Journal of Nucleic Acids最新文献

{"title":"Position-Dependent Stabilization of DNA/RNA Duplexes by Site-Specific Incorporation of LNA Nucleosides.","authors":"Elisa Tomita-Sudo, Tomoka Akita, Nae Sakimoto, Saori Tahara-Takamine, Renshin Sano, Shigenori Iwai, Junji Kawakami","doi":"10.1155/jna/7266073","DOIUrl":"10.1155/jna/7266073","url":null,"abstract":"<p><p>Owing to their enhanced functional properties, 2 ^',4 ^'-bridged nucleic acids/locked nucleic acids (2 ^',4 ^'-BNAs/LNAs) are considered promising candidates for antisense oligonucleotide therapeutics. The spatial arrangement of LNA residues within the oligonucleotide sequence is a key determinant of binding affinity to the target RNA. In this study, a series of antisense oligonucleotides containing LNA at different positions was synthesized, and their binding affinities toward the target RNA were systematically evaluated. Oligonucleotides with LNA modifications at the terminal regions exhibited approximately 100-fold lower affinity than those modified near the central region. These results offer valuable insights for the rational design of LNA-based antisense oligonucleotides.</p>","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2026 ","pages":"7266073"},"PeriodicalIF":2.7,"publicationDate":"2026-05-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13139905/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147838854","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A Biochemical Analysis of LINC00896 RNA in Cortex Neuronal Cells and Its Possible Connection to the Development of Autism.","authors":"Rachel A Hellmann Whitaker, Joshua J Storey, Isabella Vannavong, Robert S Mangiamele, Micalyn A Trihus, Donovan D Floyd, Trevor Rohder, Dylan L Cleveland, Andrew Rizea","doi":"10.1155/jna/5292315","DOIUrl":"10.1155/jna/5292315","url":null,"abstract":"<p><p>Autism spectrum disorder is a complex neurological and developmental disorder that is characterized by altered brain structures and interconnectivity, which results in a vast array of psychosocial and physiological irregularities. This is due to the complex genetic topography of autism and to the intersectionality of genetic and environmental factors that contribute to the development of this disorder. To better understand the genetic factors that cause autism, the gene linc00896, which encodes a long noncoding intergenic RNA, was biochemically and biologically analyzed primarily through circular dichroism, liquid chromatography, and mass spectrometry. From this analysis, it was determined that LINC00896 RNA has a vast interactome and that through this interactome, LINC00896 RNA influences numerous cellular processes that contribute to the symptoms of autistic patients. Additionally, the structural analysis of LINC00896 RNA indicated stable but flexible secondary and tertiary structures that support the numerous binding interactions identified in the interactome. Through these empirical findings, the linc00896 gene was identified as being an important genetic factor that contributes to the development of autism.</p>","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2026 ","pages":"5292315"},"PeriodicalIF":2.7,"publicationDate":"2026-03-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13127100/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147816552","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"RETRACTION: Genetic Clearness Novel Strategy of Group I <i>Bacillus</i> Species Isolated from Fermented Food and Beverages by Using Fibrinolytic Enzyme Gene Encoding a Serine-Like Enzyme.","authors":"Journal Of Nucleic Acids","doi":"10.1155/jna/9801841","DOIUrl":"10.1155/jna/9801841","url":null,"abstract":"<p><p>[This retracts the article DOI: 10.1155/2019/5484896.].</p>","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2026 ","pages":"9801841"},"PeriodicalIF":2.7,"publicationDate":"2026-03-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13127097/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"147816598","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Corrigendum to \"Design and Evaluation of RNA Aptamer-Mediated Delivery of C/EBP<i>β</i> siRNA for Oncological Therapy\".","authors":"","doi":"10.1155/jna/9867151","DOIUrl":"https://doi.org/10.1155/jna/9867151","url":null,"abstract":"<p><p>[This corrects the article DOI: 10.1155/jna/1461574.].