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1.
EMBO Mol Med ; 16(4): 1027-1045, 2024 Apr.
Artigo em Inglês | MEDLINE | ID: mdl-38448545

RESUMO

Clinical deployment of oligonucleotides requires delivery technologies that improve stability, target tissue accumulation and cellular internalization. Exosomes show potential as ideal delivery vehicles. However, an affordable generalizable system for efficient loading of oligonucleotides on exosomes remain lacking. Here, we identified an Exosomal Anchor DNA Aptamer (EAA) via SELEX against exosomes immobilized with our proprietary CP05 peptides. EAA shows high binding affinity to different exosomes and enables efficient loading of nucleic acid drugs on exosomes. Serum stability of thrombin inhibitor NU172 was prolonged by exosome-loading, resulting in increased blood flow after injury in vivo. Importantly, Duchenne Muscular Dystrophy PMO can be readily loaded on exosomes via EAA (EXOEAA-PMO). EXOEAA-PMO elicited significantly greater muscle cell uptake, tissue accumulation and dystrophin expression than PMO in vitro and in vivo. Systemic administration of EXOEAA-PMO elicited therapeutic levels of dystrophin restoration and functional improvements in mdx mice. Altogether, our study demonstrates that EAA enables efficient loading of different nucleic acid drugs on exosomes, thus providing an easy and generalizable strategy for loading nucleic acid therapeutics on exosomes.


Assuntos
Exossomos , Distrofia Muscular de Duchenne , Animais , Camundongos , Distrofina/genética , Camundongos Endogâmicos mdx , Exossomos/metabolismo , Morfolinos/metabolismo , Morfolinos/farmacologia , Morfolinos/uso terapêutico , Distrofia Muscular de Duchenne/tratamento farmacológico , Distrofia Muscular de Duchenne/genética , Oligonucleotídeos/metabolismo , Oligonucleotídeos/uso terapêutico
2.
Mol Pharm ; 21(3): 1204-1213, 2024 Mar 04.
Artigo em Inglês | MEDLINE | ID: mdl-38319924

RESUMO

Cytosolic DNA sensors (CDSs) recognize DNA molecules that are abnormally located in the cytosol, thus leading to the activation of the stimulator of interferon genes (STING) and the induction of type 1 interferon. In turn, type 1 interferon evokes defensive reactions against viral infections and activates the immune system; therefore, the use of agonists of CDSs as cancer therapeutics and vaccine adjuvants is expected. Double-stranded DNA molecules with dozens to thousands of bases derived from bacteria and viruses are agonists of CDSs. However, DNA is a water-soluble molecule with a high molecular weight, resulting in poor cellular uptake and endosomal escape. In contrast, long single-stranded DNA (lssDNA) obtained by rolling circle amplification is efficiently taken up and localized to endosomes. Here we constructed a CDS-targeting lssDNA via the facilitation of its intracellular transport from endosomes to the cytosol. An endosome-disrupting GALA peptide was used to deliver the lssDNA to the cytosol. A peptide-oligonucleotide conjugate (POC) was successfully obtained via the conjugation of the GALA peptide with an oligonucleotide complementary to the lssDNA. By hybridization of the POC to the complementary lssDNA (POC/lssDNA), the CDS-STING pathway in dendritic cells was efficiently stimulated. GALA peptide-conjugated DNA seems to be a helpful tool for the delivery of DNA to the cytosol.


Assuntos
DNA de Cadeia Simples , Peptídeos , Citosol/metabolismo , DNA de Cadeia Simples/metabolismo , Peptídeos/química , DNA/genética , Interferons/genética , Interferons/metabolismo , Oligonucleotídeos/metabolismo
3.
Talanta ; 272: 125824, 2024 May 15.
Artigo em Inglês | MEDLINE | ID: mdl-38422906

RESUMO

In this study, a self-powered biosensor based on an enzymatic biofuel cell was proposed for the first time for the ultrasensitive detection of soluble CD44 protein. The as-prepared biosensor was composed of the co-exist aptamer and glucose oxidase bioanode and bilirubin oxidase modified biocathode. Initially, the electron transfer from bioanode to biocathode was hindered due to the presence of the aptamer with high insulation, generating a low open-circuit voltage (EOCV). Once the target CD44 protein was present, it was recognized and captured by the aptamer at the bioanode, thus the interaction between the target CD44 protein and the immobilized aptamer caused the structural change at the surface of the electrode, which facilitated the transfer of electrons. The EOCV showed a good linear relationship with the logarithm of the CD44 protein concentrations in the range of 0.5-1000 ng mL-1 and the detection limit was 0.052 ng mL-1 (S/N = 3). The sensing platform showed excellent anti-interference performance and outstanding stability that maintained over 97% of original EOCV after 15 days. In addition, the relative standard deviation (1.40-1.96%) and recovery (100.23-101.31%) obtained from detecting CD44 protein in real-life blood samples without special pre-treatment indicated that the constructed biosensor had great potential for early cancer diagnosis.


