Aaron Frank

Aleksandra Walczak

eLife assessment
This important work introduces a method to express fluorogenic DNA aptamers in E. coli, paving the way for genetically encoded fluorescent DNA. The evidence supporting the conclusions is solid, consisting of comparisons of the aptamer's activity in vitro and within bacterial cells. This advancement described in this study is likely to become a standard technique in the DNA aptamer field, and the work will be of interest and utility to researchers in synthetic biology, molecular imaging, and bacterial genetics fields.

anonymous

Reviewer #1 (Public Review):
Summary:
The authors use an interesting expression system called a retron to express single-stranded DNA aptamers. Expressing DNA as a single-stranded sequence is very hard - DNA is naturally double-stranded. However, the successful demonstration by the authors of expressing Lettuce, which is a fluorogenic DNA aptamer, allowed visual demonstration of both expression and folding. This method will likely be the main method for expressing and testing DNA aptamers of all kinds, including fluorogenic aptamers like Lettuce and future variants/alternatives.
Strengths:
This has an overall simplicity which will lead to ready adoption. I am very excited about this work. People will be able to express other fluorogenic aptamers or DNA aptamers tagged with Lettuce with this system.
Weaknesses:
Several things are not addressed/shown:
(1) How stable are these DNA in cells? Half-life?
(2) What concentration do they achieve in cells/copy numbers? This is important since it relates to the total fluorescence output and, if the aptamer is meant to bind a protein, it will reveal if the copy number is sufficient to stoichiometrically bind target proteins. Perhaps the gels could have standards with known amounts in order to get exact amounts of aptamer expression per cell?
(3) Microscopic images of the fluorescent E. coli - why are these not shown (unless I missed them)? It would be good to see that cells are fluorescent rather than just showing flow sorting data.
(4) I would appreciate a better Figure 1 to show all the intermediate steps in the RNA processing, the subsequent beginning of the RT step, and then the final production of the ssDNA. I did not understand all the processing steps that lead to the final product, and the role of the 2'OH.
(5) I would like a better understanding or a protocol for choosing insertion sites into MSD for other aptamers - people will need simple instructions.
(6) Can the gels be stained with DFHBI/other dyes to see the Lettuce as has been done for fluorogenic RNAs?
(7) Sometimes FLAPs are called fluorogenic RNA aptamers - it might be good to mention both terms initially since some people use fluorogenic aptamer as their search term.
(8) What E coli strains are compatible with this retron system?
(9) What steps would be needed to use in mammalian cells?
(10) Is the conjugated RNA stable and does it degrade to leave just the DNA aptamer?

Reviewer #2 (Public Review):
Summary:
This manuscript explores a DNA fluorescent light-up aptamer (FLAP) with the specific goal of comparing activity in vitro to that in bacterial cells. In order to achieve expression in bacteria, the authors devise an expression strategy based on retrons and test four different constructs with the aptamer inserted at different points in the retron scaffold. They only observe binding for one scaffold in vitro, but achieve fluorescence enhancement for all four scaffolds in bacterial cells. These results demonstrate that aptamer performance can be very different in these two contexts.
Strengths:
-Given the importance of FLAPs for use in cellular imaging and the fact that these are typically evolved in vitro, understanding the difference in performance between a buffer and a cellular environment is an important research question.
-The return strategy utilized by the authors is thoughtful and well-described.
-The observation that some aptamers fail to show binding in vitro but do show enhancement in cells is interesting and surprising.
Weaknesses:
-This study hints toward an interesting observation, but would benefit from greater depth to more fully understand this phenomenon. Particularly challenging is that FLAP performance is measured in vitro by affinity and in cells by enhancement, and these may not be directly proportional. For example, it may be that some constructs have much lower affinity but a greater enhancement and this is the explanation for the seemingly different performance.
-The authors only test enhancement at one concentration of fluorophore in cells (and this experimental detail is difficult to find and would be helpful to include in the figure legend). This limits the conclusions that can be drawn from the data and limits utility for other researchers aiming to use these constructs.
-The FLAP that is used seems to have a relatively low fluorescence enhancement of only 2-3 fold in cells. It would be interesting to know if this is also the case in vitro. This is lower than typical FLAPs and it would be helpful for the authors to comment on what level of enhancement is needed for the FLAP to be of practical use for cellular imaging.

Intracellular Expression of a Fluorogenic DNA Aptamer Using Retron Eco2

Figures and data

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