RNA nanomed最新文献

{"title":"Applications of Surface Plasmon Resonance for Advanced Studies Involving Nucleic Acids.","authors":"Katelynn Pranger, Kenya Rosas, Dmitriy Khon, Emil F Khisamutdinov","doi":"10.59566/ISRNN.2024.0101044","DOIUrl":"https://doi.org/10.59566/ISRNN.2024.0101044","url":null,"abstract":"<p><p>Surface plasmon resonance (SPR) is increasingly recognized as one of the most widely used techniques for studying nucleic acid interactions. The main advantage of SPR is its ability to measure the binding affinities and association/dissociation kinetics of complexes in real-time, in a label-free environment, and using relatively small quantities of materials. The method is based on the immobilization of one of the binding partners, ligand, on a dedicated sensor surface. Immobilization is followed by the injection of the other partner, analyte, over the surface containing the ligand. The binding is monitored by subsequent changes in the refractive index of the medium close to the sensor surface upon injection of the analyte. In the field of Nucleic Acid, SPR has been intensively used in the study of various artificial and naturally occurring RNA/DNA molecules interaction with large molecular weight mass proteins and small organic molecules because of its ability to detect highly dynamic complexes that are difficult to investigate using other techniques. This mini review aims to provide a short guideline for setting up SPR experiments to identify nucleic acid complexes and assess their binding affinity or kinetics. It covers protocols for (i) nucleic acid immobilization methods, including biotin-streptavidin, metal ion-based affinity, and amine coupling, (ii) analyte-binding analysis, (iii) affinity and kinetic measurements, and (iv) data interpretation. Determining the affinity and kinetics of nucleic acid interactions through SPR is essential for gaining insights into molecular-level binding mechanisms, thus supporting advancements in nucleic acid nanotechnology. The review also highlights the various sections of SPR applications in nucleic acid research, including nucleic acid-probe immobilization, interactions with biomolecules, aptamer studies, and small molecule binding, concluding with perspectives on future developments in the field.</p>","PeriodicalId":520473,"journal":{"name":"RNA nanomed","volume":"1 1","pages":"44-60"},"PeriodicalIF":0.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11981602/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144039852","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":"Co-incubation of Short Amphiphilic Peptides with Dicer Substrate RNAs Results in <i>β</i>-Sheet Fibrils for Enhanced Gene Silencing in Cancer Cells.","authors":"Kshitij Gupta, Lorena Parlea, Mathias Viard, Katelyn Smith, Anu Puri, Joseph T Bergman, Taejin Kim, Bruce A Shapiro","doi":"10.59566/isrnn.2024.0101061","DOIUrl":"10.59566/isrnn.2024.0101061","url":null,"abstract":"<p><p>RNA can interact with positively charged, amphiphilic peptides to cooperatively assemble into fibrils that enable RNA transport across cancer cellular membranes. RNA decreases the folding energy barrier imposed by the electrostatic repulsion between these charged peptides, thus partaking in RNA-peptide self-assembly along particular pathways in the energy landscape. Specific amphiphilic peptides capable of protecting and transporting RNA across a membrane have Type II' β-turn hairpin forming motifs in their structures, which aids self-assembly into β-sheet fibrils. We employed a set of such cationic, amphiphilic peptides that have random coiled structures in the absence of folding stimuli, to characterize the (peptides):(RNA) assembly. We subjected these complexes to extensive biophysical characterization <i>in vitro</i> and in cell culture. We show that short RNAs (such as Dicer substrate RNAs) can lead these peptides to self-assemble into β-sheet fibrils that have RNA transport capabilities and can act as non-viral delivery vectors for RNA. Modulation in the peptide sequence implicitly alters the way they bind RNA and influence the peptides' ability to transport nucleic acids across membranes.</p>","PeriodicalId":520473,"journal":{"name":"RNA nanomed","volume":"1 1","pages":"61-78"},"PeriodicalIF":0.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12007892/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144005463","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":"Harnessing Computational Approaches for RNA-Targeted Drug Discovery.","authors":"Yuanzhe Zhou, Shi-Jie Chen","doi":"10.59566/isrnn.2024.0101001","DOIUrl":"10.59566/isrnn.2024.0101001","url":null,"abstract":"<p><p>RNA molecules have emerged as promising therapeutic targets due to their diverse functional and regulatory roles within cells. Computational modeling in RNA-targeted drug discovery presents a significant opportunity to expedite the discovery of novel small molecule compounds. However, this field encounters unique challenges compared to protein-targeted drug design, primarily due to limited experimental data availability and current models' inability to adequately address RNA's conformational flexibility during ligand recognition. Despite these challenges, several studies have successfully identified active RNA-targeting compounds using structure-based approaches or quantitative structure-activity relationship (QSAR) models. This review offers an overview of recent advancements in modeling RNA-small molecule interactions, emphasizing practical applications of computational methods in RNA-targeted drug discovery. Additionally, we survey existing databases that catalog nucleic acid-small molecule interactions. As interest in RNA-small molecule interactions grows and curated databases expand, the field anticipates rapid development. Novel computational models are poised to enhance the identification of potent and selective small-molecule modulators for therapeutic needs.