Assuntos
Fontes de Energia Bioelétrica , Técnicas Biossensoriais , Transporte de Elétrons , Glucose Oxidase/química , Oligonucleotídeos/metabolismo , Eletrodos , Limite de Detecção
4.
Nucleic Acids Res ; 52(7): 3924-3937, 2024 Apr 24.
Artigo em Inglês | MEDLINE | ID: mdl-38421610

RESUMO

RNA ligases are important enzymes in molecular biology and are highly useful for the manipulation and analysis of nucleic acids, including adapter ligation in next-generation sequencing of microRNAs. Thermophilic RNA ligases belonging to the RNA ligase 3 family are gaining attention for their use in molecular biology, for example a thermophilic RNA ligase from Methanobacterium thermoautotrophicum is commercially available for the adenylation of nucleic acids. Here we extensively characterise a newly identified RNA ligase from the thermophilic archaeon Palaeococcus pacificus (PpaRnl). PpaRnl exhibited significant substrate adenylation activity but low ligation activity across a range of oligonucleotide substrates. Mutation of Lys92 in motif I to alanine, resulted in an enzyme that lacked adenylation activity, but demonstrated improved ligation activity with pre-adenylated substrates (ATP-independent ligation). Subsequent structural characterisation revealed that in this mutant enzyme Lys238 was found in two alternate positions for coordination of the phosphate tail of ATP. In contrast mutation of Lys238 in motif V to glycine via structure-guided engineering enhanced ATP-dependent ligation activity via an arginine residue compensating for the absence of Lys238. Ligation activity for both mutations was higher than the wild-type, with activity observed across a range of oligonucleotide substrates with varying sequence and secondary structure.


Assuntos
RNA Ligase (ATP) , RNA Ligase (ATP)/metabolismo , RNA Ligase (ATP)/genética , RNA Ligase (ATP)/química , Especificidade por Substrato , Proteínas Arqueais/metabolismo , Proteínas Arqueais/genética , Proteínas Arqueais/química , Planococáceas/enzimologia , Planococáceas/genética , Engenharia de Proteínas , Mutação , Modelos Moleculares , Trifosfato de Adenosina/metabolismo , Oligonucleotídeos/metabolismo , Oligonucleotídeos/genética
5.
Chemistry ; 30(24): e202400137, 2024 Apr 25.
Artigo em Inglês | MEDLINE | ID: mdl-38403849

RESUMO

Besides being a key player in numerous fundamental biological processes, RNA also represents a versatile platform for the creation of therapeutic agents and efficient vaccines. The production of RNA oligonucleotides, especially those decorated with chemical modifications, cannot meet the exponential demand. Due to the inherent limits of solid-phase synthesis and in vitro transcription, alternative, biocatalytic approaches are in dire need to facilitate the production of RNA oligonucleotides. Here, we present a first step towards the controlled enzymatic synthesis of RNA oligonucleotides. We have explored the possibility of a simple protection step of the vicinal cis-diol moiety to temporarily block ribonucleotides. We demonstrate that pyrimidine nucleotides protected with acetals, particularly 2',3'-O-isopropylidene, are well-tolerated by the template-independent RNA polymerase PUP (polyU polymerase) and highly efficient coupling reactions can be achieved within minutes - an important feature for the development of enzymatic de novo synthesis protocols. Even though purines are not equally well-tolerated, these findings clearly demonstrate the possibility of using cis-diol-protected ribonucleotides combined with template-independent polymerases for the stepwise construction of RNA oligonucleotides.


