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Scientific Reports Mar 2023LNA-containing oligonucleotides bind DNA more tightly than standard DNA, so they can interact with targeted sequences and affect multiple processes. When a desired DNA...
LNA-containing oligonucleotides bind DNA more tightly than standard DNA, so they can interact with targeted sequences and affect multiple processes. When a desired DNA is present at low concentrations relative to nearly identical undesired DNAs, LNAs can block amplification of unwanted DNAs. Using a short rAAV and synthetic DNA sequence as a model, we studied the length, number, and positioning of LNA bases to improve blocker effectiveness. Oligonucleotides 18-24 bases long with LNAs at every other position were most effective. Highly degenerate targets were used to characterize the impact of mismatches on blocking. Mismatches at LNA ends had little impact on blocking activity. Single and double mismatches were tolerated with longer blockers, especially if the mismatches were near LNA ends. Shorter LNAs were more selective, with > 1 mismatch preventing effective blocking. Neither the strand to which a blocker bound nor the distance between the blocker and priming sites greatly impacted blocking efficiency. We used these findings to design blockers of wild-type DNA versus the single-base A1AT PiZ allele. Blockers are most specific when the mismatch is located away from the LNA 5' end. Pairs of partially overlapping blockers on opposite strands with a centrally-located mismatch have maximal activity and specificity.
Topics: DNA; Oligonucleotides
PubMed: 36964235
DOI: 10.1038/s41598-023-31871-7 -
Cancer Science Sep 2023Vasohihibin-2 (VASH2) is a homolog of vasohibin-1 (VASH1) and is overexpressed in various cancers. Vasohihibin-2 acts on both cancer cells and cancer microenvironmental...
Vasohihibin-2 (VASH2) is a homolog of vasohibin-1 (VASH1) and is overexpressed in various cancers. Vasohihibin-2 acts on both cancer cells and cancer microenvironmental cells. Previous analyses have shown that VASH2 promotes cancer progression and abrogation of VASH2 results in significant anticancer effects. We therefore propose VASH2 to be a practical molecular target for cancer treatment. Modifications of antisense oligonucleotide (ASO) such as bridged nucleic acids (BNA)-based modification increases the specificity and stability of ASO, and are now applied to the development of a number of oligonucleotide-based drugs. Here we designed human VASH2-ASOs, selected an optimal one, and developed 2',4'-BNA-based VASH2-ASO. When systemically administered, naked 2',4'-BNA-based VASH2-ASO accumulated in the liver and showed its gene-silencing activity. We then examined the effect of 2',4'-BNA-based VASH2-ASO in liver cancers. Intraperitoneal injection of naked 2',4'-BNA-based VASH2-ASO exerted a potent antitumor effect on orthotopically inoculated human hepatocellular carcinoma cells. The same manipulation also showed potent antitumor activity on the splenic inoculation of human colon cancer cells for liver metastasis. These results provide a novel strategy for the treatment of primary as well as metastatic liver cancers by using modified ASOs targeting VASH2.
Topics: Humans; Oligonucleotides, Antisense; Liver Neoplasms; Cell Line; Transcription Factors; Oligonucleotides; Cell Cycle Proteins; Angiogenic Proteins
PubMed: 37430466
DOI: 10.1111/cas.15897 -
Journal of Industrial Microbiology &... Dec 2021Although the study of ribonucleic acid (RNA) therapeutics started decades ago, for many years, this field of research was overshadowed by the growing interest in...
Although the study of ribonucleic acid (RNA) therapeutics started decades ago, for many years, this field of research was overshadowed by the growing interest in DNA-based therapies. Nowadays, the role of several types of RNA in cell regulation processes and the development of various diseases have been elucidated, and research in RNA therapeutics is back with force. This short literature review aims to present general aspects of many of the molecules currently used in RNA therapeutics, including in vitro transcribed mRNA (IVT mRNA), antisense oligonucleotides (ASOs), aptamers, small interfering RNAs (siRNAs), and microRNAs (miRNAs). In addition, we describe the state of the art of technologies applied for synthetic RNA manufacture and delivery. Likewise, we detail the RNA-based therapies approved by the FDA so far, as well as the ongoing clinical investigations. As a final point, we highlight the current and potential advantages of working on RNA-based therapeutics and how these could lead to a new era of accessible and personalized healthcare.
