RNA Detection

3.2 Induction of Reporter RNA Expression in Bacteria Plasmids encoding the aptamer or aptamer tagged ROI should be transformed i ...

Aliquot 0.2 mL of culture from each Erlenmeyer flask and transfer to a fresh microcentrifuge tube. Pellet the cells at 4400 gf ...

Fig. 5(a) Imaging SRB-2 aptamer in liveE. coliwith SR-DN dye. Bacteria were transformed with either pET- SRB2 or pET-tRNA plasmi ...

For background correction, Fiji/ImageJ image analysis soft- ware is used to manually pick a surface area where noE. coli cells ...

3.E. colicells expressing the GFP protein and GFP mRNA with or without DNB tandem repeats are prepared for imaging as described ...

The fluorogenic dyes RG-DN, TMR-DN, SR-DN, and TR- DN show 6-, 73-, 56-, and 15-fold fluorescence enhancement upon binding to D ...

For dual-color RNA imaging experiments, we created a single plasmid (pET-SRB2-DNB) which expresses both SRB-2 and DNB aptamers ...

Prepare the working solution of poly-D-lysine freshly each time just before it is needed. Stock solution can be stored at 4C. ...

We clearly see GFP mRNA localization at the poles of bacteria. However, this data should be interpreted very carefully. pET pla ...

Sunbul M, J€aschke A (2013) Contact- mediated quenching for RNA imaging in bac- teria with a fluorophore-binding aptamer. Angew ...

Chapter 20 Method for Imaging Live-Cell RNA Using an RNA Aptamer and a Fluorescent Probe Shin-ichi Sato, Kenji Yatsuzuka, Yousuk ...

BHQ1 aptamer, and the construction of RT aptamers that hybrid- ize to the target RNA. This imaging technology could provide new ...

21.N,N-diisopropylethylamine (e.g., Wako Pure Chemical Industries). PCR Master mix (e.g., Toyobo KOD FX Neo). 3 M sodium acetat ...

2.3 Buffers and Reaction Mixes PCR mixture: 10μL N60 template DNA, 250μL2KOD FX Neo buffer, 100μL dNTP mixture (2 mM each), 10 ...

Thermal cycler. Confocal microscope (e.g., Yokogawa Electric CV1000). LC-MS system (e.g., Shimadzu LCMS-2010EV). 2.2μm, 350 mm ...

To conjugate the fluorophore, apply 3.0μmol Cy3-NHS-ester in 36μL DMSO to the resin, and incubate it overnight at room temperat ...

The mixture is diluted and acidified with 0.6 mL of 10 v/v % TFA in acetonitrile–H 2 O (1:1). The mixture is then purified by H ...

denaturation at 98C for 10 s, annealing at 55C for 30 s, and extension at 68C for 30 s. Precipitate the DNA by adding a one- ...

Remove the supernatant and rinse the pellet with 70% ethanol. Air-dry the pellet for 5 min, and dissolve it in a 15-μL TE buffe ...

3.5 Fluorescence In Situ Hybridization (FISH) in Fixed Cells with the RT-Aptamer [25] Fix HeLa cells on 96-well plates (3.0 10 ...