Assuntos
RNA Polimerases Dirigidas por DNA , RNA , RNA/química , RNA/metabolismo , RNA Polimerases Dirigidas por DNA/metabolismo , RNA Polimerases Dirigidas por DNA/química , Oligonucleotídeos/química , Oligonucleotídeos/metabolismo , Oligonucleotídeos/síntese química , Ribonucleotídeos/química , Ribonucleotídeos/metabolismo , Nucleotídeos/química , Nucleotídeos/metabolismo , Nucleotídeos de Pirimidina/química , Nucleotídeos de Pirimidina/metabolismo
6.
Biochem Biophys Res Commun ; 703: 149650, 2024 Apr 09.
Artigo em Inglês | MEDLINE | ID: mdl-38377941

RESUMO

Tenascin-C is an extracellular matrix glycoprotein strongly expressed in coronary atherosclerotic plaque. Aptamers are single-stranded oligonucleotides that bind to specific target molecules with high affinity. This study hypothesized that tenascin-C expression at atherosclerotic plaque in vivo could be detected by tenascin-C specific aptamers using positron emission tomography (PET). This paper reports the radiosynthesis of a fluorine-18 (18F)-labeled tenascin-C aptamer for the biodistribution and PET imaging of the tenascin-C expression in apolipoprotein E-deficient (ApoE-/-) mice. The aortas ApoE-/- mice showed significantly increased positive areas of Oil red O staining than control C57BL/6 mice, and tenascin-C expression was detected in foam cells accumulated in the subendothelial lesions of ApoE-/- mice. The ex vivo biodistribution of the 18F-labeled tenascin-C aptamer showed significantly increased uptake at the aorta of ApoE-/- mice, and ex vivo autoradiography of aorta revealed the high accumulation of the 18F-labeled tenascin-C aptamer in the atherosclerotic lesions of ApoE-/- mice, which was consistent with the location of the atherosclerotic plaques detected by Oil red O staining. PET imaging of the 18F-labeled tenascin-C aptamer revealed a significantly higher mean standardized uptake in the aorta of the ApoE-/- mice than the control C57BL/6 mice. These data highlight the potential use of tenascin-C aptamer to diagnose atherosclerotic lesions in vivo.


Assuntos
Aterosclerose , Compostos Azo , Radioisótopos de Flúor , Placa Aterosclerótica , Camundongos , Animais , Placa Aterosclerótica/patologia , Tenascina/metabolismo , Distribuição Tecidual , Camundongos Endogâmicos C57BL , Aterosclerose/metabolismo , Tomografia por Emissão de Pósitrons/métodos , Matriz Extracelular/metabolismo , Oligonucleotídeos/metabolismo , Apolipoproteínas E/genética , Apolipoproteínas E/metabolismo , Modelos Animais de Doenças , Camundongos Knockout
7.
Cell Death Dis ; 15(2): 160, 2024 Feb 21.
Artigo em Inglês | MEDLINE | ID: mdl-38383492

RESUMO

Dysregulation of anti-apoptotic and pro-apoptotic protein isoforms arising from aberrant splicing is a crucial hallmark of cancers and may contribute to therapeutic resistance. Thus, targeting RNA splicing to redirect isoform expression of apoptosis-related genes could lead to promising anti-cancer phenotypes. Glioblastoma (GBM) is the most common type of malignant brain tumor in adults. In this study, through RT-PCR and Western Blot analysis, we found that BCLX pre-mRNA is aberrantly spliced in GBM cells with a favored splicing of anti-apoptotic Bcl-xL. Modulation of BCLX pre-mRNA splicing using splice-switching oligonucleotides (SSOs) efficiently elevated the pro-apoptotic isoform Bcl-xS at the expense of the anti-apoptotic Bcl-xL. Induction of Bcl-xS by SSOs activated apoptosis and autophagy in GBM cells. In addition, we found that ionizing radiation could also modulate the alternative splicing of BCLX. In contrast to heavy (carbon) ion irradiation, low energy X-ray radiation-induced an increased ratio of Bcl-xL/Bcl-xS. Inhibiting Bcl-xL through splicing regulation can significantly enhance the radiation sensitivity of 2D and 3D GBM cells. These results suggested that manipulation of BCLX pre-mRNA alternative splicing by splice-switching oligonucleotides is a novel approach to inhibit glioblastoma tumorigenesis alone or in combination with radiotherapy.


