RNA Detection

3.E. colicells expressing the GFP protein and GFP mRNA with

or without DNB tandem repeats are prepared for imaging as

described in Subheading3.3.2except for the following steps.

4. After washing the unattachedE. colicells (step 6of Subhead-
   ing3.3.2), the wells are incubated with 300μL of imaging
   solution containing 1μM of TMR-DN.


5. Both GFP protein and mRNA in live bacteria are imaged as
   mentioned in Subheading3.3.3. Filter sets for GFP are as same
   as the ones for RG-DN (seeFig. 7 andNote 17).

4 Notes

1. Contact quenching is a type of static quenching where the
   fluorophore and quencher interact with each other to form a
   nonfluorescent intramolecular ground state dimer with its own
   distinct absorption spectrum.

Fig. 6Dual-color imaging of SRB-2 and DNB aptamers in liveE. coliwith RG-DN (green,1μM) and SR-MN
(red,1μM). Fluorescence signal in bothredandgreenchannels was detected in cells expressing both DNB
and SRB-2, while cells expressing either DNB or SRB-2 showed fluorescence only in thegreenorredchannel,
respectively. Scale bar, 5μm. Images were reproduced from [22] with permission from Oxford University
Press

Visualizing RNA with Fluorogenic Aptamers in vivo 299