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Escherichia coli
Published in Yoshikatsu Murooka, Tadayuki Imanaka, Recombinant Microbes for Industrial and Agricultural Applications, 2020
Hisashi Yasueda, Hiroshi Matsui
The repetitive extragenic palindromic (REP) sequence is a highly conserved inverted repeat, with the potential for forming stable stem-loop structures in mRNA [28]. Newbury et al. have shown that the REP sequence can stabilize upstream RNA by protection from 3'→5' exonuclease attack, and have demonstrated that cloning the REP sequence downstream of a desired gene can increase protein synthesis [29]. It was also reported that processing at a cloned T7 RNase III cleavage site results in marked stabilization of the corresponding mRNA [30]. Ribonuclease III is a host nuclease that efficiently cuts RNA within the R7.7 cleavage site to leave a potential stem-and-loop structure at the 3' end of the upstream RNA, a structure that appears to stabilize the RNA against degradation.
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Published in Chad A. Mirkin, Spherical Nucleic Acids, 2020
Stacey N. Barnaby, Ryan V. Thaner, Michael B. Ross, Keith A. Brown, George C. Schatz, Chad A. Mirkin
SAXS measurements were performed to probe the interaction of nanoparticle superlattices with ribonuclease (RNase) A (Fig. 40.3), an enzyme that is known to recognize and degrade both single and double-stranded RNA duplexes [29a,b]. We hypothesized that nanoparticle superlattices would become more accessible to the enzyme as interparticle distances increased due to larger pores for diffusion [30a–c]. To eliminate a purely diffusion-based interaction, a flow-cell setup was utilized, where the enzyme and superlattice were in constant oscillation, as described in SI Materials and Methods. For the RNA superlattices, as the linker length between the nanoparticles was increased, the time span over which the superlattices retained their structure decreased dramatically (6 min for short and medium linkers and 0.25 min for long linkers; Fig. 40.3a). While pure DNA superlattices were stable in the presence of ribonuclease, one might expect that DNA/RNA superlattices would still be able to respond to enzymes due to the presence of RNA. Indeed, the ribonuclease can degrade the DNA/RNA superlattices, though they retain their order over a longer period of time than the RNA superlattices (13 min for the short linker, 8.5 min for the medium linker, and 9 min for the long linker; Fig. 40.3b,). This process is also concentration dependent. Taken together, these data show that the RNA-containing bonds in the nanoparticle superlattices are responsive to enzymes and such responses are dependent on both oligonucleotide identity and length.
Nonviral Therapeutic Approaches for Modulation of Gene Expression: Nanotechnological Strategies to Overcome Biological Challenges
Published in Ana Rute Neves, Salette Reis, Nanoparticles in Life Sciences and Biomedicine, 2018
Ana M. Cardoso, Ana L. Cardoso, Maria C. Pedroso de Lima, Amalia S. Jurado
The first approach was used to improve the stability of ONs whose function does not require their recognition and loading onto intracellular enzyme complexes. This particularity allows for extensive chemical modifications and can be applied to antisense oligonucleotides (ASOs) (reviewed in “RNA Therapeutics: Beyond RNA Interference and Antisense Oligonucleotides” [16]). ASOs are designed to bind to a specific mRNA sequence and are usually based on a phosphorothioate backbone, whose resistance to nuclease degradation is increased by nucleotide replacement by 2’-O-methoxyethyl (2’-MOE)- or 2’-O-methyl (2’-OMe)-modified residues on each end. These heavily modified portions flank an unmodified “gap,” which is recognized by ribonuclease H (RNase H), an endonuclease that specifically degrades the RNA strand of an RNA-DNA hybrid. However, the introduction of flanking 2’-OMe residues can also prevent RNase H from binding to the ASO-target mRNA duplex [36]. Alternatively, the entire ASO molecule can be 2’-MOE or 2’-OMe modified, its strong binding to the target mRNA being enough to prevent mRNA translation. Due to the increased stability of the ASO-mRNA hybrid, these molecules can act through a steric block mechanism (reviewed in “RNA Therapeutics: Beyond RNA Interference and Antisense Oligonucleotides” [16]), resulting in reduced off-target effects [36].
Enhanced anticancer potency by thermo/pH-responsive PCL-based magnetic nanoparticles
Published in Journal of Biomaterials Science, Polymer Edition, 2018
Samad Hosseini Sadr, Soodabeh Davaran, Effat Alizadeh, Roya Salehi, Ali Ramazani
The effect of DOX-MTX-loaded composite on cell cycle progression was implemented by flow cytometry analysis. In brief, about 1 × 105 MCF-7 cells were transferred in six well plates. Next day, the MCF-7 cells were treated with free DOX-MTX or DOX@MTX loaded Fe3O4@PCL grafted-poly (HEMA-co-MAA-co-NIPAAm-co-TMSPM) nanocomposites for a time period of 48 h. Subsequently, the cells were harvested and fixed with ice cold ethanol in refrigerator for 48 h. Afterward, the RNA molecules were removed with Ribonuclease A (Sinaclon). Finally, the cells were stained with Propidium Iodide (Sigma) in dark place. The DNA content was measured using Flowcytometry system (Beckton Dikinson).
A new strategy for the determination of trace Hg2+ by 5CB liquid crystal RRS probe based on nanogold amplification and Galvanic replacement reaction
Published in Liquid Crystals, 2022
Aihui Liang, Yiyi Shu, Xiaofang Huang, Dan Li, Shengfu Zhi, Chongning Li, Zhiliang Jiang
The interference of coexisting ions on the determination of 35 nmol/L Hg2+ by PMo-AuNPs-HCOOH-HCOONa-Hg2+-5CB RRS was investigated. As shown in Table S2, 10 times Fe3+; 50 times Br−, Cr3+, human serum albumin (HSA), haemoglobin, plasma protein; 100 times Mg2+, Li+, Ba2+, NO3−, Cu2+, bull serum albumin (BSA), bovine albumin, SO42-, Ca2+, IO3−, Zn2+, NH4+, Co2+, Mn2+, herring sperm DNA, and ribonuclease do not interfere with the determination. This method has good selectivity.