Assuntos
Glioblastoma , Precursores de RNA , Humanos , Processamento Alternativo/genética , Apoptose/genética , Proteína bcl-X/genética , Proteína bcl-X/metabolismo , Glioblastoma/genética , Glioblastoma/radioterapia , Oligonucleotídeos/metabolismo , Isoformas de Proteínas/metabolismo , Proteínas Proto-Oncogênicas c-bcl-2/metabolismo , Precursores de RNA/genética , Precursores de RNA/metabolismo , Splicing de RNA/genética
8.
Chembiochem ; 25(6): e202300870, 2024 03 15.
Artigo em Inglês | MEDLINE | ID: mdl-38179859

RESUMO

Tandem oligonucleotide synthesis (TOS) is an attractive strategy to increase automated oligonucleotide synthesis efficiency. TOS is accomplished via the introduction of an immolative linker within a single sequence composed of multiple oligonucleotide fragments. Here, we report the use of a commercially available building block, typically utilized for the chemical phosphorylation of DNA/RNA oligomers, to perform TOS. We show that the 2,2'-sulfonyldiethylene linker is efficiently self-immolated during the standard deprotection of DNA and RNA and presents itself as a generalizable methodology for nucleic acid TOS. Furthermore, we show the utility of this methodology by assembling a model siRNA construct, and showcase a template-directed ligation pathway to incorporate phosphoramidate or pyrophosphate linkages within DNA oligomers.


Assuntos
Oligonucleotídeos , RNA , RNA/metabolismo , Oligonucleotídeos/metabolismo , DNA , RNA Interferente Pequeno
9.
Acta Biomater ; 177: 316-331, 2024 Mar 15.
Artigo em Inglês | MEDLINE | ID: mdl-38244661

RESUMO

Parkinson's disease (PD) is the second most common neurodegenerative disorder characterized by the accumulation of α-synuclein (α-syn) aggregates called Lewy bodies leading to the gradual loss of dopaminergic (DA) neurons in the substantia nigra. Although α-syn expression can be attenuated by antisense oligonucleotides (ASOs) and heteroduplex oligonucleotide (HDO) by intracerebroventricular (ICV) injection, the challenge to peripheral targeted delivery of oligonucleotide safely and effectively into DA neurons remains unresolved. Here, we designed a new DNA/DNA double-stranded (complementary DNA, coDNA) molecule with cholesterol conjugation (Chol-HDO (coDNA)) based on an α-syn-ASO sequence and evaluated its silence efficiency. Further, Chol-HDO@LMNPs, Chol-HDO-loaded, cerebrovascular endothelial cell membrane with DSPE-PEG2000-levodopa modification (L-DOPA-CECm)-coated nanoparticles (NPs), were developed for the targeted treatment of PD by tail intravenous injection. CECm facilitated the blood-brain barrier (BBB) penetration of NPs, together with cholesterol escaped from reticuloendothelial system uptake, as well as L-DOPA was decarboxylated into dopamine which promoted the NPs toward the PD site for DA neuron regeneration. The behavioral tests demonstrated that the nanodecoys improved the efficacy of HDO on PD mice. These findings provide insights into the development of biomimetic nanodecoys loading HDO for precise therapy of PD. STATEMENT OF SIGNIFICANCE: The accumulation of α-synuclein (α-syn) aggregates is a hallmark of PD. Our previous study designed a specific antisense oligonucleotide (ASO) targeting human SNCA, but the traumatic intracerebroventricular (ICV) is not conducive to clinical application. Here, we further optimize the ASO by creating a DNA/DNA double-stranded molecule with cholesterol-conjugated, named Chol-HDO (coDNA), and develop a DA-targeted biomimetic nanodecoy Chol-HDO@LMNPs by engineering cerebrovascular endothelial cells membranes (CECm) with DSPE-PEG2000 and L-DOPA. The in vivo results demonstrated that tail vein injection of Chol-HDO@LMNPs could target DA neurons in the brain and ameliorate motor deficits in a PD mouse model. This investigation provides a promising peripheral delivery platform of L-DOPA-CECm nanodecoy loaded with a new Chol-HDO (coDNA) targeting DA neurons in PD therapy.


Assuntos
Doença de Parkinson , Camundongos , Humanos , Animais , Doença de Parkinson/genética , alfa-Sinucleína/genética , alfa-Sinucleína/metabolismo , Neurônios Dopaminérgicos/metabolismo , Levodopa , Oligonucleotídeos/farmacologia , Oligonucleotídeos/genética , Oligonucleotídeos/metabolismo , Biomimética , Células Endoteliais/metabolismo , DNA/metabolismo
10.
J Microbiol Biotechnol ; 34(1): 192-197, 2024 Jan 28.
Artigo em Inglês | MEDLINE | ID: mdl-37957116

