Oligonucleotide Probe for Transcriptome in Vivo Analysis (TIVA) of Single Neurons with Minimal Background.

Messenger RNA (mRNA) isolated from single cells can generate powerful biological insights, including the discovery of new cell types with unique functions as well as markers potentially predicting a cell's response to various therapeutic agents. We previously introduced an oligonucleotide-based technique for site-selective, photoinduced biotinylation and capture of mRNA within a living cell called transcriptome in vivo analysis (TIVA). Successful application of the TIVA technique hinges upon its oligonucleotide probe remaining completely inert (or "caged") to mRNA unless photoactivated. To improve the reliability of TIVA probe caging in diverse and challenging biological conditions, we applied a rational design process involving iterative modifications to the oligonucleotide construct. In this work, we discuss these design motivations and present an optimized probe with minimal background binding to mRNA prior to photolysis. We assess its caging performance through multiple in vitro assays including FRET analysis, native gel comigration, and pull down with model mRNA transcripts. Finally, we demonstrate that this improved probe can also isolate mRNA from single living neurons in brain tissue slices with excellent caging control.

Cytochrome c mRNA in skeletal muscles of immobilized limbs.

Even though immobilization of a slow skeletal muscle in a lengthened position prevents muscle atrophy, it is unknown whether this treatment would prevent a decrease in mitochondrial quantity. We found that, regardless of muscle length in immobilized limbs, the mRNA of a marker for mitochondrial quantity, cytochrome c, decreased. Cytochrome c mRNA per milligram of muscle was 62 and 72% less 1 wk after fixation of the soleus muscle in shortened and lengthened positions, respectively, than age-matched controls. Cytochrome c mRNA per milligram wet weight was 36 and 32% less in the tibialis anterior muscle fixed for 1 wk in the shortened and lengthened positions, respectively, compared with age-matched controls. Recently, in the 3'-untranslated region of cytochrome c mRNA a novel RNA-protein interaction that decreases in chronically stimulated rat skeletal muscle was identified. [Z. Yan, S. Salmons, Y. L. Dang, M. T. Hamilton, and F. W. Booth. Am. J. Physiol. 271 (Cell Physiol. 40): C1157-C1166, 1996]. The RNA-protein interaction in the 3'-untranslated region of cytochrome c mRNA in soleus and tibialis anterior muscles was unaffected by fixation in either shortened or lengthened position. We conclude that, whereas lengthening muscle during limb fixation abates the loss of total muscle protein, the percentage decrease in cytochrome c mRNA is proportionally greater than total protein. This suggests that the design of countermeasures to muscle atrophy should include different exercises to maintain total protein and mitochondria.