Inhibition of Influenza Virus Replication in MDCK Cells by Circular Dumbbell RNA/DNA Chimeras with Closed Alkyl Loop Structures

Hamazaki, Hiroyuki; Abe, Takayuki; Yamakawa, Hidefumi; Yokota, Tomoyuki; Shigeta, Shirô; Takaku, Hiroshi

doi:10.1002/1522-2675(200207)85:7<2183::aid-hlca2183>3.0.co;2-u

Cited by 5 publications

(3 citation statements)

References 11 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…After 2 h incubation, 36% of Db-23 retained its sequence in contrast to 6% of L-23. In this condition, no siRNA-1 was detected after 2 h. This improved stability of Db-23 can be attributed to its endless structure, as also reported for DNA dumbbells. 3e,f,4b Next, Db-23, L-23, and siRNA-1 were incubated in 20% human serum at 37 °C (Figure c). In human serum, the differences in stability were not as clear as those observed with SVPD.…”

supporting

confidence: 71%

Dumbbell-Shaped Nanocircular RNAs for RNA Interference

Abe

Ito

2007

J. Am. Chem. Soc.

View full text Add to dashboard Cite

RNA interference (RNAi) is a potent and highly specific genesilencing phenomenon that is initiated or triggered by doublestranded RNAs (dsRNAs). 1a Shortly after the development of RNAi, small interfering RNAs (siRNAs), which are 21 nucleotides in length with a 3′ nucleotide overhang, were shown to be very effective in mammalian cells. 1b Much effort has been dedicated to the application of siRNAs, both as biological tools and as therapeutic agents. 1c-e These approaches can be divided into two main classes. In the first, DNA vectors encoding the RNA polymerase II or III promoter are used to transcribe siRNAs or short hairpin RNAs (shRNAs) in mammalian cells. 1c-e In the second, chemically synthesized siRNA is introduced directly into cells. 1c-e Although the vector system is suitable for biological experiments, there are safety problems in clinical applications. 1c-e Currently, synthetic siRNA would be the method of choice for clinical purposes. 1e However, natural RNA strands are quickly degraded in biological fluids. 2a Chemically synthesized unnatural nucleotides have been developed and introduced into the siRNA strand. 1d For example, modification of the ribose moiety with a 2′-deoxy, 2′-O-methyl, or 2′-fluoro group or modification of the phosphate backbone has been examined. 1d Although these modifications improve the stability of siRNA in serum, they often cause a decrease in RNAi activity. 1d There is also concern that unnatural RNA derivatives are toxic in the human body. A method to stabilize nontoxic natural RNA strands should be very useful for applications in RNAi technology.DNA dumbbells, which consist of a double-helical stem closed by two hairpin loops, have been synthesized historically as physical models that can be used to analyze local structures in DNA. 3a,b They have more recently been applied successfully to transcriptional regulation, where they act as decoy systems because they exhibit increased stability against exonucleases and biological fluids without the need to introduce unnatural nucleotides. 3c-f A dumbbell-shaped RNA aptamer that contains two deoxynucleotides 4a and DNA/RNA chimera dumbbells for antisense applications 4b,c has been reported. Because 3′-exonuclease is a major enzyme involved in the degradation of nucleic acids in vivo, 2b RNA dumbbells are expected to be more stable than dsRNA. However, to our knowledge, this design has never been tested as an RNAi strategy. A key point to be determined is whether an RNA dumbbell is cleaved by the Dicer enzyme 5 to generate dsRNA, as shRNA is, 5c to achieve an RNAi effect in cells ( Figure 1).To test this idea, we designed and synthesized circular RNA dumbbells that contain a stem sequence encoding the firefly luciferase gene 1b and two 9-mer loops ( Figure 2a). The loop sequence is used widely in shRNA expression systems. 6 The stem sequences were designed according to a previous report, which showed that the expressed shRNA sequence worked well. 6b We added one more loop sequence on the other end of this shRNA to form dumbbel...

show abstract

supporting

confidence: 71%

Dumbbell-Shaped Nanocircular RNAs for RNA Interference

Abe

Ito

2007

J. Am. Chem. Soc.

View full text Add to dashboard Cite

show abstract

“…3 In addition, Hamazakia et al have presented circular dumbbell RNA/DNA chimeras typical of closed-alkylloop structures to achieve higher nuclease resistance. 4 In this work, we proposed a novel prodrug-type ASON that bears a dumbbell conformation with responsive disulfide switches (referred to here as "dumbbell-shaped ASON," DS-ASON). DNA dumbbell conformation consists of two hairpin domains at both ends of the strand; they have been utilized as typical models to analyze structures and functions in DNA.…”

Section: Introductionmentioning

confidence: 99%

“…Ren et al have reported that ASONs featuring an alkyl hairpin-end conformation have improved resistance to degradation by nucleases . In addition, Hamazakia et al have presented circular dumbbell RNA/DNA chimeras typical of closed-alkyl-loop structures to achieve higher nuclease resistance …”

Section: Introductionmentioning

confidence: 99%

Dumbbell-Shaped Antisense Oligonucleotide Prodrugs Showed Improved Antinuclease Stability and Anticancer Efficacy

et al. 2022

View full text Add to dashboard Cite

Antisense oligonucleotides (ASONs) have generated widespread interest as antitumor agents. Nevertheless, the utility of natural ASONs is limited due to their rapid degradation by intracellular and extracellular nucleases. In this work, we proposed a novel prodrug-type ASON with a dumbbell conformation and a responsive disulfide switch. A degradation assay showed that the dumbbell-shaped ASON (DS-ASON) exhibited stronger stability against enzymatic degradation compared with that of the linear or single-end looped ASON. The native ASON could dissociate via breakage of the disulfide switch when in the reductive microenvironment of a tumor. In addition, an optimal DS-ASON, L2, displayed robust antitumor activity both in vitro and in vivo. This paper presents a new design of nucleic acid-based therapeutics featuring a conformational change that provides improved stability and biological efficacy.

show abstract

Functional Engineering of Synthetic RNA Through Circularization

Abe¹

2022

Handbook of Chemical Biology of Nucleic Acids

View full text Add to dashboard Cite

Inhibition of Influenza Virus Replication in MDCK Cells by Circular Dumbbell RNA/DNA Chimeras with Closed Alkyl Loop Structures

Cited by 5 publications

References 11 publications

Dumbbell-Shaped Nanocircular RNAs for RNA Interference

Dumbbell-Shaped Nanocircular RNAs for RNA Interference

Dumbbell-Shaped Antisense Oligonucleotide Prodrugs Showed Improved Antinuclease Stability and Anticancer Efficacy

Functional Engineering of Synthetic RNA Through Circularization

Contact Info

Product

Resources

About