</p>","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2025 ","pages":"9867151"},"PeriodicalIF":1.8,"publicationDate":"2025-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12443502/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145086355","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Design and Evaluation of RNA Aptamer-Mediated Delivery of C/EBP<i>β</i> siRNA for Oncological Therapy.","authors":"D Vasconcelos, M H Sodergren, V Reebye, J Vasara, M S Song, K Holm, S E Khorsandi, J Rossi, N Habib, K W Huang","doi":"10.1155/jna/1461574","DOIUrl":"10.1155/jna/1461574","url":null,"abstract":"<p><p>The CCAAT/enhancer-binding protein beta (CEBPB or C/EBP<i>β</i>) is a transcription factor that plays a critical role in cellular differentiation, metabolism, and immune response. Emerging evidence has highlighted its complex involvement in both solid and hematological cancers, such as hepatocellular carcinoma (HCC) and pancreatic ductal adenocarcinoma (PDAC), where it can act as an oncogene or a tumor suppressor, depending on the context. In this study, we describe the design and evaluation of a conjugate formed by a small interfering RNA (siRNA) for CEBPB and a transferrin receptor targeting aptamer (TfR-siCEBPB). The designed conjugate is active in human and mouse cells, by transfection and by passive uptake, demonstrating target engagement with strong downregulation of CEBPB mRNA transcript. In murine models of metastatic PDAC and cirrhotic HCC, treatment with TfR-siCEBPB was associated with reduction in tumor burden and improvement in liver function biomarkers. This novel aptamer conjugate allows delivery of targeted oligonucleotide therapy and is a promising therapeutic tool to take forward to human trials.</p>","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2025 ","pages":"1461574"},"PeriodicalIF":1.8,"publicationDate":"2025-03-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11991783/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143997182","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dual Detection of Hepatitis B and C Viruses Using CRISPR-Cas Systems and Lateral Flow Assay.","authors":"Syeda Najidah Shahni, Sarah Albogami, Iqbal Azmi, Bijay Pattnaik, Rituparna Chaudhuri, Kapil Dev, Jawed Iqbal, Amit Sharma, Tanveer Ahmad","doi":"10.1155/2024/8819834","DOIUrl":"https://doi.org/10.1155/2024/8819834","url":null,"abstract":"<p><p>The development of sensitive and specific diagnostic tools for hepatitis B virus (HBV) and hepatitis C virus (HCV) remains crucial for effective disease management and control. In this study, we utilized CRISPR-Cas12 and CRISPR-Cas13 systems for the detection of HBV (DNA virus) and HCV (RNA virus), respectively. We designed and tested multiple guide RNAs (gRNAs) targeting both viruses, confirming successful cleavage of target sequences through gel electrophoresis and a fluorescent reporter assay. Using optimized gRNAs, we developed a lateral flow assay (LFA) for sensitive detection of HBV and HCV, demonstrating a concentration-dependent signal increase. Importantly, no cross-reactivity was observed with other viral targets. To further enhance sensitivity, we employed a dual-enzyme approach, combining Cas12 and Cas13 in a single reaction, which significantly improved detection limits for both viruses. Finally, we developed a dual antigen detection LFA strip capable of simultaneously detecting both HBV and HCV in a single sample. This approach holds promise for point-of-care (POC) diagnostics where the specific viral infection is unknown. This study addresses the current limitations in CRISPR-Cas based diagnostics, namely, the need for ultrasensitive detection methods and the ability to detect multiple antigens using a single test strip. Our findings demonstrate the feasibility of using CRISPR-Cas systems for highly sensitive and specific detection of HBV and HCV, paving the way for potential POC application.