Oligodesoxirribonucleótidos , Propano , Adyuvantes Inmunológicos/farmacología , Islas de CpG , Ácidos Grasos Monoinsaturados , Humanos , Oligodesoxirribonucleótidos/farmacología , Compuestos de Amonio Cuaternario/farmacología
17.
Int J Biol Macromol ; 194: 882-894, 2022 Jan 01.
Artículo en Inglés | MEDLINE | ID: mdl-34838862

RESUMEN

Guanine radical cation (G•+) is a key intermediate in many oxidative processes occurring in nucleic acids. Here, by combining mixed Quantum Mechanical/Molecular Mechanics calculations and Molecular Dynamics (MD) simulations, we study how the structural behaviour of a tract GGG(TTAGGG)3 (hereafter Tel21) of the human telomeric sequence, folded in an antiparallel quadruple helix, changes when one of the G bases is ionized to G•+ (Tel21+). Once assessed that the electron-hole is localized on a single G, we perform MD simulations of twelve Tel21+ systems, differing in the position of G•+ in the sequence. When G•+ is located in the tetrad adjacent to the diagonal loop, we observe substantial structural rearrangements, which can decrease the electrostatic repulsion with the inner Na+ ions and increase the solvent exposed surface of G•+. Analysis of solvation patterns of G•+ provides new insights on the main reactions of G•+, i.e. the deprotonation at two different sites and hydration at the C8 atom, the first steps of the processes producing 8oxo-Guanine. We suggest the main structural determinants of the relative reactivity of each position and our conclusions, consistent with the available experimental trends, can help rationalizing the reactivity of other G-quadruplex topologies.


Asunto(s)
ADN/química , G-Cuádruplex , Guanina/química , Iones/química , Simulación de Dinámica Molecular , Estrés Oxidativo , Teoría Cuántica , Telómero/química , Humanos , Modelos Moleculares , Conformación de Ácido Nucleico , Solubilidad
18.
Biomolecules ; 11(11)2021 11 01.
Artículo en Inglés | MEDLINE | ID: mdl-34827615

RESUMEN

Guanine-quadruplex-based CpG oligodeoxynucleotides (G4 CpG ODNs) have been developed as potent immunostimulatory agents with reduced sensitivity to nucleases. We designed new monomeric G4 ODNs with an antiparallel topology using antiparallel type duplex/G4 ODNs as robust scaffolds, and we characterized their topology and effects on cytokine secretion. Based on circular dichroism analysis and quantification of mRNA levels of immunostimulatory cytokines, it was found that monomeric antiparallel G4 CpG ODNs containing two CpG motifs in the first functional loop, named G2.0.0, could maintain antiparallel topology and generate a high level of immunostimulatory cytokines in RAW264 mouse macrophage-like cell lines. We also found that the flanking sequence in the CpG motif altered the immunostimulatory effects. Gc2c.0.0 and Ga2c.0.0 are monomeric antiparallel G4 CpG ODNs with one cytosine in the 3' terminal and one cytosine/adenine in the 5' terminal of CpG motifs that maintained the same resistance to degradation in serum as G2.0.0 and improved interleukin-6 production in RAW264 and bone marrow-derived macrophages. The immunostimulatory activity of antiparallel G4 CpG ODNs is superior to that of linear natural CpG ODNs. These results provide insights for the rational design of highly potent CpG ODNs using antiparallel G4 as a robust scaffold.


Asunto(s)
Guanina , Oligodesoxirribonucleótidos , Adyuvantes Inmunológicos , Animales , Ratones
19.
Nano Lett ; 21(21): 8987-8992, 2021 11 10.
Artículo en Inglés | MEDLINE | ID: mdl-34694812

RESUMEN

Throughout the past few decades, guanine quadruplex DNA structures have attracted much interest both from a fundamental material science perspective and from a technologically oriented perspective. Novel guanine octuplex DNA, formed from coiled quadruplex DNA, was recently discovered as a stable and rigid DNA-based nanostructure. A detailed electronic structure study of this new nanomaterial, performed by scanning tunneling spectroscopy on a subsingle-molecule level at cryogenic temperature, is presented herein. The electronic levels and lower energy gap of guanine octuplex DNA compared to quadruplex DNA dictate higher transverse conductivity through guanine octads than through guanine tetrads.


Asunto(s)
G-Cuádruplex , Nanoestructuras , ADN/química , Electrónica , Guanina , Conformación de Ácido Nucleico
20.
Adv Mater ; 33(8): e2006932, 2021 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-33475220

RESUMEN

Guanine quadruplex (G4)-DNA structures have sparked the interest of many scientists due to their important biological roles and their potential use in molecular nanoelectronics and nanotechnology. The high guanine content in G4-DNA endows it with mechanical stability, robustness, and improved charge transport properties-attractive attributes for a molecular nanowire. The self-driven formation of a novel G4-DNA-based nanostructure, coined guanine octuplex (G8)-DNA, is reported herein. Atomic force microscopy and scanning tunneling microscopy characterization of this molecule reveal its organized coiled-coil structure, which is found to be stable under different temperatures and surrounding conditions. G8-DNA exhibits enhanced stiffness, mechanical and thermodynamic stability when compared to its parent G4-DNA. These, along with its high guanine content, make G8-DNA a compelling new molecule, and a highly prospective candidate for molecular nanoelectronics.


Asunto(s)
ADN/química , G-Cuádruplex , Nanotecnología , Nanoestructuras
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