scholarly journals Investigation of Strand-Selective Interaction of SNA-Modified siRNA with AGO2-MID

2020 ◽  
Vol 21 (15) ◽  
pp. 5218 ◽  
Author(s):  
Yukiko Kamiya ◽  
Yuuki Takeyama ◽  
Tomonari Mizuno ◽  
Fuminori Satoh ◽  
Hiroyuki Asanuma
Keyword(s):  
Nucleic Acid ◽  
Inhibitory Effect ◽  
Guide Strand ◽  
Argonaute 2 ◽  
Passenger Strand ◽  
Nuclease Resistance ◽  
Interfering Rna ◽  
Target Activity ◽  
Rnai Activity ◽  
Target Effects

Small interfering RNA (siRNA) has been recognized as a powerful gene-silencing tool. For therapeutic application, chemical modification is often required to improve the properties of siRNA, including its nuclease resistance, activity, off-target effects, and tissue distribution. Careful siRNA guide strand selection in the RNA-induced silencing complex (RISC) is important to increase the RNA interference (RNAi) activity as well as to reduce off-target effects. The passenger strand-mediated off-target activity was previously reduced and on-target activity was enhanced by substitution with acyclic artificial nucleic acid, namely serinol nucleic acid (SNA). In the present study, the reduction of off-target activity caused by the passenger strand was investigated by modifying siRNAs with SNA. The interactions of SNA-substituted mononucleotides, dinucleotides, and (2,2,6,6-tetramethylpiperidin-1-yl)oxyl (TEMPO)-labeled double-stranded RNA (dsRNA) with the MID domain of the Argonaute 2 (AGO2) protein, which plays a pivotal role in strand selection by accommodation of the 5’-terminus of siRNA, were comprehensively analyzed. The obtained nuclear magnetic resonance (NMR) data revealed that AGO2-MID selectively bound to the guide strand of siRNA due to the inhibitory effect of the SNA backbone located at the 5’ end of the passenger strand.

scholarly journals siRNAs containing 2′-fluorinated Northern-methanocarbacyclic (2′-F-NMC) nucleotides: in vitro and in vivo RNAi activity and inability of mitochondrial polymerases to incorporate 2′-F-NMC NTPs

2021 ◽  
Author(s):  
Masaaki Akabane-Nakata ◽  
Namrata D Erande ◽  
Pawan Kumar ◽  
Rohan Degaonkar ◽  
Jason A Gilbert ◽  
...  
Keyword(s):  
Gene Silencing ◽  
Mitochondrial Rna ◽  
Seed Region ◽  
Guide Strand ◽  
Passenger Strand ◽  
Molecular Modeling Studies ◽  
Rnai Activity ◽  
Rna And Dna

Abstract We recently reported the synthesis of 2′-fluorinated Northern-methanocarbacyclic (2′-F-NMC) nucleotides, which are based on a bicyclo[3.1.0]hexane scaffold. Here, we analyzed RNAi-mediated gene silencing activity in cell culture and demonstrated that a single incorporation of 2′-F-NMC within the guide or passenger strand of the tri-N-acetylgalactosamine-conjugated siRNA targeting mouse Ttr was generally well tolerated. Exceptions were incorporation of 2′-F-NMC into the guide strand at positions 1 and 2, which resulted in a loss of the in vitro activity. Activity at position 1 was recovered when the guide strand was modified with a 5′ phosphate, suggesting that the 2′-F-NMC is a poor substrate for 5′ kinases. In mice, the 2′-F-NMC-modified siRNAs had comparable RNAi potencies to the parent siRNA. 2′-F-NMC residues in the guide seed region position 7 and at positions 10, 11 and 12 were well tolerated. Surprisingly, when the 5′-phosphate mimic 5′-(E)-vinylphosphonate was attached to the 2′-F-NMC at the position 1 of the guide strand, activity was considerably reduced. The steric constraints of the bicyclic 2′-F-NMC may impair formation of hydrogen-bonding interactions between the vinylphosphonate and the MID domain of Ago2. Molecular modeling studies explain the position- and conformation-dependent RNAi-mediated gene silencing activity of 2′-F-NMC. Finally, the 5′-triphosphate of 2′-F-NMC is not a substrate for mitochondrial RNA and DNA polymerases, indicating that metabolites should not be toxic.

