?url_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Adc&rft.relation=http%3A%2F%2Fd-scholarship-dev.library.pitt.edu%2F25604%2F&rft.title=Applications+of+Optical+Control+of+Oligonucleotide+and+Protein+Function&rft.creator=Hemphill%2C+James+B&rft.description=Optical+regulation+using+light+as+an+external+trigger+was+applied+to+the+control+of+biological+processes+with+high+spatio-temporal+resolution.+Photoremovable+caging+groups+were+site-specifically+incorporated+onto+oligonucleotides+and+proteins+to+optically+regulate+their+function+in+biological+environments%2C+typically+for+the+photochemical+control+of+gene+expression.+These+caging+group+modifications+enabled+both+OFF+%E2%86%92+ON+and+ON+%E2%86%92+OFF+optochemical+switches+for+important+chemical+biology+tools.+Oligonucleotides+containing+caging+group+modifications+were+synthesized+to+regulate+nucleic+acid+function+with+light.+Specifically%2C+photocaged+triplex-forming+oligonucleotides+were+developed+to+optochemically+control+transcription+in+cell+culture.+Light-activated+antagomirs+were+designed+for+the+optical+inhibition+of+miR-21+and+miR-122+function+in+the+regulation+of+endogenous+microRNA+activity.+This+technology+was+then+applied+to+the+study+of+miR-22+and+miR-124+function+in+cortical+neuron+migration+during+cerebral+corticogenesis.+Splice-switching+oligonucleotides+were+engineered+to+optically+control+mRNA+splicing+pathways+in+both+human+cells+and+zebrafish.+The+optical+control+of+plasmid-based+gene+expression+was+demonstrated+with+a+caged+promoter%2C+and+applied+to+the+photochemical+activation+of+transcription+in+a+live+animal+model.+The+caging+of+oligonucleotides+was+also+applied+to+DNA+computation+in+the+production+of+optically+controlled+logic+gates+and+amplification+cycles%2C+providing+spatio-temporal+control+over+hybridization+cascades+to+add+new+functionality+to+DNA+computation+modules.+These+studies+in+DNA+computation+led+to+the+development+of+novel+biosensors+for+logic+gate-based+detection+of+specific+micro+RNA+signatures+in+live+cells.+In+addition%2C+proteins+were+optically+controlled+through+the+site-specific+installation+of+caging+groups+on+amino+acid+side+chains+that+are+essential+for+protein+function+using+unnatural+amino+acid+mutagenesis+in+mammalian+cells+with+an+expanded+genetic+code.+A+caged+lysine+analogue+was+incorporated+into+T7+RNA+polymerase+to+photochemically+regulate+transcription+in+the+development+of+a+light-activated+synthetic+gene+network+and+light-triggered+RNA+interference.+A+light-activated+Cas9+endonuclease+was+engineered+through+the+installation+of+a+caged+lysine+analogue+to+optically+control+CRISPR%2FCas9+editing+of+both+exogenous+and+endogenous+genes.+Lastly%2C+a+system+for+the+incorporation+of+unnatural+amino+acids+in+zebrafish+was+studied+in+efforts+to+produce+the+first+vertebrate+species+with+an+expanded+genetic+code.&rft.date=2015-09-21&rft.type=University+of+Pittsburgh+ETD&rft.type=PeerReviewed&rft.format=application%2Fpdf&rft.language=en&rft.identifier=http%3A%2F%2Fd-scholarship-dev.library.pitt.edu%2F25604%2F4%2Fhemphill_james_2015_thesis_FINAL2.pdf&rft.identifier=++Hemphill%2C+James+B++(2015)+Applications+of+Optical+Control+of+Oligonucleotide+and+Protein+Function.++Doctoral+Dissertation%2C+University+of+Pittsburgh.++++(Unpublished)++