Topics: Aptamers, Nucleotide; Humans; MicroRNAs; Oligonucleotides, Antisense; RNA, Messenger; RNA, Small Interfering
PubMed: 34463324
DOI: 10.1093/jimb/kuab063 -
Wiley Interdisciplinary Reviews. RNA Jul 2022The COVID-19 crisis and the development of the first approved mRNA vaccine have highlighted the power of RNA-based therapeutic strategies for the development of new... (Review)
Review
The COVID-19 crisis and the development of the first approved mRNA vaccine have highlighted the power of RNA-based therapeutic strategies for the development of new medicines. Aside from RNA-vaccines, antisense oligonucleotides (ASOs) represent a new and very promising class of RNA-targeted therapy. Few drugs have already received approval from the Food and Drug Administration. Here, we underscored why and how ASOs hold the potential to change the therapeutic landscape to beat SARS-CoV-2 viral infections. This article is categorized under: RNA Interactions with Proteins and Other Molecules > Small Molecule-RNA Interactions.
Topics: Humans; Oligonucleotides; Oligonucleotides, Antisense; RNA; SARS-CoV-2; United States; Vaccines, Synthetic; mRNA Vaccines; COVID-19 Drug Treatment
PubMed: 34842345
DOI: 10.1002/wrna.1703 -
Nature Communications Aug 2023Conformational cooperativity is a universal molecular effect mechanism and plays a critical role in signaling pathways. However, it remains a challenge to develop...
Conformational cooperativity is a universal molecular effect mechanism and plays a critical role in signaling pathways. However, it remains a challenge to develop artificial molecular networks regulated by conformational cooperativity, due to the difficulties in programming and controlling multiple structural interactions. Herein, we develop a cooperative strategy by programming multiple conformational signals, rather than chemical signals, to regulate protein-oligonucleotide signal transduction, taking advantage of the programmability of allosteric DNA constructs. We generate a cooperative regulation mechanism, by which increasing the loop lengths at two different structural modules induced the opposite effects manifesting as down- and up-regulation. We implement allosteric logic operations by using two different proteins. Further, in cell culture we demonstrate the feasibility of this strategy to cooperatively regulate gene expression of PLK1 to inhibit tumor cell proliferation, responding to orthogonal protein-signal stimulation. This programmable conformational cooperativity paradigm has potential applications in the related fields.
Topics: Oligonucleotides; Allosteric Regulation; Molecular Conformation; Signal Transduction
PubMed: 37580346
DOI: 10.1038/s41467-023-40589-z -
Molecules (Basel, Switzerland) Jul 2020The chemical synthesis of modified oligoribonucleotides represents a powerful approach to study the structure, stability, and biological activity of RNAs. Selected RNA... (Review)
Review
The chemical synthesis of modified oligoribonucleotides represents a powerful approach to study the structure, stability, and biological activity of RNAs. Selected RNA modifications have been proven to enhance the drug-like properties of RNA oligomers providing the oligonucleotide-based therapeutic agents in the antisense and siRNA technologies. The important sites of RNA modification/functionalization are the nucleobase residues. Standard phosphoramidite RNA chemistry allows the site-specific incorporation of a large number of functional groups to the nucleobase structure if the building blocks are synthetically obtainable and stable under the conditions of oligonucleotide chemistry and work-up. Otherwise, the chemically modified RNAs are produced by post-synthetic oligoribonucleotide functionalization. This review highlights the post-synthetic RNA modification approach as a convenient and valuable method to introduce a wide variety of nucleobase modifications, including recently discovered native hypermodified functional groups, fluorescent dyes, photoreactive groups, disulfide crosslinks, and nitroxide spin labels.
Topics: Models, Molecular; Nucleic Acid Conformation; Oligoribonucleotides; Organophosphorus Compounds; RNA; RNA Stability
PubMed: 32717917
DOI: 10.3390/molecules25153344 -
Theranostics 2020The use of various oligonucleotide (ON) syntheses and post-synthetic strategies for targeted chemical modification enables improving their efficacy as potent modulators... (Review)
Review
The use of various oligonucleotide (ON) syntheses and post-synthetic strategies for targeted chemical modification enables improving their efficacy as potent modulators of gene expression levels in eukaryotic cells. However, the search still continues for new approaches designed for increasing internalization, lysosomal escape, and tissue specific delivery of ON. In this review we emphasized all aspects related to the synthesis and properties of ON derivatives carrying multifluorinated (MF) groups. These MF groups have unique physico-chemical properties because of their simultaneous hydrophobicity and lipophobicity. Such unusual combination of properties results in the overall modification of ON mode of interaction with the cells and making multi-fluorination highly relevant to the goal of improving potency of ON as components of new therapies. The accumulated evidence so far is pointing to high potential of ON probes, RNAi components and ON imaging beacons carrying single or multiple MF groups for improving the stability, specificity of interaction with biological targets and delivery of ONs and potentially .
