This month’s Nature methods (part 1): Spinach, blue transcription & photoacoustic imaging

This month’s Nature Methods issue has several interesting imaging items & articles, including two super-resolution reviews, two optogenetics articles, and more.

This post will be dedicated to three items in the “tools in brief” section.

Blue transcription

Optogenetics usually refers to control of ion flux via light sensitive channels. However, there are other light-responsive molecules. The item titles “Optimized optogenetic gene expression” describe a work from Kevin Gardner’s lab. They fused the transcription activating domain of the protein VP16 to the protein EL222. EL222 is a light-oxygen-voltage protein from the bacterium Erythrobacter litoralis. This protein binds to DNA when illuminated by blue light, and detaches from the DNA when the light is removed. Using this system, they could induce and repress transcription of a specific gene of interest (harboring a specific promoter recognized by EL222) in mammalian cells in tissue culture and in zebra-fish embryo. This can be a great tool.

Zebra fish egg and embryo harboring  an mCherry gene under the control of the VP-EL222 (or not) under dark or blue-light conditions. Source: Motta-Mena LB et al. (2014) Nat Chem. Biol. 10:196.

Zebra fish egg and embryo harboring an mCherry gene under the control of the VP-EL222 (or not) under dark or blue-light conditions. Source: Motta-Mena LB et al. (2014) Nat Chem. Biol. 10:196.

Photoacoustic imaging

Fluorescent molecules absorb light, and then emit light at a different wavelength. Photoacoustic molecules absorb light and emit sound waves. This is called the photoacoustic effect. This effect can be utilized to image inside whole animals, and the hope of the field is to get deep tissue penetration and a high resolution. The item titled “Activatable photoacoustic probes” presents a paper by the J. Roa’s lab at Stanford university. They developed a new polymer which absorbs at near-infrared (thus allowing good tissue penetration) and these produce a higher signal than commonly used materials for such imaging. They were also able for the first time to create a photoacoustic sensor of reactive oxygen species. This new field is very interesting and very exciting.


Spinach may deserve its own post, but briefly, Spinach and Spinach2 are RNA aptamers that can be used for the genetic encoding of fluorescent RNA. This aptamers form a unique structure which binds a specific molecule which then fluoresce. However, the optical properties of this dye were not suitable for common microscope filters. So now the group that developed Spinach developed several new dyes to enhance the fluorescent range of Spinach2.

The main problem I have with Spinach is that most of their work is based on an artificial RNA composed of 60 repeats of CGG trinucleotide and the ribosomal 5S rRNA. I haven’t followed the literature of Spinach much, but haven’t seen any single molecule imaging using Spinach. but, I guess I owe Spinach a post of its own.

ResearchBlogging.orgTools in brief (2014). Chemical biology: Optimized optogenetic gene expression Nature Methods, 11 (3), 230-230 DOI: 10.1038/nmeth.2867
Tools in brief (2014). Sensors and probes: Expanding Spinach2’s spectral properties Nature Methods, 11 (3), 230-230 DOI: 10.1038/nmeth.2865
Tools in brief (2014). Imaging: Activatable photoacoustic probes Nature Methods, 11 (3), 230-230 DOI: 10.1038/nmeth.2868
Pu K, Shuhendler AJ, Jokerst JV, Mei J, Gambhir SS, Bao Z, & Rao J (2014). Semiconducting polymer nanoparticles as photoacoustic molecular imaging probes in living mice. Nature nanotechnology PMID: 24463363
Motta-Mena LB, Reade A, Mallory MJ, Glantz S, Weiner OD, Lynch KW, & Gardner KH (2014). An optogenetic gene expression system with rapid activation and deactivation kinetics. Nature chemical biology, 10 (3), 196-202 PMID: 24413462
Song W, Strack RL, Svensen N, & Jaffrey SR (2014). Plug-and-Play Fluorophores Extend the Spectral Properties of Spinach. Journal of the American Chemical Society, 136 (4), 1198-201 PMID: 24393009
Strack RL, Disney MD, & Jaffrey SR (2013). A superfolding Spinach2 reveals the dynamic nature of trinucleotide repeat-containing RNA. Nature methods, 10 (12), 1219-24 PMID: 24162923

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