</p>","PeriodicalId":520473,"journal":{"name":"RNA nanomed","volume":"1 1","pages":"1-15"},"PeriodicalIF":0.0,"publicationDate":"2024-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11975998/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143813328","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":"Conversion of Chemical Drugs into Targeting Ligands on RNA Nanoparticles and Assessing Payload Stoichiometry for Optimal Biodistribution in Cancer Treatment.","authors":"Congcong Xu, Hongran Yin, Tesla Yudhistira, Zhefeng Li, Daniel W Binzel, Peixuan Guo","doi":"10.59566/isrnn.2024.0101109","DOIUrl":"10.59566/isrnn.2024.0101109","url":null,"abstract":"<p><p>Active targeting-mediated nanodelivery takes advantages of ligand-receptor specificity to avoid non-specific distribution, holding great promise for the treatment of a spectrum of diseases. RNA nanoparticles have demonstrated rapid spontaneous tumor targeting and very little organ accumulation due to rapid renal clearance of non-tumor accumulated RNA nanoparticles. However available ligands for specific cells are limited, yet many chemical entities possess receptor targeting capability and remains unexplored. To provide specific tumor accumulation, a multivalent targeting strategy on RNA nanoparticles to control their <i>in vivo</i> fate is implemented. Methotrexate (MTX), a clinically approved chemotherapy was used as a tumor-targeting ligand through conjugation to our RNA nanoparticle with controlled conjugation of various copy numbers. As copies of conjugated MTX increased on the nanoparticle, the specific binding to overexpressed folate receptor was enhanced as demonstrated by flow cytometry analysis and confocal microscopy imaging. Increasing the amounts of conjugated MTX did not significantly change the nanoparticle size, Zeta potential, or cytokine induction. Increased amounts of conjugated MTX resulted in improved cell inhibition due to MTX release following cell internalization. However, increasing conjugated MTX to the RNA nanoparticles reduced the melting temperature of RNA nanoparticles and increased <i>in vitro</i> serum protein binding to the nanoparticles. Thus, <i>in vivo</i> biodistribution profiles of RNA nanoparticles revealed different behaviors based on MTX conjugation in cancer targeting and clearance. Increased copies of MTX changed the ability of nanoparticles to target tumors, accumulate in healthy organs, and rapidly clear through the urine. Nanoparticle design must be closely considered for optimized cancer targeting and therapy, providing the rationale for a proper design of RNA nanodelivery in cancer treatment.</p>","PeriodicalId":520473,"journal":{"name":"RNA nanomed","volume":"1 1","pages":"109-123"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11926850/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143694834","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":"The Reduction of Traumatic Spinal Cord Secondary Injury by Anti-RhoA siRNA Functionalized Nucleic Acid Nanoparticles (NANPs).","authors":"Damian Beasock, Morgan Chandler, Yasmine Radwan, Zhen Liao, Fuying Ma, Ken Webb, Martin Panigaj, Jeoung Soo Lee, Kirill A Afonin","doi":"10.59566/isrnn.2024.0101079","DOIUrl":"10.59566/isrnn.2024.0101079","url":null,"abstract":"<p><p>Primary injury of the spinal cord is caused by a mechanical traumatic event which is rapidly followed by a secondary injury cascade that may evolve for several months leading to biological and functional changes. During the secondary injury, many pathophysiological pathways and process are activated including inflammation, oxidative stress, demyelination, excitotoxicity, axon degeneration, and cell death. The RhoA/Rho kinase pathway significantly contributes to spinal degeneration and regeneration and therefore represents a potential therapeutic target. Nucleic acid nanoparticles (NANPs) offer easy rational and programable design with the potential to carry on multiple synergistic therapeutic nucleic acid functional motifs. In this context we designed, synthesized, and assembled several representative NANPs decorated with multiple copies of siRNAs targeting RhoA. Subsequently we assessed NANPs' physicochemical properties, toxicity, and immunorecognition upon delivery with the nanocarrier PLGA-g-PEI (PgP), developed with the aim to select for the most immunoquiescent type of formulations. In addition, we observed that L1 neural cell adhesion molecule conjugated PgP (L1-PgP) efficiently delivered NANP-siRhoA in cultured neuroblastoma (B35) cells. RhoA mRNA expression was significantly reduced by all L1-PgP/ NANP-siRhoA relative to the untreated control, while no significant differences were observed between the different NANP-siRhoAs.