RESUMO

Refractory infections, such as hospital-acquired pneumonia, can be better diagnosed with the assistance of precise methicillin-resistant Staphylococcus aureus (MRSA) testing. However, traditional methods necessitate high-tech tools, rigorous temperature cycling, and the extraction of genetic material from MRSA cells. Herein, we propose a sensitive, specific, and extraction-free strategy for MRSA detection by integrating allosteric probe-based target recognition and exonuclease-III (Exo-III)-enhanced color reaction. The penicillin-binding protein 2a (PBP2a) aptamer in the allosteric probe binds with MRSA to convert protein signals to nucleic acid signals. This is followed by the DNA polymerase-assisted target recycle and the production of numerous single-strand DNA (ssDNA) chains which bind with silver ion (Ag+) aptamer to form a blunt terminus that can be identified by Exo-III. As a result, the Ag+ aptamer pre-coupled to magnetic nanoparticles is digested. After magnetic separation, the Ag+ in liquid supernatant catalyzes 3,3',5,5'-tetramethylbenzidine (TMB) for a color reaction. In addition, a concentration of 54 cfu/mL is predicted to be the lowest detectable value. Based on this, our assay has a wide linear detection range, covering 5 orders of magnitude and demonstrating a high specificity, which allows it to accurately distinguish the target MRSA from other microorganisms.


Assuntos
Staphylococcus aureus Resistente à Meticilina , Staphylococcus aureus Resistente à Meticilina/genética , Proteínas de Ligação às Penicilinas/genética , Oligonucleotídeos/metabolismo
11.
Angew Chem Int Ed Engl ; 63(4): e202314262, 2024 Jan 22.
Artigo em Inglês | MEDLINE | ID: mdl-38012811

RESUMO

Molecular profiling of protein markers on small extracellular vesicles (sEVs) is a promising strategy for the precise detection and classification of ovarian cancers. However, this strategy is challenging owing to the lack of simple and practical detection methods. In this work, using an aptamer-based nanoflow cytometry (nFCM) detection strategy, a simple and rapid method for the molecular profiling of multiple protein markers on sEVs was developed. The protein markers can be easily labeled with aptamer probes and then rapidly profiled by nFCM. Seven cancer-associated protein markers, including CA125, STIP1, CD24, EpCAM, EGFR, MUC1, and HER2, on plasma sEVs were profiled for the molecular detection and classification of ovarian cancers. Profiling these seven protein markers enabled the precise detection of ovarian cancer with a high accuracy of 94.2 %. In addition, combined with machine learning algorithms, such as linear discriminant analysis (LDA) and random forest (RF), the molecular classifications of ovarian cancer cell lines and subtypes were achieved with overall accuracies of 82.9 % and 55.4 %, respectively. Therefore, this simple, rapid, and non-invasive method exhibited considerable potential for the auxiliary diagnosis and molecular classification of ovarian cancers in clinical practice.


Assuntos
Vesículas Extracelulares , Neoplasias Ovarianas , Humanos , Feminino , Biomarcadores Tumorais/metabolismo , Neoplasias Ovarianas/patologia , Oligonucleotídeos/metabolismo , Proteínas de Choque Térmico/metabolismo , Vesículas Extracelulares/metabolismo
12.
Small ; 20(8): e2306760, 2024 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-37821404

RESUMO

Autophagosome-tethering compound (ATTEC) technology has recently been emerging as a novel approach for degrading proteins of interest (POIs). However, it still faces great challenges in how to design target-specific ATTEC molecules. Aptamers are single-stranded DNA or RNA oligonucleotides that can recognize their target proteins with high specificity and affinity. Here, ATTEC is combined with aptamers for POIs degradation. As a proof of concept, pathological protein α-synuclein (α-syn) is chosen as the target and an efficient α-syn degrader is generated. Aptamer as a targeting warhead of α-syn is conjugated with LC3B-binding compound 5,7-dihydroxy-4-phenylcoumarin (DP) via bioorthogonal click reaction. It is demonstrated that the aptamer conjugated with DP is capable of clearing α-syn through LC3 and autophagic degradation. These results indicate that aptamer-based ATTECs are a versatile approach to degrade POIs by taking advantage of the well-defined different aptamers for targeting diverse proteins, which provides a new way for the design of ATTECs to degradation of targeted proteins.