scholarly journals Aptamer Chimeras for Therapeutic Delivery: The Challenging Perspectives

Genes ◽  
2018 ◽  
Vol 9 (11) ◽  
pp. 529 ◽  
Author(s):  
Carla Esposito ◽  
Silvia Catuogno ◽  
Gerolama Condorelli ◽  
Paola Ungaro ◽  
Vittorio de Franciscis
Keyword(s):  
Nucleic Acid ◽  
Therapeutic Delivery ◽  
Specific Recognition ◽  
Efficient Delivery ◽  
Target Effects

Nucleic acid-based aptamers have emerged as efficient delivery carriers of therapeutics. Thanks to their unique features, they can be, to date, considered one of the best targeting moieties, allowing the specific recognition of diseased cells and avoiding unwanted off-target effects on healthy tissues. In this review, we revise the most recent contributes on bispecific and multifunctional aptamer therapeutic chimeras. We will discuss key examples of aptamer-mediated delivery of nucleic acid and peptide-based therapeutics underlying their great potentiality and versatility. Achieved objectives and challenges will be highlighted as well.

scholarly journals Study on rapid screening technology of antisense oligonucleotides for SARS-CoV-2

2021 ◽  
Author(s):  
Huawei Shen
Keyword(s):  
Nucleic Acid ◽  
Antisense Oligonucleotides ◽  
Structural Characteristics ◽  
Inhibitory Effect ◽  
Rapid Screening ◽  
Short Term ◽  
Physical Isolation ◽  
The World ◽  
Actual Use ◽  
Screening Technology

Abstract According to the structural characteristics of SARS-CoV-2 nucleic acid,SARS-CoV-2 genomes were virtually segmented.After comparing with human genome,44707 SARS-CoV-2 genomes and 26 primates' genomes, 19 antisense oligonucleotides sequences were selected.Experimental results show that the combined inhibitory effect reaches 100% . Significance statement：Currently, effective methods of controlling the spread of SARS-CoV-2 are very limited, only physical isolation and vaccination.Although physical isolation can achieve some short-term results, but can not fundamentally solve the problem of epidemic spread.The time between the development of a vaccine and its actual use is very long.It often happens that the vaccine is developed successfully, but the epidemic situation is beyond control.If a mutant strain emerges, it will take longer.I hope that the rapid screening technology of SARS-CoV-2 antisense oligonucleotides will light up new hope for the future of mankind and contribute oriental wisdom to the world.

scholarly journals Effect of kinetin on nucleic acid synthesis in senescing and young leaves in Brassica oleracea L. var. gongylodes L.

2015 ◽  
Vol 44 (4) ◽  
pp. 553-565
Author(s):  
J. Legocka ◽  
A. Szweykowska
Keyword(s):  
Molecular Weight ◽  
Nucleic Acid ◽  
Acid Synthesis ◽  
Inhibitory Effect ◽  
Rrna Synthesis ◽  
Low Molecular Weight ◽  
Chlorophyll B ◽  
Mature Leaves ◽  
Young Leaves ◽  
Brassica Oleracea L

In detached kohlrabi leaves senescing in the dark, the decrease in chlorophyll to was more pronounced than in chlorophyll a. The retardation by kinetin of the chlorophyll loss was also markedly stronger in the case of chlorophyll b. Using the fractionation of nucleic acids on polyacrylamide gels it has been shown that during leaf senescence the level of all RNA species decreased, whereas the amount of DNA was more or less constant. In the presence of kinetin, the loss of RNA was inhibited and the incorporation of precursor into the cytoplasmic rRNA as well as into low molecular weight RNA species was supported. Chloroplast rRNA synthesis has not been detected in mature leaves and kinetin showed no effect in this respect. In young expanding leaves detached and kept in light, the synthesis of cytoplasmic rRNA was strongly stimulated by kinetin, whereas in the case of Chloroplast rRNA only an inhibitory effect of kinetin could be found. The results suggest that the cytokinins are primarily involved in processes of the synthesis of cytoplasmic rRNA and low molecular RNA fractions, and in this way affect the development of plastids, in particular the course of their senescence.

