III, Louis James Maher

AbstractRecent advances in peroxidase‐mediated biotin tyramide (BT) signal amplification technology have resulted in high‐resolution and subcellular compartment‐specific mapping of protein and RNA localization. Horseradish peroxidase (HRP) in the presence of H2O2 is known to activate phenolic compounds for phenoxy radical reaction with nucleic acids, where biotinylation by BT is a practical example. BT reactivity with RNA and DNA is not understood in detail. We report that BT phenoxy radicals react in a sequence‐independent manner with guanosine bases in RNA. In contrast, DNA reactivity with BT cannot be detected by our methods under the same conditions. Remarkably, we show that fluorescein conjugates DNA rapidly and selectively reacts with BT phenoxy radicals, allowing convenient and practical biotinylation of DNA on fluorescein with retention of fluorescence.

Abstract Mutations in any of the genes encoding the four subunits of succinate dehydrogenase (SDH), a mitochondrial membrane‐bound enzyme complex that is involved in both the tricarboxylic acid cycle and the electron transport chain, can lead to a variety of disorders. Recognized conditions with such mutations include Leigh syndrome and hereditary tumors such as pheochromocytoma and paraganglioma (PPGL), renal cell carcinoma, and gastrointestinal stromal tumor. Tumors appear in SDH mutation carriers with dominant inheritance due to loss of heterozygosity in susceptible cells. Here, we describe a mouse model intended to reproduce hereditary PPGL through Cre‐mediated loss of SDHC in cells that express tyrosine hydroxylase (TH), a compartment where PPGL is known to originate. We report that while there is modest expansion of TH + glomus cells in the carotid body upon SDHC loss, PPGL is not observed in such mice, even in the presence of a conditional dominant negative p53 protein and chronic hypoxia. Instead, we report an unexpected phenotype of nondiabetic obesity beginning at about 20 weeks of age. We hypothesize that this obesity is caused by TH + cell loss or altered phenotype in key compartments of the central nervous system responsible for regulating feeding behavior, coupled with metabolic changes due to loss of peripheral catecholamine production.

Using DNA ligase‐catalyzed cyclization assays, the in vitro persistence length of DNA has been determined to be about 150 base pairs (bp). In living E. coli bacteria, where DNA loops regulate the lac operon, DNA looping appears to be much more probable than expected from in vitro data. Why? A possible explanation for this paradox is that DNA loops in bacteria are bridged by proteins, reducing the amount of required costly DNA bending. Current in vitro methods to measure DNA flexibility are tedious and artificial, in that they require DNA cyclization, not just DNA looping. No high‐throughput method has been described to measure DNA flexibility for loops involving bridging proteins of different sizes. We are developing a high‐throughput method to measure the probability of DNA looping when bridged by a fusion protein that includes PCV2 and micrococcal nuclease domains. A bead‐tethered 1000‐bp DNA molecule of a known sequence is conjugated to this fusion protein through the PCV2 domain, and looping allows self‐cleavage such that the distribution of cleavage sites revealed by next generation sequencing reflects the energetics of DNA looping. We hypothesize that this distribution will be affected as a function of bridging protein size. Measuring how the size of bridging proteins affects tight DNA loop probability enables improved understanding of genetic switches.

Leigh syndrome embodies degenerative disorders with a collection of symptoms secondary to inborn errors of metabolism. Combinations of hypomorphic and loss‐of‐function alleles in many genes have been shown to result in Leigh syndrome. Interestingly, deficiency for the tricarboxylic acid cycle enzyme succinate dehydrogenase (SDH) can lead to Leigh‐like syndrome in some circumstances and to cancer (paraganglioma, renal cell carcinoma, gastrointestinal stromal tumor) in others. In our experiments originally intended to create an inducible whole‐body SDH‐loss mouse model of tumorigenesis, we generated a condition reminiscent of Leigh‐like syndrome that is lethal to mice within 4 wk. Remarkably, as has been shown for other mitochondrial diseases, chronic hypoxia offers substantial protection to mice from this condition after systemic SDH loss, allowing survival in the context of profoundly impaired oxidative metabolism.—Al Khazal, F., Holte, M. N., Bolon, B., White, T. A., LeBrasseur, N., Maher, L. J. III. A conditional mouse model of complex II deficiency manifesting as Leigh‐like syndrome. FASEB J. 33, 13189–13201 (2019). www.fasebj.org

We previously reported the in vitro selection and characterization of a DNA aptamer capable of stimulating remyelination in a mouse model of multiple sclerosis. This aptamer was selected for its ability to bind to suspensions of crude murine myelin in vitro . Our initial studies in vitro and in vivo involved a 40-nucleotide derivative (LJM-3064) of the original 100-nucleotide aptamer. LJM-3064 retained robust myelin-binding properties. Structural characterization of LJM-3064 revealed that the guanosine-rich 5′ half of the sequence forms different G-quadruplex-type structures that are variably stable in the presence of physiologically relevant ions. We hypothesized that this structured domain is sufficient for myelin binding. In this study, we confirm that a 20-nucleotide DNA, corresponding to the 5′ half of LJM-3064, retains myelin-binding properties. We then optimize this minimal myelin-binding aptamer via systematic evolution of ligands by exponential enrichment after sparse rerandomization. We report a sequence variant (LJM-5708) of the 20-nucleotide myelin-binding aptamer with enhanced myelin-binding properties and the ability to bind cultured human oligodendroglioma cells in vitro , providing the first evidence of cross-species reactivity of this myelin-binding aptamer. As our formulation of DNA aptamers for in vivo remyelination therapy involves conjugation to streptavidin, we verified that the myelin-binding properties of LJM-5708 were retained in conjugates to avidin, streptavidin, and neutravidin. DNA aptamer LJM-5708 is a lead for further preclinical development of remyelinating aptamer technologies.