Assuntos
Autofagossomos , alfa-Sinucleína , alfa-Sinucleína/metabolismo , Autofagossomos/metabolismo , Autofagia , Lisossomos/metabolismo , Oligonucleotídeos/metabolismo
13.
Nature ; 623(7989): 1001-1008, 2023 Nov.
Artigo em Inglês | MEDLINE | ID: mdl-37968393

RESUMO

Cyclic oligonucleotide-based antiphage signalling systems (CBASS) protect prokaryotes from viral (phage) attack through the production of cyclic oligonucleotides, which activate effector proteins that trigger the death of the infected host1,2. How bacterial cyclases recognize phage infection is not known. Here we show that staphylococcal phages produce a structured RNA transcribed from the terminase subunit genes, termed CBASS-activating bacteriophage RNA (cabRNA), which binds to a positively charged surface of the CdnE03 cyclase and promotes the synthesis of the cyclic dinucleotide cGAMP to activate the CBASS immune response. Phages that escape the CBASS defence harbour mutations that lead to the generation of a longer form of the cabRNA that cannot activate CdnE03. As the mammalian cyclase OAS1 also binds viral double-stranded RNA during the interferon response, our results reveal a conserved mechanism for the activation of innate antiviral defence pathways.


Assuntos
Bactérias , Nucleotidiltransferases , RNA Viral , Fagos de Staphylococcus , Animais , 2',5'-Oligoadenilato Sintetase/metabolismo , Bactérias/enzimologia , Bactérias/imunologia , Evolução Molecular , Imunidade Inata , Nucleotidiltransferases/metabolismo , Oligonucleotídeos/imunologia , Oligonucleotídeos/metabolismo , RNA Viral/imunologia , RNA Viral/metabolismo , Transdução de Sinais/imunologia , Fagos de Staphylococcus/genética , Fagos de Staphylococcus/imunologia
14.
Nucleic Acids Res ; 51(19): e99, 2023 10 27.
Artigo em Inglês | MEDLINE | ID: mdl-37739412

RESUMO

The first step in gene expression is the transcription of DNA sequences into RNA. Regulation at the level of transcription leads to changes in steady-state concentrations of RNA transcripts, affecting the flux of downstream functions and ultimately cellular phenotypes. Changes in transcript levels are routinely followed in cellular contexts via genome-wide sequencing techniques. However, in vitro mechanistic studies of transcription have lagged with respect to throughput. Here, we describe the use of a real-time, fluorescent-aptamer-based method to quantitate steady-state transcription rates of the Mycobacterium tuberculosis RNA polymerase. We present clear controls to show that the assay specifically reports on promoter-dependent, full-length RNA transcription rates that are in good agreement with the kinetics determined by gel-resolved, α-32P NTP incorporation experiments. We illustrate how the time-dependent changes in fluorescence can be used to measure regulatory effects of nucleotide concentrations and identity, RNAP and DNA concentrations, transcription factors, and antibiotics. Our data showcase the ability to easily perform hundreds of parallel steady-state measurements across varying conditions with high precision and reproducibility to facilitate the study of the molecular mechanisms of bacterial transcription.


Assuntos
Mycobacterium tuberculosis , Transcrição Gênica , RNA Polimerases Dirigidas por DNA/genética , RNA Polimerases Dirigidas por DNA/metabolismo , Mycobacterium tuberculosis/genética , Mycobacterium tuberculosis/metabolismo , Oligonucleotídeos/metabolismo , Reprodutibilidade dos Testes , RNA/metabolismo , Fatores de Transcrição/metabolismo
15.
Bioconjug Chem ; 34(10): 1822-1834, 2023 10 18.
Artigo em Inglês | MEDLINE | ID: mdl-37733627

RESUMO

The formation of noncovalent complexes by mixing of positively charged polymers with negatively charged oligonucleotides (ONs) is a widely explored concept in nanomedicine to achieve cellular delivery of ONs. Uptake of ON complexes occurs through endocytosis, which then requires release of ON from endosomes. As one type of polymer, cell-penetrating peptides (CPPs) are being used which are peptides of about 8-30 amino acids in length. However, only a few CPPs yield effective cytosolic ON delivery and activity. Several strategies have been devised to increase cellular uptake and enhance endosomal release, among which an increase of osmotic pressure through the so-called proton sponge effect, disruption of membrane integrity through membrane activity, and disulfide-mediated polymerization. Here, we address the relevance of these concepts for mRNA delivery by incorporating structural features into the human lactoferrin-derived CPP, which shows uptake but not delivery. The incorporation of histidines was explored to address osmotic pressure and structural motifs of the delivery-active CPP PepFect14 (PF14) to address membrane disturbance, and finally, the impact of polymerization was explored. Whereas oligomerization increased the stability of polyplexes against heparin-induced decomplexation, neither this approach nor the incorporation of histidine residues to promote a proton-sponge effect yielded activity. Also, the replacement of arginine residues with lysine or ornithine residues, as in PF14, was without effect, even though all polyplexes showed cellular uptake. Ultimately, sufficient activity could only be achieved by transferring amphipathic sequence motifs from PF14 into the hLF context with some benefit of oligomerization demonstrating overarching principles of delivery for CPPs, lipid nanoparticles, and other types of delivery polymers.


