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Item Open Access Modification of orthogonal tRNAs: unexpected consequences for sense codon reassignment(Colorado State University. Libraries, 2016-10-23) Biddle, Wil, author; Schmitt, Margaret A., author; Fisk, John D., author; Oxford University Press, publisherBreaking the degeneracy of the genetic code via sense codon reassignment has emerged as a way to incorporate multiple copies of multiple non-canonical amino acids into a protein of interest. Here, we report the modification of a normally orthogonal tRNA by a host enzyme and show that this adventitious modification has a direct impact on the activity of the orthogonal tRNA in translation. We observed nearly equal decoding of both histidine codons, CAU and CAC, by an engineered orthogonal M. jannaschii tRNA with an AUG anticodon: tRNAOpt. We suspected a modification of the tRNAOptAUG anticodon was responsible for the anomalous lack of codon discrimination and demonstrate that adenosine 34 of tRNAOptAUG is converted to inosine. We identified tRNAOptAUG anticodon loop variants that increase reassignment of the histidine CAU codon, decrease incorporation in response to the histidine CAC codon, and improve cell health and growth profiles. Recognizing tRNA modification as both a potential pitfall and avenue of directed alteration will be important as the field of genetic code engineering continues to infiltrate the genetic codes of diverse organisms.Item Open Access 1/ƒ noise for intermittent quantum dots exhibits nonstationarity and critical exponents(Colorado State University. Libraries, 2014-11) Sadegh, Sanaz, author; Barkai, Eli, author; Krapf, Diego, author; IOP Publishing Ltd., publisherThe power spectrum of quantum dot (QD) fluorescence exhibits 1/ƒ β noise, related to the intermittency of these nanosystems. As in other systems exhibiting 1/ƒ noise, this power spectrum is not integrable at low frequencies, which appears to imply infinite total power. We report measurements of individual QDs that address this long-standing paradox. We find that the level of 1/ƒ β noise decays with the observation time. The change of the spectrum with time places a bound on the total power. These observations are in stark contrast with most measurements of noise in macroscopic systems which do not exhibit any evidence for non-stationarity. We show that the traditional description of the power spectrum with a single exponent β is incomplete and three additional critical exponents characterize the dependence on experimental time.