</p>","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2024 ","pages":"8819834"},"PeriodicalIF":1.3,"publicationDate":"2024-10-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11470818/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142467924","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Synthesis and Evaluation of MGB Polyamide-Oligonucleotide Conjugates as Gene Expression Control Compounds.","authors":"Kazuo Kamaike,&nbsp;Mutsumi Sano,&nbsp;Daisuke Sakata,&nbsp;Yu Nishihara,&nbsp;Hiroaki Amino,&nbsp;Akihiro Ohtsuki,&nbsp;Yui Okada,&nbsp;Takafumi Miyakawa,&nbsp;Makoto Kogawara,&nbsp;Mai Tsutsumi,&nbsp;Misato Takahashi,&nbsp;Etsuko Kawashima,&nbsp;Koichiro Ota,&nbsp;Hiroaki Miyaoka","doi":"10.1155/2023/2447998","DOIUrl":"https://doi.org/10.1155/2023/2447998","url":null,"abstract":"<p><p>MGB polyamide-oligonucleotide conjugates <b>ON 1</b>-<b>4</b> with linked MGB polyamides at the 2-exocyclic amino group of a guanine base using aminoalkyl linkers were synthesized and evaluated in terms of binding affinity for complementary DNA containing the MGB polyamide binding sequence using <i>T</i> _m and CD analyses. The MGB polyamides comprised pyrrole polyamides (Py₄- and Py₃-), which possess binding affinity for A-T base pairs, and imidazole (Im₃-) and pyrrole-<i>γ</i>-imidazole (Py₃-<i>γ</i>-Im₃-) polyamide hairpin motifs, which possess binding affinity for C-G base pairs. It was found that the stability of modified dsDNA was greatly influenced by the linker length. Py₄- and Py₃-oligonucleotide conjugates (<b>ON 1</b> (<i>n</i> = 4) and <b>ON 2</b> (<i>n</i> = 4)) containing the 4-aminobutyl linker formed stable dsDNA with complementary DNA. Although Im₃-oligonucleotide conjugate <b>ON 3</b> (<i>n</i> = 4) containing the 4-aminobutyl linker formed stable dsDNA with complementary DNA, stabilization of dsDNA by the imidazole amide moiety of <b>ON 3</b> (<i>n</i> = 4) was lower compared with the pyrrole amide moiety of <b>ON 2</b> (<i>n</i> = 4). The Py₃-<i>γ</i>-Im₃-oligonucleotide conjugate <b>ON 4</b> (<i>n</i> = 2), which possesses binding affinity for C-G base pairs via a pyrrole/imidazole combination and contains a 2-aminoethyl linker, showed high binding ability for complementary DNA. Furthermore, the DNA sequence recognition of MGB polyamide-oligonucleotide conjugates was investigated using single-base mismatch DNAs, which possess a mismatch base in the MGB polyamide binding sequence. The Py₃-<i>γ</i>-Im₃-oligonucleotide conjugate <b>ON 4</b> (<i>n</i> = 2) showed high sequence recognition ability for complementary DNA.</p>","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2023 ","pages":"2447998"},"PeriodicalIF":2.3,"publicationDate":"2023-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10030224/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9523227","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Comparing Two Methods for the Isolation of Exosomes.","authors":"Mohammad A Aziz,&nbsp;Benedict Seo,&nbsp;Haizal M Hussaini,&nbsp;Merilyn Hibma,&nbsp;Alison M Rich","doi":"10.1155/2022/8648373","DOIUrl":"https://doi.org/10.1155/2022/8648373","url":null,"abstract":"<p><p>Exosomes are membrane-bound nanovesicles released by cells into their extracellular environment. They carry different types of RNA including mRNA which may be useful in the diagnosis of various diseases. Exosome isolation has been a challenge because of their small size; therefore, two exosome isolation methods were compared in this study. The Exoquick-TC PLUS™ exosome isolation kit (kit) was compared with the classic ultracentrifugation (UC) method for exosome isolation. In samples obtained using both methods, cryo-electron microscopy showed round or slightly elongated vesicles with diameters ranging from 50 to 150 nm and delimited by a bilayered membrane. Dynamic light scattering resulted in multiple peaks for kit exosomes, whereas a single peak was observed for UC exosomes. Significantly, more total RNA was present in UC exosomes in contrast to kit exosomes (<i>P</i> < 0.0001). This was reflected in subsequent mRNA analysis using qPCR, where UC exosomes had lower Ct values compared to kit exosomes. In conclusion, exosome characterization revealed the presence of exosomes in both UC and the kit samples. The kit samples presented additional peaks from DLS which might be due to impurities. Overall, due to a higher total RNA and mRNA content, UC is a better option for subsequent mRNA analysis; nevertheless, the kit can still be used if an ultracentrifuge is not available as four out of the five genes selected were detected and quantified using the kit.