Assuntos
Peptídeos Penetradores de Células , Humanos , Peptídeos Penetradores de Células/química , Prótons , Oligonucleotídeos/metabolismo , Endocitose , Polímeros
16.
Bioconjug Chem ; 34(10): 1780-1788, 2023 10 18.
Artigo em Inglês | MEDLINE | ID: mdl-37736001

RESUMO

Proteolysis-targeting chimeras (PROTACs) have attracted attention as a chemical method of protein knockdown via the ubiquitin-proteasome system. Some oligonucleotide-based PROTACs have recently been developed for disease-related proteins that do not have optimal small-molecule ligands such as transcription factors. We have previously developed the PROTAC LCL-ER(dec), which uses a decoy oligonucleotide as a target ligand for estrogen receptor α (ERα) as a model transcription factor. However, LCL-ER(dec) has a low intracellular stability because it comprises natural double-stranded DNA sequences. In the present study, we developed PROTACs containing chemically modified decoys to address this issue. Specifically, we introduced phosphorothioate modifications and hairpin structures into LCL-ER(dec). Among the newly designed PROTACs, LCL-ER(dec)-H46, with a T4 loop structure at the end of the decoy, showed long-term ERα degradation activity while acquiring enzyme tolerance. These findings suggest that the introduction of hairpin structures is a useful modification of oligonucleotides in decoy oligonucleotide-based PROTACs.


Assuntos
Receptor alfa de Estrogênio , Quimera de Direcionamento de Proteólise , Receptores de Estrogênio , Receptor alfa de Estrogênio/metabolismo , Oligonucleotídeos/metabolismo , Complexo de Endopeptidases do Proteassoma/metabolismo , Proteólise , Receptores de Estrogênio/metabolismo , Fatores de Transcrição/metabolismo , Ubiquitina-Proteína Ligases , Humanos
17.
Methods Mol Biol ; 2701: 77-90, 2023.
Artigo em Inglês | MEDLINE | ID: mdl-37574476

RESUMO

Many chemicals cause mutation or cancer in animals and humans by forming DNA lesions, including base adducts, which play a critical role in mutagenesis and carcinogenesis. A large number of such adducts are repaired by the DNA glycosylase-mediated base excision repair (BER) pathway, and some are processed by nucleotide excision repair (NER) and nucleotide incision repair (NIR). To understand what structural features determine repair enzyme specificity and mechanism in chemically modified DNA in vitro, we developed and optimized a DNA cleavage assay using defined oligonucleotides containing a single, site specifically placed lesion. This assay can be used to investigate novel activities against any newly identified derivatives from chemical compounds, substrate specificity and cleavage efficiency of repair enzymes, and quantitative structure-function relationships. Overall, the methodology is highly sensitive and can also be modified to explore whether a lesion is processed by NER or NIR activity, as well as to study its miscoding properties in translesion DNA synthesis (TLS).


Assuntos
DNA Glicosilases , Oligonucleotídeos , Humanos , Animais , Oligonucleotídeos/genética , Oligonucleotídeos/metabolismo , Clivagem do DNA , Reparo do DNA , DNA Glicosilases/metabolismo , DNA/genética
18.
Nat Commun ; 14(1): 5153, 2023 08 24.
Artigo em Inglês | MEDLINE | ID: mdl-37620381

RESUMO

DNA methylation is important for gene expression and alterations in DNA methylation are involved in the development and progression of cancer and other major diseases. Analysis of DNA methylation patterns has until now been dependent on either a chemical or an enzymatic pre-treatment, which are both time consuming procedures and potentially biased due to incomplete treatment. We present a qPCR technology, EpiDirect®, that allows for direct PCR quantification of DNA methylations using untreated DNA. EpiDirect® is based on the ability of Intercalating Nucleic Acids (INA®) to differentiate between methylated and unmethylated cytosines in a special primer design. With this technology, we develop an assay to analyze the methylation status of a region of the MGMT promoter used in treatment selection and prognosis of glioblastoma patients. We compare the assay to two bisulfite-relying, methyl-specific PCR assays in a study involving 42 brain tumor FFPE samples, revealing high sensitivity, specificity, and the clinical utility of the method.