Topics: Animals; Cell Line; Fluorine; Humans; Magnetic Resonance Imaging; Nanoparticles; Oligonucleotides; Permeability; Precision Medicine
PubMed: 31938071
DOI: 10.7150/thno.37936 -
Biosensors Mar 2023Mycotoxins are naturally occurring toxic secondary metabolites produced by fungi in cereals and foodstuffs during the stages of cultivation and storage. Electrochemical... (Review)
Review
Mycotoxins are naturally occurring toxic secondary metabolites produced by fungi in cereals and foodstuffs during the stages of cultivation and storage. Electrochemical biosensing has emerged as a rapid, efficient, and economical approach for the detection and quantification of mycotoxins in different sample media. An electrochemical biosensor consists of two main units, a recognition receptor and a signal transducer. Natural or artificial antibodies, aptamers, molecularly imprinted polymers (MIP), peptides, and DNAzymes have been extensively employed as selective recognition receptors for the electrochemical biosensing of mycotoxins. This article affords a detailed discussion of the recent advances and future prospects of various types of recognition receptors exploited in the electrochemical biosensing of mycotoxins.
Topics: Mycotoxins; Fungi; Peptides; Biosensing Techniques; Aptamers, Nucleotide
PubMed: 36979603
DOI: 10.3390/bios13030391 -
ALTEX 2022Oligonucleotide therapeutics (ONTs) encompass classes of medicines that selectively target and potentially ameliorate previously untreatable and often rare diseases.... (Review)
Review
Oligonucleotide therapeutics (ONTs) encompass classes of medicines that selectively target and potentially ameliorate previously untreatable and often rare diseases. Several unique classes of ONTs provide versatility, enabling direct modulation of gene expression by virtue of Watson-Crick base pairing or modulation of cell signaling through structural mimicry or interference with protein-receptor interactions. Due to a lack of suitable in vitro models capable of recapitulating or predicting in vivo effects of ONTs, their discovery and optimization has relied heavily on animal studies for predicting efficacy and safety in humans. Since ONTs often lack cross-species activity, animal models with genetic humanization and/or species-specific surrogate ONTs are often required. Human microphysiological systems (MPS) offer an opportunity to reduce the use of animals and may enable evaluation of drug mechanisms, optimization of cell and tissue targeting ligands or delivery vehicles, and characterization of pharmacokinetics (PK), pharmacodynamics (PD), and safety of candidate ONTs. The lack of published examples for MPS applications with ONT demonstrates the need for a focused effort to characterize and build confidence in their utility. The goals of this review are to summarize the current landscape of ONTs and highlight potential opportunities and challenges for application of MPS during ONT discovery and development. In addition, this review aims to raise awareness with ONT drug developers and regulatory authorities on the potential impact of MPS with respect to characterizing pharmacology, ADME, and toxicity and to educate MPS platform developers on unique design attributes needed to fully appreciate MPS advantages in ONT development.
Topics: Animals; Oligonucleotides; Pharmaceutical Preparations
PubMed: 34766620
DOI: 10.14573/altex.2108241 -
International Journal of Oncology Jun 2022Cancer‑related deaths remain a challenging and devastating obstacle to defeat despite the tremendous advances in cancer treatment. Cancer metastasis is the major cause... (Review)
Review
Cancer‑related deaths remain a challenging and devastating obstacle to defeat despite the tremendous advances in cancer treatment. Cancer metastasis is the major cause of these cancer‑related deaths. Metastasis involves sequential steps during cancer cells' journey to a new site. These steps are coordinately regulated by specific intracellular regulators and cellular interactions between the cancer cells and the supporting microenvironment of the different organs. The development of aptamer‑based therapeutics is a promising strategy to fight cancer metastasis as it holds potential advantages. Oligonucleotide and peptide aptamers are short sequences of single‑stranded nucleic acids or amino acids, respectively, that target proteins, genetic materials, and cells. Antimetastatic aptamer‑based therapeutics exert their pharmacological effect by direct interaction with the signaling pathways inside the cancer cells or the communications between cancer cells and the tumor microenvironment. In addition, aptamers have been utilized as a guiding ligand to deliver a therapeutic moiety to cancer cells or the supporting microenvironment. The selected aptamer possesses high specificity since it is designed to recognize and interact with its target. This review summarizes recent advances in the development of aptamer‑based therapeutics targeting mediators of cancer metastasis. In addition, potential opportunities are discussed to inspire researchers in the field to develop novel aptamer‑based antimetastatic treatments.
Topics: Aptamers, Nucleotide; Drug Delivery Systems; Humans; Neoplasms; Tumor Microenvironment
PubMed: 35425991
DOI: 10.3892/ijo.2022.5355