</p>","PeriodicalId":520473,"journal":{"name":"RNA nanomed","volume":"1 1","pages":"79-90"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC12043328/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"144016202","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":"pH-responsive bond as a linker for the release of chemical drugs from RNA-drug complexes in endosome or lysosome.","authors":"Piotr Rychahou, Sijin Guo, Yinan Zhang, Nicole Rychagov, Yekaterina Y Zaytseva, Heidi L Weiss, B Mark Evers, Peixuan Guo","doi":"10.59566/isrnn.2024.0101091","DOIUrl":"10.59566/isrnn.2024.0101091","url":null,"abstract":"<p><p>Emerging phenomena have signaled that RNA therapeutics will be the third milestone in pharmaceutical drug development. RNA nanoparticles display motile and deformable properties that lead to (1) fast and efficient tumor accumulation via both spontaneous and active targeting, and (2) fast renal excretion of non-tumor-accumulated nanoparticles due to RNA's negative charge and dynamic property; thus, undetectable toxicity. Here, we report the use of RNA nanoparticles to harbor the cancer-targeting ligand and chemical drugs and the design of the pH-responsive bond as a linker for the release of chemical drugs from RNA-drug complexes in endosomes or lysosomes. RNA nanoparticles constructed from a three-way junction (3WJ) core of bacteriophage phi29 packaging RNA (pRNA) offer an advanced strategy for receptor-selective drug delivery into cancer cells and has the potential to enhance the efficacy of anti-cancer therapies while mitigating dose-limiting toxicity in patients with colorectal cancer (CRC). We investigated conjugation of small-molecule drugs targeting the PI3K/mTOR pathway to 3WJ RNA nanoparticles and confirmed intracellular drug delivery by 3WJ RNA nanoparticles into CRC cells. 3WJ a, a single strand of 3WJ nanoparticle, was constructed with a pH-sensitive linkage conjugated to a dual PI3K/mTOR inhibitor, PI-103-azide. We demonstrated PI-103 conjugation to RNA under normal physiologic pH conditions and rapid pH-dependent drug release in an acidic environment. Next, we assembled FA-3WJ-PI103 nanoparticles from three single-stranded RNA, 3WJ a-PI-103, 3WJ b and 3WJ c-folate, to specifically target folate receptor alpha (FRα). Our tests demonstrated receptor-mediated uptake of FA-pRNA-PI-103 nanoparticles, pH-responsive PI-103 drug release from lysosomes and inhibition of the PI3K/mTOR pathway in CRC cells and tumor spheroids. These results confirm receptor-mediated cytosolic drug delivery by pH-responsive RNA nanoparticles and demonstrate potential of the 3WJ-drug complex as a novel strategy for receptor-selective drug delivery to cancer cells with high FRα expression.</p>","PeriodicalId":520473,"journal":{"name":"RNA nanomed","volume":"1 1","pages":"91-108"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11925213/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143672241","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":"Targeted Delivery of Potent Chemical Drugs and RNAi to Drug-Resistant Breast Cancer Using RNA-Nanotechnology and RNA-Ligand Displaying Extracellular vesicles.","authors":"Yuan Soon Ho, Tzu-Chun Cheng, Peixuan Guo","doi":"10.59566/isrnn.2024.0101016","DOIUrl":"10.59566/isrnn.2024.0101016","url":null,"abstract":"<p><p>This review describes a new technology to treat breast-cancer-drug-resistance by targeting the ABC as the multi-homo-subunit ATPase, enlightening by the Christmas-lighting budge with serial circuit and the asymmetrical homo-hexamer of the phi29 DNA packaging motor with sequential revolving mechanism. Chemotherapeutics has been widely used in breast cancer treatments, but drug resistance has raised a serious concern. RNA therapeutics has emerged as the third milestone in pharmaceutical drug development. RNA nanoparticles are dynamic, mild, and deformative, resulting in spontaneous, rapid, and efficient accumulation in tumor vasculature after IV injection. Their negative charge and favorable size bypass the nonspecific targeting of vital organs and normal cells. This motile and deformable nature also led to the fast passing of glomerular filters and their movement into the urine for rapid body clearance for those non-tumor-accumulated nanoparticles, resulting in undetectable toxicity. Extracellular vesicles have shown potential as a delivery system for RNAi and chemotherapeutic drugs <i>in vivo</i>, contributing to the efficacy of cancer remission. However, the lack of cell-targeting ligands on extracellular vesicles and the nonspecific entry into healthy cells has led to safety concerns. This review addresses how to apply RNA nanotechnology and RNA-ligand displaying extracellular vesicles for specific delivery to breast cancer. The particular focus is on using and combining the RNA and extracellular vesicle technology to deal with breast cancer drug resistance. The targeting capabilities and drug safety can be improved through extracellular vesicle engineering techniques, such as affixing ligands on the extracellular vesicle surface utilizing arrow-tail RNA nanoparticles, ultimately addressing off-target effects and toxicity. Using RNA ligands for specific targeting and the efficient membrane fusion of extracellular vesicles has enabled the development of ligand-displayed extracellular vesicles capable of delivering both RNAi and chemical drugs to cells with precision, effectively inhibiting tumor growth. The negative charge inherent in the vesicles results in electrostatic repulsion, reducing non-specific binding to healthy cells that contain negatively charged lipid membranes. By leveraging the principles of RNA nanotechnology, the engineering of extracellular vesicles offers a promising avenue for addressing breast cancer drug resistance. This review also discusses applying the series of circuit mechanisms in Christmas-decorating-lighting to develop effective therapeutics to combat breast cancer chemoresistance by targeting the ABC drug transporter and breast cancer surface receptors.</p>","PeriodicalId":520473,"journal":{"name":"RNA nanomed","volume":"1 1","pages":"16-43"},"PeriodicalIF":0.0,"publicationDate":"2024-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11927007/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143695048","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}