</p>","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":" ","pages":"8648373"},"PeriodicalIF":2.3,"publicationDate":"2022-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9626211/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40443240","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Update on the Development of Toehold Switch-Based Approach for Molecular Diagnostic Tests of COVID-19","authors":"Almando Geraldi, N. N. T. Puspaningsih, Fatiha Khairunnisa","doi":"10.1155/2022/7130061","DOIUrl":"https://doi.org/10.1155/2022/7130061","url":null,"abstract":"A high volume of diagnostic tests is needed during the coronavirus disease 2019 (COVID-19) pandemic to obtain representative results. These results can help to design and implement effective policies to prevent the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Diagnosis using current gold standard methods, i.e., real-time quantitative PCR (RT-qPCR), is challenging, especially in areas with limited trained personnel and health-related infrastructure. The toehold switch-based diagnostic system is a promising alternative method for detecting SARS-CoV-2 that has advantages such as inexpensive cost per testing, rapid, and highly sensitive and specific analysis. Moreover, the system can be applied to paper-based platforms, simplifying the distribution and utilization in low-resource settings. This review provides insight into the development of toehold switch-based diagnostic devices as the most recent methods for detecting SARS-CoV-2.","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":"2022 1","pages":""},"PeriodicalIF":2.3,"publicationDate":"2022-05-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48508335","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Exposure to a Pathological Condition May Be Required for the Cells to Secrete Exosomes Containing mtDNA Aberration","authors":"Manjusha Vaidya, Sandeep Sreerama, Mariana Gaviria, K. Sugaya","doi":"10.1155/2022/7960198","DOIUrl":"https://doi.org/10.1155/2022/7960198","url":null,"abstract":"Exosomes, nanovesicles secreted by all cells, carry out intercellular communication by transmitting biologically active cargo comprising DNA, RNA, and proteins. These biomolecules reflect the status of their parent cells and can be altered by pathological conditions. Therefore, the researchers have been investigating differential sequences and quantities of DNA associated with exosomes as valuable biomarkers of diseases. Exosomes carry different types of DNA molecules, including genomic, cytoplasmic, and mitochondrial (mtDNA). The mtDNA aberrations are reported to be a hallmark of diseases involving oxidative stress, such as cancer and neurodegenerative diseases. Establishing robust in vitro models comprising appropriate cell lineages is the first step towards investigating disease-specific anomalies and testing therapeutics. Induced pluripotent stem (iPS) cells from patients with diseases have been used for this purpose since they can differentiate into various cells. The current study investigated mtDNA aberrations in exosomes secreted by primary cancer cells and neural stem cells (NSCs) differentiated from iPS cells. The primary cancer cells were isolated from surgically removed glioblastoma multiforme (GBM) tissue, and the iPS cells were produced from control and Alzheimer's disease (AD) subjects' B lymphocytes. We detected aberrations in mtDNA associated with exosomes secreted from GBM cells but not from the NSCs. This result indicates that the cells may not secrete exosomes carrying mtDNA aberration without exposure to a pathological condition. Thus, we may need to consider this fact when we use iPS cell-derived cells as an in vitro disease model.","PeriodicalId":16575,"journal":{"name":"Journal of Nucleic Acids","volume":" ","pages":""},"PeriodicalIF":2.3,"publicationDate":"2022-03-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48842269","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}