Assuntos
Reação em Cadeia da Polimerase , Reação em Cadeia da Polimerase/instrumentação , Reação em Cadeia da Polimerase/métodos , DNA/metabolismo , Metilação de DNA , Temperatura , Oligonucleotídeos/metabolismo , Ilhas de CpG
19.
Mikrochim Acta ; 190(8): 295, 2023 07 17.
Artigo em Inglês | MEDLINE | ID: mdl-37458810

RESUMO

The development and performance of a DNA probe adsorbing Mn2+-modified black phosphorus (BP@Mn2+/DNA) hybrid nanosensor is reported that enables rapid detection of cancer-derived exosomal microRNAs (miRNAs) and exosomes. This two-dimensional (2D) nanosensor can spontaneously penetrate the lipid bilayer of exosome membranes owing to its ultra-thin geometry. Subsequently, the adsorbed probe specifically hybridizes with the target miRNA and then dissociates from the nanosensor surface, generating fluorescent signals. Therefore, the BP@Mn2+/DNA nanosensor can differentiate between colorectal cancer (CRC) cell-derived exosomes and those derived from intestinal epithelial cells through sensing of exosomal miRNAs. Furthermore, when the epithelial cell adhesion molecule (EpCAM) aptamer is adsorbed onto BP@Mn2+ instead of the miRNA probe, the nanosensor is able to distinguish exosomes derived from the plasma of CRC patients from those of healthy controls by the recognition ability of the EpCAM aptamer. By utilizing this nanosensor, we were able to effectively differentiate cancer-derived exosomes through the direct detection of miRNA-21 within the exosomes, as well as the identification of specific exosomal membrane proteins. This nanosensor design paves the way for the development of rapid and efficient cancer-derived exosomal miRNA and exosome biosensing nanoplatforms.


Assuntos
Exossomos , MicroRNAs , Neoplasias , Humanos , Exossomos/metabolismo , Molécula de Adesão da Célula Epitelial/metabolismo , Neoplasias/metabolismo , Oligonucleotídeos/metabolismo
20.
J Inherit Metab Dis ; 46(6): 1147-1158, 2023 11.
Artigo em Inglês | MEDLINE | ID: mdl-37467014

RESUMO

Glycogen storage disease type-Ia (GSD-Ia), characterized by impaired blood glucose homeostasis, is caused by a deficiency in glucose-6-phosphatase-α (G6Pase-α or G6PC). Using the G6pc-R83C mouse model of GSD-Ia, we explored a CRISPR/Cas9-based double-strand DNA oligonucleotide (dsODN) insertional strategy that uses the nonhomologous end-joining repair mechanism to correct the pathogenic p.R83C variant in G6pc exon-2. The strategy is based on the insertion of a short dsODN into G6pc exon-2 to disrupt the native exon and to introduce an additional splice acceptor site and the correcting sequence. When transcribed and spliced, the edited gene would generate a wild-type mRNA encoding the native G6Pase-α protein. The editing reagents formulated in lipid nanoparticles (LNPs) were delivered to the liver. Mice were treated either with one dose of LNP-dsODN at age 4 weeks or with two doses of LNP-dsODN at age 2 and 4 weeks. The G6pc-R83C mice receiving successful editing expressed ~4% of normal hepatic G6Pase-α activity, maintained glucose homeostasis, lacked hypoglycemic seizures, and displayed normalized blood metabolite profile. The outcomes are consistent with preclinical studies supporting previous gene augmentation therapy which is currently in clinical trials. This editing strategy may offer the basis for a therapeutic approach with an earlier clinical intervention than gene augmentation, with the additional benefit of a potentially permanent correction of the GSD-Ia phenotype.


Assuntos
Doença de Depósito de Glicogênio Tipo I , Oligonucleotídeos , Camundongos , Animais , Oligonucleotídeos/metabolismo , Sistemas CRISPR-Cas , Doença de Depósito de Glicogênio Tipo I/genética , Doença de Depósito de Glicogênio Tipo I/terapia , Doença de Depósito de Glicogênio Tipo I/metabolismo , Fígado/metabolismo , Glucose-6-Fosfatase/genética , Glucose-6-Fosfatase/metabolismo
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