Proving 2-aminobiphenyl nitric oxide probes in cells and designing sequence-defined oligomers for sequencing




Escamilla, Pedro Rogelio

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The simple diatom radical nitric oxide (NO) has numerous roles in biology. In organisms, healthy nanomolar NO levels are highly regulated. Deficiencies in NO can lead to atherosclerosis, diabetes, glaucoma, and many other conditions. Yet organisms also purposefully increase NO concentrations to micromolar levels in combatting pathogens. However, these high levels can backfire and damage cells and tissues, as found for Parkinson’s disease and ischemia, among others. Fluorescent NO probes enable live cell, tissue, and sometimes whole-animal imaging with minimal perturbation of their biological environment. 2-aminobiphenyl-based probe NO550 brought about a novel mechanism of detection in which NO-surrogate nitrosonium cation is assimilated into the nascent cinnoline fluorophore, resulting in low background and increased sensitivity. A family of second-generation 2-aminobiphenyl based probes were designed, producing four top performers in abiotic conditions. Chapter 1 describes the synthesis of these top candidates and their evaluation in cells. Two emerged as promising options for NO researchers. Chapter 2 describes the design and synthesis of sequence-defined non-natural oligomers that are sequenceable. Biological polymers peptides and DNA/RNA’s exquisitely complex properties are dictated by their sequence; changing the sequence sufficiently may have detrimental effects on their performance. Both their synthesis and sequencing continue being optimized; a human genome that once required thirteen years to sequence now takes one day.
Not as developed but growing rapidly is the field of non-natural sequence-defined polymers. Without the constraints of biology, limitless options exist for backbone structures and sidechains. Such diversity discourages the focused development of sequencing technologies on par with those for biological polymers. Consequently, tandem MS is the favored form of analysis. We sought to change the approach to polymer design by factoring in the sequencing of the polymer in addition to its synthesis. Oligourethanes based on β-aminoalcohols were designed so that the terminal unit could be derivatized to sequence by cyclizing upon itself and thereby releasing the remainder of the oligomer. Several derivatizations were investigated, to find that the oligomer sequenced itself without any terminal unit transformation, rather by self-immolation under conditions that slowed the “unzipping” of the polymer sufficiently to be able to detect the intermediate sequences.



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