scholarly journals A Single Amide Linkage in the Passenger Strand Suppresses Its Activity and Enhances Guide Strand Targeting of siRNAs

2018 ◽  
Vol 13 (3) ◽  
pp. 533-536 ◽  
Author(s):  
Travis Hardcastle ◽  
Irina Novosjolova ◽  
Venubabu Kotikam ◽  
Samwel K. Cheruiyot ◽  
Daniel Mutisya ◽  
...  
Keyword(s):  
Guide Strand ◽  
Amide Linkage ◽  
Passenger Strand

scholarly journals Structurally modulated codelivery of siRNA and Argonaute 2 for enhanced RNA interference

2018 ◽  
Vol 115 (12) ◽  
pp. E2696-E2705 ◽  
Author(s):  
Jiahe Li ◽  
Connie Wu ◽  
Wade Wang ◽  
Yanpu He ◽  
Elad Elkayam ◽  
...  
Keyword(s):  
Molecular Structure ◽  
Rna Interference ◽  
Small Interfering Rna ◽  
Sirna Delivery ◽  
Effector Protein ◽  
Side Group ◽  
Argonaute 2 ◽  
Fundamental Research ◽  
Delivery Vehicles ◽  
Interfering Rna

Small interfering RNA (siRNA) represents a promising class of inhibitors in both fundamental research and the clinic. Numerous delivery vehicles have been developed to facilitate siRNA delivery. Nevertheless, achieving highly potent RNA interference (RNAi) toward clinical translation requires efficient formation of RNA-induced gene-silencing complex (RISC) in the cytoplasm. Here we coencapsulate siRNA and the central RNAi effector protein Argonaute 2 (Ago2) via different delivery carriers as a platform to augment RNAi. The physical clustering between siRNA and Ago2 is found to be indispensable for enhanced RNAi. Moreover, by utilizing polyamines bearing the same backbone but distinct cationic side-group arrangements of ethylene diamine repeats as the delivery vehicles, we find that the molecular structure of these polyamines modulates the degree of siRNA/Ago2-mediated improvement of RNAi. We apply this strategy to silence the oncogene STAT3 and significantly prolong survival in mice challenged with melanoma. Our findings suggest a paradigm for RNAi via the synergistic coassembly of RNA with helper proteins.

scholarly journals Role of Lipid-Based and Polymer-Based Non-Viral Vectors in Nucleic Acid Delivery for Next-Generation Gene Therapy

Molecules ◽  
2020 ◽  
Vol 25 (12) ◽  
pp. 2866 ◽  
Author(s):  
Aniket Wahane ◽  
Akaash Waghmode ◽  
Alexander Kapphahn ◽  
Karishma Dhuri ◽  
Anisha Gupta ◽  
...  
Keyword(s):  
Gene Therapy ◽  
Nucleic Acid ◽  
Messenger Rna ◽  
Viral Vectors ◽  
Cationic Lipids ◽  
Nucleic Acid Delivery ◽  
Nucleic Acid Analogs ◽  
Organ Specific ◽  
Interfering Rna

The field of gene therapy has experienced an insurgence of attention for its widespread ability to regulate gene expression by targeting genomic DNA, messenger RNA, microRNA, and short-interfering RNA for treating malignant and non-malignant disorders. Numerous nucleic acid analogs have been developed to target coding or non-coding sequences of the human genome for gene regulation. However, broader clinical applications of nucleic acid analogs have been limited due to their poor cell or organ-specific delivery. To resolve these issues, non-viral vectors based on nanoparticles, liposomes, and polyplexes have been developed to date. This review is centered on non-viral vectors mainly comprising of cationic lipids and polymers for nucleic acid-based delivery for numerous gene therapy-based applications.

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